Journal articles: 'Origins'

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Leslie, M. "ORIGINS: On the Origin of Photosynthesis." Science 323, no. 5919 (March 6, 2009): 1286–87. http://dx.doi.org/10.1126/science.323.5919.1286.

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Joshi, Ishita, Jie Peng, Gina Alvino, Elizabeth Kwan, and Wenyi Feng. "Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains." PLOS ONE 17, no. 2 (February 14, 2022): e0263569. http://dx.doi.org/10.1371/journal.pone.0263569.

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We performed a comparative analysis of replication origin activation by genome-wide single-stranded DNA mapping in two yeast strains challenged by hydroxyurea, an inhibitor of the ribonucleotide reductase. We gained understanding of the impact on origin activation by three factors: S-phase checkpoint control, DNA sequence polymorphisms, and relative positioning of origin and transcription unit. Wild type W303 showed a significant reduction of fork progression accompanied by an elevated level of Rad53 phosphorylation as well as physical presence at origins compared to A364a. Moreover, a rad53K227A mutant in W303 activated more origins, accompanied by global reduction of ssDNA across all origins, compared to A364a. Sequence polymorphism in the consensus motifs of origins plays a minor role in determining strain-specific activity. Finally, we identified a new class of origins only active in checkpoint-proficient cells, which we named “Rad53-dependent origins”. Our study presents a comprehensive list of differentially used origins and provide new insights into the mechanisms of origin activation.

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Nash, Catherine. "Irish Origins, Celtic Origins." Irish Studies Review 14, no. 1 (February 2006): 11–37. http://dx.doi.org/10.1080/09670880500439760.

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Liu, Jun, Kristopher McConnell, Michael Dixon, and Brian R. Calvi. "Analysis of model replication origins in Drosophila reveals new aspects of the chromatin landscape and its relationship to origin activity and the prereplicative complex." Molecular Biology of the Cell 23, no. 1 (January 2012): 200–212. http://dx.doi.org/10.1091/mbc.e11-05-0409.

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Epigenetic regulation exerts a major influence on origins of DNA replication during development. The mechanisms for this regulation, however, are poorly defined. We showed previously that acetylation of nucleosomes regulates the origins that mediate developmental gene amplification during Drosophila oogenesis. Here we show that developmental activation of these origins is associated with acetylation of multiple histone lysines. Although these modifications are not unique to origin loci, we find that the level of acetylation is higher at the active origins and quantitatively correlated with the number of times these origins initiate replication. All of these acetylation marks were developmentally dynamic, rapidly increasing with origin activation and rapidly declining when the origins shut off and neighboring promoters turn on. Fine-scale analysis of the origins revealed that both hyperacetylation of nucleosomes and binding of the origin recognition complex (ORC) occur in a broad domain and that acetylation is highest on nucleosomes adjacent to one side of the major site of replication initiation. It was surprising to find that acetylation of some lysines depends on binding of ORC to the origin, suggesting that multiple histone acetyltransferases may be recruited during origin licensing. Our results reveal new insights into the origin epigenetic landscape and lead us to propose a chromatin switch model to explain the coordination of origin and promoter activity during development.

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Spencer, Joshua, and Chris Tillman. "Necessity of origins and multi-origin art." Inquiry 62, no. 7 (May 8, 2018): 741–54. http://dx.doi.org/10.1080/0020174x.2018.1470567.

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Edler, Lutz, and Annette Kopp-Schneider. "Origins of the mutational origin of cancer." International Journal of Epidemiology 34, no. 5 (July 26, 2005): 1168–70. http://dx.doi.org/10.1093/ije/dyi134.

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Dershowitz, A., and C. S. Newlon. "The effect on chromosome stability of deleting replication origins." Molecular and Cellular Biology 13, no. 1 (January 1993): 391–98. http://dx.doi.org/10.1128/mcb.13.1.391-398.1993.

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The observed spacing between chromosomal DNA replication origins in Saccharomyces cerevisiae is at least four times shorter than should be necessary to ensure complete replication of chromosomal DNA during the S phase. To test whether all replication origins are required for normal chromosome stability, the loss rates of derivatives of chromosome III from which one or more origins had been deleted were measured. In the case of a 61-kb circular derivative of the chromosome that has two highly active origins and one origin that initiates only 10 to 20% of the time, deletion of either highly active origin increased its rate of loss two- to fourfold. Deletion of both highly active origins caused the ring chromosome to be lost in approximately 20% of cell divisions. This very high rate of loss demonstrates that there are no efficient cryptic origins on the ring chromosome that are capable of ensuring its replication in the absence of the origins that are normally used. Deletion of the same two origins from the full-length chromosome III, which contains more than six replication origins, had no effect on its rate of loss. These results suggest that the increase in the rate of loss of the small circular chromosome from which a single highly active origin was deleted was caused by the failure of the remaining highly active origin to initiate replication in a small fraction (approximately 0.003) of cell cycles.

