Relevant bibliographies by topics / CTCF protein

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Academic literature on the topic 'CTCF protein'

Author: Grafiati
Published: 18 May 2024

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Journal articles on the topic "CTCF protein"

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Voutsadakis, Ioannis. "Molecular Lesions of Insulator CTCF and Its Paralogue CTCFL (BORIS) in Cancer: An Analysis from Published Genomic Studies." High-Throughput 7, no. 4 (October 1, 2018): 30. http://dx.doi.org/10.3390/ht7040030.

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CTCF (CCCTC-binding factor) is a transcription regulator with hundreds of binding sites in the human genome. It has a main function as an insulator protein, defining together with cohesins the boundaries of areas of the genome called topologically associating domains (TADs). TADs contain regulatory elements such as enhancers which function as regulators of the transcription of genes inside the boundaries of the TAD while they are restricted from regulating genes outside these boundaries. This paper will examine the most common genetic lesions of CTCF as well as its related protein CTCFL (CTCF-like also called BORIS) in cancer using publicly available data from published genomic studies. Cancer types where abnormalities in the two genes are more common will be examined for possible associations with underlying repair defects or other prevalent genetic lesions. The putative functional effects in CTCF and CTCFL lesions will also be explored.
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MacPherson, Melissa J., Linda G. Beatty, Wenjing Zhou, Minjie Du, and Paul D. Sadowski. "The CTCF Insulator Protein Is Posttranslationally Modified by SUMO." Molecular and Cellular Biology 29, no. 3 (November 24, 2008): 714–25. http://dx.doi.org/10.1128/mcb.00825-08.

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ABSTRACT The CTCF protein is a highly conserved zinc finger protein that is implicated in many aspects of gene regulation and nuclear organization. Its functions include the ability to act as a repressor of genes, including the c-myc oncogene. In this paper, we show that the CTCF protein can be posttranslationally modified by the small ubiquitin-like protein SUMO. CTCF is SUMOylated both in vivo and in vitro, and we identify two major sites of SUMOylation in the protein. The posttranslational modification of CTCF by the SUMO proteins does not affect its ability to bind to DNA in vitro. SUMOylation of CTCF contributes to the repressive function of CTCF on the c-myc P2 promoter. We also found that CTCF and the repressive Polycomb protein, Pc2, are colocalized to nuclear Polycomb bodies. The Pc2 protein may act as a SUMO E3 ligase for CTCF, strongly enhancing its modification by SUMO 2 and 3. These studies expand the repertoire of posttranslational modifications of CTCF and suggest roles for such modifications in its regulation of epigenetic states.
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Pugacheva, Elena M., Naoki Kubo, Dmitri Loukinov, Md Tajmul, Sungyun Kang, Alexander L. Kovalchuk, Alexander V. Strunnikov, Gabriel E. Zentner, Bing Ren, and Victor V. Lobanenkov. "CTCF mediates chromatin looping via N-terminal domain-dependent cohesin retention." Proceedings of the National Academy of Sciences 117, no. 4 (January 14, 2020): 2020–31. http://dx.doi.org/10.1073/pnas.1911708117.

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The DNA-binding protein CCCTC-binding factor (CTCF) and the cohesin complex function together to shape chromatin architecture in mammalian cells, but the molecular details of this process remain unclear. Here, we demonstrate that a 79-aa region within the CTCF N terminus is essential for cohesin positioning at CTCF binding sites and chromatin loop formation. However, the N terminus of CTCF fused to artificial zinc fingers was not sufficient to redirect cohesin to non-CTCF binding sites, indicating a lack of an autonomously functioning domain in CTCF responsible for cohesin positioning. BORIS (CTCFL), a germline-specific paralog of CTCF, was unable to anchor cohesin to CTCF DNA binding sites. Furthermore, CTCF–BORIS chimeric constructs provided evidence that, besides the N terminus of CTCF, the first two CTCF zinc fingers, and likely the 3D geometry of CTCF–DNA complexes, are also involved in cohesin retention. Based on this knowledge, we were able to convert BORIS into CTCF with respect to cohesin positioning, thus providing additional molecular details of the ability of CTCF to retain cohesin. Taken together, our data provide insight into the process by which DNA-bound CTCF constrains cohesin movement to shape spatiotemporal genome organization.
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Klenova, E. M., R. H. Nicolas, H. F. Paterson, A. F. Carne, C. M. Heath, G. H. Goodwin, P. E. Neiman, and V. V. Lobanenkov. "CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms." Molecular and Cellular Biology 13, no. 12 (December 1993): 7612–24. http://dx.doi.org/10.1128/mcb.13.12.7612-7624.1993.

