1
|
Chang EYC, Tsai S, Aristizabal MJ, Wells JP, Coulombe Y, Busatto FF, Chan YA, Kumar A, Dan Zhu Y, Wang AYH, Fournier LA, Hieter P, Kobor MS, Masson JY, Stirling PC. MRE11-RAD50-NBS1 promotes Fanconi Anemia R-loop suppression at transcription-replication conflicts. Nat Commun 2019; 10:4265. [PMID: 31537797 PMCID: PMC6753070 DOI: 10.1038/s41467-019-12271-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
Ectopic R-loop accumulation causes DNA replication stress and genome instability. To avoid these outcomes, cells possess a range of anti-R-loop mechanisms, including RNaseH that degrades the RNA moiety in R-loops. To comprehensively identify anti-R-loop mechanisms, we performed a genome-wide trigenic interaction screen in yeast lacking RNH1 and RNH201. We identified >100 genes critical for fitness in the absence of RNaseH, which were enriched for DNA replication fork maintenance factors including the MRE11-RAD50-NBS1 (MRN) complex. While MRN has been shown to promote R-loops at DNA double-strand breaks, we show that it suppresses R-loops and associated DNA damage at transcription-replication conflicts. This occurs through a non-nucleolytic function of MRE11 that is important for R-loop suppression by the Fanconi Anemia pathway. This work establishes a novel role for MRE11-RAD50-NBS1 in directing tolerance mechanisms at transcription-replication conflicts.
Collapse
Affiliation(s)
| | - Shuhe Tsai
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - James P Wells
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yan Coulombe
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Franciele F Busatto
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Yujia A Chan
- The Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
| | - Arun Kumar
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Yi Dan Zhu
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | | | | | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Vancouver, V5Z 4H4, Canada
| | - Jean-Yves Masson
- Centre Hospitalier Universitaire de Québec-Universite Laval, Oncology Axis, Quebec City, G1R 2J6, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, G1V 0A6, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, Canada.
| |
Collapse
|
2
|
Girgis HZ, Velasco A, Reyes ZE. HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures. BMC Bioinformatics 2018; 19:310. [PMID: 30176808 PMCID: PMC6122555 DOI: 10.1186/s12859-018-2312-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Histone modifications play important roles in gene regulation, heredity, imprinting, and many human diseases. The histone code is complex and consists of more than 100 marks. Therefore, biologists need computational tools to characterize general signatures representing the distributions of tens of chromatin marks around thousands of regions. RESULTS To this end, we developed a software tool, HebbPlot, which utilizes a Hebbian neural network in learning a general chromatin signature from regions with a common function. Hebbian networks can learn the associations between tens of marks and thousands of regions. HebbPlot presents a signature as a digital image, which can be easily interpreted. Moreover, signatures produced by HebbPlot can be compared quantitatively. We validated HebbPlot in six case studies. The results of these case studies are novel or validating results already reported in the literature, indicating the accuracy of HebbPlot. Our results indicate that promoters have a directional chromatin signature; several marks tend to stretch downstream or upstream. H3K4me3 and H3K79me2 have clear directional distributions around active promoters. In addition, the signatures of high- and low-CpG promoters are different; H3K4me3, H3K9ac, and H3K27ac are the most different marks. When we studied the signatures of enhancers active in eight tissues, we observed that these signatures are similar, but not identical. Further, we identified some histone modifications - H3K36me3, H3K79me1, H3K79me2, and H4K8ac - that are associated with coding regions of active genes. Other marks - H4K12ac, H3K14ac, H3K27me3, and H2AK5ac - were found to be weakly associated with coding regions of inactive genes. CONCLUSIONS This study resulted in a novel software tool, HebbPlot, for learning and visualizing the chromatin signature of a genetic element. Using HebbPlot, we produced a visual catalog of the signatures of multiple genetic elements in 57 cell types available through the Roadmap Epigenomics Project. Furthermore, we made a progress toward a functional catalog consisting of 22 histone marks. In sum, HebbPlot is applicable to a wide array of studies, facilitating the deciphering of the histone code.
