1
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Wang Q, Lin J. Homeostasis of mRNA concentrations through coupling transcription, export, and degradation. iScience 2024; 27:110531. [PMID: 39175768 PMCID: PMC11338957 DOI: 10.1016/j.isci.2024.110531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 04/16/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024] Open
Abstract
Many experiments showed that eukaryotic cells maintain a constant mRNA concentration upon various perturbations by actively regulating mRNA production and degradation rates, known as mRNA buffering. However, the underlying mechanism is still unknown. In this work, we unveil a mechanistic model of mRNA buffering: the releasing-shuttling (RS) model. The model incorporates two crucial proteins, X and Y, which play several roles, including transcription, decay, and export factors, in the different stages of mRNA metabolism. The RS model predicts the constant mRNA concentration under genome-wide genetic perturbations and cell volume changes, the slowed-down mRNA degradation after Pol II depletion, and the temporal transcription dynamics after exonuclease depletion, in agreement with multiple experiments. Finally, we present a list of X and Y candidates and propose an experimental method to identify X. Our work uncovers potentially universal pathways coupling transcription, export, and degradation that help cells maintain mRNA homeostasis.
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Affiliation(s)
- Qirun Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jie Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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2
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Wong LH, Tremethick DJ. Multifunctional histone variants in genome function. Nat Rev Genet 2024:10.1038/s41576-024-00759-1. [PMID: 39138293 DOI: 10.1038/s41576-024-00759-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 08/15/2024]
Abstract
Histones are integral components of eukaryotic chromatin that have a pivotal role in the organization and function of the genome. The dynamic regulation of chromatin involves the incorporation of histone variants, which can dramatically alter its structural and functional properties. Contrary to an earlier view that limited individual histone variants to specific genomic functions, new insights have revealed that histone variants exert multifaceted roles involving all aspects of genome function, from governing patterns of gene expression at precise genomic loci to participating in genome replication, repair and maintenance. This conceptual change has led to a new understanding of the intricate interplay between chromatin and DNA-dependent processes and how this connection translates into normal and abnormal cellular functions.
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Affiliation(s)
- Lee H Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capial Territory, Australia.
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3
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Tremblay BJM, Santini CP, Cheng Y, Zhang X, Rosa S, Qüesta JI. Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition. Nat Commun 2024; 15:1724. [PMID: 38409232 PMCID: PMC10897432 DOI: 10.1038/s41467-024-46082-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.
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Affiliation(s)
- Benjamin J M Tremblay
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Cristina P Santini
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Yajiao Cheng
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Xue Zhang
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain.
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4
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Ye Y, Zhang S, Gao L, Zhu Y, Zhang J. Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205162. [PMID: 36658736 PMCID: PMC10015865 DOI: 10.1002/advs.202205162] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/15/2022] [Indexed: 06/17/2023]
Abstract
The exploration of single-cell 3D genome maps reveals that chromatin domains are indeed physical structures presenting in single cells, and domain boundaries vary from cell to cell. However, systematic analysis of the association between regulatory factor binding and elements and the formation of chromatin domains in single cells has not yet emerged. To this end, a hierarchical chromatin domain structure identification algorithm (named as HiCS) is first developed from individual single-cell Hi-C maps, with superior performance in both accuracy and efficiency. The results suggest that in addition to the known CTCF-cohesin complex, Polycomb, TrxG, pluripotent protein families, and other multiple factors also contribute to shaping chromatin domain boundaries in single embryonic stem cells. Different cooperation patterns of these regulatory factors drive genomic position categories with differential preferences forming boundaries, and the most extensive six types of retrotransposons are differentially distributed in these genomic position categories with preferential localization. The above results suggest that these different retrotransposons within genomic regions interplay with regulatory factors navigating the preference of genomic positions forming boundaries, driving the formation of higher-order chromatin structures, and thus regulating cell functions in single mouse embryonic stem cells.
