Journal articles: 'Chromosomal domain'

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Chen, Bo-Wei, Ming-Hsing Lin, Chen-Hsi Chu, Chia-En Hsu, and Yuh-Ju Sun. "Insights into ParB spreading from the complex structure of Spo0J and parS." Proceedings of the National Academy of Sciences 112, no. 21 (May 11, 2015): 6613–18. http://dx.doi.org/10.1073/pnas.1421927112.

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Spo0J (stage 0 sporulation protein J, a member of the ParB superfamily) is an essential component of the ParABS (partition system of ParA, ParB, and parS)-related bacterial chromosome segregation system. ParB (partition protein B) and its regulatory protein, ParA, act cooperatively through parS (partition S) DNA to facilitate chromosome segregation. ParB binds to chromosomal DNA at specific parS sites as well as the neighboring nonspecific DNA sites. Various ParB molecules can associate together and spread along the chromosomal DNA. ParB oligomer and parS DNA interact together to form a high-order nucleoprotein that is required for the loading of the structural maintenance of chromosomes proteins onto the chromosome for chromosomal DNA condensation. In this report, we characterized the binding of parS and Spo0J from Helicobacter pylori (HpSpo0J) and solved the crystal structure of the C-terminal domain truncated protein (Ct-HpSpo0J)-parS complex. Ct-HpSpo0J folds into an elongated structure that includes a flexible N-terminal domain for protein–protein interaction and a conserved DNA-binding domain for parS binding. Two Ct-HpSpo0J molecules bind with one parS. Ct-HpSpo0J interacts vertically and horizontally with its neighbors through the N-terminal domain to form an oligomer. These adjacent and transverse interactions are accomplished via a highly conserved arginine patch: RRLR. These interactions might be needed for molecular assembly of a high-order nucleoprotein complex and for ParB spreading. A structural model for ParB spreading and chromosomal DNA condensation that lead to chromosome segregation is proposed.

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Krasikova, Alla, and Tatiana Kulikova. "Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes." Non-Coding RNA 6, no. 1 (December 25, 2019): 1. http://dx.doi.org/10.3390/ncrna6010001.

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In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs.

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Krithivas, Anita, Masahiro Fujimuro, Magdalena Weidner, David B. Young, and S. Diane Hayward. "Protein Interactions Targeting the Latency-Associated Nuclear Antigen of Kaposi's Sarcoma-Associated Herpesvirus to Cell Chromosomes." Journal of Virology 76, no. 22 (November 15, 2002): 11596–604. http://dx.doi.org/10.1128/jvi.76.22.11596-11604.2002.

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ABSTRACT Maintenance of Kaposi's sarcoma-associated herpesvirus (KSHV) latent infection depends on the viral episomes in the nucleus being distributed to daughter cells following cell division. The latency-associated nuclear antigen (LANA) is constitutively expressed in all KSHV-infected cells. LANA binds sequences in the terminal repeat regions of the KSHV genome and tethers the viral episomes to chromosomes. To better understand the mechanism of chromosomal tethering, we performed glutathione S-transferase (GST) affinity and yeast two-hybrid assays to identify LANA-interacting proteins with known chromosomal association. Two of the interactors were the methyl CpG binding protein MeCP2 and the 43-kDa protein DEK. The interactions of MeCP2 and DEK with LANA were confirmed by coimmunoprecipitation. The MeCP2-interacting domain was mapped to the previously described chromatin binding site in the N terminus of LANA, while the DEK-interacting domain mapped to LANA amino acids 986 to 1043 in the C terminus. LANA was unable to associate with mouse chromosomes in chromosome spreads of transfected NIH 3T3 cells. However, LANA was capable of targeting to mouse chromosomes in the presence of human MeCP2 or DEK. The data indicate that LANA is tethered to chromosomes through two independent chromatin binding domains that interact with different protein partners.

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Baxter, Michael K., Maria G. McPhillips, Keiko Ozato, and Alison A. McBride. "The Mitotic Chromosome Binding Activity of the Papillomavirus E2 Protein Correlates with Interaction with the Cellular Chromosomal Protein, Brd4." Journal of Virology 79, no. 8 (April 15, 2005): 4806–18. http://dx.doi.org/10.1128/jvi.79.8.4806-4818.2005.

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ABSTRACT The papillomavirus transcriptional activator, E2, is involved in key functions of the viral life cycle. These include transcriptional regulation, viral DNA replication, and viral genome segregation. The transactivation domain of E2 is required for each of these functions. To identify the regions of the domain that mediate binding to mitotic chromosomes, a panel of mutations has been generated and their effect on various E2 functions has been analyzed. A structural model of the bovine papillomavirus type 1 (BPV1) E2 transactivation domain was generated based on its homology with the solved structure of the human papillomavirus type 16 (HPV16) domain. This model was used to identify distinct surfaces of the domain to be targeted by point mutation to further delineate the functional region of the transactivation domain responsible for mitotic chromosome association. The mutated E2 proteins were assessed for mitotic chromosome binding and, in addition, transcriptional activation and transcriptional repression activities. Mutation of amino acids R37 and I73, which are located on a surface of the domain that in HPV16 E2 is reported to mediate self-interaction, completely eliminated mitotic chromosome binding. Mitotic chromosome binding activity was found to correlate well with the ability to interact with the cellular chromosomal associated factor Brd4, which has recently been proposed to mediate the association between BPV1 E2 and mitotic chromosomes.

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Fischer, K., P. Horrocks, M. Preuss, J. Wiesner, S. Wünsch, A. A. Camargo, and M. Lanzer. "Expression of var genes located within polymorphic subtelomeric domains of Plasmodium falciparum chromosomes." Molecular and Cellular Biology 17, no. 7 (July 1997): 3679–86. http://dx.doi.org/10.1128/mcb.17.7.3679.

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Plasmodium falciparum var genes encode a diverse family of proteins, located on the surfaces of infected erythrocytes, which are implicated in the pathology of human malaria through antigenic variation and adhesion of infected erythrocytes to the microvasculature. We have constructed a complete representative telomere-to-telomere yeast artificial chromosome (YAC) contig map of the P. falciparum chromosome 8 for studies on the chromosomal organization, distribution, and expression of var genes. Three var gene loci were identified on chromosome 8, two of which map close to the telomeres at either end of the chromosome. Analysis of the previously described chromosome 2 contig map and random P. falciparum telomeric YAC clones revealed that most, if not all, 14 P. falciparum chromosomes contain var genes in a subtelomeric location. Mapping the chromosomal location of var genes expressed in a long-term culture of the P. falciparum isolate Dd2 revealed that four of the five different expressed var genes identified map within subtelomeric locations. Expression of var genes from a chromosomal domain known for frequent rearrangements has important implications for the mechanism of var gene switching and the generation of novel antigenic and adhesive phenotypes.

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LaSalle, Janine M., and Marc Lalande. "Domain organization of allele-specific DNA replication within the GABAA receptor gene cluster." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 766–67. http://dx.doi.org/10.1017/s0424820100140208.