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Dershowitz, A., and C. S. Newlon. "The effect on chromosome stability of deleting replication origins." Molecular and Cellular Biology 13, no. 1 (January 1993): 391–98. http://dx.doi.org/10.1128/mcb.13.1.391.

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The observed spacing between chromosomal DNA replication origins in Saccharomyces cerevisiae is at least four times shorter than should be necessary to ensure complete replication of chromosomal DNA during the S phase. To test whether all replication origins are required for normal chromosome stability, the loss rates of derivatives of chromosome III from which one or more origins had been deleted were measured. In the case of a 61-kb circular derivative of the chromosome that has two highly active origins and one origin that initiates only 10 to 20% of the time, deletion of either highly active origin increased its rate of loss two- to fourfold. Deletion of both highly active origins caused the ring chromosome to be lost in approximately 20% of cell divisions. This very high rate of loss demonstrates that there are no efficient cryptic origins on the ring chromosome that are capable of ensuring its replication in the absence of the origins that are normally used. Deletion of the same two origins from the full-length chromosome III, which contains more than six replication origins, had no effect on its rate of loss. These results suggest that the increase in the rate of loss of the small circular chromosome from which a single highly active origin was deleted was caused by the failure of the remaining highly active origin to initiate replication in a small fraction (approximately 0.003) of cell cycles.

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Theis, James F., and Carol S. Newlon. "Two Compound Replication Origins in Saccharomyces cerevisiae Contain Redundant Origin Recognition Complex Binding Sites." Molecular and Cellular Biology 21, no. 8 (April 15, 2001): 2790–801. http://dx.doi.org/10.1128/mcb.21.8.2790-2801.2001.

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ABSTRACT While many of the proteins involved in the initiation of DNA replication are conserved between yeasts and metazoans, the structure of the replication origins themselves has appeared to be different. As typified by ARS1, replication origins inSaccharomyces cerevisiae are <150 bp long and have a simple modular structure, consisting of a single binding site for the origin recognition complex, the replication initiator protein, and one or more accessory sequences. DNA replication initiates from a discrete site. While the important sequences are currently less well defined, metazoan origins appear to be different. These origins are large and appear to be composed of multiple, redundant elements, and replication initiates throughout zones as large as 55 kb. In this report, we characterize two S. cerevisiae replication origins, ARS101 and ARS310, which differ from the paradigm. These origins contain multiple, redundant binding sites for the origin recognition complex. Each binding site must be altered to abolish origin function, while the alteration of a single binding site is sufficient to inactivate ARS1. This redundant structure may be similar to that seen in metazoan origins.

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Tian, Mengxue, Zhenjia Wang, Chongzhi Zang, Zhangli Su, Etsuko Shibata, Yoshiyuki Shibata, and Anindya Dutta. "Abstract 3174: Integrative analysis of genome-wide DNA replication origins in human cells." Cancer Research 83, no. 7_Supplement (April 4, 2023): 3174. http://dx.doi.org/10.1158/1538-7445.am2023-3174.

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Abstract Dysregulated DNA replication is associated with cancer development. DNA replication initiates from ~50,000 sites in each cell cycle. Genome-wide profiles of replication origins can be generated using various sequencing-based methods following different molecular capture strategies. No previous study has integrated the results from these different experiments to characterize the most reproducible origins or their association with the replication initiation factor, Origin Recognition Complex (ORC), known to be important for origin-specification. We conducted an integrative analysis of 98 human origin profiling datasets from four different techniques including NS-seq, Repli-seq, Rerep-seq and Bubble-seq, and identified a total of 1,460,610 origins in the human genome. Of these, only 0.12% (1,746) were high-confidence “shared origins” that were detected by all four techniques. Compared with all origins, the shared origins have higher GC content and overlap more with gene promoters, CTCF binding sites, transcription factor (TF) binding hotspots, G-quadruplex sites and activating histone marks. Only ~20% of the shared origins (343) overlap with known ORC binding sites. Despite the low overlap between shared origins and ORC binding sites, permutation tests suggest that the overlap between shared origins, ORC binding sites, R-loops and promoters are all significantly higher than random expectation. The variability in origin identification by different techniques and by same techniques in different groups suggests that replication origins are specified by highly variable stochastic events influenced by epigenetic variability. Citation Format: Mengxue Tian, Zhenjia Wang, Chongzhi Zang, Zhangli Su, Etsuko Shibata, Yoshiyuki Shibata, Anindya Dutta. Integrative analysis of genome-wide DNA replication origins in human cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3174.

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Bachant, Jeff, Elizabeth A. Hoffman, Chris Caridi, Constance I. Nugent, and Wenyi Feng. "The yeast Dbf4 Zn2+ finger domain suppresses single-stranded DNA at replication forks initiated from a subset of origins." Current Genetics 68, no. 2 (February 11, 2022): 253–65. http://dx.doi.org/10.1007/s00294-022-01230-6.