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Affiliation(s)
- Yusen Ye
- School of Computer Science and TechnologyXidian UniversityXi'anShaanxi710071P. R. China
| | - Shihua Zhang
- NCMISCEMSRCSDSAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing100190P. R. China
- School of Mathematical SciencesUniversity of Chinese Academy of SciencesBeijing100049P. R. China
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming650223P. R. China
| | - Lin Gao
- School of Computer Science and TechnologyXidian UniversityXi'anShaanxi710071P. R. China
| | - Yuqing Zhu
- Center for Stem Cell and Translational MedicineSchool of Life SciencesAnhui UniversityHefeiAnhui230601P. R. China
| | - Jin Zhang
- Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310003P. R. China
- Zhejiang Laboratory for Systems and Precision MedicineZhejiang University Medical CenterHangzhouZhejiang311121P. R. China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310058P. R. China
- Center of Gene/Cell Engineering and Genome MedicineHangzhouZhejiang310058P. R. China
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5
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Chierzi S, Kacerovsky JB, Fok AHK, Lahaie S, Shibi Rosen A, Farmer WT, Murai KK. Astrocytes Transplanted during Early Postnatal Development Integrate, Mature, and Survive Long Term in Mouse Cortex. J Neurosci 2023; 43:1509-1529. [PMID: 36669885 PMCID: PMC10008063 DOI: 10.1523/jneurosci.0544-22.2023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 12/15/2022] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
Astrocytes have complex structural, molecular, and physiological properties and form specialized microenvironments that support circuit-specific functions in the CNS. To better understand how astrocytes acquire their unique features, we transplanted immature mouse cortical astrocytes into the developing cortex of male and female mice and assessed their integration, maturation, and survival. Within days, transplanted astrocytes developed morphologies and acquired territories and tiling behavior typical of cortical astrocytes. At 35-47 d post-transplantation, astrocytes appeared morphologically mature and expressed levels of EAAT2/GLT1 similar to nontransplanted astrocytes. Transplanted astrocytes also supported excitatory/inhibitory (E/I) presynaptic terminals within their territories, and displayed normal Ca2+ events. Transplanted astrocytes showed initially reduced expression of aquaporin 4 (AQP4) at endfeet and elevated expression of EAAT1/GLAST, with both proteins showing normalized expression by 110 d and one year post-transplantation, respectively. To understand how specific brain regions support astrocytic integration and maturation, we transplanted cortical astrocytes into the developing cerebellum. Cortical astrocytes interlaced with Bergmann glia (BG) in the cerebellar molecular layer to establish discrete territories. However, transplanted astrocytes retained many cortical astrocytic features including higher levels of EAAT2/GLT1, lower levels of EAAT1/GLAST, and the absence of expression of the AMPAR subunit GluA1. Collectively, our findings demonstrate that immature cortical astrocytes integrate, mature, and survive (more than one year) following transplantation and retain cortical astrocytic properties. Astrocytic transplantation can be useful for investigating cell-autonomous (intrinsic) and non-cell-autonomous (environmental) mechanisms contributing to astrocytic development/diversity, and for determining the optimal timing for transplanting astrocytes for cellular delivery or replacement in regenerative medicine.SIGNIFICANCE STATEMENT The mechanisms that enable astrocytes to acquire diverse molecular and structural properties remain to be better understood. In this study, we systematically analyzed the properties of cortical astrocytes following their transplantation to the early postnatal brain. We found that immature cortical astrocytes transplanted into cerebral cortex during early postnatal mouse development integrate and establish normal astrocytic properties, and show long-term survival in vivo (more than one year). In contrast, transplanted cortical astrocytes display reduced or altered ability to integrate into the more mature cerebral cortex or developing cerebellum, respectively. This study demonstrates the developmental potential of transplanted cortical astrocytes and provides an approach to tease apart cell-autonomous (intrinsic) and non-cell-autonomous (environmental) mechanisms that determine the structural, molecular, and physiological phenotype of astrocytes.
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Affiliation(s)
- Sabrina Chierzi
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec H3G 1A4, Canada
| | - J Benjamin Kacerovsky
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec H3G 1A4, Canada
| | - Albert H K Fok
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec H3G 1A4, Canada
| | - Sylvie Lahaie
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec H3G 1A4, Canada
| | - Arielle Shibi Rosen
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec H3G 1A4, Canada
| | - W Todd Farmer
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec H3G 1A4, Canada
| | - Keith K Murai
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec H3G 1A4, Canada
- Quantitative Life Sciences Graduate Program, McGill University, Montreal, Quebec H3A 2A7, Canada
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6
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Powers EN, Chan C, Doron-Mandel E, Llacsahuanga Allcca L, Kim Kim J, Jovanovic M, Brar GA. Bidirectional promoter activity from expression cassettes can drive off-target repression of neighboring gene translation. eLife 2022; 11:e81086. [PMID: 36503721 PMCID: PMC9754628 DOI: 10.7554/elife.81086] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Targeted selection-based genome-editing approaches have enabled many fundamental discoveries and are used routinely with high precision. We found, however, that replacement of DBP1 with a common selection cassette in budding yeast led to reduced expression and function for the adjacent gene, MRP51, despite all MRP51 coding and regulatory sequences remaining intact. Cassette-induced repression of MRP51 drove all mutant phenotypes detected in cells deleted for DBP1. This behavior resembled the 'neighboring gene effect' (NGE), a phenomenon of unknown mechanism whereby cassette insertion at one locus reduces the expression of a neighboring gene. Here, we leveraged strong off-target mutant phenotypes resulting from cassette replacement of DBP1 to provide mechanistic insight into the NGE. We found that the inherent bidirectionality of promoters, including those in expression cassettes, drives a divergent transcript that represses MRP51 through combined transcriptional interference and translational repression mediated by production of a long undecoded transcript isoform (LUTI). Divergent transcript production driving this off-target effect is general to yeast expression cassettes and occurs ubiquitously with insertion. Despite this, off-target effects are often naturally prevented by local sequence features, such as those that terminate divergent transcripts between the site of cassette insertion and the neighboring gene. Thus, cassette-induced off-target effects can be eliminated by the insertion of transcription terminator sequences into the cassette, flanking the promoter. Because the driving features of this off-target effect are broadly conserved, our study suggests it should be considered in the design and interpretation of experiments using integrated expression cassettes in other eukaryotic systems, including human cells.