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Parental imprinting is a gamete-specific modification that distinguishes the paternal and maternal chromosomes in higher eukaryotes, resulting in allele-specific changes in chromatin organization, transcription and replication. One example of parental imprinting in humans is revealed by two distinct genetic diseases, Prader-Willi syndrome (PWS) and Angelman syndrome (AS) which both map to chromosome 15q11-13. PWS is caused by the absence of a paternal contribution to 15q11-13, while AS results from the lack of a maternal copy of the region. Within this chromosomal subregion lies a cluster of GABAA receptor β3 and α5 subunit genes (GABRB3 and GABRA5) which are separated by about 100 kb and arranged in opposite transcritional orientations (Figure 1). Allele-specific asynchronous DNA replication has previously been found to be associated with imprinted chromosomal regions.In order to further study the association between DNA replication and imprinting, allele-specific replication was assayed by fluorescence in situ hybridization (FISH). Biotin-labeled phage probes detected by FITC hybridized to each chromosome as either a singlet (unreplicated state) or a doublet (replicated state). Cells demonstrating asynchronous replication (one singlet and one doublet) for each probe are shown in Figure 2.

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Hilliker, Arthur J. "Assaying chromosome arrangement in embryonic interphase nuclei of Drosophila melanogaster by radiation induced interchanges." Genetical Research 47, no. 1 (February 1986): 13–18. http://dx.doi.org/10.1017/s0016672300024459.

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SummaryDespite recent advances in our understanding of chromatin ultrastructure, little is known of the arrangement of chromosomes during interphase, the portion of the cell cycle associated with somatic gene transcription. An experimental procedure is described which has allowed the determination of the nature of the relative arrangement during interphase of chromosomes in a specific diploid cell type of Drosophila, the salivary gland anlage of the 10–14-h-old embryo. At this stage of development the salivary gland cells have ceased mitotic divisions. Embryos of 10–14 h in age were irradiated with 12000 rads of gamma radiation and then allowed to develop into third instar larvae. The polytene chromosomes of these larvae were examined for radiation-induced interchanges. From the distribution of observed interchanges, three major features of interphase chromosome arrangement were inferred. (1) Each euchromatic chromosomal arm occupies a specific domain within the interphase nucleus which does not appreciably overlap with those of other arms. (2) Within these chromosomal domains DNA folding is very extensive. (3) The heterochromatic regions of each chromosomal arm are sequestered from the euchromatic regions. An additional point of interest concerns the nature of the interchanges observed. No reciprocal interchanges were observed – all appeared to be partial exchanges, possibly subchromatid interchanges involving only one DNA strand from each of the two exchange sites.

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Doyle, Michael, and Michael F. Jantsch. "Distinct in vivo roles for double-stranded RNA-binding domains of the Xenopus RNA-editing enzyme ADAR1 in chromosomal targeting." Journal of Cell Biology 161, no. 2 (April 28, 2003): 309–19. http://dx.doi.org/10.1083/jcb.200301034.

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The RNA-editing enzyme adenosine deaminase that acts on RNA (ADAR1) deaminates adenosines to inosines in double-stranded RNA substrates. Currently, it is not clear how the enzyme targets and discriminates different substrates in vivo. However, it has been shown that the deaminase domain plays an important role in distinguishing various adenosines within a given substrate RNA in vitro. Previously, we could show that Xenopus ADAR1 is associated with nascent transcripts on transcriptionally active lampbrush chromosomes, indicating that initial substrate binding and possibly editing itself occurs cotranscriptionally. Here, we demonstrate that chromosomal association depends solely on the three double-stranded RNA-binding domains (dsRBDs) found in the central part of ADAR1, but not on the Z-DNA–binding domain in the NH2 terminus nor the catalytic deaminase domain in the COOH terminus of the protein. Most importantly, we show that individual dsRBDs are capable of recognizing different chromosomal sites in an apparently specific manner. Thus, our results not only prove the requirement of dsRBDs for chromosomal targeting, but also show that individual dsRBDs have distinct in vivo localization capabilities that may be important for initial substrate recognition and subsequent editing specificity.

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Riddle, Nicole C., Christopher D. Shaffer, and Sarah C. R. Elgin. "A lot about a little dot — lessons learned from Drosophila melanogaster chromosome 4This paper is one of a selection of papers published in this Special Issue, entitled 29th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process." Biochemistry and Cell Biology 87, no. 1 (February 2009): 229–41. http://dx.doi.org/10.1139/o08-119.

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The fourth chromosome of Drosophila melanogaster has a number of unique properties that make it a convenient model for the study of chromatin structure. Only 4.2 Mb overall, the 1.2 Mb distal arm of chromosome 4 seen in polytene chromosomes combines characteristics of heterochromatin and euchromatin. This domain has a repeat density of ~35%, comparable to some pericentric chromosome regions, while maintaining a gene density similar to that of the other euchromatic chromosome arms. Studies of position-effect variegation have revealed that heterochromatic and euchromatic domains are interspersed on chromosome 4, and both cytological and biochemical studies have demonstrated that chromosome 4 is associated with heterochromatic marks, such as heterochromatin protein 1 and histone 3 lysine 9 methylation. Chromosome 4 is also marked by POF (painting-of-fourth), a chromosome 4-specific chromosomal protein, and utilizes a dedicated histone methyltransferase, EGG. Studies of chromosome 4 have helped to shape our understanding of heterochromatin domains and their establishment and maintenance. In this review, we provide a synthesis of the work to date and an outlook to the future.

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Hasanova, Aytakin. "CHARACTERIZATION OF HUMAN CHROMOSOMAL CONSTITUTIVE HETEROCHROMATIN." Gulustan-Black Sea Scientific Journal of Academic Research 53, no. 02 (April 15, 2020): 08–11. http://dx.doi.org/10.36962/gbssjar5302202008.

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Heterochromatin of centromeric chromosome regions contains late replicating, largely repetitive DNA. It is suggested that heterochromatin participates in chromosome pairing, crossing-over and in chromosome disjunction control (1,3). Centromeric heterochromatin, a variety of heterochromatin, is a tightly packed form of DNA.Centromeric heterochromatin is a constituent in the formation ofactive centromeres in most higher-order organisms; the domain exists on both mitotic and interphase chromosomes. (4,5,6,8) Centromeric heterochromatin is usually formed on alpha satellite DNA in humans; however, there have been cases where centric heterochromatin and centromeres have formed on originally euchromatin domains lacking alpha satellite DNA; this usually happens as a result of a chromosome breakage event and the formed centromere is called a neocentromere.

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Shopland, Lindsay S., Carol V. Johnson, Meg Byron, John McNeil, and Jeanne B. Lawrence. "Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains." Journal of Cell Biology 162, no. 6 (September 15, 2003): 981–90. http://dx.doi.org/10.1083/jcb.200303131.

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Typically, eukaryotic nuclei contain 10–30 prominent domains (referred to here as SC-35 domains) that are concentrated in mRNA metabolic factors. Here, we show that multiple specific genes cluster around a common SC-35 domain, which contains multiple mRNAs. Nonsyntenic genes are capable of associating with a common domain, but domain “choice” appears random, even for two coordinately expressed genes. Active genes widely separated on different chromosome arms associate with the same domain frequently, assorting randomly into the 3–4 subregions of the chromosome periphery that contact a domain. Most importantly, visualization of six individual chromosome bands showed that large genomic segments (∼5 Mb) have striking differences in organization relative to domains. Certain bands showed extensive contact, often aligning with or encircling an SC-35 domain, whereas others did not. All three gene-rich reverse bands showed this more than the gene-poor Giemsa dark bands, and morphometric analyses demonstrated statistically significant differences. Similarly, late-replicating DNA generally avoids SC-35 domains. These findings suggest a functional rationale for gene clustering in chromosomal bands, which relates to nuclear clustering of genes with SC-35 domains. Rather than random reservoirs of splicing factors, or factors accumulated on an individual highly active gene, we propose a model of SC-35 domains as functional centers for a multitude of clustered genes, forming local euchromatic “neighborhoods.”