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AbstractDbf4 is the cyclin-like subunit for the Dbf4-dependent protein kinase (DDK), required for activating the replicative helicase at DNA replication origin that fire during S phase. Dbf4 also functions as an adaptor, targeting the DDK to different groups of origins and substrates. Here we report a genome-wide analysis of origin firing in a budding yeast mutant, dbf4-zn, lacking the Zn2+ finger domain within the C-terminus of Dbf4. At one group of origins, which we call dromedaries, we observe an unanticipated DNA replication phenotype: accumulation of single-stranded DNA spanning ± 5kbp from the center of the origins. A similar accumulation of single-stranded DNA at origins occurs more globally in pri1-m4 mutants defective for the catalytic subunit of DNA primase and rad53 mutants defective for the S phase checkpoint following DNA replication stress. We propose the Dbf4 Zn2+ finger suppresses single-stranded gaps at replication forks emanating from dromedary origins. Certain origins may impose an elevated requirement for the DDK to fully initiate DNA synthesis following origin activation. Alternatively, dbf4-zn may be defective for stabilizing/restarting replication forks emanating from dromedary origins during replication stress.

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Armon, Adi. "The “Origins of The Origins”." Arendt Studies 3 (2019): 49–68. http://dx.doi.org/10.5840/arendtstudies2018102417.

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Unlike “Imperialism” and “Totalitarianism,” the last two chapters in Hannah Arendt’s The Origins of Totalitarianism (1951), written in the United States in the 1940s, the completion of the first chapter, “Antisemitism”, was preceded by more than two decades of writing in Europe and in the United States, during which Arendt found it increasingly necessary to address issues related to the Jews’ political and social situation. The chapter may be only one part of the book, but it is in fact the “origin of The Origins” and its cornerstone. In order to trace several themes of this seminal chapter, we must analyze the contribution of the French Jewish thinker, Bernard Lazare, to Arendt’s thinking. Without him, “Antisemitism” would never have coalesced and seen the light of day as a political analysis of the phenomenon. Without the “Antisemitism” chapter, The Origins of Totalitarianism would not have become a canonical work of twentieth-century political thought.

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Patel, Prasanta K., Benoit Arcangioli, Stephen P. Baker, Aaron Bensimon, and Nicholas Rhind. "DNA Replication Origins Fire Stochastically in Fission Yeast." Molecular Biology of the Cell 17, no. 1 (January 2006): 308–16. http://dx.doi.org/10.1091/mbc.e05-07-0657.

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DNA replication initiates at discrete origins along eukaryotic chromosomes. However, in most organisms, origin firing is not efficient; a specific origin will fire in some but not all cell cycles. This observation raises the question of how individual origins are selected to fire and whether origin firing is globally coordinated to ensure an even distribution of replication initiation across the genome. We have addressed these questions by determining the location of firing origins on individual fission yeast DNA molecules using DNA combing. We show that the firing of replication origins is stochastic, leading to a random distribution of replication initiation. Furthermore, origin firing is independent between cell cycles; there is no epigenetic mechanism causing an origin that fires in one cell cycle to preferentially fire in the next. Thus, the fission yeast strategy for the initiation of replication is different from models of eukaryotic replication that propose coordinated origin firing.

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Collins, I., and C. S. Newlon. "Chromosomal DNA replication initiates at the same origins in meiosis and mitosis." Molecular and Cellular Biology 14, no. 5 (May 1994): 3524–34. http://dx.doi.org/10.1128/mcb.14.5.3524-3534.1994.

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Autonomously replicating sequence (ARS) elements are identified by their ability to promote high-frequency transformation and extrachromosomal replication of plasmids in the yeast Saccharomyces cerevisiae. Six of the 14 ARS elements present in a 200-kb region of Saccharomyces cerevisiae chromosome III are mitotic chromosomal replication origins. The unexpected observation that eight ARS elements do not function at detectable levels as chromosomal replication origins during mitotic growth suggested that these ARS elements may function as chromosomal origins during premeiotic S phase. Two-dimensional agarose gel electrophoresis was used to map premeiotic replication origins in a 100-kb segment of chromosome III between HML and CEN3. The pattern of origin usage in premeiotic S phase was identical to that in mitotic S phase, with the possible exception of ARS308, which is an inefficient mitotic origin associated with CEN3. CEN3 was found to replicate during premeiotic S phase, demonstrating that the failure of sister chromatids to disjoin during the meiosis I division is not due to unreplicated centromeres. No origins were found in the DNA fragments without ARS function. Thus, in both mitosis and meiosis, chromosomal replication origins are coincident with ARS elements but not all ARS elements have chromosomal origin function. The efficiency of origin use and the patterns of replication termination are similar in meiosis and in mitosis. DNA replication termination occurs over a broad distance between active origins.

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Collins, I., and C. S. Newlon. "Chromosomal DNA replication initiates at the same origins in meiosis and mitosis." Molecular and Cellular Biology 14, no. 5 (May 1994): 3524–34. http://dx.doi.org/10.1128/mcb.14.5.3524.

