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Zepeda-Mendoza CJ, Ibn-Salem J, Kammin T, Harris DJ, Rita D, Gripp KW, MacKenzie JJ, Gropman A, Graham B, Shaheen R, Alkuraya FS, Brasington CK, Spence EJ, Masser-Frye D, Bird LM, Spiegel E, Sparkes RL, Ordulu Z, Talkowski ME, Andrade-Navarro MA, Robinson PN, Morton CC. Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. Am J Hum Genet 2017; 101:206-217. [PMID: 28735859 PMCID: PMC5544382 DOI: 10.1016/j.ajhg.2017.06.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/19/2017] [Indexed: 01/08/2023] Open
Abstract
Interpretation of variants of uncertain significance, especially chromosomal rearrangements in non-coding regions of the human genome, remains one of the biggest challenges in modern molecular diagnosis. To improve our understanding and interpretation of such variants, we used high-resolution three-dimensional chromosomal structural data and transcriptional regulatory information to predict position effects and their association with pathogenic phenotypes in 17 subjects with apparently balanced chromosomal abnormalities. We found that the rearrangements predict disruption of long-range chromatin interactions between several enhancers and genes whose annotated clinical features are strongly associated with the subjects' phenotypes. We confirm gene-expression changes for a couple of candidate genes to exemplify the utility of our analysis of position effect. These results highlight the important interplay between chromosomal structure and disease and demonstrate the need to utilize chromatin conformational data for the prediction of position effects in the clinical interpretation of non-coding chromosomal rearrangements.
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Affiliation(s)
- Cinthya J Zepeda-Mendoza
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Tammy Kammin
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David J Harris
- Harvard Medical School, Boston, MA 02115, USA; Boston Children's Hospital, Boston, MA 02115, USA
| | - Debra Rita
- Cytogenetics Lab, ACL laboratories, Rosemont, IL 60018, USA
| | - Karen W Gripp
- Nemours Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | | | - Andrea Gropman
- Children's National Medical Center, Washington, DC 20010, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh 12713, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Campbell K Brasington
- Clinical Genetics Division, Department of Pediatrics, Levine Children's Hospital at Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Edward J Spence
- Clinical Genetics Division, Department of Pediatrics, Levine Children's Hospital at Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Diane Masser-Frye
- Genetics and Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA
| | - Lynne M Bird
- Genetics and Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA; University of California, San Diego, La Jolla, CA 92093, USA
| | - Erica Spiegel
- Maternal Fetal Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Rebecca L Sparkes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Zehra Ordulu
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael E Talkowski
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Departments of Neurology and Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Peter N Robinson
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, USA; Johannes Gutenberg University, Mainz 55122, Germany; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Centre, Manchester M13 9NT, UK.
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Li W, Yi J, Agbu P, Zhou Z, Kelley RL, Kallgren S, Jia S, He X. Replication stress affects the fidelity of nucleosome-mediated epigenetic inheritance. PLoS Genet 2017; 13:e1006900. [PMID: 28749973 PMCID: PMC5549764 DOI: 10.1371/journal.pgen.1006900] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 08/08/2017] [Accepted: 06/29/2017] [Indexed: 02/06/2023] Open
Abstract
The fidelity of epigenetic inheritance or, the precision by which epigenetic information is passed along, is an essential parameter for measuring the effectiveness of the process. How the precision of the process is achieved or modulated, however, remains largely elusive. We have performed quantitative measurement of epigenetic fidelity, using position effect variegation (PEV) in Schizosaccharomyces pombe as readout, to explore whether replication perturbation affects nucleosome-mediated epigenetic inheritance. We show that replication stresses, due to either hydroxyurea treatment or various forms of genetic lesions of the replication machinery, reduce the inheritance accuracy of CENP-A/Cnp1 nucleosome positioning within centromere. Mechanistically, we demonstrate that excessive formation of single-stranded DNA, a common molecular abnormality under these conditions, might have correlation with the reduction in fidelity of centromeric chromatin duplication. Furthermore, we show that replication stress broadly changes chromatin structure at various loci in the genome, such as telomere heterochromatin expanding and mating type locus heterochromatin spreading out of the boundaries. Interestingly, the levels of inheritable expanding at sub-telomeric heterochromatin regions are highly variable among independent cell populations. Finally, we show that HU treatment of the multi-cellular organisms C. elegans and D. melanogaster affects epigenetically programmed development and PEV, illustrating the evolutionary conservation of the phenomenon. Replication stress, in addition to its demonstrated role in genetic instability, promotes variable epigenetic instability throughout the epigenome. In this study, we found replication stresses reduce the fidelity of nucleosome-mediated epigenetic inheritance. Using Position Effect Variegation (PEV) in centromere as an indicator of chromatin epigenetic stability, we quantified the precision of nucleosomal inheritance and found replication stresses reduce the fidelity of nucleosome-mediated epigenetic inheritance. Further analysis of genome-wide heterochromatin distribution showed that replication stresses affect chromatin structure by expanding of heterochromatin with locus specificity. Mechanistically, we provide evidence suggesting that excessive formation of single-stranded DNA might have correlation with the reduction in fidelity of centromeric chromatin duplication. Finally, we demonstrated replication stress perturb the development process by reducing the fidelity of chromatin organization duplication in fruit fly and worm, illustrating the broadness and the evolutionary conservation of the phenomenon. Together, our results shed light on the importance of replication stresses cause epigenetic instability in addition to genetic stability.