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Theis, J. F., and C. S. Newlon. "Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function." Molecular and Cellular Biology 14, no. 11 (November 1994): 7652–59. http://dx.doi.org/10.1128/mcb.14.11.7652.

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ARS307 is highly active as a replication origin in its native location on chromosome III of Saccharomyces cerevisiae. Its ability to confer autonomous replication activity on plasmids requires the presence of an 11-bp autonomously replicating sequence (ARS) consensus sequence (ACS), which is also required for chromosomal origin function, as well as approximately 100 bp of sequence flanking the ACS called domain B. To further define the sequences required for ARS function, a linker substitution mutagenesis of domain B was carried out. The mutations defined two sequences, B1 and B2, that contribute to ARS activity. Therefore, like ARS1, domain B of ARS307 is composed of functional subdomains. Constructs carrying mutations in the B1 element were used to replace the chromosomal copy of ARS307. These mutations caused a reduction in chromosomal origin activity, demonstrating that the B1 element is required for efficient chromosomal origin function.

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Theis, J. F., and C. S. Newlon. "Domain B of ARS307 contains two functional elements and contributes to chromosomal replication origin function." Molecular and Cellular Biology 14, no. 11 (November 1994): 7652–59. http://dx.doi.org/10.1128/mcb.14.11.7652-7659.1994.

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ARS307 is highly active as a replication origin in its native location on chromosome III of Saccharomyces cerevisiae. Its ability to confer autonomous replication activity on plasmids requires the presence of an 11-bp autonomously replicating sequence (ARS) consensus sequence (ACS), which is also required for chromosomal origin function, as well as approximately 100 bp of sequence flanking the ACS called domain B. To further define the sequences required for ARS function, a linker substitution mutagenesis of domain B was carried out. The mutations defined two sequences, B1 and B2, that contribute to ARS activity. Therefore, like ARS1, domain B of ARS307 is composed of functional subdomains. Constructs carrying mutations in the B1 element were used to replace the chromosomal copy of ARS307. These mutations caused a reduction in chromosomal origin activity, demonstrating that the B1 element is required for efficient chromosomal origin function.

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Yang, Chao, Bingyan Hu, Stephan Michael Portheine, Pichaporn Chuenban, and Arp Schnittger. "State changes of the HORMA protein ASY1 are mediated by an interplay between its closure motif and PCH2." Nucleic Acids Research 48, no. 20 (June 19, 2020): 11521–35. http://dx.doi.org/10.1093/nar/gkaa527.

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Abstract HORMA domain-containing proteins (HORMADs) play an essential role in meiosis in many organisms. The meiotic HORMADs, including yeast Hop1, mouse HORMAD1 and HORMAD2, and Arabidopsis ASY1, assemble along chromosomes at early prophase and the closure motif at their C-termini has been hypothesized to be instrumental for this step by promoting HORMAD oligomerization. In late prophase, ASY1 and its homologs are progressively removed from synapsed chromosomes promoting chromosome synapsis and recombination. The conserved AAA+ ATPase PCH2/TRIP13 has been intensively studied for its role in removing HORMADs from synapsed chromosomes. In contrast, not much is known about how HORMADs are loaded onto chromosomes. Here, we reveal that the PCH2-mediated dissociation of the HORMA domain of ASY1 from its closure motif is important for the nuclear targeting and subsequent chromosomal loading of ASY1. This indicates that the promotion of ASY1 to an ‘unlocked’ state is a prerequisite for its nuclear localization and chromosomal assembly. Likewise, we find that the closure motif is also necessary for the removal of ASY1 by PCH2 later in prophase. Our work results in a unified new model for PCH2 and HORMADs function in meiosis and suggests a mechanism to contribute to unidirectionality in meiosis.

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Yamashita, Daisuke, Keishi Shintomi, Takao Ono, Ioannis Gavvovidis, Detlev Schindler, Heidemarie Neitzel, Marc Trimborn, and Tatsuya Hirano. "MCPH1 regulates chromosome condensation and shaping as a composite modulator of condensin II." Journal of Cell Biology 194, no. 6 (September 12, 2011): 841–54. http://dx.doi.org/10.1083/jcb.201106141.

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Mutations in human MCPH1 (hMCPH1) cause primary microcephaly, which is characterized by a marked reduction of brain size. Interestingly, hMCPH1 mutant patient cells display unique cellular phenotypes, including premature chromosome condensation (PCC), in G2 phase. To test whether hMCPH1 might directly participate in the regulation of chromosome condensation and, if so, how, we developed a cell-free assay using Xenopus laevis egg extracts. Our results demonstrate that an N-terminal domain of hMCPH1 specifically inhibits the action of condensin II by competing for its chromosomal binding sites in vitro. This simple and powerful assay allows us to dissect mutations causing primary microcephaly in vivo and evolutionary substitutions among different species. A complementation assay using patient cells revealed that, whereas the N-terminal domain of hMCPH1 is sufficient to rescue the PCC phenotype, its central domain plays an auxiliary role in shaping metaphase chromosomes by physically interacting with condensin II. Thus, hMCPH1 acts as a composite modulator of condensin II to regulate chromosome condensation and shaping.

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Zheng, Peng-Sheng, Jane Brokaw, and Alison A. McBride. "Conditional Mutations in the Mitotic Chromosome Binding Function of the Bovine Papillomavirus Type 1 E2 Protein." Journal of Virology 79, no. 3 (February 1, 2005): 1500–1509. http://dx.doi.org/10.1128/jvi.79.3.1500-1509.2005.

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ABSTRACT The papillomavirus E2 protein is required for viral transcriptional regulation, DNA replication and genome segregation. We have previously shown that the E2 transactivator protein and BPV1 genomes are associated with mitotic chromosomes; E2 links the genomes to cellular chromosomes to ensure efficient segregation to daughter nuclei. The transactivation domain of the E2 protein is necessary and sufficient for association of the E2 protein with mitotic chromosomes. To determine which residues of this 200-amino-acid domain are important for chromosomal interaction, E2 proteins with amino acid substitutions in each conserved residue of the transactivation domain were tested for their ability to associate with mitotic chromosomes. Chromatin binding was assessed by using immunofluorescence on both spread and directly fixed mitotic chromosomes. E2 proteins defective in the transactivation and replication functions were unable to associate with chromosomes, and those that were competent in these functions were attached to mitotic chromosomes. However, several mutated proteins that were defective for chromosomal interaction could associate with chromosomes after treatment with agents that promote protein folding or when cells were incubated at lower temperatures. These results indicate that precise folding of the E2 transactivation domain is crucial for its interaction with mitotic chromosomes and that this association can be modulated.

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Strehl, S., J. M. LaSalle, and M. Lalande. "High-resolution analysis of DNA replication domain organization across an R/G-band boundary." Molecular and Cellular Biology 17, no. 10 (October 1997): 6157–66. http://dx.doi.org/10.1128/mcb.17.10.6157.