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Autonomously replicating sequence (ARS) elements are identified by their ability to promote high-frequency transformation and extrachromosomal replication of plasmids in the yeast Saccharomyces cerevisiae. Six of the 14 ARS elements present in a 200-kb region of Saccharomyces cerevisiae chromosome III are mitotic chromosomal replication origins. The unexpected observation that eight ARS elements do not function at detectable levels as chromosomal replication origins during mitotic growth suggested that these ARS elements may function as chromosomal origins during premeiotic S phase. Two-dimensional agarose gel electrophoresis was used to map premeiotic replication origins in a 100-kb segment of chromosome III between HML and CEN3. The pattern of origin usage in premeiotic S phase was identical to that in mitotic S phase, with the possible exception of ARS308, which is an inefficient mitotic origin associated with CEN3. CEN3 was found to replicate during premeiotic S phase, demonstrating that the failure of sister chromatids to disjoin during the meiosis I division is not due to unreplicated centromeres. No origins were found in the DNA fragments without ARS function. Thus, in both mitosis and meiosis, chromosomal replication origins are coincident with ARS elements but not all ARS elements have chromosomal origin function. The efficiency of origin use and the patterns of replication termination are similar in meiosis and in mitosis. DNA replication termination occurs over a broad distance between active origins.

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Li, Feng, Jianhua Chen, Eduardo Solessio, and David M. Gilbert. "Spatial distribution and specification of mammalian replication origins during G1 phase." Journal of Cell Biology 161, no. 2 (April 21, 2003): 257–66. http://dx.doi.org/10.1083/jcb.200211127.

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We have examined the distribution of early replicating origins on stretched DNA fibers when nuclei from CHO cells synchronized at different times during G1 phase initiate DNA replication in Xenopus egg extracts. Origins were differentially labeled in vivo versus in vitro to allow a comparison of their relative positions and spacing. With nuclei isolated in the first hour of G1 phase, in vitro origins were distributed throughout a larger number of DNA fibers and did not coincide with in vivo origins. With nuclei isolated 1 h later, a similar total number of in vitro origins were clustered within a smaller number of DNA fibers but still did not coincide with in vivo origins. However, with nuclei isolated later in G1 phase, the positions of many in vitro origins coincided with in vivo origin sites without further change in origin number or density. These results highlight two distinct G1 steps that establish a spatial and temporal program for replication.

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Zhang, Ren, and Chun-Ting Zhang. "Identification of replication origins in archaeal genomes based on theZ-curve method." Archaea 1, no. 5 (2005): 335–46. http://dx.doi.org/10.1155/2005/509646.

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TheZ-curve is a three-dimensional curve that constitutes a unique representation of a DNA sequence, i.e., both theZ-curve and the given DNA sequence can be uniquely reconstructed from the other. We employedZ-curve analysis to identify one replication origin in theMethanocaldococcus jannaschiigenome, two replication origins in theHalobacteriumspecies NRC-1 genome and one replication origin in theMethanosarcina mazeigenome. One of the predicted replication origins ofHalobacteriumspecies NRC-1 is the same as a replication origin later identified by in vivo experiments. TheZ-curve analysis of theSulfolobus solfataricusP2 genome suggested the existence of three replication origins, which is also consistent with later experimental results. This review aims to summarize applications of theZ-curve in identifying replication origins of archaeal genomes, and to provide clues about the locations of as yet unidentified replication origins of theAeropyrum pernixK1,Methanococcus maripaludisS2,Picrophilus torridusDSM 9790 andPyrobaculum aerophilumstr. IM2 genomes.

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Karnani, Neerja, Christopher M. Taylor, Ankit Malhotra, and Anindya Dutta. "Genomic Study of Replication Initiation in Human Chromosomes Reveals the Influence of Transcription Regulation and Chromatin Structure on Origin Selection." Molecular Biology of the Cell 21, no. 3 (February 2010): 393–404. http://dx.doi.org/10.1091/mbc.e09-08-0707.

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DNA replication in metazoans initiates from multiple chromosomal loci called origins. Currently, there are two methods to purify origin-centered nascent strands: lambda exonuclease digestion and anti-bromodeoxyuridine immunoprecipitation. Because both methods have unique strengths and limitations, we purified nascent strands by both methods, hybridized them independently to tiling arrays (1% genome) and compared the data to have an accurate view of genome-wide origin distribution. By this criterion, we identified 150 new origins that were reproducible across the methods. Examination of a subset of these origins by chromatin immunoprecipitation against origin recognition complex (ORC) subunits 2 and 3 showed 93% of initiation peaks to localize at/within 1 kb of ORC binding sites. Correlation of origins with functional elements of the genome revealed origin activity to be significantly enriched around transcription start sites (TSSs). Consistent with proximity to TSSs, we found a third of initiation events to occur at or near the RNA polymerase II binding sites. Interestingly, ∼50% of the early origin activity was localized within 5 kb of transcription regulatory factor binding region clusters. The chromatin signatures around the origins were enriched in H3K4-(di- and tri)-methylation and H3 acetylation modifications on histones. Affinity of origins for open chromatin was also reiterated by their proximity to DNAse I-hypersensitive sites. Replication initiation peaks were AT rich, and >50% of the origins mapped to evolutionarily conserved regions of the genome. In summary, these findings indicate that replication initiation is influenced by transcription initiation and regulation as well as chromatin structure.