Collapse
Affiliation(s)
- Hani Z. Girgis
- Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104-9700 OK USA
| | - Alfredo Velasco
- Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104-9700 OK USA
| | - Zachary E. Reyes
- Tandy School of Computer Science, University of Tulsa, 800 South Tucker Drive, Tulsa, 74104-9700 OK USA
| |
Collapse
|
3
|
Chang EYC, Novoa CA, Aristizabal MJ, Coulombe Y, Segovia R, Chaturvedi R, Shen Y, Keong C, Tam AS, Jones SJM, Masson JY, Kobor MS, Stirling PC. RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability. J Cell Biol 2017; 216:3991-4005. [PMID: 29042409 PMCID: PMC5716281 DOI: 10.1083/jcb.201703168] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/16/2017] [Accepted: 09/18/2017] [Indexed: 01/01/2023] Open
Abstract
Sgs1, the orthologue of human Bloom's syndrome helicase BLM, is a yeast DNA helicase functioning in DNA replication and repair. We show that SGS1 loss increases R-loop accumulation and sensitizes cells to transcription-replication collisions. Yeast lacking SGS1 accumulate R-loops and γ-H2A at sites of Sgs1 binding, replication pausing regions, and long genes. The mutation signature of sgs1Δ reveals copy number changes flanked by repetitive regions with high R-loop-forming potential. Analysis of BLM in Bloom's syndrome fibroblasts or by depletion of BLM from human cancer cells confirms a role for Sgs1/BLM in suppressing R-loop-associated genome instability across species. In support of a potential direct effect, BLM is found physically proximal to DNA:RNA hybrids in human cells, and can efficiently unwind R-loops in vitro. Together, our data describe a conserved role for Sgs1/BLM in R-loop suppression and support an increasingly broad view of DNA repair and replication fork stabilizing proteins as modulators of R-loop-mediated genome instability.
Collapse
Affiliation(s)
| | - Carolina A Novoa
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | | | - Yan Coulombe
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Romulo Segovia
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Richa Chaturvedi
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Yaoqing Shen
- Michael Smith Genome Sciences Centre, Vancouver, Canada
| | - Christelle Keong
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
| | - Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre Hospitalier Universitaire de Québec Research Center, Québec City, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada .,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| |
Collapse
|
4
|
Sowpati DT, Srivastava S, Dhawan J, Mishra RK. C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search. BMC Bioinformatics 2017; 18:392. [PMID: 28929968 PMCID: PMC5606219 DOI: 10.1186/s12859-017-1786-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of novel epigenetic patterns and their visualization across gene subsets remains a challenge. Results We developed a fast and interactive web app, C-State (Chromatin-State), to query and plot chromatin landscapes across multiple loci and cell types. C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer, pre-processing and prior programming knowledge. Conclusions C-State is unique in its ability to extract and analyze multi-gene epigenetic information. It allows for powerful GUI-based pattern searching and visualization. We include a case study to demonstrate its potential for identifying user-defined epigenetic trends in context of gene expression profiles. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1786-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | - Jyotsna Dhawan
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rakesh K Mishra
- CSIR- Centre for Cellular and Molecular Biology, Hyderabad, India.
| |
Collapse
|
5
|
Young CP, Hillyer C, Hokamp K, Fitzpatrick DJ, Konstantinov NK, Welty JS, Ness SA, Werner-Washburne M, Fleming AB, Osley MA. Distinct histone methylation and transcription profiles are established during the development of cellular quiescence in yeast. BMC Genomics 2017; 18:107. [PMID: 28122508 PMCID: PMC5267397 DOI: 10.1186/s12864-017-3509-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 01/18/2017] [Indexed: 12/19/2022] Open
Abstract
Background Quiescent cells have a low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we defined the genome-wide profiles of three species of histone methylation associated with active transcription between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and transcripts. Results Quiescent cells retained histone methylations normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained significant levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase. The RNA polymerase II associated with genes in quiescent cells displayed a distinct occupancy profile compared to its pattern of occupancy across genes in actively growing cells. Although transcription is generally repressed in quiescent cells, analysis of individual genes identified a period of active transcription during the development of quiescence. Conclusions The data suggest that the transcript profile and histone methylation marks in quiescent cells were established both in growing cells and during the development of quiescence and then retained in these cells. Together, this might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3509-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Conor P Young
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Cory Hillyer
- Department of Microbiology and Molecular Genetics, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Karsten Hokamp
- Smurfit Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Darren J Fitzpatrick
- Smurfit Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | | | | | - Scott A Ness
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | | | - Alastair B Fleming
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, University of Dublin, Trinity College Dublin, Dublin, Ireland.
| | - Mary Ann Osley
- Department of Microbiology and Molecular Genetics, University of New Mexico School of Medicine, Albuquerque, NM, USA.