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Establishing how mammalian chromosome replication is regulated and how groups of replication origins are organized into replication bands will significantly increase our understanding of chromosome organization. Replication time bands in mammalian chromosomes show overall congruency with structural R- and G-banding patterns as revealed by different chromosome banding techniques. Thus, chromosome bands reflect variations in the longitudinal structure and function of the chromosome, but little is known about the structural basis of the metaphase chromosome banding pattern. At the microscopic level, both structural R and G bands and replication bands occupy discrete domains along chromosomes, suggesting separation by distinct boundaries. The purpose of this study was to determine replication timing differences encompassing a boundary between differentially replicating chromosomal bands. Using competitive PCR on replicated DNA from flow-sorted cell cycle fractions, we have analyzed the replication timing of markers spanning roughly 5 Mb of human chromosome 13q14.3/q21.1. This is only the second report of high-resolution analysis of replication timing differences across an R/G-band boundary. In contrast to previous work, however, we find that band boundaries are defined by a gradient in replication timing rather than by a sharp boundary separating R and G bands into functionally distinct chromatin compartments. These findings indicate that topographical band boundaries are not defined by specific sequences or structures.

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Berrios, Soledad. "Nuclear Architecture of Mouse Spermatocytes: Chromosome Topology, Heterochromatin, and Nucleolus." Cytogenetic and Genome Research 151, no. 2 (2017): 61–71. http://dx.doi.org/10.1159/000460811.

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The nuclear organization of spermatocytes in meiotic prophase I is primarily determined by the synaptic organization of the bivalents that are bound by their telomeres to the nuclear envelope and described as arc-shaped trajectories through the 3D nuclear space. However, over this basic meiotic organization, a spermatocyte nuclear architecture arises that is based on higher-ordered patterns of spatial associations among chromosomal domains from different bivalents that are conditioned by the individual characteristics of chromosomes and the opportunity for interactions between their domains. Consequently, the nuclear architecture is species-specific and prone to modification by chromosomal rearrangements. This model is valid for the localization of any chromosomal domain in the meiotic prophase nucleus. However, constitutive heterochromatin plays a leading role in shaping nuclear territories. Thus, the nuclear localization of nucleoli depends on the position of NORs in nucleolar bivalents, but the association among nucleolar chromosomes mainly depends on the presence of constitutive heterochromatin that does not affect the expression of the ribosomal genes. Constitutive heterochromatin and nucleoli form complex nuclear territories whose distribution in the nuclear space is nonrandom, supporting the hypothesis regarding the existence of a species-specific nuclear architecture in first meiotic prophase spermatocytes.

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Liang, Jian, Leonard Prouty, B. Jill Williams, Mark A. Dayton, and Kerry L. Blanchard. "Acute Mixed Lineage Leukemia With an inv(8)(p11q13) Resulting in Fusion of the Genes for MOZ and TIF2." Blood 92, no. 6 (September 15, 1998): 2118–22. http://dx.doi.org/10.1182/blood.v92.6.2118.

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Abstract Chromosomal abnormalities in acute leukemia have led to the discovery of many genes involved in normal hematopoiesis and in malignant transformation. We have identified the fusion partners in an inv(8)(p11q13) from a patient with acute mixed lineage leukemia. We show by fluorescence in situ hybridization (FISH) analysis, Southern blotting, and reverse transcriptase-polymerase chain reaction (RT-PCR) that the genes for MOZ, monocytic leukemiazinc finger protein, and TIF2,transcriptional intermediary factor 2, are involved in the inv(8)(p11q13). We demonstrate that the inversion creates a fusion between the 5′ end of MOZ mRNA and the 3′ end of TIF2 mRNA maintaining the translational frame of the protein. The predicted fusion protein contains the zinc finger domains, the nuclear localization domains, the histone acetyltransferase (HAT) domain, and a portion of the acidic domain ofMOZ, coupled to the CREB-binding protein (CBP) interaction domain and the activation domains of TIF2. The breakpoint is distinct from the breakpoint in the t(8;16)(p11;p13) translocation in acute monocytic leukemia with erythrophagocytosis that fuses MOZ with CBP. The reciprocalTIF2-MOZ fusion gene is not expressed, perhaps as a result of a deletion near the chromosome 8 centromere. TheMOZ-TIF2 fusion is one of a new family of chromosomal rearrangements that associate HAT activity, transcriptional coactivation, and acute leukemia. © 1998 by The American Society of Hematology.

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Liang, Jian, Leonard Prouty, B. Jill Williams, Mark A. Dayton, and Kerry L. Blanchard. "Acute Mixed Lineage Leukemia With an inv(8)(p11q13) Resulting in Fusion of the Genes for MOZ and TIF2." Blood 92, no. 6 (September 15, 1998): 2118–22. http://dx.doi.org/10.1182/blood.v92.6.2118.418k09_2118_2122.

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Chromosomal abnormalities in acute leukemia have led to the discovery of many genes involved in normal hematopoiesis and in malignant transformation. We have identified the fusion partners in an inv(8)(p11q13) from a patient with acute mixed lineage leukemia. We show by fluorescence in situ hybridization (FISH) analysis, Southern blotting, and reverse transcriptase-polymerase chain reaction (RT-PCR) that the genes for MOZ, monocytic leukemiazinc finger protein, and TIF2,transcriptional intermediary factor 2, are involved in the inv(8)(p11q13). We demonstrate that the inversion creates a fusion between the 5′ end of MOZ mRNA and the 3′ end of TIF2 mRNA maintaining the translational frame of the protein. The predicted fusion protein contains the zinc finger domains, the nuclear localization domains, the histone acetyltransferase (HAT) domain, and a portion of the acidic domain ofMOZ, coupled to the CREB-binding protein (CBP) interaction domain and the activation domains of TIF2. The breakpoint is distinct from the breakpoint in the t(8;16)(p11;p13) translocation in acute monocytic leukemia with erythrophagocytosis that fuses MOZ with CBP. The reciprocalTIF2-MOZ fusion gene is not expressed, perhaps as a result of a deletion near the chromosome 8 centromere. TheMOZ-TIF2 fusion is one of a new family of chromosomal rearrangements that associate HAT activity, transcriptional coactivation, and acute leukemia. © 1998 by The American Society of Hematology.

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De, Sandip, Yuzhong Cheng, Ming-an Sun, Natalie D. Gehred, and Judith A. Kassis. "Structure and function of an ectopic Polycomb chromatin domain." Science Advances 5, no. 1 (January 2019): eaau9739. http://dx.doi.org/10.1126/sciadv.aau9739.

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Polycomb group proteins (PcGs) drive target gene repression and form large chromatin domains. InDrosophila, DNA elements known as Polycomb group response elements (PREs) recruit PcGs to the DNA. We have shown that, within theinvected-engrailed(inv-en) Polycomb domain, strong, constitutive PREs are dispensable for Polycomb domain structure and function. We suggest that the endogenous chromosomal location imparts stability to this Polycomb domain. To test this possibility, a 79-kbentransgene was inserted into other chromosomal locations. This transgene is functional and forms a Polycomb domain. The spreading of the H3K27me3 repressive mark, characteristic of PcG domains, varies depending on the chromatin context of the transgene. Unlike at the endogenous locus, deletion of the strong, constitutive PREs from the transgene leads to both loss- and gain-of function phenotypes, demonstrating the important role of these regulatory elements. Our data show that chromatin context plays an important role in Polycomb domain structure and function.

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Sullivan, K. F., M. Hechenberger, and K. Masri. "Human CENP-A contains a histone H3 related histone fold domain that is required for targeting to the centromere." Journal of Cell Biology 127, no. 3 (November 1, 1994): 581–92. http://dx.doi.org/10.1083/jcb.127.3.581.