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Lebofsky, Ronald, Roland Heilig, Max Sonnleitner, Jean Weissenbach, and Aaron Bensimon. "DNA Replication Origin Interference Increases the Spacing between Initiation Events in Human Cells." Molecular Biology of the Cell 17, no. 12 (December 2006): 5337–45. http://dx.doi.org/10.1091/mbc.e06-04-0298.

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Mammalian DNA replication origins localize to sites that range from base pairs to tens of kilobases. A regular distribution of initiations in individual cell cycles suggests that only a limited number of these numerous potential start sites are converted into activated origins. Origin interference can silence redundant origins; however, it is currently unknown whether interference participates in spacing functional human initiation events. By using a novel hybridization strategy, genomic Morse code, on single combed DNA molecules from primary keratinocytes, we report the initiation sites present on 1.5 Mb of human chromosome 14q11.2. We confirm that initiation zones are widespread in human cells, map to intergenic regions, and contain sequence motifs found at other mammalian initiation zones. Origins used per cell cycle are less abundant than the potential sites of initiation, and their limited use increases the spacing between initiation events. Between-zone interference decreases in proportion to the distance from the active origin, whereas within-zone interference is 100% efficient. These results identify a hierarchical organization of origin activity in human cells. Functional origins govern the probability that nearby origins will fire in the context of multiple potential start sites of DNA replication, and this is mediated by origin interference.

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Oehlmann, Maren, Alan J. Score, and J. Julian Blow. "The role of Cdc6 in ensuring complete genome licensing and S phase checkpoint activation." Journal of Cell Biology 165, no. 2 (April 19, 2004): 181–90. http://dx.doi.org/10.1083/jcb.200311044.

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Before S phase, cells license replication origins for initiation by loading them with Mcm2-7 heterohexamers. This process is dependent on Cdc6, which is recruited to unlicensed origins. Using Xenopus egg extracts we show that although each origin can load many Mcm2-7 hexamers, the affinity of Cdc6 for each origins drops once it has been licensed by loading the first hexamers. This encourages the distribution of at least one Mcm2-7 hexamer to each origin, and thereby helps to ensure that all origins are licensed. Although Cdc6 is not essential for DNA replication once licensing is complete, Cdc6 regains a high affinity for origins once replication forks are initiated and Mcm2-7 has been displaced from the origin DNA. We show that the presence of Cdc6 during S phase is essential for the checkpoint kinase Chk1 to become activated in response to replication inhibition. These results show that Cdc6 plays multiple roles in ensuring precise chromosome duplication.

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Sharma, Karuna, Martin Weinberger, and Joel A. Huberman. "Roles for Internal and Flanking Sequences in Regulating the Activity of Mating-Type-Silencer-Associated Replication Origins in Saccharomyces cerevisiae." Genetics 159, no. 1 (September 1, 2001): 35–45. http://dx.doi.org/10.1093/genetics/159.1.35.

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Abstract ARS301 and ARS302 are inactive replication origins located at the left end of budding yeast (Saccharomyces cerevisiae) chromosome III, where they are associated with the HML-E and -I silencers of the HML mating type cassette. Although they function as replication origins in plasmids, they do not serve as origins in their normal chromosomal locations, because they are programmed to fire so late in S phase that they are passively replicated by the replication fork from neighboring early-firing ARS305 before they have a chance to fire on their own. We asked whether the nucleotide sequences required for plasmid origin function of these silencer-associated chromosomally inactive origins differ from the sequences needed for plasmid origin function by nonsilencer-associated chromosomally active origins. We could not detect consistent differences in sequence requirements for the two types of origins. Next, we asked whether sequences within or flanking these origins are responsible for their chromosomal inactivity. Our results demonstrate that both flanking and internal sequences contribute to chromosomal inactivity, presumably by programming these origins to fire late in S phase. In ARS301, the function of the internal sequences determining chromosomal inactivity is dependent on the checkpoint proteins Mec1p and Rad53p.

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Blow, J. Julian, Peter J. Gillespie, Dennis Francis, and Dean A. Jackson. "Replication Origins in XenopusEgg Extract Are 5–15 Kilobases Apart and Are Activated in Clusters That Fire at Different Times." Journal of Cell Biology 152, no. 1 (January 8, 2001): 15–26. http://dx.doi.org/10.1083/jcb.152.1.15.