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A novel sequence-specific DNA-binding protein, CTCF, which interacts with the chicken c-myc gene promoter, has been identified and partially characterized (V. V. Lobanenkov, R. H. Nicolas, V. V. Adler, H. Paterson, E. M. Klenova, A. V. Polotskaja, and G. H. Goodwin, Oncogene 5:1743-1753, 1990). In order to test directly whether binding of CTCF to one specific DNA region of the c-myc promoter is important for chicken c-myc transcription, we have determined which nucleotides within this GC-rich region are responsible for recognition of overlapping sites by CTCF and Sp1-like proteins. Using missing-contact analysis of all four nucleotides in both DNA strands and homogeneous CTCF protein purified by sequence-specific chromatography, we have identified three sets of nucleotides which contact either CTCF or two Sp1-like proteins binding within the same DNA region. Specific mutations of 3 of 15 purines required for CTCF binding were designed to eliminate binding of CTCF without altering the binding of other proteins. Electrophoretic mobility shift assay of nuclear extracts showed that the mutant DNA sequence did not bind CTCF but did bind two Sp1-like proteins. When introduced into a 3.3-kbp-long 5'-flanking noncoding c-myc sequence fused to a reporter CAT gene, the same mutation of the CTCF binding site resulted in 10- and 3-fold reductions, respectively, of transcription in two different (erythroid and myeloid) stably transfected chicken cell lines. Isolation and analysis of the CTCF cDNA encoding an 82-kDa form of CTCF protein shows that DNA-binding domain of CTCF is composed of 11 Zn fingers: 10 are of C2H2 class, and 1 is of C2HC class. CTCF was found to be abundant and conserved in cells of vertebrate species. We detected six major nuclear forms of CTCF protein differentially expressed in different chicken cell lines and tissues. We conclude that isoforms of 11-Zn-finger factor CTCF which are present in chicken hematopoietic HD3 and BM2 cells can act as a positive regulator of the chicken c-myc gene transcription. Possible functions of other CTCF forms are discussed.
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Klenova, E. M., R. H. Nicolas, H. F. Paterson, A. F. Carne, C. M. Heath, G. H. Goodwin, P. E. Neiman, and V. V. Lobanenkov. "CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms." Molecular and Cellular Biology 13, no. 12 (December 1993): 7612–24. http://dx.doi.org/10.1128/mcb.13.12.7612.

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A novel sequence-specific DNA-binding protein, CTCF, which interacts with the chicken c-myc gene promoter, has been identified and partially characterized (V. V. Lobanenkov, R. H. Nicolas, V. V. Adler, H. Paterson, E. M. Klenova, A. V. Polotskaja, and G. H. Goodwin, Oncogene 5:1743-1753, 1990). In order to test directly whether binding of CTCF to one specific DNA region of the c-myc promoter is important for chicken c-myc transcription, we have determined which nucleotides within this GC-rich region are responsible for recognition of overlapping sites by CTCF and Sp1-like proteins. Using missing-contact analysis of all four nucleotides in both DNA strands and homogeneous CTCF protein purified by sequence-specific chromatography, we have identified three sets of nucleotides which contact either CTCF or two Sp1-like proteins binding within the same DNA region. Specific mutations of 3 of 15 purines required for CTCF binding were designed to eliminate binding of CTCF without altering the binding of other proteins. Electrophoretic mobility shift assay of nuclear extracts showed that the mutant DNA sequence did not bind CTCF but did bind two Sp1-like proteins. When introduced into a 3.3-kbp-long 5'-flanking noncoding c-myc sequence fused to a reporter CAT gene, the same mutation of the CTCF binding site resulted in 10- and 3-fold reductions, respectively, of transcription in two different (erythroid and myeloid) stably transfected chicken cell lines. Isolation and analysis of the CTCF cDNA encoding an 82-kDa form of CTCF protein shows that DNA-binding domain of CTCF is composed of 11 Zn fingers: 10 are of C2H2 class, and 1 is of C2HC class. CTCF was found to be abundant and conserved in cells of vertebrate species. We detected six major nuclear forms of CTCF protein differentially expressed in different chicken cell lines and tissues. We conclude that isoforms of 11-Zn-finger factor CTCF which are present in chicken hematopoietic HD3 and BM2 cells can act as a positive regulator of the chicken c-myc gene transcription. Possible functions of other CTCF forms are discussed.
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Wang, Jie, Yumei Wang, and Luo Lu. "De-SUMOylation of CCCTC Binding Factor (CTCF) in Hypoxic Stress-induced Human Corneal Epithelial Cells." Journal of Biological Chemistry 287, no. 15 (February 21, 2012): 12469–79. http://dx.doi.org/10.1074/jbc.m111.286641.

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Epigenetic factor CCCTC binding factor (CTCF) plays important roles in the genetic control of cell fate. Previous studies found that CTCF is positively and negatively regulated at the transcriptional level by epidermal growth factor (EGF) and ultraviolet (UV) stimulation, respectively. However, it is unknown whether other stresses modify the CTCF protein. Here, we report that regulation of CTCF by de-SUMOylation is dependent upon hypoxic and oxidative stresses. We found that stimulation of human corneal epithelial cells with hypoxic stress suppressed a high molecular mass form of CTCF (150 kDa), but not a lower molecular weight form of CTCF (130 kDa). Further investigation revealed that the hypoxic stress-suppressed 150-kDa CTCF was a small ubiquitin-related modifier (SUMO)ylated form of the protein. Hypoxic stress-induced de-SUMOylation of human CTCF was associated with lysine 74 and 689 residues, but not to the phosphorylation of CTCF. Overexpression of SENP1 induced de-SUMOylation of CTCF. However, knockdown of SENP1 could not rescue hypoxic stress-induced CTCF de-SUMOylation. Overexpression of SUMO1 and SUMO2 increased SUMOylation of CTCF and partially blocked hypoxic stress-induced CTCF de-SUMOylation, suggesting that free cellular SUMO proteins play roles in regulating hypoxia-induced CTCF de-SUMOylation. In addition, hypoxic stress significantly inhibited PAX6 mRNA and protein expressions by suppression of PAX6-P0 promoter activity. The result was further supported by data showing that knockdown of CTCF significantly enhanced expression of PAX6 and abolished hypoxia-induced suppression of PAX6. Thus, we conclude that hypoxic stress induces de-SUMOylation of CTCF to functionally regulate CTCF activity.
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Lehman, Bettina J., Fernando J. Lopez-Diaz, Thom P. Santisakultarm, Linjing Fang, Maxim N. Shokhirev, Kenneth E. Diffenderfer, Uri Manor, and Beverly M. Emerson. "Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress." PLOS Genetics 17, no. 1 (January 7, 2021): e1009277. http://dx.doi.org/10.1371/journal.pgen.1009277.