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Centromeres are the differentiated chromosomal domains that specify the mitotic behavior of chromosomes. To examine the molecular basis for the specification of centromeric chromatin, we have cloned a human cDNA that encodes the 17-kD histone-like centromere antigen, CENP-A. Two domains are evident in the 140 aa CENP-A polypeptide: a unique NH2-terminal domain and a 93-amino acid COOH-terminal domain that shares 62% identity with nucleosomal core protein, histone H3. An epitope tagged derivative of CENP-A was faithfully targeted to centromeres when expressed in a variety of animal cells and this targeting activity was shown to reside in the histone-like COOH-terminal domain of CENP-A. These data clearly indicate that the assembly of centromeres is driven, at least in part, by the incorporation of a novel core histone into centromeric chromatin.

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Martin, Rui Pires, and Stephen A. Krawetz. "Characterizing a Human Lysyl Oxidase Chromosomal Domain." Molecular Biotechnology 15, no. 3 (2000): 225–36. http://dx.doi.org/10.1385/mb:15:3:225.

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24

Sofueva, Sevil, Eitan Yaffe, Wen-Ching Chan, Dimitra Georgopoulou, Matteo Vietri Rudan, Hegias Mira-Bontenbal, Steven M. Pollard, Gary P. Schroth, Amos Tanay, and Suzana Hadjur. "Cohesin-mediated interactions organize chromosomal domain architecture." EMBO Journal 32, no. 24 (November 1, 2013): 3119–29. http://dx.doi.org/10.1038/emboj.2013.237.

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25

Xia, Yu-Rong, Bogi Andersen, Margarete Mehrabian, Anh T. Diep, Craig H. Warden, T. Mohandas, Robert J. McEvilly, Michael G. Rosenfeld, and Aldons J. Lusis. "Chromosomal Organization of Mammalian POU Domain Factors." Genomics 18, no. 1 (October 1993): 126–30. http://dx.doi.org/10.1006/geno.1993.1435.

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26

Bonner, Mary Kate, Julian Haase, Hayden Saunders, Hindol Gupta, Biyun Iris Li, and Alexander E. Kelly. "The Borealin dimerization domain interacts with Sgo1 to drive Aurora B–mediated spindle assembly." Molecular Biology of the Cell 31, no. 20 (September 15, 2020): 2207–18. http://dx.doi.org/10.1091/mbc.e20-05-0341.

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This study provides the molecular mechanism for the interaction of Sgo1 with the chromosomal passenger complex and explores the specific role of Sgo1 in regulating Aurora B functions that ensure the equal segregation of chromosomes.

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27

Essers, Jeroen, Wiggert A. van Cappellen, Arjan F. Theil, Ellen van Drunen, Nicolaas G. J. Jaspers, Jan H. J. Hoeijmakers, Claire Wyman, Wim Vermeulen, and Roland Kanaar. "Dynamics of Relative Chromosome Position during the Cell Cycle." Molecular Biology of the Cell 16, no. 2 (February 2005): 769–75. http://dx.doi.org/10.1091/mbc.e04-10-0876.

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The position of chromosomal neighborhoods in living cells was followed using three different methods for marking chromosomal domains occupying arbitrary locations in the nucleus; photobleaching of GFP-labeled histone H2B, local UV-marked DNA, and photobleaching of fluorescently labeled DNA. All methods revealed that global chromosomal organization can be reestablished through one cell division from mother to daughters. By simultaneously monitoring cell cycle stage in the cells in which relative chromosomal domain positions were tracked, we observed that chromosomal neighborhood organization is apparently lost in the early G1 phase of the cell cycle. However, the daughter cells eventually regain the general chromosomal organization pattern of their mothers, suggesting an active mechanism could be at play to reestablish chromosomal neighborhoods.

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Laloraya, Shikha, Vincent Guacci, and Douglas Koshland. "Chromosomal Addresses of the Cohesin Component Mcd1p." Journal of Cell Biology 151, no. 5 (November 27, 2000): 1047–56. http://dx.doi.org/10.1083/jcb.151.5.1047.

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We identified the chromosomal addresses of a cohesin subunit, Mcd1p, in vivo by chromatin immunoprecipitation coupled with high resolution PCR-based chromosomal walking. The mapping of new Mcd1p-binding sites (cohesin-associated regions [CARs]) in single-copy sequences of several chromosomes establish their spacing (∼9 kb), their sequestration to intergenic regions, and their association with AT-rich sequences as general genomic properties of CARs. We show that cohesins are not excluded from telomere proximal regions, and the enrichment of cohesins at the centromere at mitosis reflects de novo loading. The average size of a CAR is 0.8–1.0 kb. They lie at the boundaries of transcriptionally silenced regions, suggesting they play a direct role in defining the silent chromatin domain. Finally, we identify CARs in tandem (rDNA) and interspersed repetitive DNA (Ty2 and subtelomeric repeats). Each 9-kb rDNA repeat has a single CAR proximal to the 5S gene. Thus, the periodicity of CARs in single-copy regions and the rDNA repeats is conserved. The presence and spacing of CARs in repetitive DNA has important implications for genomic stability and chromosome packaging/condensation.

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Migliazza, A., L. Lombardi, M. Rocchi, D. Trecca, CC Chang, R. Antonacci, NS Fracchiolla, P. Ciana, AT Maiolo, and A. Neri. "Heterogeneous chromosomal aberrations generate 3' truncations of the NFKB2/lyt-10 gene in lymphoid malignancies." Blood 84, no. 11 (December 1, 1994): 3850–60. http://dx.doi.org/10.1182/blood.v84.11.3850.bloodjournal84113850.

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The NFKB2(lyt-10) gene codes for a protein that is a member of the NK- kappa B/rel family of transcription factors containing a DNA-binding rel domain and a carboxy-terminal ankyrin-like domain. The NFKB2 gene represents a candidate proto-oncogene, since it has been found to be involved in a chromosomal translocation t(10;14)(q24;q32) in one case of B-cell lymphoma and in gene rearrangements in various types of lymphoid malignancies. To elucidate the structural and functional consequences of NFKB2 rearrangements, we report the molecular characterization of three novel rearranged NFKB2 genes in lymphoid tumors. In one case of multiple myeloma (MM), cloning and sequencing analysis of reciprocal breakpoint sites showed that they occurred within intron 15 of the NFKB2 gene and led to the complete deletion of the 32 portion of the gene coding for the ankyrin domain. Fluorescent in situ hybridization (FISH) analysis showed that the novel regions involved in the NFKB2 rearrangement originated from chromosome 7q34, thus implying the occurrence of a t(7;10)(q34;q24) reciprocal chromosomal translocation. In one case of T-cell cutaneous lymphoma (CTCL) and in one of B-cell chronic lymphocytic leukemia (B-CLL), NFKB2 rearrangements occurred, respectively, within exons 18 and 20 of the gene and involved recombinations with distinct regions of chromosome 10q24. Molecular analysis suggested that these rearrangements may occur as a consequence of small internal chromosomal deletions. In both of these cases, the rearrangements led to specific carboxy-terminal truncations of NFKB2 generating abnormal transcripts that coded for proteins lacking portions of the ankyrin domain. These proteins localize in the nucleus, suggesting their constitutive activation in vivo. Overall, our results indicate that NFKB2 rearrangements in lymphoid neoplasia may occur by heterogeneous mechanisms, including internal chromosomal deletion or chromosomal translocation. The common consequence of these rearrangements appears to be the deletion of 32 sequences of NFKB2 leading to the production of carboxy-truncated constitutively nuclear proteins that may be involved in tumorigenesis.