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Affiliation(s)
- Emily Nicole Powers
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Charlene Chan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ella Doron-Mandel
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | | | - Jenny Kim Kim
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Gloria Ann Brar
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkleyBerkleyUnited States
- Center for Computational Biology, University of California, BerkeleyBerkeleyUnited States
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7
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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8
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Sefer E. ProbC: joint modeling of epigenome and transcriptome effects in 3D genome. BMC Genomics 2022; 23:287. [PMID: 35397520 PMCID: PMC8994916 DOI: 10.1186/s12864-022-08498-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/23/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Hi-C and its high nucleosome resolution variant Micro-C provide a window into the spatial packing of a genome in 3D within the cell. Even though both techniques do not directly depend on the binding of specific antibodies, previous work has revealed enriched interactions and domain structures around multiple chromatin marks; epigenetic modifications and transcription factor binding sites. However, the joint impact of chromatin marks in Hi-C and Micro-C interactions have not been globally characterized, which limits our understanding of 3D genome characteristics. An emerging question is whether it is possible to deduce 3D genome characteristics and interactions by integrative analysis of multiple chromatin marks and associate interactions to functionality of the interacting loci. RESULT We come up with a probabilistic method PROBC to decompose Hi-C and Micro-C interactions by known chromatin marks. PROBC is based on convex likelihood optimization, which can directly take into account both interaction existence and nonexistence. Through PROBC, we discover histone modifications (H3K27ac, H3K9me3, H3K4me3, H3K4me1) and CTCF as particularly predictive of Hi-C and Micro-C contacts across cell types and species. Moreover, histone modifications are more effective than transcription factor binding sites in explaining the genome's 3D shape through these interactions. PROBC can successfully predict Hi-C and Micro-C interactions in given species, while it is trained on different cell types or species. For instance, it can predict missing nucleosome resolution Micro-C interactions in human ES cells trained on mouse ES cells only from these 5 chromatin marks with above 0.75 AUC. Additionally, PROBC outperforms the existing methods in predicting interactions across almost all chromosomes. CONCLUSION Via our proposed method, we optimally decompose Hi-C interactions in terms of these chromatin marks at genome and chromosome levels. We find a subset of histone modifications and transcription factor binding sites to be predictive of both Hi-C and Micro-C interactions and TADs across human, mouse, and different cell types. Through learned models, we can predict interactions on species just from chromatin marks for which Hi-C data may be limited.
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Affiliation(s)
- Emre Sefer
- Department of Computer Science, Ozyegin University, Istanbul, Turkey.
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9
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Bryll AR, Peterson CL. Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis. Genes Dev 2021; 36:17-22. [PMID: 34916303 PMCID: PMC8763048 DOI: 10.1101/gad.348923.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022]
Abstract
In this study, Bryll et al. found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is accentuated by loss of deposition of histone variant H2A.Z. They identify the mRNA for the sirtuin deacetylase Hst3 as a key target for the RNA exosome that mediates communication between RNA degradation and transcription machineries. Eukaryotic cells maintain an optimal level of mRNAs through unknown mechanisms that balance RNA synthesis and degradation. We found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is accentuated by loss of deposition of histone variant H2A.Z. We identify the mRNA for the sirtuin deacetylase Hst3 as a key target for the RNA exosome that mediates communication between RNA degradation and transcription machineries. These findings reveal how the RNA exosome and H2A.Z function together to control a deacetylase, ensuring proper levels of transcription in response to changes in RNA degradation.
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Affiliation(s)
- Alysia R Bryll
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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10
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Guest T, Haycocks JRJ, Warren GZL, Grainger DC. Genome-wide mapping of Vibrio cholerae VpsT binding identifies a mechanism for c-di-GMP homeostasis. Nucleic Acids Res 2021; 50:149-159. [PMID: 34908143 PMCID: PMC8754643 DOI: 10.1093/nar/gkab1194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
Many bacteria use cyclic dimeric guanosine monophosphate (c-di-GMP) to control changes in lifestyle. The molecule, synthesized by proteins having diguanylate cyclase activity, is often a signal to transition from motile to sedentary behaviour. In Vibrio cholerae, c-di-GMP can exert its effects via the transcription factors VpsT and VpsR. Together, these proteins activate genes needed for V. cholerae to form biofilms. In this work, we have mapped the genome-wide distribution of VpsT in a search for further regulatory roles. We show that VpsT binds 23 loci and recognises a degenerate DNA palindrome having the consensus 5'-W-5R-4[CG]-3Y-2W-1W+1R+2[GC]+3Y+4W+5-3'. Most genes targeted by VpsT encode functions related to motility, biofilm formation, or c-di-GMP metabolism. Most notably, VpsT activates expression of the vpvABC operon that encodes a diguanylate cyclase. This creates a positive feedback loop needed to maintain intracellular levels of c-di-GMP. Mutation of the key VpsT binding site, upstream of vpvABC, severs the loop and c-di-GMP levels fall accordingly. Hence, as well as relaying the c-di-GMP signal, VpsT impacts c-di-GMP homeostasis.