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When Xenopus eggs and egg extracts replicate DNA, replication origins are positioned randomly with respect to DNA sequence. However, a completely random distribution of origins would generate some unacceptably large interorigin distances. We have investigated the distribution of replication origins in Xenopus sperm nuclei replicating in Xenopus egg extract. Replicating DNA was labeled with [3H]thymidine or bromodeoxyuridine and the geometry of labeled sites on spread DNA was examined. Most origins were spaced 5–15 kb apart. This regular distribution provides an explanation for how complete chromosome replication can be ensured although origins are positioned randomly with respect to DNA sequence. Origins were grouped into small clusters (typically containing 5–10 replicons) that fired at approximately the same time, with different clusters being activated at different times in S phase. This suggests that a temporal program of origin firing similar to that seen in somatic cells also exists in the Xenopus embryo. When the quantity of origin recognition complexes (ORCs) on the chromatin was restricted, the average interorigin distance increased, and the number of origins in each cluster decreased. This suggests that the binding of ORCs to chromatin determines the regular spacing of origins in this system.

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Newlon, Carol S. "The replication of yeast chromosomes: lessons fromSaccharomyces cerevisiaechromosome III." Canadian Journal of Botany 73, S1 (December 31, 1995): 208–14. http://dx.doi.org/10.1139/b95-248.

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To understand how a eukaryotic chromosome is replicated, a systematic analysis of chromosome III of Saccharomyces cerevisiae has been undertaken. Replication origins are specified by autonomously replicating sequence (ARS) elements, whose sequences can be dissected using a simple plasmid assay. Only a subset of ARS elements are active as chromosomal replication origins. Replication origins are required for normal chromosome transmission, but they appear to be redundant; several origins can be deleted without affecting chromosome stability. Replication origin position has been conserved on chromosome III in diverged strains, suggesting that origin position is important for chromosome function. The inability of some ARS elements to function as chromosomal replication origins appears likely to result from chromosomal context or position effects. Replication termination occurs over broad regions between active replication origins. The position of termination can be altered by deleting origins, suggesting that no specific replication termination elements are required. Replication forks appear to move at a relatively constant rate through the chromosome. A replication pause site associated with the centromere results from the kinetochore protein complex that binds the centromere to mediate chromosome segregation. Key words: Saccharomyces cerevisiae, ARS elements, replication origins, replication termination, DNA replication intermediates.

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Aparicio, Jennifer G., Christopher J. Viggiani, Daniel G. Gibson, and Oscar M. Aparicio. "The Rpd3-Sin3 Histone Deacetylase Regulates Replication Timing and Enables Intra-S Origin Control in Saccharomyces cerevisiae." Molecular and Cellular Biology 24, no. 11 (June 1, 2004): 4769–80. http://dx.doi.org/10.1128/mcb.24.11.4769-4780.2004.

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ABSTRACT The replication of eukaryotic genomes follows a temporally staged program, in which late origin firing often occurs within domains of altered chromatin structure(s) and silenced genes. Histone deacetylation functions in gene silencing in some late-replicating regions, prompting an investigation of the role of histone deacetylation in replication timing control in Saccharomyces cerevisiae. Deletion of the histone deacetylase Rpd3 or its interacting partner Sin3 caused early activation of late origins at internal chromosomal loci but did not alter the initiation timing of early origins or a late-firing, telomere-proximal origin. By delaying initiation relative to the earliest origins, Rpd3 enables regulation of late origins by the intra-S replication checkpoint. RPD3 deletion suppresses the slow S phase of clb5Δ cells by enabling late origins to fire earlier, suggesting that Rpd3 modulates the initiation timing of many origins throughout the genome. Examination of factors such as Ume6 that function together with Rpd3 in transcriptional repression indicates that Rpd3 regulates origin initiation timing independently of its role in transcriptional repression. This supports growing evidence that for much of the S. cerevisiae genome transcription and replication timing are not linked.

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Gerhardt, Jeannine, Samira Jafar, Mark-Peter Spindler, Elisabeth Ott, and Aloys Schepers. "Identification of New Human Origins of DNA Replication by an Origin-Trapping Assay." Molecular and Cellular Biology 26, no. 20 (September 5, 2006): 7731–46. http://dx.doi.org/10.1128/mcb.01392-06.

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ABSTRACT Metazoan genomes contain thousands of replication origins, but only a limited number have been characterized so far. We developed a two-step origin-trapping assay in which human chromatin fragments associated with origin recognition complex (ORC) in vivo were first enriched by chromatin immunoprecipitation. In a second step, these fragments were screened for transient replication competence in a plasmid-based assay utilizing the Epstein-Barr virus latent origin oriP. oriP contains two elements, an origin (dyad symmetry element [DS]) and the family of repeats, that when associated with the viral protein EBNA1 facilitate extrachromosomal stability. Insertion of the ORC-binding human DNA fragments in oriP plasmids in place of DS enabled us to screen functionally for their abilities to restore replication. Using the origin-trapping assay, we isolated and characterized five previously unknown human origins. The assay was validated with nascent strand abundance assays that confirm these origins as active initiation sites in their native chromosomal contexts. Furthermore, ORC and MCM2-7 components localized at these origins during G1 phase of the cell cycle but were not detected during mitosis. This finding extends the current understanding of origin-ORC dynamics by suggesting that replication origins must be reestablished during the early stages of each cell division cycle and that ORC itself participates in this process.