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Filipski, J., E. Svetlova, N. Avril-Fournout, P. Deschavanne, and M. Bellis. "New approaches to the mapping of chromosomal domains." Acta Biochimica Polonica 43, no. 2 (June 30, 1996): 289–92. http://dx.doi.org/10.18388/abp.1996_4496.

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Although it is generally accepted that the chromosome is divided into elementary subunits, the structural and functional domains, the organisation of these structures at the molecular level is not well understood. In particular, the domain boundaries are not easily identifiable. Several possible candidates such as MARs/SARs, insulators, LCRs, palindromic sequences, or easily melting sequences have been found in the regions having properties one would except for boundaries. None of these elements, however, has been found in all of the constructs functioning as boundaries in tests in vivo. Recent work suggests that the common denominator might be the presence og GC-rich oligonucleotide stretches and the formation of the chromatin hypersensitive sites. A model is discussed in which "unusual" structures, in particular the four-stranded DNA sequence elements containing unpaired bases, play the role of domain boundaries.

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Kapoor, Priya, and Lori Frappier. "EBNA1 Partitions Epstein-Barr Virus Plasmids in Yeast Cells by Attaching to Human EBNA1-Binding Protein 2 on Mitotic Chromosomes." Journal of Virology 77, no. 12 (June 15, 2003): 6946–56. http://dx.doi.org/10.1128/jvi.77.12.6946-6956.2003.

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ABSTRACT Epstein-Barr virus (EBV) episomal genomes are stably maintained in human cells and are partitioned during cell division by mitotic chromosome attachment. Partitioning is mediated by the viral EBNA1 protein, which binds both the EBV segregation element (FR) and a mitotic chromosomal component. We previously showed that the segregation of EBV-based plasmids can be reconstituted in Saccharomyces cerevisiae and is absolutely dependent on EBNA1, the EBV FR sequence, and the human EBNA1-binding protein 2 (EBP2). We have now used this yeast system to elucidate the functional contribution of human EBP2 to EBNA1-mediated plasmid partitioning. Human EBP2 was found to attach to yeast mitotic chromosomes in a cell cycle-dependent manner and cause EBNA1 to associate with the mitotic chromosomes. The domain of human EBP2 that binds both yeast and human chromosomes was mapped and shown to be functionally distinct from the EBNA1-binding domain. The functionality and localization of human EBP2 mutants and fusion proteins indicated that the attachment of EBNA1 to mitotic chromosomes is crucial for EBV plasmid segregation in S. cerevisiae, as it is in humans, and that this is the contribution of human EBP2. The results also indicate that plasmid segregation in S. cerevisiae can occur through chromosome attachment.

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Noselli, S., F. Payre, and A. Vincent. "Zinc fingers and other domains cooperate in binding of Drosophila sry beta and delta proteins at specific chromosomal sites." Molecular and Cellular Biology 12, no. 2 (February 1992): 724–33. http://dx.doi.org/10.1128/mcb.12.2.724.

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The closely related Drosophila serendipity (sry) beta and delta zinc finger proteins display consensus in vitro DNA recognition sequences differing by 4 of 13 nucleotide positions and bind in vivo to distinct sets of sites on polytene chromosomes. We compared the pattern of in vivo chromosomal binding of deleted forms of the sry delta protein fused to beta-galactosidase and expressed in Drosophila transgenic lines. Results show that the carboxy-terminal DNA-binding finger domain is required and sufficient for binding at specific chromosomal sites but that this binding does not nearly reproduce the wild-type pattern. An NH2-terminal domain of the sry delta protein is essential to its specificity of in vivo interaction with chromatin. In vitro and in vivo experiments using reciprocal finger swap between the sry beta and delta proteins suggest that the in vivo specificity is dependent on selective protein-protein contacts at defined chromosomal sites, in addition to DNA specific recognition.

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33

Noselli, S., F. Payre, and A. Vincent. "Zinc fingers and other domains cooperate in binding of Drosophila sry beta and delta proteins at specific chromosomal sites." Molecular and Cellular Biology 12, no. 2 (February 1992): 724–33. http://dx.doi.org/10.1128/mcb.12.2.724-733.1992.

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The closely related Drosophila serendipity (sry) beta and delta zinc finger proteins display consensus in vitro DNA recognition sequences differing by 4 of 13 nucleotide positions and bind in vivo to distinct sets of sites on polytene chromosomes. We compared the pattern of in vivo chromosomal binding of deleted forms of the sry delta protein fused to beta-galactosidase and expressed in Drosophila transgenic lines. Results show that the carboxy-terminal DNA-binding finger domain is required and sufficient for binding at specific chromosomal sites but that this binding does not nearly reproduce the wild-type pattern. An NH2-terminal domain of the sry delta protein is essential to its specificity of in vivo interaction with chromatin. In vitro and in vivo experiments using reciprocal finger swap between the sry beta and delta proteins suggest that the in vivo specificity is dependent on selective protein-protein contacts at defined chromosomal sites, in addition to DNA specific recognition.

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34

Howe, Kerstin, Philipp H. Schiffer, Julia Zielinski, Thomas Wiehe, Gavin K. Laird, John C. Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. "Structure and evolutionary history of a large family of NLR proteins in the zebrafish." Open Biology 6, no. 4 (April 2016): 160009. http://dx.doi.org/10.1098/rsob.160009.

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Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system.

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Rulten, Stuart L., Felipe Cortes-Ledesma, Liandi Guo, Natasha J. Iles, and Keith W. Caldecott. "APLF (C2orf13) Is a Novel Component of Poly(ADP-Ribose) Signaling in Mammalian Cells." Molecular and Cellular Biology 28, no. 14 (May 12, 2008): 4620–28. http://dx.doi.org/10.1128/mcb.02243-07.

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ABSTRACT APLF is a novel protein of unknown function that accumulates at sites of chromosomal DNA strand breakage via forkhead-associated (FHA) domain-mediated interactions with XRCC1 and XRCC4. APLF can also accumulate at sites of chromosomal DNA strand breaks independently of the FHA domain via an unidentified mechanism that requires a highly conserved C-terminal tandem zinc finger domain. Here, we show that the zinc finger domain binds tightly to poly(ADP-ribose), a polymeric posttranslational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. Protein poly(ADP-ribosyl)ation is tightly regulated and defects in either its synthesis or degradation slow global rates of chromosomal single-strand break repair. Interestingly, APLF negatively affects poly(ADP-ribosyl)ation in vitro, and this activity is dependent on its capacity to bind the polymer. In addition, transient overexpression in human A549 cells of full-length APLF or a C-terminal fragment encoding the tandem zinc finger domain greatly suppresses the appearance of poly(ADP-ribose), in a zinc finger-dependent manner. We conclude that APLF can accumulate at sites of chromosomal damage via zinc finger-mediated binding to poly(ADP-ribose) and is a novel component of poly(ADP-ribose) signaling in mammalian cells.

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36

Lu, L., and J. Tower. "A transcriptional insulator element, the su(Hw) binding site, protects a chromosomal DNA replication origin from position effects." Molecular and Cellular Biology 17, no. 4 (April 1997): 2202–6. http://dx.doi.org/10.1128/mcb.17.4.2202.

