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Saha D, Animireddy S, Lee J, Thommen A, Murvin MM, Lu Y, Calabrese JM, Bartholomew B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1's AT-hook, and SWI/SNF recruitment. Mol Cell 2024:S1097-2765(24)00223-5. [PMID: 38593804 DOI: 10.1016/j.molcel.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 11/24/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
RNA transcribed from enhancers, i.e., eRNA, has been suggested to directly activate transcription by recruiting transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find that the AT-hook of SWI/SNF preferentially binds RNA and, as part of the esBAF complex, associates with eRNA transcribed from intronic and intergenic regions. Our data suggest that SWI/SNF is globally recruited in cis by eRNA to cell-type-specific enhancers, representative of two distinct stages that mimic early mammalian development, and not at enhancers that are shared between the two stages. In this manner, SWI/SNF facilitates recruitment and/or activation of MLL3/4, p300/CBP, and Mediator to stage-specific enhancers and super-enhancers that regulate the transcription of metabolic and cell lineage priming-related genes. These findings highlight a connection between ATP-dependent chromatin remodeling and eRNA in cell identity and typical- and super-enhancer activation.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Anna Thommen
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - McKenzie M Murvin
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA
| | - J Mauro Calabrese
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA.
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2
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Kim M, Wang P, Clow PA, Chien I(E, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei CL, Casellas R, Cheng AW, Ruan Y. Multifaceted roles of cohesin in regulating transcriptional loops. bioRxiv 2024:2024.03.25.586715. [PMID: 38585764 PMCID: PMC10996690 DOI: 10.1101/2024.03.25.586715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.
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Affiliation(s)
- Minji Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Present address: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Equal contributions
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Equal contributions
| | - Patricia A. Clow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Equal contributions
| | - I (Eli) Chien
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Xiaotao Wang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai, China
| | - Jianhao Peng
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Haoxi Chai
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Xiyuan Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, P.R. China
| | - Byoungkoo Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, 06030, USA
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Rafael Casellas
- Hematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Albert W. Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
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3
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Lewis BA. The role of O-GlcNAcylation in RNA polymerase II transcription. J Biol Chem 2024; 300:105705. [PMID: 38311176 PMCID: PMC10906531 DOI: 10.1016/j.jbc.2024.105705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Eukaryotic RNA polymerase II (RNAPII) is responsible for the transcription of the protein-coding genes in the cell. Enormous progress has been made in discovering the protein activities that are required for transcription to occur, but the effects of post-translational modifications (PTMs) on RNAPII transcriptional regulation are much less understood. Most of our understanding relates to the cyclin-dependent kinases (CDKs), which appear to act relatively early in transcription. However, it is becoming apparent that other PTMs play a crucial role in the transcriptional cycle, and it is doubtful that any sort of complete understanding of this regulation is attainable without understanding the spectra of PTMs that occur on the transcriptional machinery. Among these is O-GlcNAcylation. Recent experiments have shown that the O-GlcNAc PTM likely has a prominent role in transcription. This review will cover the role of the O-GlcNAcylation in RNAPII transcription during initiation, pausing, and elongation, which will hopefully be of interest to both O-GlcNAc and RNAPII transcription researchers.
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Affiliation(s)
- Brian A Lewis
- Gene Regulation Section/LP, Center for Cancer Research, National Cancer Institute/NIH, Bethesda, Maryland, USA.
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4
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Atsumi Y, Iwata R, Kimura H, Vanderhaeghen P, Yamamoto N, Sugo N. Repetitive CREB-DNA interactions at gene loci predetermined by CBP induce activity-dependent gene expression in human cortical neurons. Cell Rep 2024; 43:113576. [PMID: 38128530 DOI: 10.1016/j.celrep.2023.113576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/10/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Neuronal activity-dependent transcription plays a key role in plasticity and pathology in the brain. An intriguing question is how neuronal activity controls gene expression via interactions of transcription factors with DNA and chromatin modifiers in the nucleus. By utilizing single-molecule imaging in human embryonic stem cell (ESC)-derived cortical neurons, we demonstrate that neuronal activity increases repetitive emergence of cAMP response element-binding protein (CREB) at histone acetylation sites in the nucleus, where RNA polymerase II (RNAPII) accumulation and FOS expression occur rapidly. Neuronal activity also enhances co-localization of CREB and CREB-binding protein (CBP). Increased binding of a constitutively active CREB to CBP efficiently induces CREB repetitive emergence. On the other hand, the formation of histone acetylation sites is dependent on CBP histone modification via acetyltransferase (HAT) activity but is not affected by neuronal activity. Taken together, our results suggest that neuronal activity promotes repetitive CREB-CRE and CREB-CBP interactions at predetermined histone acetylation sites, leading to rapid gene expression.