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Affiliation(s)
- Thomas Guest
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - James R J Haycocks
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gemma Z L Warren
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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11
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Gowthaman U, Ivanov M, Schwarz I, Patel HP, Müller NA, García‐Pichardo D, Lenstra TL, Marquardt S. The Hda1 histone deacetylase limits divergent non-coding transcription and restricts transcription initiation frequency. EMBO J 2021; 40:e108903. [PMID: 34661296 PMCID: PMC8634119 DOI: 10.15252/embj.2021108903] [Citation(s) in RCA: 1] [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: 06/07/2021] [Revised: 08/31/2021] [Accepted: 09/28/2021] [Indexed: 01/01/2023] Open
Abstract
Nucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA and a divergent non-coding (DNC) transcript of unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. Using high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements, we identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC transcription. Nascent transcription profiling showed a genome-wide role of Hda1C in repression of DNC transcription. Live-cell imaging of transcription revealed that mutations in the Hda3 subunit increased the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC transcription regions, supporting DNC transcription repression by histone deacetylation. Our data support the interpretation that DNC transcription results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.
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Affiliation(s)
- Uthra Gowthaman
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Maxim Ivanov
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Isabel Schwarz
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Heta P Patel
- Division of Gene RegulationThe Netherlands Cancer Institute (NKI)Oncode InstituteAmsterdamThe Netherlands
| | - Niels A Müller
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Present address:
Thünen Institute of Forest GeneticsGrosshansdorfGermany
| | - Desiré García‐Pichardo
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Tineke L Lenstra
- Division of Gene RegulationThe Netherlands Cancer Institute (NKI)Oncode InstituteAmsterdamThe Netherlands
| | - Sebastian Marquardt
- Copenhagen Plant Science CentreDepartment of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
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12
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Kochan DZ, Mawer JSP, Massen J, Tishinov K, Parekh S, Graef M, Spang A, Tessarz P. The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription. J Cell Sci 2021; 134:jcs259051. [PMID: 34350963 PMCID: PMC8353526 DOI: 10.1242/jcs.259051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression involves regulation of chromatin structure and transcription, as well as processing of the transcribed mRNA. While there are feedback mechanisms, it is not clear whether these include crosstalk between chromatin architecture and mRNA decay. To address this, we performed a genome-wide genetic screen using a Saccharomyces cerevisiae strain harbouring the H3K56A mutation, which is known to perturb chromatin structure and nascent transcription. We identified Puf5 (also known as Mpt5) as essential in an H3K56A background. Depletion of Puf5 in this background leads to downregulation of Puf5 targets. We suggest that Puf5 plays a role in post-transcriptional buffering of mRNAs, and support this by transcriptional shutoff experiments in which Puf5 mRNA targets are degraded slower in H3K56A cells compared to wild-type cells. Finally, we show that post-transcriptional buffering of Puf5 targets is widespread and does not occur only in an H3K56A mutant, but also in an H3K4R background, which leads to a global increase in nascent transcription. Our data suggest that Puf5 determines the fate of its mRNA targets in a context-dependent manner acting as an mRNA surveillance hub balancing deregulated nascent transcription to maintain physiological mRNA levels.
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Affiliation(s)
- David Z. Kochan
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Julia S. P. Mawer
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Jennifer Massen
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Kiril Tishinov
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Swati Parekh
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Martin Graef
- Max Planck Research Group ‘Autophagy and Cellular Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Anne Spang
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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13
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Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry. Nat Microbiol 2021; 6:746-756. [PMID: 33958766 PMCID: PMC7612053 DOI: 10.1038/s41564-021-00898-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023]
Abstract
Transcription initiates at promoters, DNA regions recognized by a DNA-dependent RNA polymerase. We previously identified horizontally acquired Escherichia coli promoters from which the direction of transcription was unclear. In the present study, we show that more than half of these promoters are bidirectional and drive divergent transcription. Using genome-scale approaches, we demonstrate that 19% of all transcription start sites detected in E. coli are associated with a bidirectional promoter. Bidirectional promoters are similarly common in diverse bacteria and archaea, and have inherent symmetry: specific bases required for transcription initiation are reciprocally co-located on opposite DNA strands. Bidirectional promoters enable co-regulation of divergent genes and are enriched in both intergenic and horizontally acquired regions. Divergent transcription is conserved among bacteria, archaea and eukaryotes, but the underlying mechanisms for bidirectionality are different.