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The nuclear protein CCCTC-binding factor (CTCF) has diverse roles in chromatin architecture and gene regulation. Functionally, CTCF associates with thousands of genomic sites and interacts with proteins, such as cohesin, or non-coding RNAs to facilitate specific transcriptional programming. In this study, we examined CTCF during the cellular stress response in human primary cells using immune-blotting, quantitative real time-PCR, chromatin immunoprecipitation-sequence (ChIP-seq) analysis, mass spectrometry, RNA immunoprecipitation-sequence analysis (RIP-seq), and Airyscan confocal microscopy. Unexpectedly, we found that CTCF is exquisitely sensitive to diverse forms of stress in normal patient-derived human mammary epithelial cells (HMECs). In HMECs, a subset of CTCF protein forms complexes that localize to Serine/arginine-rich splicing factor (SC-35)-containing nuclear speckles. Upon stress, this species of CTCF protein is rapidly downregulated by changes in protein stability, resulting in loss of CTCF from SC-35 nuclear speckles and changes in CTCF-RNA interactions. Our ChIP-seq analysis indicated that CTCF binding to genomic DNA is largely unchanged. Restoration of the stress-sensitive pool of CTCF protein abundance and re-localization to nuclear speckles can be achieved by inhibition of proteasome-mediated degradation. Surprisingly, we observed the same characteristics of the stress response during neuronal differentiation of human pluripotent stem cells (hPSCs). CTCF forms stress-sensitive complexes that localize to SC-35 nuclear speckles during a specific stage of neuronal commitment/development but not in differentiated neurons. We speculate that these particular CTCF complexes serve a role in RNA processing that may be intimately linked with specific genes in the vicinity of nuclear speckles, potentially to maintain cells in a certain differentiation state, that is dynamically regulated by environmental signals. The stress-regulated activity of CTCF is uncoupled in persistently stressed, epigenetically re-programmed “variant” HMECs and certain cancer cell lines. These results reveal new insights into CTCF function in cell differentiation and the stress-response with implications for oxidative damage-induced cancer initiation and neuro-degenerative diseases.
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Daruliza Kernain and Shaharum Shamsuddin. "Interaction between Two Transcriptional Factors CTCF and YB-1 – Truncated domains in Brain Cancer Cell line." International Journal of Research in Pharmaceutical Sciences 10, no. 4 (October 16, 2019): 3332–38. http://dx.doi.org/10.26452/ijrps.v10i4.1642.

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CTCF is a protein involved in the regulation of transcription, insulator function, and the X-chromosome inactivation. It is an 11 ZF transcriptional factor which is highly conserved between the species. Identification of proteins interacting with CTCF can help to elucidate the function in the cell. Previously reported studies had identified numerous CTCF protein interacting partners, and one of the interacting partners chosen in this study is YB-1. Brain cancer cell –RGBM was selected as a model to study the interaction between CTCF and YB-1. Firstly, proteins were transformed and expressed in the bacterial expression system, and these proteins were chosen to further map the interaction via pull-down assay. Results showed CTCF-ZF was the only domain able to binds to YB-1 CSD. Other truncated areas did not show any interaction hence demonstrating the interaction between these two proteins took place at the ZF for CTCF and CSD for YB-1. Next, the significant of the interaction was further characterized using the mammalian two-hybrid system. Results show strong interaction when both we co-transfected into RGBM cells. Thus, this study shows a significant binding between CTCF/YB-1 interaction in the brain cell line.
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Chernukhin, Igor, Shaharum Shamsuddin, Sung Yun Kang, Rosita Bergström, Yoo-Wook Kwon, WenQiang Yu, Joanne Whitehead, et al. "CTCF Interacts with and Recruits the Largest Subunit of RNA Polymerase II to CTCF Target Sites Genome-Wide." Molecular and Cellular Biology 27, no. 5 (January 8, 2007): 1631–48. http://dx.doi.org/10.1128/mcb.01993-06.

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ABSTRACT CTCF is a transcription factor with highly versatile functions ranging from gene activation and repression to the regulation of insulator function and imprinting. Although many of these functions rely on CTCF-DNA interactions, it is an emerging realization that CTCF-dependent molecular processes involve CTCF interactions with other proteins. In this study, we report the association of a subpopulation of CTCF with the RNA polymerase II (Pol II) protein complex. We identified the largest subunit of Pol II (LS Pol II) as a protein significantly colocalizing with CTCF in the nucleus and specifically interacting with CTCF in vivo and in vitro. The role of CTCF as a link between DNA and LS Pol II has been reinforced by the observation that the association of LS Pol II with CTCF target sites in vivo depends on intact CTCF binding sequences. “Serial” chromatin immunoprecipitation (ChIP) analysis revealed that both CTCF and LS Pol II were present at the β-globin insulator in proliferating HD3 cells but not in differentiated globin synthesizing HD3 cells. Further, a single wild-type CTCF target site (N-Myc-CTCF), but not the mutant site deficient for CTCF binding, was sufficient to activate the transcription from the promoterless reporter gene in stably transfected cells. Finally, a ChIP-on-ChIP hybridization assay using microarrays of a library of CTCF target sites revealed that many intergenic CTCF target sequences interacted with both CTCF and LS Pol II. We discuss the possible implications of our observations with respect to plausible mechanisms of transcriptional regulation via a CTCF-mediated direct link of LS Pol II to the DNA.
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Maksimenko, Oksana G., Dariya V. Fursenko, Elena V. Belova, and Pavel G. Georgiev. "CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers." Acta Naturae 13, no. 1 (March 15, 2021): 31–46. http://dx.doi.org/10.32607/actanaturae.11206.