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Affiliation(s)
- Yuri Atsumi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryohei Iwata
- VIB-KU Leuven, Center for Brain & Disease Research and KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Pierre Vanderhaeghen
- VIB-KU Leuven, Center for Brain & Disease Research and KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Nobuhiko Yamamoto
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China.
| | - Noriyuki Sugo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
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5
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Bruno F, Coronel-Guisado C, González-Aguilera C. Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin. Mol Cell 2024; 84:221-233.e6. [PMID: 38151016 DOI: 10.1016/j.molcel.2023.11.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/23/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
DNA replication produces a global disorganization of chromatin structure that takes hours to be restored. However, how these chromatin rearrangements affect the regulation of gene expression and the maintenance of cell identity is not clear. Here, we use ChOR-seq and ChrRNA-seq experiments to analyze RNA polymerase II (RNAPII) activity and nascent RNA synthesis during the first hours after chromatin replication in human cells. We observe that transcription elongation is rapidly reactivated in nascent chromatin but that RNAPII abundance and distribution are altered, producing heterogeneous changes in RNA synthesis. Moreover, this first wave of transcription results in RNAPII blockages behind the replication fork, leading to changes in alternative splicing. Altogether, our results deepen our understanding of how transcriptional programs are regulated during cell division and uncover molecular mechanisms that explain why chromatin replication is an important source of gene expression variability.
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Affiliation(s)
- Federica Bruno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Cristóbal Coronel-Guisado
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Universidad Pablo de Olavide, 41092, Seville, Spain; Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013, Seville, Spain.
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6
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Erdos E, Sandor K, Young-Erdos CL, Halasz L, Smith SR, Osborne TF, Divoux A. Transcriptional Control of Subcutaneous Adipose Tissue by the Transcription Factor CTCF Modulates Heterogeneity in Fat Distribution in Women. Cells 2023; 13:86. [PMID: 38201289 PMCID: PMC10778492 DOI: 10.3390/cells13010086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Determining the mechanism driving body fat distribution will provide insights into obesity-related health risks. We used functional genomics tools to profile the epigenomic landscape to help infer the differential transcriptional potential of apple- and pear-shaped women's subcutaneous adipose-derived stem cells (ADSCs). We found that CCCTC-binding factor (CTCF) expression and its chromatin binding were increased in ADSCs from pear donors compared to those from apple donors. Interestingly, the pear enriched CTCF binding sites were located predominantly at the active transcription start sites (TSSs) of genes with active histone marks and YY1 motifs and were also associated with pear enriched RNAPII binding. In contrast, apple enriched CTCF binding sites were mainly found at intergenic regions and when identified at TSS, they were enriched with the bivalent chromatin signatures. Altogether, we provide evidence that CTCF plays an important role in differential regulation of subcutaneous ADSCs gene expression and may influence the development of apple vs. pear body shape.
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Affiliation(s)
- Edina Erdos
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Katalin Sandor
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | | | - Laszlo Halasz
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Steven R. Smith
- Translational Research Institute, Adventhealth, Orlando, FL 32804, USA
| | - Timothy F. Osborne
- Division of Diabetes Endocrinology and Metabolism, Departments of Medicine, Biological Chemistry and Pediatrics, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Adeline Divoux
- Translational Research Institute, Adventhealth, Orlando, FL 32804, USA
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7
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Martin BJE, Ablondi EF, Goglia C, Mimoso CA, Espinel-Cabrera PR, Adelman K. Global identification of SWI/SNF targets reveals compensation by EP400. Cell 2023; 186:5290-5307.e26. [PMID: 37922899 DOI: 10.1016/j.cell.2023.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/11/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Mammalian SWI/SNF chromatin remodeling complexes move and evict nucleosomes at gene promoters and enhancers to modulate DNA access. Although SWI/SNF subunits are commonly mutated in disease, therapeutic options are limited by our inability to predict SWI/SNF gene targets and conflicting studies on functional significance. Here, we leverage a fast-acting inhibitor of SWI/SNF remodeling to elucidate direct targets and effects of SWI/SNF. Blocking SWI/SNF activity causes a rapid and global loss of chromatin accessibility and transcription. Whereas repression persists at most enhancers, we uncover a compensatory role for the EP400/TIP60 remodeler, which reestablishes accessibility at most promoters during prolonged loss of SWI/SNF. Indeed, we observe synthetic lethality between EP400 and SWI/SNF in cancer cell lines and human cancer patient data. Our data define a set of molecular genomic features that accurately predict gene sensitivity to SWI/SNF inhibition in diverse cancer cell lines, thereby improving the therapeutic potential of SWI/SNF inhibitors.