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Affiliation(s)
- Wenzhu Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jia Yi
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pamela Agbu
- Department of Biochemistry and Molecular Biology
| | - Zheng Zhou
- Department of Biochemistry and Molecular Biology
| | - Richard L. Kelley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Scott Kallgren
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Xiangwei He
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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3
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McElroy KA, Jung YL, Zee BM, Wang CI, Park PJ, Kuroda MI. upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks. G3 (Bethesda) 2017; 7:625-635. [PMID: 28064188 PMCID: PMC5295607 DOI: 10.1534/g3.116.037788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022]
Abstract
Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications (PTMs) of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by, these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here, we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells that are mutant for upSET We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone PTM quantification. To test whether this finding was consistent in the whole organism, we deleted the upSET coding sequence using CRISPR/Cas-9, which we found to be lethal in both sexes in flies. We were able to rescue this lethality using a tagged upSET transgene, and found that UpSET protein localizes to transcriptional start sites (TSS) of active genes throughout the genome. Misregulated heterochromatin is apparent by suppressed position effect variegation of the wm4 allele in heterozygous upSET-deleted flies. Using nascent-RNA sequencing in the upSET-mutant S2 lines, we show that this result applies to heterochromatin genes generally. Our findings support a critical role for UpSET in maintaining heterochromatin, perhaps by delimiting the active chromatin environment.
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Affiliation(s)
- Kyle A McElroy
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Youngsook L Jung
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115
| | - Barry M Zee
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Charlotte I Wang
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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Leman DV, Parshikov AF, Georgiev PG, Maksimenko OG. [Organization of the Drosophila melanogaster SF1 insulator and its role in transcription regulation in transgenic lines]. Genetika 2014; 50:392-399. [PMID: 25715441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The SF1 insulator was found to contain a polyadenylation signal, which corresponded to the functional polyadenylation signal in embryonic S2 cells and the transgenic lines of Drosophila and bi-directional promoter that functioned in S2 cells. The studies performed did not confirm the ability of the SF1 insulator to protect expression of reporter gene white from the chromosome position effect in transgenic lines.
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McCracken A, Locke J. Mutations in CG8878, a novel putative protein kinase, enhance P element dependent silencing (PDS) and position effect variegation (PEV) in Drosophila melanogaster. PLoS One 2014; 9:e71695. [PMID: 24614804 PMCID: PMC3948951 DOI: 10.1371/journal.pone.0071695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/04/2013] [Indexed: 11/20/2022] Open
Abstract
Genes in multicellular organisms are expressed as part of a developmental program that is largely dependent on self-perpetuating higher-order chromatin states. The mechanism of establishing and maintaining these epigenetic events is well studied in Drosophila. The first known example of an epigenetic effect was that of (PEV) in Drosophila, which has been shown to be due to gene silencing via heterochromatin formation. We are investigating a process similar to Position Effect Variegation (PEV) using a mini-w transgene, called Pci, inserted in the upstream regulatory region of ci. The mini-white+ transgene in Pci is expressed throughout the adult eye; however, when other P or KP elements are present, a variegated eye phenotype results indicating random w+ silencing during development. This P element dependent silencing (PDS) can be modified by the haplo-suppressors/triplo-enhancers, Su(var)205 and Su(var)3-7, indicating that these heterochromatic modifiers also act dose dependently in PDS. Here we use a spontaneous derivative mutation of Pci called PciE1 (E1) that variegates like PDS in the absence of P elements, presumably due to an adjacent gypsy element insertion, to screen for second-site modifier mutations that enhance variable silencing of white+ in E1. We isolated 7 mutations in CG8878, an essential gene, that enhance the E1 variegated phenotype. CG8878, a previously uncharacterized gene, potentially encodes a serine/threonine kinase whose closest Drosophila paralogue, ballchen (nhk-1), phosphorylates histones. These mutant alleles enhance both PDS at E1 and Position Effect Variegation (PEV) at w(m4), indicating a previously unknown common silencing mechanism between the two.