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14
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Welle A, Kasakow CV, Jungmann AM, Gobbo D, Stopper L, Nordström K, Salhab A, Gasparoni G, Scheller A, Kirchhoff F, Walter J. Epigenetic control of region-specific transcriptional programs in mouse cerebellar and cortical astrocytes. Glia 2021; 69:2160-2177. [PMID: 34028094 DOI: 10.1002/glia.24016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 01/07/2023]
Abstract
Astrocytes from the cerebral cortex (CTX) and cerebellum (CB) share basic molecular programs, but also form distinct spatial and functional subtypes. The regulatory epigenetic layers controlling such regional diversity have not been comprehensively investigated so far. Here, we present an integrated epigenome analysis of methylomes, open chromatin, and transcriptomes of astroglia populations isolated from the cortex or cerebellum of young adult mice. Besides a basic overall similarity in their epigenomic programs, cortical astrocytes and cerebellar astrocytes exhibit substantial differences in their overall open chromatin structure and in gene-specific DNA methylation. Regional epigenetic differences are linked to differences in transcriptional programs encompassing genes of region-specific transcription factor networks centered around Lhx2/Foxg1 in CTX astrocytes and the Zic/Irx families in CB astrocytes. The distinct epigenetic signatures around these transcription factor networks point to a complex interconnected and combinatorial regulation of region-specific transcriptomes. These findings suggest that key transcription factors, previously linked to temporal, regional, and spatial control of neurogenesis, also form combinatorial networks important for astrocytes. Our study provides a valuable resource for the molecular basis of regional astrocyte identity and physiology.
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Affiliation(s)
- Anna Welle
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Carmen V Kasakow
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Annemarie M Jungmann
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Davide Gobbo
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Laura Stopper
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Karl Nordström
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Abdulrahman Salhab
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Gilles Gasparoni
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
| | - Anja Scheller
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Frank Kirchhoff
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine, University of Saarland, Homburg, Germany
| | - Jörn Walter
- Department of Genetics and EpiGenetics, University of Saarland, Saarbrücken, Germany
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15
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Lee JE, Kim MY. Cancer epigenetics: Past, present and future. Semin Cancer Biol 2021; 83:4-14. [PMID: 33798724 DOI: 10.1016/j.semcancer.2021.03.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022]
Abstract
Cancer was thought to be caused solely by genetic mutations in oncogenes and tumor suppressor genes. In the last 35 years, however, epigenetic changes have been increasingly recognized as another primary driver of carcinogenesis and cancer progression. Epigenetic deregulation in cancer often includes mutations and/or aberrant expression of chromatin-modifying enzymes, their associated proteins, and even non-coding RNAs, which can alter chromatin structure and dynamics. This leads to changes in gene expression that ultimately contribute to the emergence and evolution of cancer cells. Studies of the deregulation of chromatin modifiers in cancer cells have reshaped the way we approach cancer and guided the development of novel anticancer therapeutics that target epigenetic factors. There remain, however, a number of unanswered questions in this field that are the focus of present research. Areas of particular interest include the actions of emerging classes of epigenetic regulators of carcinogenesis and the tumor microenvironment, as well as epigenetic tumor heterogeneity. In this review, we discuss past findings on epigenetic mechanisms of cancer, current trends in the field of cancer epigenetics, and the directions of future research that may lead to the identification of new prognostic markers for cancer and the development of more effective anticancer therapeutics.
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Affiliation(s)
- Jae Eun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Mi-Young Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; KAIST Institute for the BioCentury, Cancer Metastasis Control Center, Daejeon, Republic of Korea.
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16
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Genome-wide chromatin accessibility is restricted by ANP32E. Nat Commun 2020; 11:5063. [PMID: 33033242 PMCID: PMC7546623 DOI: 10.1038/s41467-020-18821-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide chromatin state underlies gene expression potential and cellular function. Epigenetic features and nucleosome positioning contribute to the accessibility of DNA, but widespread regulators of chromatin state are largely unknown. Our study investigates how coordination of ANP32E and H2A.Z contributes to genome-wide chromatin state in mouse fibroblasts. We define H2A.Z as a universal chromatin accessibility factor, and demonstrate that ANP32E antagonizes H2A.Z accumulation to restrict chromatin accessibility genome-wide. In the absence of ANP32E, H2A.Z accumulates at promoters in a hierarchical manner. H2A.Z initially localizes downstream of the transcription start site, and if H2A.Z is already present downstream, additional H2A.Z accumulates upstream. This hierarchical H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor binding, and increased expression of neighboring genes. Thus, ANP32E dramatically influences genome-wide chromatin accessibility through subtle refinement of H2A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels. Chromatin state underlies cellular function, and transcription factor binding patterns along with epigenetic marks define chromatin state. Here the authors show that the histone chaperone ANP32E functions through regulation of H2A.Z to restrict genome-wide chromatin accessibility and to inhibit gene transcriptional activation.