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In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.
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Dissertations / Theses on the topic "CTCF protein"

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Fischer, Sabine. "Inducible systems for the characterization of insulating and repressing motifs." kostenfrei, 2009. http://d-nb.info/999863568/34.

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Nobelen, Suzanne van de. "Touched by CTCF analysis of a multi-functional zinc finger protein /." [S.l.] : Rotterdam : [The Author] ; Erasmus University [Host], 2008. http://hdl.handle.net/1765/12282.

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Panzer, Imke [Verfasser]. "Identifizierung und Analyse von Protein-Interaktionspartnern des Isolationsfaktors CTCF / Imke Panzer." Gießen : Universitätsbibliothek, 2012. http://d-nb.info/1063954177/34.

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Zielke, Katrin [Verfasser], and Andreas [Akademischer Betreuer] Burkovski. "The insulator protein CTCF and cohesins are critical for Herpesvirus saimiri genome maintenance = Das Insulatorprotein CTCF und Kohäsine sind kritisch für die Erhaltung der Genome von Herpesvirus saimiri / Katrin Zielke. Betreuer: Andreas Burkovski." Erlangen : Universitätsbibliothek der Universität Erlangen-Nürnberg, 2012. http://d-nb.info/1021259632/34.

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Segueni, Julie. "DNA methylation changes CTCF binding and reorganizes 3D genome structure in breast cancer cells." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASL020.

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Les génomes des mammifères adoptent une organisation 3D fonctionnelle où les interactions entre les enhancers et les promoteurs des gènes sont contenues à l'intérieur de domaines d'association topologique (TADs). La protéine insulatrice CTCF a deux rôles dans ce processus : sa liaison aux promoteurs permettant la formation de boucles enhancers-promoteurs (structure intra-TAD) et sa liaison aux frontières des TADs empêchant la formation de boucles ectopiques entre domaines voisins. Surtout, les perturbations de la liaison de la protéine CTCF à des sites particuliers dans des cellules cancéreuses peuvent être dues à des changements de séquences d'ADN (mutations) ou à des changements de méthylation de l'ADN (épi-mutations). Nous avons d'abord réalisé des expériences calibrées de CTCF ChIP-seq et avons trouvé qu'un grand nombre de sites ont une liaison différente de CTCF, avec une grande fraction de sites différemment liés étant partagés parmi les lignées cancéreuses. Ces changements de liaison de CTCF peuvent être des gains ou des pertes de liaison et sont souvent situés près de gènes associés à la transformation cancéreuse. Nous avons trouvé une remarquable corrélation entre les changements de liaison de CTCF et les changements d'enrichissement de la marque H3K27ac, indiquant un lien entre la liaison de CTCF et l'activité d'éléments cis-régulateurs (CREs). Grâce à des expériences de Hi-C à haute résolution, nous avons évalué l'impact de ces changements de liaison de CTCF sur la structure de la chromatine, caractérisant une réorganisation considérable de la structure 3D du génome à des loci de gènes qui contiennent des pics CTCF perturbés. De manière inattendue, nous trouvons les exemples les plus drastiques de réorganisation à l'intérieur des TADs, au niveau des boucles enhancers-promoteurs. Ensuite, nous avons identifié les changements de méthylation de l'ADN comme la cause de la dérégulation de la liaison de CTCF dans notre modèle. En utilisant un agent retirant la méthylation de l'ADN sur l'ensemble du génome, nous avons réussi à partiellement inverser des changements de liaison de CTCF que nous avons observés et les changements d'expression induits. Ainsi, notre étude identifie une réorganisation invasive de la liaison de CTCF et des structures intra-TADs, induite par la méthylation de l'ADN. Ces épi-mutations récurrentes peuvent expliquer les mécanismes de dérégulation commune des gènes dans les cancers
Mammalian genomes adopt a functional 3D organization where enhancer-promoter interactions are constrained within Topologically Associating Domains (TADs). The CTCF insulator protein has a dual role in this process, with binding at promoters resulting in the formation of enhancer-promoter loops (intra-TAD structure) and binding at TAD boundaries preventing the formation of inappropriate loops between neighboring domains. Importantly, perturbations of CTCF binding at specific sites in cancer cells can be caused by both changes to the DNA sequence (mutations) or DNA methylation changes (epi-mutations). We first performed precisely-calibrated CTCF ChIP-seq experiments and found that a large number of sites are differentially bound, with a substantial fraction of differential CTCF binding peaks shared among cancer cell lines. Differential CTCF peaks can both be gained and lost and are often localized close to genes associated with breast cancer transformation. We found a striking correlation between CTCF binding changes and H3K27ac changes indicating a link between CTCF binding and the activity of cis-regulatory elements (CREs). Using high-resolution Hi-C, we assessed the impact of differential CTCF binding on chromatin structure, characterizing considerable 3D genome reorganization at gene loci with perturbed CTCF peaks. Unexpectedly, we find the most drastic examples of reorganization within TADs, at the level of enhancer-promoter loops. Then, we identified DNA methylation changes as the upstream cause of CTCF binding deregulation in our breast cancer model. Using genome-wide hypomethylating agent, we were able to partially reverse observed CTCF binding changes and the gene expression changes they induced. Our work thus identifies a pervasive DNA-methylation-guided reorganization of CTCF binding and intra-TAD structure. Such recurrent patterns of epi-mutations can provide a mechanistic explanation for shared gene deregulation in cancers
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Malashchuk, Ogor. "Epigenetic regulation of skin development and postnatal homeostasis : the role of chromatin architectural protein Ctcf in the control of keratinocyte differentiation and epidermal barrier formation." Thesis, University of Bradford, 2016. http://hdl.handle.net/10454/14791.