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Affiliation(s)
- Allen McCracken
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John Locke
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Chang SP, Opsahl ML, Whitelaw CBA, Morley SD, West JD. Relative transgene expression frequencies in homozygous versus hemizygous transgenic mice. Transgenic Res 2013; 22:1143-54. [PMID: 23873612 DOI: 10.1007/s11248-013-9732-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 07/06/2013] [Indexed: 11/26/2022]
Abstract
We have used a simple binomial model of stochastic transgene inactivation at the level of the chromosome or transgene, rather than the cellular level, for the analysis of two mouse transgenic lines that show variegated patterns of expression. This predicts the percentages of cells that express one, both or neither alleles of the transgene in homozygotes from the observed percentages of cells, which express the transgene in hemizygotes. It adequately explained the relationship between the numbers of cells expressing the transgene in hemizygous and homozygous mosaic 21OH/LacZ mouse adrenals and mosaic BLG/7 mouse mammary glands. The binomial model also predicted that a small proportion of cells in mosaic mammary glands of BLG/7 homozygotes would express both BLG/7 alleles but published data indicated that all cells expressing the transgene showed monoallelic expression. Although it didn't fit all of the BLG/7 data as precisely as a more complex model, which used several ad hoc assumptions to explain these results, the simple binomial model was able to explain the relationship in observed transgene expression frequencies between hemizygous and homozygous mosaic tissues for both 21OH/LacZ and BLG/7 mice. It may prove to be a useful general model for analysing other transgenic animals showing mosaic transgene expression.
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Affiliation(s)
- Su-Ping Chang
- Genes and Development Group, Centre for Integrative Physiology, School of Clinical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
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Lavrov SA, Shatskikh AS, Kibanov MV, Gvozdev VA. [Correlation on a cellular level of gene transcriptional silencing and heterochromatin compartment dragging in case of PEV-producing eu-heterochromatin rearrangement in Drosophila melanogaster]. Mol Biol (Mosk) 2013; 47:286-91. [PMID: 23808163 DOI: 10.7868/s0026898413020080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Eu-heterochromatic rearrangements transfer genes into the heterochromatin and cause their variegated inactivation (PEV). Genes affected by PEV often demonstrate association with heterochromatic nuclear compartment (a distinct area composed of heterochromatin sequences like satellite DNA and enriched in specific chromatin proteins e.g. HP1). Here, we investigate the nuclear localization and the expression levels of the genes subjected to PEV caused by chromosome inversion, In(2)A4. We demonstrate that the degree of PEV-caused gene inactivation depends on a developmental stage, and the maximum of repression corresponds to the gene expression activation period. In the case of In(2)A4 rearrangement we detect the dragging of affected euchromatic region into heterochromatic nuclear compartment and the increase in HP1 occupancy in this region. We developed a protocol of simultaneous RNA-DNA-protein staining to demonstrate firstly in a single cell a strong correlation between transcriptional activity of affected gene and its distance from chromosome 2 satellite DNA.
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Valentine ME, Wolyniak MJ, Rutter MT. Extensive phenotypic variation among allelic T-DNA inserts in Arabidopsis thaliana. PLoS One 2012; 7:e44981. [PMID: 23028719 PMCID: PMC3441624 DOI: 10.1371/journal.pone.0044981] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/15/2012] [Indexed: 11/19/2022] Open
Abstract
T-DNA insertion mutants are a tool used widely in Arabidopsis thaliana to disrupt gene function. We phenotyped multiple homozygous T-DNA A. thaliana mutants at each of two loci (AT1G11060 and AT4G00210). We measured life history traits, including germination, size at reproduction and fruit production. Allelic T-DNA lines differed for most traits at AT1G11060 but not at AT4G00210. However, insertions in exons differed from other insertion positions in AT4G00210 but not in AT1G11060. We found evidence for additional insertions in approximately half of the lines, but found few phenotypic consequences. In general, our results suggest that a cautious interpretation of T-DNA phenotypes is warranted.