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Balter, M. "ORIGINS: On the Origin of Art and Symbolism." Science 323, no. 5915 (February 6, 2009): 709–11. http://dx.doi.org/10.1126/science.323.5915.709.

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Kearns, Lionel. "Origins." College English 50, no. 8 (December 1988): 876. http://dx.doi.org/10.2307/377986.

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Majaj, Lisa Suhair. "Origins." World Literature Today 78, no. 3/4 (2004): 21. http://dx.doi.org/10.2307/40158479.

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Parms. "Origins." Fourth Genre: Explorations in Nonfiction 17, no. 2 (2015): 53. http://dx.doi.org/10.14321/fourthgenre.17.2.0053.

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Moller, Torsten. "Origins." IEEE Computer Graphics and Applications 40, no. 1 (January 1, 2020): 14–19. http://dx.doi.org/10.1109/mcg.2019.2957689.

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Williams, Donald T. "Origins." Theology Today 51, no. 4 (January 1995): 607. http://dx.doi.org/10.1177/004057369505100417.

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Bailey, Richard W. "Origins." Dictionaries: Journal of the Dictionary Society of North America 17, no. 1 (1996): 1–16. http://dx.doi.org/10.1353/dic.1996.0014.

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Foster, Zelda. "Origins:." Hospice Journal, The 14, no. 3/4 (November 9, 1999): 9–13. http://dx.doi.org/10.1300/j011v14n03_02.

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Dyrud, Jarl E. "Origins." Contemporary Psychoanalysis 32, no. 4 (October 1996): 670–73. http://dx.doi.org/10.1080/00107530.1996.10746344.

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Long, Naomi. "Origins." Manoa 14, no. 2 (2002): 221. http://dx.doi.org/10.1353/man.2003.0037.

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McCarthy, Nicola. "Origins." Nature Reviews Cancer 11, no. 2 (January 20, 2011): 80–81. http://dx.doi.org/10.1038/nrc3008.

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Brooksbank, Cath. "Origins." Nature Reviews Cancer 2, no. 6 (June 2002): 401. http://dx.doi.org/10.1038/nrc826.

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Schulman, Grace. "Origins." Prairie Schooner 81, no. 1 (2007): 56–57. http://dx.doi.org/10.1353/psg.2007.0098.

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Magasanik, Boris. "Origins." Journal of Biological Chemistry 280, no. 24 (April 19, 2005): 22557–59. http://dx.doi.org/10.1074/jbc.x500003200.

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Van Schie, Gerwin. "Origins." TMG Journal for Media History 21, no. 2 (November 1, 2018): 67. http://dx.doi.org/10.18146/2213-7653.2018.367.

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In this article, categorisation based on origins is investigated in the Dutch census reports produced between 1899 and 2018. Through this analysis, I will argue that the conceptual pair of autochthon and allochthon (until 2017 used to describe ‘native’ and ‘non-native’ Dutch people) is not a social construct, but rather a sociotechnical construct. Through this analysis, it becomes clear that where the category of the ‘foreigner’ at the beginning of the twentieth century was mainly related to a passport and place of birth, later national origins became a racially tainted concept. Pre-1980, counting machines at CBS only counted people’s information as selfdescribed; since 1980, computers have determined the identity of Dutch citizens. Today, governmental statistics based on the origins of Dutch people are available online for free and can be used by third parties for a variety of applications. Through this historical analysis, it becomes clear that the current practices are not the ‘standard’ way of categorisation, but rather one of the possibilities that are historically, socially and technologically situated.

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Weinberg, S. "Origins." Science 230, no. 4721 (October 4, 1985): 15–18. http://dx.doi.org/10.1126/science.230.4721.15.

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Lezama Lima, Jose, and Stephen D. Gingerich. "Origins." CR: The New Centennial Review 2, no. 2 (2002): 19–21. http://dx.doi.org/10.1353/ncr.2002.0024.

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Tran, Vu. "Origins." Ploughshares 45, no. 2 (2019): 183–91. http://dx.doi.org/10.1353/plo.2019.0067.

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Ridley, Mark. "Origins." Trends in Ecology & Evolution 4, no. 4 (April 1989): 118. http://dx.doi.org/10.1016/0169-5347(89)90063-3.

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Amiotte, Lowell, and Charles Woodard. "Origins." Studies in American Indian Literatures 35, no. 3-4 (September 2023): 1–2. http://dx.doi.org/10.1353/ail.2023.a928896.