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Eukaryotic chromosomes are organized into domains of activity for both transcription and DNA replication. Transcriptional "border," or "insulator," elements have been implicated in mediating the organization of transcriptional domains. However, the DNA sequence elements which might demarcate domains of DNA replication activity are unknown. su(Hw) protein binding sites [su(Hw)BSs] are potent transcriptional insulator elements which can block enhancer action, as well as positive and negative chromosomal position effects. Here we report that flanking su(Hw)BSs can also create a chromosomal domain permissible for activity of the chorion gene DNA replication origin. During Drosophila oogenesis the chorion (eggshell) gene loci are amplified approximately 80-fold through repeated initiation of DNA replication. The cis-acting amplification control element, on the third chromosome (ACE3), is required for high levels of amplification initiating at the nearby major origin of replication, Ori-beta. A transgenic chorion locus construct containing ACE3 and Ori-beta was able to amplify but was extremely sensitive to position effects: only 7 of 21 independent insertions amplified >10-fold. The inclusion of flanking su(Hw)BSs in the construct dramatically protected DNA replication from position effects: 31 of 31 insertions now amplified >10-fold, and this protection was reduced in a su(Hw) mutant background. Amplification was equal on both sides of the su(Hw)BS, demonstrating that replication fork passage is not significantly impeded by these sites. Inclusion of only a single su(Hw)BS in the construct did not detectably protect the chorion gene DNA replication origin from position effects.

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Logsdon, Glennis A., Evelyne J. Barrey, Emily A. Bassett, Jamie E. DeNizio, Lucie Y. Guo, Tanya Panchenko, Jennine M. Dawicki-McKenna, Patrick Heun, and Ben E. Black. "Both tails and the centromere targeting domain of CENP-A are required for centromere establishment." Journal of Cell Biology 208, no. 5 (February 23, 2015): 521–31. http://dx.doi.org/10.1083/jcb.201412011.

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The centromere—defined by the presence of nucleosomes containing the histone H3 variant, CENP-A—is the chromosomal locus required for the accurate segregation of chromosomes during cell division. Although the sequence determinants of human CENP-A required to maintain a centromere were reported, those that are required for early steps in establishing a new centromere are unknown. In this paper, we used gain-of-function histone H3 chimeras containing various regions unique to CENP-A to investigate early events in centromere establishment. We targeted histone H3 chimeras to chromosomally integrated Lac operator sequences by fusing each of the chimeras to the Lac repressor. Using this approach, we found surprising contributions from a small portion of the N-terminal tail and the CENP-A targeting domain in the initial recruitment of two essential constitutive centromere proteins, CENP-C and CENP-T. Our results indicate that the regions of CENP-A required for early events in centromere establishment differ from those that are required for maintaining centromere identity.

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Deshpande, A. M., and C. S. Newlon. "The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae." Molecular and Cellular Biology 12, no. 10 (October 1992): 4305–13. http://dx.doi.org/10.1128/mcb.12.10.4305.

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Replication origins have been mapped to positions that coincide, within experimental error (several hundred base pairs), with ARS elements. To determine whether the DNA sequences required for ARS function on plasmids are required for chromosomal origin function, the chromosomal copy of ARS306 was deleted and the chromosomal copy of ARS307 was replaced with mutant derivatives of ARS307 containing single point mutations in domain A within the ARS core consensus sequence. The chromosomal origin function of these derivatives was assayed by two-dimensional agarose gel electrophoresis. Deletion of ARS306 deleted the associated replication origin. The effects on chromosomal origin function of mutations in domain A paralleled their effects on ARS function, as measured by plasmid stability. These results demonstrate that chromosomal origin function is a property of the ARS element itself.

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Deshpande, A. M., and C. S. Newlon. "The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae." Molecular and Cellular Biology 12, no. 10 (October 1992): 4305–13. http://dx.doi.org/10.1128/mcb.12.10.4305-4313.1992.

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Replication origins have been mapped to positions that coincide, within experimental error (several hundred base pairs), with ARS elements. To determine whether the DNA sequences required for ARS function on plasmids are required for chromosomal origin function, the chromosomal copy of ARS306 was deleted and the chromosomal copy of ARS307 was replaced with mutant derivatives of ARS307 containing single point mutations in domain A within the ARS core consensus sequence. The chromosomal origin function of these derivatives was assayed by two-dimensional agarose gel electrophoresis. Deletion of ARS306 deleted the associated replication origin. The effects on chromosomal origin function of mutations in domain A paralleled their effects on ARS function, as measured by plasmid stability. These results demonstrate that chromosomal origin function is a property of the ARS element itself.

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40

Uzawa, S., and M. Yanagida. "Visualization of centromeric and nucleolar DNA in fission yeast by fluorescence in situ hybridization." Journal of Cell Science 101, no. 2 (February 1, 1992): 267–75. http://dx.doi.org/10.1242/jcs.101.2.267.

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The nucleolar and centromeric DNAs of the fission yeast Schizosaccharomyces pombe were visualized in the nucleus by fluorescence in situ hybridization using repetitive ribosomal and centromeric DNAs as the probes. The rDNAs were seen in the nuclear domain previously assigned as nucleolar, that is, the region into which the rod-like chromatin protrudes from the hemispherical chromosomal domain. Using mitotically-arrested cells containing condensed chromosomes, it was demonstrated that the rDNAs were present on the smallest chromosome III, consistent with genetic data. Using a centromeric repetitive element as the hybridization probe, the centromere of chromosome III, cen3, which contains the largest number of the repetitive elements, was visualized. The centromere in interphase cells is located near the periphery of the nucleus as a single dot. Early in mitosis, however, it divides into two and is situated in the middle of the short mitotic spindle. After spindle extension in anaphase, the centromeric DNA is present at both ends of the spindle, that is, near the spindle pole bodies. The movement of cen3 during mitosis (anaphase A and B) is discussed in relation to spindle dynamics and chromosome separation.

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Soler-Vila, Paula, Pol Cuscó, Irene Farabella, Marco Di Stefano, and Marc A. Marti-Renom. "Hierarchical chromatin organization detected by TADpole." Nucleic Acids Research 48, no. 7 (February 21, 2020): e39-e39. http://dx.doi.org/10.1093/nar/gkaa087.

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Abstract The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse.

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Lawrence, Jeanne B., and Christine M. Clemson. "Gene associations: true romance or chance meeting in a nuclear neighborhood?" Journal of Cell Biology 182, no. 6 (September 22, 2008): 1035–38. http://dx.doi.org/10.1083/jcb.200808121.

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Many recent studies have raised interest in the nuclear associations of coregulated genes from different chromosomes, often evoking interpretations of gene–gene interactions, communication, and even “romance.” However, in some cases, the associations may be indirect and infrequent and may reflect the segregation of active and inactive genes into different nuclear compartments. The study by Brown et al. (see p. 1083 of this issue) reports that the apparent association of erythroid genes is not a direct interaction nor colocalization to one tiny transcription factory but arises as a result of the known clustering of many active genes with larger splicing factor–rich speckles (a.k.a., SC35-defined domains). This clustering appears largely stochastic but is impacted by the chromosomal neighborhood of the gene as well as its transcriptional status. The study adds a new twist by examining the same gene in a foreign chromosomal context, providing evidence that this impacts a gene's propensity to form gene–domain (or apparent gene–gene) associations within nuclei.

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Qian, Chengmin, Qiang Zhang, SiDe Li, Lei Zeng, Martin J. Walsh, and Ming-Ming Zhou. "Structure and chromosomal DNA binding of the SWIRM domain." Nature Structural & Molecular Biology 12, no. 12 (November 20, 2005): 1078–85. http://dx.doi.org/10.1038/nsmb1022.

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Kim, Heui-Soo. "Human cts18.1 gene: chromosomal localization and PH-domain analysis." Genes & Genetic Systems 73, no. 5 (1998): 293–96. http://dx.doi.org/10.1266/ggs.73.293.