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Epigenetic regulatory mechanisms play important roles in the control of lineage-specific differentiation during development. However, mechanisms that regulate higher-order chromatin remodelling and transcription of keratinocyte-specific genes that are clustered in the genome into three distinct loci (Keratin type I/II loci and Epidermal Differentiation Complex (EDC)) during differentiation of the epidermis are poorly understood. By using 3D-Fluorescent In Situ Hybridization (FISH), we determined that in the epidermal keratinocytes, the KtyII and EDC loci are located closely to each other in the nuclear compartment enriched by the nuclear speckles. However, in KtyII locus knockout mice, EDC locus moved away from the KtyII locus flanking regions and nuclear speckles towards the nuclear periphery, which is associated with marked changes in gene expression described previously. Chromatin architectural protein Ctcf has previously been implicated in the control of long-range enhancer-promoter contacts and inter-chromosomal interactions. Ctcf is broadly expressed in the skin including epidermal keratinocytes and hair follicles. Conditional Keratin 14-driven Ctcf ablation in mice results in the increase of the epidermal thickness, proliferation, alterations of the epidermal barrier and the development of epidermal pro-inflammatory response. Epidermal barrier defects in Krt14CreER/Ctcf fl/fl mice are associated with marked changes in gene expression in the EDC and KtyII loci, which become topologically segregated in the nucleus upon Ctcf ablation. Therefore, these data suggest that Ctcf serves as critical determinant regulating higher-order chromatin organization in lineage-specific gene loci in epidermal keratinocytes, which is required for the proper control of gene expression, maintenance of the epidermal barrier and its function.
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Malashchuk, Igor. "Epigenetic Regulation of Skin Development and Postnatal Homeostasis The role of chromatin architectural protein Ctcf in the control of Keratinocyte Differentiation and Epidermal Barrier Formation." Thesis, University of Bradford, 2016. http://hdl.handle.net/10454/14791.

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Epigenetic regulatory mechanisms play important roles in the control of lineage-specific differentiation during development. However, mechanisms that regulate higher-order chromatin remodelling and transcription of keratinocyte-specific genes that are clustered in the genome into three distinct loci (Keratin type I/II loci and Epidermal Differentiation Complex (EDC) during differentiation of the epidermis are poorly understood. By using 3D-Fluorescent In Situ Hybridization (FISH), we determined that in the epidermal keratinocytes, the KtyII and EDC loci are located closely to each other in the nuclear compartment enriched by the nuclear speckles. However, in KtyII locus knockout mice, EDC locus moved away from the KtyII locus flanking regions and nuclear speckles towards the nuclear periphery, which is associated with marked changes in gene expression described previously. Chromatin architectural protein Ctcf has previously been implicated in the control of long-range enhancer-promoter contacts and inter-chromosomal interactions. Ctcf is broadly expressed in the skin including epidermal keratinocytes and hair follicles. Conditional Keratin 14-driven Ctcf ablation in mice results in the increase of the epidermal thickness, proliferation, alterations of the epidermal barrier and the development of epidermal pro-inflammatory response. Epidermal barrier defects in Krt14CreER/Ctcf fl/fl mice are associated with marked changes in gene expression in the EDC and KtyII loci, which become topologically segregated in the nucleus upon Ctcf ablation. Therefore, these data suggest that Ctcf serves as critical determinant regulating higher-order chromatin organization in lineage-specific gene loci in epidermal keratinocytes, which is required for the proper control of gene expression, maintenance of the epidermal barrier and its function.
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Shamsuddin, S. "Biochemical characterization of the interactions between a transcription factor, CTCF and its partners Y-Box binding protein-1, and the large subunit of RNA polymerase II." Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269484.

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Alharbi, Adel Braik M. "Characterising the Roles of Zinc Finger Proteins CTCF and ZRANB2 in Modulating Alternative Splicing." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/27996.

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Zinc finger (ZF) proteins constitute the most abundant protein class and are involved in multiple biological processes including development, differentiation, tumour suppression and apoptosis. CTCF and ZRANB2 are two ZF proteins that have been recently linked to modulation of alternative splicing (AS). AS is a complex biological process enriching transcriptome and proteome diversity by facilitating the production of multiple mRNA and protein isoforms from individual genes. However, the genome-wide impact of Ctcf and Zranb2 dosage on AS has not been investigated. The present study examined the effect of Ctcf haploinsufficiency and Zranb2 deficiency on gene expression and AS in Ctcf hemizygous (Ctcf+/-) and conditional Zranb2 knockout (Zranb2-/-) mice, respectively. Reduced Ctcf and Zranb2 levels caused distinct differences in gene expression and AS. In Ctcf+/- mice, these differences were tissue-specific and exhibited a significant increase in intron retention in Ctcf+/- liver and kidney. Interestingly, Ctcf binding sites were enriched proximal to the genomic regions of the intron-retaining genes in Ctcf+/- liver. Proteomic analysis of Ctcf interacting partners in five mouse tissues identified the Small RNA Binding Exonuclease Protection Factor La (Ssb) as a novel Ctcf interactor in all the examined tissues. Tissue-specific protein interactions with Ctcf were also observed. In the brain, co-immunoprecipitation was used to experimentally validate Ctcf interactions with Tra2β, C1qbp, Cpsf6 as well as Atxn1, which are known to be involved in pre-mRNA splicing and brain development, respectively. This study provides new insights into effects of Ctcf haploinsufficiency and Zranb2 deficiency on the transcriptome and highlights a new role for Ctcf in mediating tissue-specific intron retention and protein interactions.
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Ball, DeAnna K. "Establishment of a recombinant CTGF expression system in vitro that models CTGF processing in vivo : structural and functional characterization of multiple mass CTGF proteins /." The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486397841221133.