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Vujcic, Marija, Charles A. Miller, and David Kowalski. "Activation of Silent Replication Origins at Autonomously Replicating Sequence Elements near the HML Locus in Budding Yeast." Molecular and Cellular Biology 19, no. 9 (September 1, 1999): 6098–109. http://dx.doi.org/10.1128/mcb.19.9.6098.

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ABSTRACT In the budding yeast, Saccharomyces cerevisiae, replicators can function outside the chromosome as autonomously replicating sequence (ARS) elements; however, within chromosome III, certain ARSs near the transcriptionally silent HML locus show no replication origin activity. Two of these ARSs comprise the transcriptional silencers E (ARS301) and I (ARS302). Another, ARS303, resides betweenHML and the CHA1 gene, and its function is not known. Here we further localized and characterized ARS303and in the process discovered a new ARS, ARS320. BothARS303 and ARS320 are competent as chromosomal replication origins since origin activity was seen when they were inserted at a different position in chromosome III. However, at their native locations, where the two ARSs are in a cluster withARS302, the I silencer, no replication origin activity was detected regardless of yeast mating type, special growth conditions that induce the transcriptionally repressed CHA1 gene,trans-acting mutations that abrogate transcriptional silencing at HML (sir3, orc5), orcis-acting mutations that delete the E and I silencers containing ARS elements. These results suggest that, for theHML ARS cluster (ARS303, ARS320, and ARS302), inactivity of origins is independent of local transcriptional silencing, even though origins and silencers share keycis- and trans-acting components. Surprisingly, deletion of active replication origins located 25 kb (ORI305) and 59 kb (ORI306) away led to detection of replication origin function at theHML ARS cluster, as well as at ARS301, the E silencer. Thus, replication origin silencing at HML ARSs is mediated by active replication origins residing at long distances fromHML in the chromosome. The distal active origins are known to fire early in S phase, and we propose that their inactivation delays replication fork arrival at HML, providing additional time for HML ARSs to fire as origins.

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Dubey, Swasti. "Factual Origins of Myths." International Journal of Social Science And Human Research 05, no. 10 (October 12, 2022): 4491–93. http://dx.doi.org/10.47191/ijsshr/v5-i10-11.

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Many cultures have developed myths and legends rooted in the ideas of vampirism, lycanthropy, and witchcraft. According to anthropological currents, these stories don’t come up from nothing, but follow a process of transformation of elements drawn from real experiences eventually transformed into fictional stories depending on the message they are meant to spread. Every legend has an origin in history, an event with no plausible explanation at the time due to lack of scientific technology and resources. Although, reality can be described in scientific terms. These possible facts connected to mythology do not entirely explain the success of myth in folklore, but only some more or less impressive aspects following these legends. These facts when turned and twisted by imagination and superstitious thinking create these inexplicable enthralling stories which undoubtedly would be passed down to generations as souvenirs of history, culture, and civilization.

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Paneth, Nigel. "Commentary: The origins of fetal origins." International Journal of Epidemiology 45, no. 2 (April 2016): 319–20. http://dx.doi.org/10.1093/ije/dyw066.

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Thelen, Esther. "Origins of origins of motor control." Behavioral and Brain Sciences 18, no. 4 (December 1995): 780–83. http://dx.doi.org/10.1017/s0140525x00041030.

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AbstractExamination of infant spontaneous and goal-directed arm movements supports Feldman and Levin's hypothesis of a functional hierarchy. Early infant movements are dominated by biomechanical and dynamic factors without external frames of reference. Development involves not only learning to generate these frames of reference, but also protecting the higher-level goal of the movement from internal and external perturbations.

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Feng, Yuchao, TianXin Fu, Liyuan Zhang, Changyuan Wang, and Dongjie Zhang. "Research on Differential Metabolites in Distinction of Rice (Oryza sativa L.) Origin Based on GC-MS." Journal of Chemistry 2019 (January 15, 2019): 1–7. http://dx.doi.org/10.1155/2019/1614504.

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The analytical method for the metabolomics of the 60 rice seeds from two main rice origins in Heilongjiang Province was developed based on gas chromatography coupled with mass spectrum. The specific differential metabolites between two rice origins were identified, and the distinguish of the two main origins was illustrated by using the R software platform with XCMS software package for gas chromatography coupled with mass spectrum data processing, combined with multivariate statistical analysis software. The result indicated that the 173 peaks were detected, and 54 of which were structurally identified, covering amino acids, aliphatic acid, sugar, polyols, and so on. By comparing the data of Wuchang and Jiansanjiang origins, it was found that there were 9 special metabolites in Wuchang origin and 8 special metabolites in Jiansanjiang origin. The 10 differential metabolites with significant changes (P<0.05, VIP ≥ 1) were filtrated. It is indicated that the differential metabolites of rice carry information of their origin and there are the differences in the metabolites of rice in two main origins. The proposed method is expected to be useful for the metabolomic researches of rice.

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Journal articles on the topic 'Origins'

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