| |
Collapse
|
6
|
Aristizabal MJ, Negri GL, Kobor MS. The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition. PLoS Genet 2015; 11:e1005608. [PMID: 26496706 PMCID: PMC4619828 DOI: 10.1371/journal.pgen.1005608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 09/27/2015] [Indexed: 12/14/2022] Open
Abstract
RNA polymerase II (RNAPII) contains a unique C-terminal domain that is composed of heptapeptide repeats and which plays important regulatory roles during gene expression. RNAPII is responsible for the transcription of most protein-coding genes, a subset of non-coding genes, and retrotransposons. Retrotransposon transcription is the first step in their multiplication cycle, given that the RNA intermediate is required for the synthesis of cDNA, the material that is ultimately incorporated into a new genomic location. Retrotransposition can have grave consequences to genome integrity, as integration events can change the gene expression landscape or lead to alteration or loss of genetic information. Given that RNAPII transcribes retrotransposons, we sought to investigate if the RNAPII-CTD played a role in the regulation of retrotransposon gene expression. Importantly, we found that the RNAPII-CTD functioned to maintaining genome integrity through inhibition of retrotransposon gene expression, as reducing CTD length significantly increased expression and transposition rates of Ty1 elements. Mechanistically, the increased Ty1 mRNA levels in the rpb1-CTD11 mutant were partly due to Cdk8-dependent alterations to the RNAPII-CTD phosphorylation status. In addition, Cdk8 alone contributed to Ty1 gene expression regulation by altering the occupancy of the gene-specific transcription factor Ste12. Loss of STE12 and TEC1 suppressed growth phenotypes of the RNAPII-CTD truncation mutant. Collectively, our results implicate Ste12 and Tec1 as general and important contributors to the Cdk8, RNAPII-CTD regulatory circuitry as it relates to the maintenance of genome integrity.
Collapse
Affiliation(s)
- Maria J. Aristizabal
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Department of Molecular Oncology, BC Cancer Research Center, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
7
|
Rossetto D, Cramet M, Wang AY, Steunou AL, Lacoste N, Schulze JM, Côté V, Monnet-Saksouk J, Piquet S, Nourani A, Kobor MS, Côté J. Eaf5/7/3 form a functionally independent NuA4 submodule linked to RNA polymerase II-coupled nucleosome recycling. EMBO J 2014; 33:1397-415. [PMID: 24843044 DOI: 10.15252/embj.201386433] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The NuA4 histone acetyltransferase complex is required for gene regulation, cell cycle progression, and DNA repair. Dissection of the 13-subunit complex reveals that the Eaf7 subunit bridges Eaf5 with Eaf3, a H3K36me3-binding chromodomain protein, and this Eaf5/7/3 trimer is anchored to NuA4 through Eaf5. This trimeric subcomplex represents a functional module, and a large portion exists in a native form outside the NuA4 complex. Gene-specific and genome-wide location analyses indicate that Eaf5/7/3 correlates with transcription activity and is enriched over the coding region. In agreement with a role in transcription elongation, the Eaf5/7/3 trimer interacts with phosphorylated RNA polymerase II and helps its progression. Loss of Eaf5/7/3 partially suppresses intragenic cryptic transcription arising in set2 mutants, supporting a role in nucleosome destabilization. On the other hand, loss of the trimer leads to an increase of replication-independent histone exchange over the coding region of transcribed genes. Taken together, these results lead to a model where Eaf5/7/3 associates with elongating polymerase to promote the disruption of nucleosomes in its path, but also their refolding in its wake.
Collapse
Affiliation(s)
- Dorine Rossetto
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Myriam Cramet
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Alice Y Wang
- Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada
| | - Anne-Lise Steunou
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Nicolas Lacoste
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Julia M Schulze
- Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Julie Monnet-Saksouk
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Sandra Piquet
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Amine Nourani
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| | - Michael S Kobor
- Center for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, BC, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center Centre de Recherche du CHU de Québec-Axe Oncologie Hôtel-Dieu de Québec, Quebec City, QC, Canada
| |
Collapse
|
8
|
Chan YA, Aristizabal MJ, Lu PYT, Luo Z, Hamza A, Kobor MS, Stirling PC, Hieter P. Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. PLoS Genet 2014; 10:e1004288. [PMID: 24743342 PMCID: PMC3990523 DOI: 10.1371/journal.pgen.1004288] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/21/2014] [Indexed: 12/17/2022] Open
Abstract
DNA:RNA hybrid formation is emerging as a significant cause of genome instability in biological systems ranging from bacteria to mammals. Here we describe the genome-wide distribution of DNA:RNA hybrid prone loci in Saccharomyces cerevisiae by DNA:RNA immunoprecipitation (DRIP) followed by hybridization on tiling microarray. These profiles show that DNA:RNA hybrids preferentially accumulated at rDNA, Ty1 and Ty2 transposons, telomeric repeat regions and a subset of open reading frames (ORFs). The latter are generally highly transcribed and have high GC content. Interestingly, significant DNA:RNA hybrid enrichment was also detected at genes associated with antisense transcripts. The expression of antisense-associated genes was also significantly altered upon overexpression of RNase H, which degrades the RNA in hybrids. Finally, we uncover mutant-specific differences in the DRIP profiles of a Sen1 helicase mutant, RNase H deletion mutant and Hpr1 THO complex mutant compared to wild type, suggesting different roles for these proteins in DNA:RNA hybrid biology. Our profiles of DNA:RNA hybrid prone loci provide a resource for understanding the properties of hybrid-forming regions in vivo, extend our knowledge of hybrid-mitigating enzymes, and contribute to models of antisense-mediated gene regulation. A summary of this paper was presented at the 26th International Conference on Yeast Genetics and Molecular Biology, August 2013.