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Affiliation(s)
- Megan E. Valentine
- Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
| | - Michael J. Wolyniak
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, Virginia, United States of America
| | - Matthew T. Rutter
- Department of Biology, College of Charleston, Charleston, South Carolina, United States of America
- * E-mail:
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9
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Shabarina AN, Glazkov MV. [Nuclear envelope attachment sites of interphase chromosomes: barrier elements but not insulators]. Genetika 2012; 48:1012-1016. [PMID: 23035555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A neDNA fragment that protects a transgene from position effect variegation when flanking it was tested for insulator properties. The fragment did not act as an insulator. A similarity of neDNA and various barrier elements was examined, and Drosophila melanogaster and Mus musculus chromosome DNA regions homologous to neDNA were analyzed. Additional conserved sites and DNA duplex destabilization sites were found in the neDNA sequence, and DNA conformational specifics were assumed for the chromosomal neighborhood of neDNA sites of the D. melanogaster and M. musculus genomes.
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Batenchuk C, St-Pierre S, Tepliakova L, Adiga S, Szuto A, Kabbani N, Bell JC, Baetz K, Kærn M. Chromosomal position effects are linked to sir2-mediated variation in transcriptional burst size. Biophys J 2011; 100:L56-8. [PMID: 21575565 DOI: 10.1016/j.bpj.2011.04.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 03/31/2011] [Accepted: 04/07/2011] [Indexed: 11/19/2022] Open
Abstract
Gene expression noise varies with genomic position and is a driving force in the evolution of chromosome organization. Nevertheless, position effects remain poorly characterized. Here, we present a systematic analysis of chromosomal position effects by characterizing single-cell gene expression from euchromatic positions spanning the length of a eukaryotic chromosome. We demonstrate that position affects gene expression by modulating the size of transcriptional bursts, rather than their frequency, and that the histone deacetylase Sir2 plays a role in this process across the chromosome.
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Affiliation(s)
- Cory Batenchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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Abstract
The susceptibility to recombination of a plasmid inserted into a chromosome varies with its genomic position. This recombination position effect is known to correlate with the average G+C content of the flanking sequences. Here we propose that this effect could be mediated by changes in the susceptibility to superhelical duplex destabilization that would occur. We use standard nonparametric statistical tests, regression analysis and principal component analysis to identify statistically significant differences in the destabilization profiles calculated for the plasmid in different contexts, and correlate the results with their measured recombination rates. We show that the flanking sequences significantly affect the free energy of denaturation at specific sites interior to the plasmid. These changes correlate well with experimentally measured variations of the recombination rates within the plasmid. This correlation of recombination rate with superhelical destabilization properties of the inserted plasmid DNA is stronger than that with average G+C content of the flanking sequences. This model suggests a possible mechanism by which flanking sequence base composition, which is not itself a context-dependent attribute, can affect recombination rates at positions within the plasmid.
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Affiliation(s)
- Cheryl L Sershen
- Baylor College of Medicine, Houston, Texas, United States of America.
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Power P, Jeffery D, Rehman MA, Chatterji A, Yankulov K. Sub-telomeric core X and Y' elements in S. cerevisiae suppress extreme variations in gene silencing. PLoS One 2011; 6:e17523. [PMID: 21437278 PMCID: PMC3060084 DOI: 10.1371/journal.pone.0017523] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 02/04/2011] [Indexed: 11/23/2022] Open
Abstract
Telomere Position Effect (TPE) is governed by strong repression signals emitted by telomeres via the Sir2/3/4 Histone Deacetylase complex. These signals are then relayed by weak proto-silencers residing in the subtelomeric core X and Y' elements. Subtelomeres also contain Sub-Telomeric Anti-silencing Regions (STARs). In this study we have prepared telomeres built of different combinations of core X, Y' and STARs and have analyzed them in strains lacking Histone-Acetyltransferase genes as well as in cdc6-1 and Δrif1 strains. We show that core X and Y' dramatically reduce both positive and negative variations in TPE, that are caused by these mutations. We also show that the deletion of Histone-Acetyltransferase genes reduce the silencing activity of an ACS proto-silencer, but also reduce the anti-silencing activity of a STAR. We postulate that core X and Y' act as epigenetic “cushioning” cis-elements.
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Affiliation(s)
- Patricia Power
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Daniel Jeffery
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Muhammad Attiq Rehman
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Arjun Chatterji
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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