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Book chapters on the topic "CTCF protein"

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Nanni, Luca. "Computational Inference of DNA Folding Principles: From Data Management to Machine Learning." In Special Topics in Information Technology, 79–88. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-85918-3_7.

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AbstractDNA is the molecular basis of life and would total about three meters if linearly untangled. To fit in the cell nucleus at the micrometer scale, DNA has, therefore, to fold itself into several layers of hierarchical structures, which are thought to be associated with functional compartmentalization of genomic features like genes and their regulatory elements. For this reason, understanding the mechanisms of genome folding is a major biological research problem. Studying chromatin conformation requires high computational resources and complex data analyses pipelines. In this chapter, we first present the PyGMQL software for interactive and scalable data exploration for genomic data. PyGMQL allows the user to inspect genomic datasets and design complex analysis pipelines. The software presents itself as a easy-to-use Python library and interacts seamlessly with other data analysis packages. We then use the software for the study of chromatin conformation data. We focus on the epigenetic determinants of Topologically Associating Domains (TADs), which are region of high self chromatin interaction. The results of this study highlight the existence of a “grammar of genome folding” which dictates the formation of TADs and boundaries, which is based on the CTCF insulator protein. Finally we focus on the relationship between chromatin conformation and gene expression, designing a graph representation learning model for the prediction of gene co-expression from gene topological features obtained from chromatin conformation data. We demonstrate a correlation between chromatin topology and co-expression, shedding a new light on this debated topic and providing a novel computational framework for the study of co-expression networks.
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Eguchi, Takanori, Satoshi Kubota, Kazumi Kawata, Yoshiki Mukudai, Junji Uehara, Toshihiro Ohgawara, Soichiro Ibaragi, Akira Sasaki, Takuo Kuboki, and Masaharu Takigawa. "Novel Transcriptional Regulation of CCN2/CTGF by Nuclear Translocation of MMP3." In CCN Proteins in Health and Disease, 255–64. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3779-4_19.

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Wang, Weihan, Cynthia Jose, Nicholas Kenney, Bethanie Morrison, and Mary Lou Cutler. "Global Expression Profiling Reveals a Role for CTGF/CCN2 in Lactogenic Differentiation of Mouse Mammary Epithelial Cells." In CCN Proteins in Health and Disease, 141–62. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3779-4_12.

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Riser, Bruce L., Feridoon Najmabadi, Bernard Perbal, Jo Ann Rambow, Melisa L. Riser, Ernest Sukowski, Herman Yeger, Sarah C. Riser, and Darryl R. Peterson. "CCN3 (NOV): A Negative Regulator of CCN2 (CTGF) Activity and an Endogenous Inhibitor of Fibrosis in Experimental Diabetic Nephropathy." In CCN Proteins in Health and Disease, 163–81. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3779-4_13.

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Filippova, Galina N. "Genetics and Epigenetics of the Multifunctional Protein CTCF." In Current Topics in Developmental Biology, 337–60. Elsevier, 2007. http://dx.doi.org/10.1016/s0070-2153(07)80009-3.

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Lucchesi, John C. "Architectural organization of the genome." In Epigenetics, Nuclear Organization & Gene Function, 125–39. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198831204.003.0010.

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In the nucleus, chromosomes occupy particular positions (territories) based on their size and gene content. Within each territory, chromosomes are subdivided into loops that contain mostly active or inactive genes. These loops associate, respectively, into domains called topologically associating domains (TADs). These domains are defined by binding sites present at their borders and occupied by architectural proteins that, in mammals, include CTCF (CCCTC-binding factor), cohesin complexes and TFIIIC (a transcription factor for RNA polymerase III). Enhancers and their target promoters are located within the same TAD where they are prevented from promiscuous interactions with other promoters by the presence of insulators. In Drosophila, architectural protein binding sites associate to group TADs together and form insulator bodies thought to facilitate the rare inter-TAD interactions that may bring into proximity genes that should be co-regulated. A similar situation appears to exist for regions within and between TADs that are enriched for Polycomb group (PCG) repressive complexes; grouping of these regions forms PcG bodies.
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Takigawa, Masaharu, Takashi Nishida, and Satoshi Kubota. "ROLES OF CCN2/CTGF IN THE CONTROL OF GROWTH AND REGENERATION." In CCN Proteins, 19–59. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2005. http://dx.doi.org/10.1142/9781860946899_0002.

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Ping Lin, Peter. "Liquid Biopsy Analysis of Circulating Tumor Biomarkers in Lung Cancer." In Lung Cancer - Modern Multidisciplinary Management [Working Title]. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.95422.