Collapse
Affiliation(s)
- Yujia A. Chan
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Maria J. Aristizabal
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada
| | - Phoebe Y. T. Lu
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada
| | - Zongli Luo
- Wine Research Centre, University of British Columbia, Vancouver, Canada
| | - Akil Hamza
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter C. Stirling
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
- * E-mail: (PCS); (PH)
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- * E-mail: (PCS); (PH)
| |
Collapse
|
9
|
Aristizabal MJ, Negri GL, Benschop JJ, Holstege FCP, Krogan NJ, Kobor MS. High-throughput genetic and gene expression analysis of the RNAPII-CTD reveals unexpected connections to SRB10/CDK8. PLoS Genet 2013; 9:e1003758. [PMID: 24009531 PMCID: PMC3757075 DOI: 10.1371/journal.pgen.1003758] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/15/2013] [Indexed: 12/21/2022] Open
Abstract
The C-terminal domain (CTD) of RNA polymerase II (RNAPII) is composed of heptapeptide repeats, which play a key regulatory role in gene expression. Using genetic interaction, chromatin immunoprecipitation followed by microarrays (ChIP-on-chip) and mRNA expression analysis, we found that truncating the CTD resulted in distinct changes to cellular function. Truncating the CTD altered RNAPII occupancy, leading to not only decreases, but also increases in mRNA levels. The latter were largely mediated by promoter elements and in part were linked to the transcription factor Rpn4. The mediator subunit Cdk8 was enriched at promoters of these genes, and its removal not only restored normal mRNA and RNAPII occupancy levels, but also reduced the abnormally high cellular amounts of Rpn4. This suggested a positive role of Cdk8 in relationship to RNAPII, which contrasted with the observed negative role at the activated INO1 gene. Here, loss of CDK8 suppressed the reduced mRNA expression and RNAPII occupancy levels of CTD truncation mutants.
Collapse
Affiliation(s)
- Maria J. Aristizabal
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Joris J. Benschop
- Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Frank C. P. Holstege
- Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, United States of America
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
10
|
Nelson CJ, Ausió J. 55th Annual Canadian Society for Molecular Biosciences Conference on Epigenetics and Genomic Stability. Whistler, British Columbia, Canada, 14–18 March 2012. Epigenomics 2012; 4:255-9. [PMID: 22690661 DOI: 10.2217/epi.12.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The 55th Annual Canadian Society for Molecular Biosciences Conference on Epigenetics and Genomic Stability in Whistler, Canada, 14-18 March 2012, brought together 31 speakers from different nationalities. The organizing committee, led by Jim Davie (Chair) at the University of Manitoba (Manitoba, Canada), consisted of several established researchers in the fields of chromatin and epigenetics from across Canada. The meeting was centered on the contribution of epigenetics to gene expression, DNA damage and repair, and the role of environmental factors. A few interesting talks on replication added some insightful information on the controversial issue of histone post-translational modifications as genuine epigenetic marks that are inherited through cell division.
Collapse
Affiliation(s)
- Christopher J Nelson
- Department of Biochemistry & Microbiology, University of Victoria, British Columbia, Canada
| | | |
Collapse
|
11
|
Histone H3 lysine 36 methylation targets the Isw1b remodeling complex to chromatin. Mol Cell Biol 2012; 32:3479-85. [PMID: 22751925 DOI: 10.1128/mcb.00389-12] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Histone H3 lysine 36 methylation is a ubiquitous hallmark of productive transcription elongation. Despite the prevalence of this histone posttranslational modification, however, the downstream functions triggered by this mark are not well understood. In this study, we showed that H3K36 methylation promoted the chromatin interaction of the Isw1b chromatin-remodeling complex in Saccharomyces cerevisiae. Similar to H3K36 methylation, Isw1b was found at the mid- and 3' regions of transcribed genes genome wide, and its presence at active genes was dependent on H3K36 methylation and the PWWP domain of the Isw1b subunit, Ioc4. Moreover, purified Isw1b preferentially interacted with recombinant nucleosomes that were methylated at lysine 36, and this interaction also required the Ioc4 PWWP domain. While H3K36 methylation has been shown to regulate the binding of numerous factors, this is the first time that it has been shown to facilitate targeting of a chromatin-remodeling complex.
Collapse
|