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Affiliation(s)
- Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Eileen F Ablondi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christine Goglia
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Piero R Espinel-Cabrera
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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8
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Nagy-Mikó B, Németh-Szatmári O, Faragó-Mészáros R, Csókási A, Bognár B, Ördög N, Borsos BN, Majoros H, Ujfaludi Z, Oláh-Németh O, Nikolényi A, Dobi Á, Kószó R, Sántha D, Lázár G, Simonka Z, Paszt A, Ormándi K, Pankotai T, Boros IM, Villányi Z, Vörös A. Predictive Potential of RNA Polymerase B (II) Subunit 1 (RPB1) Cytoplasmic Aggregation for Neoadjuvant Chemotherapy Failure. Int J Mol Sci 2023; 24:15869. [PMID: 37958852 PMCID: PMC10650411 DOI: 10.3390/ijms242115869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
We aimed to investigate the contribution of co-translational protein aggregation to the chemotherapy resistance of tumor cells. Increased co-translational protein aggregation reflects altered translation regulation that may have the potential to buffer transcription under genotoxic stress. As an indicator for such an event, we followed the cytoplasmic aggregation of RPB1, the aggregation-prone largest subunit of RNA polymerase II, in biopsy samples taken from patients with invasive carcinoma of no special type. RPB1 frequently aggregates co-translationally in the absence of proper HSP90 chaperone function or in ribosome mutant cells as revealed formerly in yeast. We found that cytoplasmic foci of RPB1 occur in larger sizes in tumors that showed no regression after therapy. Based on these results, we propose that monitoring the cytoplasmic aggregation of RPB1 may be suitable for determining-from biopsy samples taken before treatment-the effectiveness of neoadjuvant chemotherapy.
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Affiliation(s)
- Bence Nagy-Mikó
- Department of Biochemistry and Molecular Biology, University of Szeged, 52 Középfasor, H-6726 Szeged, Hungary
| | - Orsolya Németh-Szatmári
- Department of Biochemistry and Molecular Biology, University of Szeged, 52 Középfasor, H-6726 Szeged, Hungary
| | - Réka Faragó-Mészáros
- Department of Biochemistry and Molecular Biology, University of Szeged, 52 Középfasor, H-6726 Szeged, Hungary
| | - Aliz Csókási
- Department of Biochemistry and Molecular Biology, University of Szeged, 52 Középfasor, H-6726 Szeged, Hungary
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
| | - Bence Bognár
- Department of Biochemistry and Molecular Biology, University of Szeged, 52 Középfasor, H-6726 Szeged, Hungary
| | - Nóra Ördög
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
| | - Barbara N. Borsos
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
| | - Hajnalka Majoros
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
| | - Zsuzsanna Ujfaludi
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
| | - Orsolya Oláh-Németh
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
| | - Aliz Nikolényi
- Department of Oncotherapy, Albert Szent-Györgyi Health Centre, University of Szeged, 12 Korányi Fasor, H-6720 Szeged, Hungary
| | - Ágnes Dobi
- Department of Oncotherapy, Albert Szent-Györgyi Health Centre, University of Szeged, 12 Korányi Fasor, H-6720 Szeged, Hungary
| | - Renáta Kószó
- Department of Oncotherapy, Albert Szent-Györgyi Health Centre, University of Szeged, 12 Korányi Fasor, H-6720 Szeged, Hungary
| | - Dóra Sántha
- Department of Oncotherapy, Albert Szent-Györgyi Health Centre, University of Szeged, 12 Korányi Fasor, H-6720 Szeged, Hungary
| | - György Lázár
- Department of Surgery, Albert Szent-Györgyi Health Centre, University of Szeged, 8 Semmelweis Street, H-6725 Szeged, Hungary
| | - Zsolt Simonka
- Department of Surgery, Albert Szent-Györgyi Health Centre, University of Szeged, 8 Semmelweis Street, H-6725 Szeged, Hungary
| | - Attila Paszt
- Department of Surgery, Albert Szent-Györgyi Health Centre, University of Szeged, 8 Semmelweis Street, H-6725 Szeged, Hungary
| | - Katalin Ormándi
- Department of Radiology, Albert Szent-Györgyi Health Centre, University of Szeged, 6 Semmelweis Street, H-6725 Szeged, Hungary