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Risk stratification, prognostication and longitudinal monitoring of therapeutic efficacy in lung cancer patients remains highly challenging. It is imperative to establish robust surrogate biomarkers for identifying eligible patients, predicting and effectively monitoring clinical response as well as timely detecting emerging resistance to therapeutic regimens. Circulating tumor biomarkers, analyzed by liquid biopsy, are primarily composed of nucleic acid-based circulating tumor DNA (ctDNA) and an aneuploid cell-based category of circulating tumor cells (CTCs) and circulating tumor-derived endothelial cells (CTECs). Unlike ctDNA, cancer cells are the origin of all categories of various tumor biomarkers. Involvement of aneuploid CTCs and CTECs in tumorigenesis, neoangiogenesis, tumor progression, cancer metastasis and post-therapeutic recurrence has been substantially investigated. Both CTCs and CTECs possessing an active interplay and crosstalk constitute a unique category of cellular circulating tumor biomarkers. These cells concurrently harbor the intact cancer-related genetic signatures and full tumor marker expression profiles in sync with disease progression and therapeutic process. Recent progress in clinical implementation of non-invasive liquid biopsy has made it feasible to frequently carry out ctDNA analysis and unbiased detection of a full spectrum of non-hematologic circulating rare cells including CTCs and CTECs in lung cancer patients, regardless of variation in heterogeneous cell size and cancer cell surface anchor protein expression. In situ phenotypic and karyotypic comprehensive characterization of aneuploid CTCs and CTECs, in combination with single cell-based genotyping and improved ctDNA analyses, will facilitate and benefit multidisciplinary management of lung cancer.
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Somegowda, Madhusudana, Achur N. Rajeshwara, S. Raghavendra, Siddanakoppalu N. Pramod, R. Sagar, G. N. Thippeshappa, and Shankarappa Shridhara. "Phenylpropanoid Pathway for Lignin Biosynthesis and Protein Defensive Strategy against Melon Fly." In Current Topics on Chemistry and Biochemistry Vol. 3, 173–97. Book Publisher International (a part of SCIENCEDOMAIN International), 2022. http://dx.doi.org/10.9734/bpi/ctcb/v3/2608a.

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suwairi, Wafaa, and matthew L. Warman. "WISP3 and Progressive Pseudorheumatoid Dysplasia." In Inborn Errors Of Development, 336–39. Oxford University PressNew York, NY, 2008. http://dx.doi.org/10.1093/oso/9780195306910.003.0027.

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Abstract Mutation in Wnt-1 inducible signaling pathway protein 3 (WISP3) (CCN6), a member of the CCN (CTGF, CEF10/Cyr61, Nov, and, now, WISP1, WISP2, and WISP3) family of secreted growth regulators causes the autosomal recessive disorder progressive pseudorheumatoid dysplasia (PPD) (Hurvitz et al., 1999). Of the six members of the CCN gene family, only WISP3 has been associated with a human Mendelian disease phenotype. The precise developmental pathway by which WISP3 causes disease is unknown. The ability to regulate diverse pathways [e.g., bone morphogenetic protein, Wnt, transforming growth factor-β (TGF-β), Integrin, and insulin-like growth factor 1 (IGF1)] has been identi3ed among CCN family members. However, most activities have been identi3ed ex vivo or using nonphysiologic levels of messenger RNA (mRNA)/protein in vivo. Consequently, the roles of Wisp3 and the other CCN family members in the physiologic, in vivo, regulation of developmental and homeostatic pathways require further investigation.
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Conference papers on the topic "CTCF protein"

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Myung, Ja Hye, Cari A. Launiere, Khyati A. Gajjar, David T. Eddington, and Seungpyo Hong. "Enhanced Tumor Cell Separation by Surfaces Functionalized With Combinations of Bioadhesive Proteins." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13210.

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Effective detection of circulating tumor cells (CTCs) can provide important diagnostic and prognostic information of metastatic cancer. However, CTCs are extremely rare and estimated to be only in the range of one tumor cell in the background of 106–109 normal blood cells, hindering clinically significant detection.[1–2] The specific capturing and potential enrichment of CTCs using anti-epithelial cell adhesion molecule (anti-EpCAM)[3] and selectin, respectively, inspire a biofunctionalized surface that mimics biological complexity may detect and isolate target cells at a greater sensitivity and specificity. This concept is supported by the initial physiological interactions between CTCs and endothelium in the bloodstream, which include concurrent rolling and stationary binding steps. Towards this aim, we investigated the following: i) two proteins with distinct biofunctions (selectin to induce rolling and anti-EpCAM to statically capture target cells) can be co-immobilized; ii) a combined rolling and stationary binding can be induced by the mixture of the proteins; and iii) the biomimetic combination enhances overall capture efficiency of the surface. As a proof-of-concept study for the hypothesis of enhanced separation capacity and capture efficiency using protein mixtures, the surfaces are tested using in vitro cell lines (MCF-7 cells as a CTC model and HL-60 cells as a leukocyte model) under flow conditions. The effects of the combination of rolling (E-selectin) and stationary binding (anti-EpCAM) on capture efficiency are compared to a surface functionalized solely with anti-EpCAM.
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Liu, Wenye, Cong Sun, Yechao Han, and Laifu Du. "Predicition of Three-Dimensional Structure of CTGF Protein." In 2015 7th International Conference on Information Technology in Medicine and Education (ITME). IEEE, 2015. http://dx.doi.org/10.1109/itme.2015.176.

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Rivandi, M., A. Franken, A. Abramova, L. Yang, B. Gierke, J. Eberhardt, M. Beer, et al. "ZeptoCTC: a high-sensitivity method for protein analysis in single CTCs." In 42. Jahreskongress der Deutschen Gesellschaft für Senologie e.V. (DGS). Georg Thieme Verlag, 2023. http://dx.doi.org/10.1055/s-0043-1769159.

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Agerbæk, Mette Ø., Sara R. Bang-Christensen, Ming-Hsin Yang, Thomas M. Clausen, Sisse B. Ditlev, Marina A. Pereira, Morten A. Nielsen, et al. "Abstract 4595: The VAR2CSA malaria protein efficiently retrieves CTCs from a broad spectrum of cancers." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-4595.

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Simone, E. R., T. A. Davies, N. A. Zabe, S. M. Greenberg-seperaky, and N. E. Larsen. "EARLY PLATELET-THROMBIN RECEPTORS AND THEIR FUNCTIONS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643730.