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17
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Squillaro T, Peluso G, Galderisi U, Di Bernardo G. Long non-coding RNAs in regulation of adipogenesis and adipose tissue function. eLife 2020; 9:59053. [PMID: 32730204 PMCID: PMC7392603 DOI: 10.7554/elife.59053] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Complex interaction between genetics, epigenetics, environment, and nutrition affect the physiological activities of adipose tissues and their dysfunctions, which lead to several metabolic diseases including obesity or type 2 diabetes. Here, adipogenesis appears to be a process characterized by an intricate network that involves many transcription factors and long noncoding RNAs (lncRNAs) that regulate gene expression. LncRNAs are being investigated to determine their contribution to adipose tissue development and function. LncRNAs possess multiple cellular functions, and they regulate chromatin remodeling, along with transcriptional and post-transcriptional events; in this way, they affect gene expression. New investigations have demonstrated the pivotal role of these molecules in modulating white and brown/beige adipogenic tissue development and activity. This review aims to provide an update on the role of lncRNAs in adipogenesis and adipose tissue function to promote identification of new drug targets for treating obesity and related metabolic diseases.
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Affiliation(s)
- Tiziana Squillaro
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Umberto Galderisi
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Giovanni Di Bernardo
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, University of Campania Luigi Vanvitelli, Naples, Italy
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18
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Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast. Nat Commun 2019; 10:4372. [PMID: 31558720 PMCID: PMC6763489 DOI: 10.1038/s41467-019-12400-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/06/2019] [Indexed: 01/22/2023] Open
Abstract
Dynamic disruption and reassembly of promoter-proximal nucleosomes is a conserved hallmark of transcriptionally active chromatin. Histone H3-K56 acetylation (H3K56Ac) enhances these turnover events and promotes nucleosome assembly during S phase. Here we sequence nascent transcripts to investigate the impact of H3K56Ac on transcription throughout the yeast cell cycle. We find that H3K56Ac is a genome-wide activator of transcription. While H3K56Ac has a major impact on transcription initiation, it also appears to promote elongation and/or termination. In contrast, H3K56Ac represses promiscuous transcription that occurs immediately following replication fork passage, in this case by promoting efficient nucleosome assembly. We also detect a stepwise increase in transcription as cells transit S phase and enter G2, but this response to increased gene dosage does not require H3K56Ac. Thus, a single histone mark can exert both positive and negative impacts on transcription that are coupled to different cell cycle events.
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19
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Feldman JL, Peterson CL. Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability. Cell Rep 2019; 27:2978-2989.e5. [PMID: 31167142 PMCID: PMC6640630 DOI: 10.1016/j.celrep.2019.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Accepted: 05/01/2019] [Indexed: 01/08/2023] Open
Abstract
The mammalian sirtuin, SIRT6, is a key tumor suppressor that maintains genome stability and regulates transcription, though how SIRT6 family members control genome stability is unclear. Here, we use multiple genome-wide approaches to demonstrate that the yeast SIRT6 homologs, Hst3 and Hst4, prevent genome instability by tuning levels of both coding and noncoding transcription. While nascent RNAs are elevated in the absence of Hst3 and Hst4, a global impact on steady-state mRNAs is masked by the nuclear exosome, indicating that sirtuins and the exosome provide two levels of regulation to maintain transcription homeostasis. We find that, in the absence of Hst3 and Hst4, increased transcription is associated with excessive DNA-RNA hybrids (R-loops) that appear to lead to new DNA double-strand breaks. Importantly, dissolution of R-loops suppresses the genome instability phenotypes of hst3 hst4 mutants, suggesting that the sirtuins maintain genome stability by acting as a rheostat to prevent promiscuous transcription.
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Affiliation(s)
- Jessica L Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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20
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Wu AC, Van Werven FJ. Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription. Transcription 2019; 10:164-170. [PMID: 31057041 PMCID: PMC6602560 DOI: 10.1080/21541264.2019.1608716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/11/2019] [Accepted: 04/13/2019] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, divergent transcription is a major source of noncoding RNAs. Recent studies have uncovered that in yeast, the transcription factor Rap1 restricts transcription in the divergent direction and thereby controls promoter directionality. Here, we summarize these findings, propose regulatory principles, and discuss the implications for eukaryotic gene regulation.