| | - Tibor Pankotai
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Dugonics tér 13, H-6720 Szeged, Hungary
- Genome Integrity and DNA Repair Core Group, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), University of Szeged, Budapesti út 9, H-6728 Szeged, Hungary
| | - Imre M. Boros
- Department of Biochemistry and Molecular Biology, University of Szeged, 52 Középfasor, H-6726 Szeged, Hungary
| | - Zoltán Villányi
- Department of Biochemistry and Molecular Biology, University of Szeged, 52 Középfasor, H-6726 Szeged, Hungary
| | - András Vörös
- Department of Pathology, Albert Szent-Györgyi Medical School, University of Szeged, Állomás utca 1, H-6725 Szeged, Hungary
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9
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Chanarat S. Transcription machinery of the minimalist: comparative genomic analysis provides insights into the (de)regulated transcription mechanism of microsporidia - fungal-relative parasites. Transcription 2023; 14:1-17. [PMID: 36757099 PMCID: PMC10353337 DOI: 10.1080/21541264.2023.2174765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Microsporidia are eukaryotic obligate intracellular parasites closely related to fungi. Co-evolving with infected hosts, microsporidia have highly reduced their genomes and lacked several biological components. As it is beneficial for intracellular parasites like microsporidia to reduce their genome size, it is therefore reasonable to assume that genes encoding multifactorial complex machinery of transcription could be a potential target to be excluded from microsporidian genomes during the reductive evolution. In such a case, an evolutionary dilemma occurs because microsporidia cannot remove all transcription-machinery-encoding genes, products of which are essential for initialthe initial steps of gene expression. Here, I propose that while genes encoding core machinery are conserved, several genes known to function in fine-tune regulation of transcription are absent. This genome compaction strategy may come at the cost of loosely regulated or less controllable transcription. Alternatively, analogous to microsporidian polar tube, the parasites may have specialized factors to regulate their RNA synthesis.
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Affiliation(s)
- Sittinan Chanarat
- Laboratory of Molecular Cell Biology, Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
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10
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Bhowmick R, Mehta KPM, Lerdrup M, Cortez D. Integrator facilitates RNAPII removal to prevent transcription-replication collisions and genome instability. Mol Cell 2023:S1097-2765(23)00371-4. [PMID: 37295432 DOI: 10.1016/j.molcel.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/17/2023] [Accepted: 05/10/2023] [Indexed: 06/12/2023]
Abstract
DNA replication preferentially initiates close to active transcription start sites (TSSs) in the human genome. Transcription proceeds discontinuously with an accumulation of RNA polymerase II (RNAPII) in a paused state near the TSS. Consequently, replication forks inevitably encounter paused RNAPII soon after replication initiates. Hence, dedicated machinery may be needed to remove RNAPII and facilitate unperturbed fork progression. In this study, we discovered that Integrator, a transcription termination machinery involved in the processing of RNAPII transcripts, interacts with the replicative helicase at active forks and promotes the removal of RNAPII from the path of the replication fork. Integrator-deficient cells have impaired replication fork progression and accumulate hallmarks of genome instability including chromosome breaks and micronuclei. The Integrator complex resolves co-directional transcription-replication conflicts to facilitate faithful DNA replication.
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Affiliation(s)
- Rahul Bhowmick
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA.
| | - Kavi P M Mehta
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Mads Lerdrup
- Center for Chromosome Stability, Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA.