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Human platelets possess less than 1000 high affinity [Kd=10-9]and 50-100,000 receptors of lower [Kd=10-7] affinity for o(α-thrombin. The selective derivatization of thrombin with the bifunctional crosslinking agent, DNCO, has enabled us to identify these receptorsvia covalent binding of either active siteinhibited tosyllyslmethylketothrombin (TLCK-T) or active Ctf-thrombin (T).Kinetic studies of the inhibition of the platelet-thrombin response by covalently and noncovalently bound TLCK-T have helped to elucidate the roles of the high and low affinity thrombin receptors. The activation parameters examined were initial membrane depolarization, cytoplasmic alkalinization,dense granule secretion of serotonin and lysosomal secretion of β-glucuronidase.Isolation and characterization of the thrombin receptors after covalent photocoupling of the TLCK-T or active T- were performed after solubilization by gel filtration. The intact, high affinity receptor moiety, a glycoprotein, has an approximate molecular weight of∽lSO.OOO daltons; occasionally this protein is found as a dimer of ∽360,000 daltons. When exposed to o(α-T the receptor undergoes proteolysis, leaving a protein of∽80,000 daltons and releasing the remaining glycoprotein into the medium.Higher doses of active T have been shown to bind with lower affinity to a larger protein of approximate molecular weight 600,000 daltons anda smaller protein of 46,000 daltons. Both proteins are nonsusceptible to thrombin proteolysis. Reduction and alkylation of the600,000 dalton complex yielded two and possibly three high molecular weight components (200,000, 160,000, and possibly 145,000daltons) which may correspond to previously suggested GP-Ia and GP-Ib of the GP-I complex. Under different solubilization conditions, two other membrane proteins have been found to be part of the GP-I complex; one which is not a glycoprotein, GP-Ic, while the other is associated with the glycocalyx and is called glycocalicin. Glycocalicin and GP-Icdo inhibit thrombin binding,implying that the low affinity receptor is indeed the previously suggested GP-I complex and does not appear to be directly involved withplatelet activation.Examination of the effect of dose and duration of incubation with non-covalently binding TLCK-T on subsequent α-thrombin response suggests the existence of positive cooperativity among thrombin receptors.Although TLCK-T has the same affinity for platelets (Kd) as T , the rateof binding and therefore that of dissociation are lower. Thus for incubation times of 1 minute or less with up to a 2x saturating TLCK-T dose, the subsequent depolarization response to a saturating T dose was enhanced. Exposure to higher TLCK-T (5x saturating)doses led to significant inhibition.Verification of the potentiation observed in noncovalent TLCK-T studies was performed using TLCK-T covalently bound to the platelet receptor with DNCO. Several hundred thrombin molecules were bound to the platelet when a subsaturating dose of TLCK-T(0.0025 U/ml) was used to crosslink, whileseveral thousand resulted with a saturating (0.05 U/ml) TLCK-T dose. Positive cooperativity was observed with low αT doses (0.005 U/ml) when several hundred high affinity receptors are blocked. The parameters studied which exhibited this positive cooperativity were depolarization, pH change and serotonin secretion, α-Glucuronidase secretion was normal. The presence and degreeof enhancement were donor-variableand suggest different threshhold thrombin dose requirements. The enhancement observed can be attributed to either an increased rate of binding (increased affinity) or to an increased number of exposed binding sites. Since little difference was found between the number of TLCK-T molecules bound after30 versus 60 seconds, we conclude that thepotentiation is more likely due to an increased number of exposed binding sites. Results from covalent crosslinks using a fluorescein and rhodamine labeled-TLCK-T and the fluorescence activated cellsorter support this hypothesis. The sensitization of the high affinity binding sitesby partial occupancy implies these bindingsites are responsible for depolarization, pH change and dense granule secretion (the rapid initial activation response), while βglucuronidase secretion, a secondary response, is otherwise controlled.
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Ontiveros, Priscilla, Connie Landaverde, Maren K. Levin, Sarah Hippely, Mark Landers, Yipeng Wang, Ryan Dittamore, and Joyce A. O'Shaughnessy. "Abstract 457: HER2, AR protein expression and chromosomal instability in circulating tumor cells (CTCs) of metastatic breast cancer (MBC) patients (pts)." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-457.

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Ontiveros, Priscilla, Connie Landaverde, Maren K. Levin, Sarah Hippely, Mark Landers, Yipeng Wang, Ryan Dittamore, and Joyce A. O'Shaughnessy. "Abstract 457: HER2, AR protein expression and chromosomal instability in circulating tumor cells (CTCs) of metastatic breast cancer (MBC) patients (pts)." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-457.

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Renier, Corinne, Charles L. Wilkerson, SJ Claire Hur, Da Eun Rachel Park, Clementine A. Lemaire, Melissa Matsumoto, James Carroll, et al. "Abstract 3664: A workflow to evaluate PD-L1 protein expression on circulating tumor cells (CTCs) from non-small cell lung cancer (NSCLC)." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-3664.

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Fernandez, Luisa, John Poirier, Angel Rodriguez, Melanie Hulling, Robin Richardson, Ramsay Sutton, Rhett Jiles, et al. "Abstract 1348: Characterization of SLFN11 protein expression in circulating tumor cells (CTCs) of patients with metastatic castration resistant prostate cancer (mCRPC) prior to platinum based chemotherapy." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1348.

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Fernandez, Luisa, John Poirier, Angel Rodriguez, Melanie Hulling, Robin Richardson, Ramsay Sutton, Rhett Jiles, et al. "Abstract 1348: Characterization of SLFN11 protein expression in circulating tumor cells (CTCs) of patients with metastatic castration resistant prostate cancer (mCRPC) prior to platinum based chemotherapy." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-1348.

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