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Affiliation(s)
- Andrew C.K. Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
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21
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Sokpor G, Castro-Hernandez R, Rosenbusch J, Staiger JF, Tuoc T. ATP-Dependent Chromatin Remodeling During Cortical Neurogenesis. Front Neurosci 2018; 12:226. [PMID: 29686607 PMCID: PMC5900035 DOI: 10.3389/fnins.2018.00226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly. ATP-dependent chromatin remodeling complexes regulate gene expression through utilization of energy from ATP hydrolysis to reorganize chromatin structure. These chromatin remodeling complexes are characteristically multimeric, with some capable of adopting functionally distinct conformations via subunit reconstitution to perform specific roles in major aspects of cortical neurogenesis. In this review, we highlight the functions of such chromatin remodelers during cortical development. We also bring together various proposed mechanisms by which ATP-dependent chromatin remodelers function individually or in concert, to specifically modulate vital steps in cortical neurogenesis.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Ricardo Castro-Hernandez
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
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22
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Poli J, Gasser SM, Papamichos-Chronakis M. The INO80 remodeller in transcription, replication and repair. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0290. [PMID: 28847827 DOI: 10.1098/rstb.2016.0290] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Montpellier and Centre de Recherche en Biologie Cellulaire (CRBM), UMR5237, CNRS, Montpellier 34095, Cedex 5, France
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland .,Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Manolis Papamichos-Chronakis
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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23
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du Mee DJM, Ivanov M, Parker JP, Buratowski S, Marquardt S. Efficient termination of nuclear lncRNA transcription promotes mitochondrial genome maintenance. eLife 2018; 7:31989. [PMID: 29504936 PMCID: PMC5837560 DOI: 10.7554/elife.31989] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/08/2018] [Indexed: 12/27/2022] Open
Abstract
Most DNA in the genomes of higher organisms does not code for proteins. RNA Polymerase II (Pol II) transcribes non-coding DNA into long non-coding RNAs (lncRNAs), but biological roles of lncRNA are unclear. We find that mutations in the yeast lncRNA CUT60 result in poor growth. Defective termination of CUT60 transcription causes read-through transcription across the ATP16 gene promoter. Read-through transcription localizes chromatin signatures associated with Pol II elongation to the ATP16 promoter. The act of Pol II elongation across this promoter represses functional ATP16 expression by a Transcriptional Interference (TI) mechanism. Atp16p function in the mitochondrial ATP-synthase complex promotes mitochondrial DNA stability. ATP16 repression by TI through inefficient termination of CUT60 therefore triggers mitochondrial genome loss. Our results expand the functional and mechanistic implications of non-coding DNA in eukaryotes by highlighting termination of nuclear lncRNA transcription as mechanism to stabilize an organellar genome.
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Affiliation(s)
- Dorine Jeanne Mariëtte du Mee
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Joseph Paul Parker
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
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24
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Chiu AC, Suzuki HI, Wu X, Mahat DB, Kriz AJ, Sharp PA. Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP. Mol Cell 2018; 69:648-663.e7. [PMID: 29398447 DOI: 10.1016/j.molcel.2018.01.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/21/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022]
Abstract
Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. These PAS termination events are enriched at the first few stable nucleosomes flanking CpG islands and suppressed by U1 snRNP. Thus, promoter-proximal Pol II pausing consists of two processes: TSS-proximal and +1 stable nucleosome pausing, with PAS termination coinciding with the latter. While pausing factors NELF/DSIF only function in the former step, flavopiridol-sensitive mechanism(s) and Myc modulate both steps. We propose that premature PAS termination near the nucleosome-associated pause site represents a common transcriptional elongation checkpoint regulated by U1 snRNP recognition, nucleosome stability, and Myc activity.
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Affiliation(s)
- Anthony C Chiu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiroshi I Suzuki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xuebing Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dig B Mahat
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrea J Kriz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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25
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Klopf E, Schmidt HA, Clauder-Münster S, Steinmetz LM, Schüller C. INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res 2017; 45:3752-3766. [PMID: 28025392 PMCID: PMC5397147 DOI: 10.1093/nar/gkw1292] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/13/2016] [Indexed: 12/19/2022] Open
Abstract
The conserved INO80 chromatin remodeling complex is involved in regulation of DNA damage repair, replication and transcription. It is commonly recruited to the transcription start region and contributes to the establishment of promoter-proximal nucleosomes. We find a substantial influence of INO80 on nucleosome dynamics and gene expression during stress induced transcription. Transcription induced by osmotic stress leads to genome-wide remodeling of promoter proximal nucleosomes. INO80 function is required for timely return of evicted nucleosomes to the 5΄ end of induced genes. Reduced INO80 function in Arp8-deficient cells leads to correlated prolonged transcription and nucleosome eviction. INO80 and the related complex SWR1 regulate incorporation of the H2A.Z isoform at promoter proximal nucleosomes. However, H2A.Z seems not to influence osmotic stress induced gene regulation. Furthermore, we show that high rates of transcription promote INO80 recruitment to promoter regions, suggesting a connection between active transcription and promoter proximal nucleosome remodeling. In addition, we find that absence of INO80 enhances bidirectional promoter activity at highly induced genes and expression of a number of stress induced transcripts. We suggest that INO80 has a direct repressive role via promoter proximal nucleosome remodeling to limit high levels of transcription in yeast.
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Affiliation(s)
- Eva Klopf
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, Campus Vienna Biocenter 5 (VBC5), 1030 Vienna, Austria
| | - Sandra Clauder-Münster
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
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Neves LT, Douglass S, Spreafico R, Venkataramanan S, Kress TL, Johnson TL. The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae. Genes Dev 2017; 31:702-717. [PMID: 28446598 PMCID: PMC5411710 DOI: 10.1101/gad.295188.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/27/2017] [Indexed: 01/01/2023]
Abstract
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation. Here we show that splicing of intron-containing genes in cells lacking H2A.Z is impaired, particularly under suboptimal splicing conditions. Cells lacking H2A.Z are especially dependent on a functional U2 snRNP (small nuclear RNA [snRNA] plus associated proteins), as H2A.Z shows extensive genetic interactions with U2 snRNP-associated proteins, and RNA sequencing (RNA-seq) reveals that introns with nonconsensus branch points are particularly sensitive to H2A.Z loss. Consistently, H2A.Z promotes efficient spliceosomal rearrangements involving the U2 snRNP, as H2A.Z loss results in persistent U2 snRNP association and decreased recruitment of downstream snRNPs to nascent RNA. H2A.Z impairs transcription elongation, suggesting that spliceosome rearrangements are tied to H2A.Z's role in elongation. Depletion of disassembly factor Prp43 suppresses H2A.Z-mediated splice defects, indicating that, in the absence of H2A.Z, stalled spliceosomes are disassembled, and unspliced RNAs are released. Together, these data demonstrate that H2A.Z is required for efficient pre-mRNA splicing and indicate a role for H2A.Z in coordinating the kinetics of transcription elongation and splicing.