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11
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Bay LTE, Stokke T, Syljuåsen RG, Landsverk HB. Analysis of RNA Polymerase II Chromatin Binding by Flow Cytometry. Bio Protoc 2023; 13:e4659. [PMID: 37113330 PMCID: PMC10127051 DOI: 10.21769/bioprotoc.4659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/20/2022] [Accepted: 03/05/2023] [Indexed: 04/29/2023] Open
Abstract
RNA polymerase II (RNAPII) transcribes DNA into mRNA and thereby plays a critical role in cellular protein production. In addition, RNAPII plays a central role in DNA damage responses. Measurements of RNAPII on chromatin may thus give insight into several essential processes in eukaryotic cells. During transcription, the C-terminal domain of RNAPII becomes post-translationally modified, and phosphorylation on serine 5 and serine 2 can be used as markers for the promoter proximal and productively elongating forms of RNAPII, respectively. Here, we provide a detailed protocol for the detection of chromatin-bound RNAPII and its serine 5- and serine 2-phosphorylated forms in individual human cells through the cell cycle. We have recently shown that this method can be used to study the effects of ultraviolet DNA damage on RNAPII chromatin binding and that it can even be used to reveal new knowledge about the transcription cycle itself. Other commonly used methods to study RNAPII chromatin binding include chromatin immunoprecipitation followed by sequencing or chromatin fractionation followed by western blotting. However, such methods are frequently based on lysates made from a large number of cells, which may mask population heterogeneity, e.g., due to cell cycle phase. With strengths such as single-cell analysis, speed of use, and accurate quantitative readouts, we envision that our flow cytometry method can be widely used as a complementary approach to sequencing-based methods to study effects of different stimuli and inhibitors on RNAPII-mediated transcription. Graphical overview.
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Affiliation(s)
- Lilli T. E. Bay
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Trond Stokke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Department of Core Facilities, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Randi G. Syljuåsen
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- *For correspondence: ;
| | - Helga B. Landsverk
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- *For correspondence: ;
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12
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Abstract
The positive transcription elongation factor b (P-TEFb) is composed of cyclins T1 or T2 and cyclin-dependent kinase 9 that regulate the elongation phase of transcription by RNA polymerase II. By antagonizing negative elongation factors and phosphorylating the C-terminal domain of RNA polymerase II, P-TEFb facilitates the elongation and co-transcriptional processing of nascent transcripts. This step is critical for the expression of most eukaryotic genes. In growing cells, P-TEFb is regulated negatively by its reversible associations with HEXIM1/2 in the 7SK snRNP and positively by a number of transcription factors, as well as the super elongation complex. In resting cells, P-TEFb falls apart, and cyclin T1 is degraded by the proteasome. This complex regulation of P-TEFb has evolved for the precise temporal and spatial regulation of gene expression in the organism. Its dysregulation contributes to inflammatory and neoplastic conditions.
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Affiliation(s)
- Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA.
| | - Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA.
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13
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Ohishi H, Ochiai H. STREAMING-Tag System: Technology to Enable Visualization of Transcriptional Activity and Subnuclear Localization of Specific Endogenous Genes. Methods Mol Biol 2023; 2577:103-122. [PMID: 36173569 DOI: 10.1007/978-1-0716-2724-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system enables imaging of nuclear localization as well as the transcription activity of a specific endogenous gene at sub-100-nm resolution in living cells. The use of this system combined with imaging of epigenome states enables a detailed analysis of the impact of epigenome status on transcriptional dynamics. In this chapter, we describe a method for quantifying distances between Nanog gene and clusters of cofactor BRD4 using the STREAMING-tag system in mouse embryonic stem cells.
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Affiliation(s)
- Hiroaki Ohishi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
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14
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Gregersen LH, Mitter R, Svejstrup JQ. Elongation factor-specific capture of RNA polymerase II complexes. Cell Rep Methods 2022; 2:100368. [PMID: 36590686 PMCID: PMC9795356 DOI: 10.1016/j.crmeth.2022.100368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/25/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022]
Abstract
Transcription of protein-coding genes is regulated by dynamic association of co-factors with RNA polymerase II (RNAPII). The function of these factors and their relationship with RNAPII is often poorly understood. Here, we present an approach for elongation-factor-specific mNET capture (ELCAP) of RNAPII complexes for sequencing and mass spectrometry analysis aimed at investigating the function of such RNAPII regulatory proteins. As proof of principle, we apply ELCAP to the RNAPII-associated proteins SCAF4 and SCAF8, which share an essential role as mRNA anti-terminators but have individual roles at the 3' end of genes. Mass spectrometry analysis shows that both SCAF4 and SCAF8 are part of RNAPII elongation complexes containing 3' end processing factors but depleted of splicing components. Importantly, the ELCAP sequencing (ELCAP-seq) profiles of SCAF4- and SCAF8-RNAPII complexes nicely reflect their function as mRNA-anti-terminators and their competing functions at the end of genes, where they prevent or promote transcriptional readthrough.