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Wray, Justin, Elizabeth A. Williamson, Sean Chester, Jacqueline Farrington, Rosa Sterk, David M. Weinstock, Maria Jasin, Suk-Hee Lee, Jac A. Nickoloff, and Robert Hromas. "The transposase domain protein Metnase/SETMAR suppresses chromosomal translocations." Cancer Genetics and Cytogenetics 200, no. 2 (July 2010): 184–90. http://dx.doi.org/10.1016/j.cancergencyto.2010.04.011.

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Kellum, R., and P. Schedl. "A group of scs elements function as domain boundaries in an enhancer-blocking assay." Molecular and Cellular Biology 12, no. 5 (May 1992): 2424–31. http://dx.doi.org/10.1128/mcb.12.5.2424.

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Chromosomes of higher eukaryotes are thought to be organized into a series of discrete and topologically independent higher-order domains. In addition to providing a mechanism for chromatin compaction, these higher-order domains are thought to define independent units of gene activity. Implicit in most models for the folding of the chromatin fiber are special nucleoprotein structures, the domain boundaries, which serve to delimit each higher-order chromosomal domain. We have used an "enhancer-blocking assay" to test putative domain boundaries for boundary function in vivo. This assay is based on the notion that in delimiting independent units of gene activity, domain boundaries should be able to restrict the scope of activity of enhancer elements to genes which reside within the same domain. In this case, interposing a boundary between an enhancer and a promoter should block the action of the enhancer. In the experiments reported here, we have used the yolk protein-1 enhancer element and an hsp70 promoter:lacZ fusion gene to test putative boundary DNA segments for enhancer-blocking activity. We have found that several scs-like elements are capable of blocking the action of the yp-1 enhancer when placed between it and the hsp70 promoter. In contrast, a MAR/SAR DNA segment and another spacer DNA segment had no apparent effect on enhancer activity.

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Kellum, R., and P. Schedl. "A group of scs elements function as domain boundaries in an enhancer-blocking assay." Molecular and Cellular Biology 12, no. 5 (May 1992): 2424–31. http://dx.doi.org/10.1128/mcb.12.5.2424-2431.1992.

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Chromosomes of higher eukaryotes are thought to be organized into a series of discrete and topologically independent higher-order domains. In addition to providing a mechanism for chromatin compaction, these higher-order domains are thought to define independent units of gene activity. Implicit in most models for the folding of the chromatin fiber are special nucleoprotein structures, the domain boundaries, which serve to delimit each higher-order chromosomal domain. We have used an "enhancer-blocking assay" to test putative domain boundaries for boundary function in vivo. This assay is based on the notion that in delimiting independent units of gene activity, domain boundaries should be able to restrict the scope of activity of enhancer elements to genes which reside within the same domain. In this case, interposing a boundary between an enhancer and a promoter should block the action of the enhancer. In the experiments reported here, we have used the yolk protein-1 enhancer element and an hsp70 promoter:lacZ fusion gene to test putative boundary DNA segments for enhancer-blocking activity. We have found that several scs-like elements are capable of blocking the action of the yp-1 enhancer when placed between it and the hsp70 promoter. In contrast, a MAR/SAR DNA segment and another spacer DNA segment had no apparent effect on enhancer activity.

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Dorris, David R., and Kevin Struhl. "Artificial Recruitment of TFIID, but Not RNA Polymerase II Holoenzyme, Activates Transcription in Mammalian Cells." Molecular and Cellular Biology 20, no. 12 (June 15, 2000): 4350–58. http://dx.doi.org/10.1128/mcb.20.12.4350-4358.2000.

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ABSTRACT In yeast cells, transcriptional activation occurs when the RNA polymerase II (Pol II) machinery is artificially recruited to a promoter by fusing individual components of this machinery to a DNA-binding domain. Here, we show that artificial recruitment of components of the TFIID complex can activate transcription in mammalian cells. Surprisingly, artificial recruitment of TATA-binding protein (TBP) activates transiently transfected and chromosomally integrated promoters with equal efficiency, whereas artificial recruitment of TBP-associated factors activates only chromosomal reporters. In contrast, artificial recruitment of various components of the mammalian Pol II holoenzyme does not confer transcriptional activation, nor does it result in synergistic activation in combination with natural activation domains. In the one case examined in more detail, the Srb7 fusion failed to activate despite being associated with the Pol II holoenzyme and being directly recruited to the promoter. Interestingly, some acidic activation domains are less effective when the promoter is chromosomally integrated rather than transiently transfected, whereas the Sp1 glutamine-rich activation domain is more effective on integrated reporters. Thus, yeast and mammalian cells differ with respect to transcriptional activation by artificial recruitment of the Pol II holoenzyme.

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Magnitov, Mikhail D., Veronika S. Kuznetsova, Sergey V. Ulianov, Sergey V. Razin, and Alexander V. Tyakht. "Benchmark of software tools for prokaryotic chromosomal interaction domain identification." Bioinformatics 36, no. 17 (August 27, 2020): 4560–67. http://dx.doi.org/10.1093/bioinformatics/btaa555.

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Abstract Motivation The application of genome-wide chromosome conformation capture (3C) methods to prokaryotes provided insights into the spatial organization of their genomes and identified patterns conserved across the tree of life, such as chromatin compartments and contact domains. Prokaryotic genomes vary in GC content and the density of restriction sites along the chromosome, suggesting that these properties should be considered when planning experiments and choosing appropriate software for data processing. Diverse algorithms are available for the analysis of eukaryotic chromatin contact maps, but their potential application to prokaryotic data has not yet been evaluated. Results Here, we present a comparative analysis of domain calling algorithms using available single-microbe experimental data. We evaluated the algorithms’ intra-dataset reproducibility, concordance with other tools and sensitivity to coverage and resolution of contact maps. Using RNA-seq as an example, we showed how orthogonal biological data can be utilized to validate the reliability and significance of annotated domains. We also suggest that in silico simulations of contact maps can be used to choose optimal restriction enzymes and estimate theoretical map resolutions before the experiment. Our results provide guidelines for researchers investigating microbes and microbial communities using high-throughput 3C assays such as Hi-C and 3C-seq. Availability and implementation The code of the analysis is available at https://github.com/magnitov/prokaryotic_cids. Supplementary information Supplementary data are available at Bioinformatics online.

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Bi, Xin. "Domains of Gene Silencing Near the Left End of Chromosome III inSaccharomyces cerevisiae." Genetics 160, no. 4 (April 1, 2002): 1401–7. http://dx.doi.org/10.1093/genetics/160.4.1401.

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AbstractIn Saccharomyces cerevisiae the HM loci and regions adjacent to the telomeres are transcriptionally silent. HML is situated 11 kb from the left telomere of chromosome III. I have systematically examined gene silencing along this 11-kb chromosomal region. I found that silencing extends at least 1.1 kb beyond HML, indicating that the HML E silencer acts on both sides. Moreover, I obtained evidence indicating that a 0.71-kb sequence near the E silencer acts as a barrier to the spread of silencing and coincides with the left boundary of the silent HML domain. I also showed that silencing at the telomere is limited to an ~2-kb domain. On the other hand, an ~7-kb region between HML and the telomere is not silenced by HML or the telomere. These results provide a clear example of organization of the eukaryotic genome into interspersed domains with distinct potentials for gene expression.

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Journal articles on the topic 'Chromosomal domain'

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