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Affiliation(s)
- Lauren T Neves
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA.,Graduate Program in Molecular Biology Interdepartmental Program, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Stephen Douglass
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Srivats Venkataramanan
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA
| | - Tracy L Kress
- Department of Biology, The College of New Jersey, Ewing, New Jersey 08628, USA
| | - Tracy L Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095 USA.,Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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Jin Y, Eser U, Struhl K, Churchman LS. The Ground State and Evolution of Promoter Region Directionality. Cell 2017; 170:889-898.e10. [PMID: 28803729 DOI: 10.1016/j.cell.2017.07.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/06/2017] [Accepted: 07/07/2017] [Indexed: 01/22/2023]
Abstract
Eukaryotic promoter regions are frequently divergently transcribed in vivo, but it is unknown whether the resultant antisense RNAs are a mechanistic by-product of RNA polymerase II (Pol II) transcription or biologically meaningful. Here, we use a functional evolutionary approach that involves nascent transcript mapping in S. cerevisiae strains containing foreign yeast DNA. Promoter regions in foreign environments lose the directionality they have in their native species. Strikingly, fortuitous promoter regions arising in foreign DNA produce equal transcription in both directions, indicating that divergent transcription is a mechanistic feature that does not imply a function for these transcripts. Fortuitous promoter regions arising during evolution promote bidirectional transcription and over time are purged through mutation or retained to enable new functionality. Similarly, human transcription is more bidirectional at newly evolved enhancers and promoter regions. Thus, promoter regions are intrinsically bidirectional and are shaped by evolution to bias transcription toward coding versus non-coding RNAs.
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Affiliation(s)
- Yi Jin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Umut Eser
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol 2017; 18:407-422. [PMID: 28512350 DOI: 10.1038/nrm.2017.26] [Citation(s) in RCA: 713] [Impact Index Per Article: 101.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize diverse ATP-dependent nucleosome-remodelling complexes to carry out histone sliding, ejection or the incorporation of histone variants, suggesting that different mechanisms of action are used by the various chromatin-remodelling complex subfamilies. However, all chromatin-remodelling complex subfamilies contain an ATPase-translocase 'motor' that translocates DNA from a common location within the nucleosome. In this Review, we discuss (and illustrate with animations) an alternative, unifying mechanism of chromatin remodelling, which is based on the regulation of DNA translocation. We propose the 'hourglass' model of remodeller function, in which each remodeller subfamily utilizes diverse specialized proteins and protein domains to assist in nucleosome targeting or to differentially detect nucleosome epitopes. These modules converge to regulate a common DNA translocation mechanism, to inform the conserved ATPase 'motor' on whether and how to apply DNA translocation, which together achieve the various outcomes of chromatin remodelling: nucleosome assembly, chromatin access and nucleosome editing.
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Affiliation(s)
- Cedric R Clapier
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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29
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Yu L, Rege M, Peterson CL, Volkert MR. RNA polymerase II depletion promotes transcription of alternative mRNA species. BMC Mol Biol 2016; 17:20. [PMID: 27578267 PMCID: PMC5004267 DOI: 10.1186/s12867-016-0074-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/18/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cells respond to numerous internal and external stresses, such as heat, cold, oxidative stress, DNA damage, and osmotic pressure changes. In most cases, the primary response to stress is transcriptional induction of genes that assist the cells in tolerating the stress and facilitate the repair of the cellular damage. However, when the transcription machinery itself is stressed, responding by such standard mechanisms may not be possible. RESULTS In this study, we demonstrate that depletion or inactivation of RNA polymerase II (RNAPII) changes the preferred polyadenylation site usage for several transcripts, and leads to increased transcription of a specific subset of genes. Surprisingly, depletion of RNA polymerase I (RNAPI) also promotes altered polyadenylation site usage, while depletion of RNA polymerase III (RNAPIII) does not appear to have an impact. CONCLUSIONS Our results demonstrate that stressing the transcription machinery by depleting either RNAPI or RNAPII leads to a novel transcriptional response that results in induction of specific mRNAs and altered polyadenylation of many of the induced transcripts.
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Affiliation(s)
- Lijian Yu
- Microbiological and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Mayuri Rege
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA, 01605, USA.
| | - Michael R Volkert
- Microbiological and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
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