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Affiliation(s)
- Lea H. Gregersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jesper Q. Svejstrup
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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15
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Chan J, Kumar A, Kono H. RNAPII driven post-translational modifications of nucleosomal histones. Trends Genet 2022; 38:1076-1095. [PMID: 35618507 DOI: 10.1016/j.tig.2022.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
Abstract
The current understanding of how specific distributions of histone post-translational modifications (PTMs) are achieved throughout the chromatin remains incomplete. This review focuses on the role of RNA polymerase II (RNAPII) in establishing H2BK120/K123 ubiquitination and H3K4/K36 methylation distribution. The rate of RNAPII transcription is mainly a function of the RNAPII elongation and recruitment rates. Two major mechanisms link RNAPII's transcription rate to the distribution of PTMs. First, the phosphorylation patterns of Ser2P/Ser5P in the C-terminal domain of RNAPII change as a function of time, since the start of elongation, linking them to the elongation rate. Ser2P/Ser5P recruits specific histone PTM enzymes/activators to the nucleosome. Second, multiple rounds of binding and catalysis by the enzymes are required to establish higher methylations (H3K4/36me3). Thus, methylation states are determined by the transcription rate. In summary, the first mechanism determines the location of methylations in the gene, while the second mechanism determines the methylation state.
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Affiliation(s)
- Justin Chan
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
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16
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Erdos E, Divoux A, Sandor K, Halasz L, Smith SR, Osborne TF. Unique role for lncRNA HOTAIR in defining depot-specific gene expression patterns in human adipose-derived stem cells. Genes Dev 2022; 36:566-581. [PMID: 35618313 PMCID: PMC9186385 DOI: 10.1101/gad.349393.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/12/2022] [Indexed: 01/12/2023]
Abstract
In this study, Erdos et al. investigated the role of HOX transcript antisense intergenic RNA (HOTAIR) in adipose tissue biology. Using three different approaches (silencing of HOTAIR in GF human adipose-derived stem cells [GF hASCs], overexpression of HOTAIR in ABD hASCs, and ChIRP-seq) to localize HOTAIR binding in GF hASC chromatin, they found that HOTAIR binds and modulates expression, both positively and negatively, of genes involved in adipose tissue-specific pathways, including adipogenesis, and demonstrate a unique function for HOTAIR in hASC depot-specific regulation of gene expression. Accumulation of fat above the waist is an important risk factor in developing obesity-related comorbidities independently of BMI or total fat mass. Deciphering the gene regulatory programs of the adipose tissue precursor cells within upper body or abdominal (ABD) and lower body or gluteofemoral (GF) depots is important to understand their differential capacity for lipid accumulation, maturation, and disease risk. Previous studies identified the HOX transcript antisense intergenic RNA (HOTAIR) as a GF-specific lncRNA; however, its role in adipose tissue biology is still unclear. Using three different approaches (silencing of HOTAIR in GF human adipose-derived stem cells [GF hASCs], overexpression of HOTAIR in ABD hASCs, and ChIRP-seq) to localize HOTAIR binding in GF hASC chromatin, we found that HOTAIR binds and modulates expression, both positively and negatively, of genes involved in adipose tissue-specific pathways, including adipogenesis. We further demonstrate a direct interaction between HOTAIR and genes with high RNAPII binding in their gene bodies, especially at their 3′ ends or transcription end sites. Computational analysis suggests HOTAIR binds preferentially to the 3′ ends of genes containing predicted strong RNA–RNA interactions with HOTAIR. Together, these results reveal a unique function for HOTAIR in hASC depot-specific regulation of gene expression.
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Affiliation(s)
- Edina Erdos
- Division of Diabetes Endocrinology and Metabolism, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Medicine, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Adeline Divoux
- Translational Research Institute, AdventHealth, Orlando, Florida 32804, USA
| | - Katalin Sandor
- Division of Diabetes Endocrinology and Metabolism, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Medicine, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Laszlo Halasz
- Division of Diabetes Endocrinology and Metabolism, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Medicine, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Steven R Smith
- Translational Research Institute, AdventHealth, Orlando, Florida 32804, USA
| | - Timothy F Osborne
- Division of Diabetes Endocrinology and Metabolism, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Medicine, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
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17
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Mandal R, Raab M, Rödel F, Krämer A, Kostova I, Peña-Llopis S, Häupl B, Oellerich T, Gasimli K, Sanhaji M, Becker S, Strebhardt K. The non-apoptotic function of Caspase-8 in negatively regulating the CDK9-mediated Ser2 phosphorylation of RNA polymerase II in cervical cancer. Cell Mol Life Sci 2022; 79:597. [PMID: 36399280 DOI: 10.1007/s00018-022-04598-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022]
Abstract
Cervical cancer is the fourth most frequently diagnosed and fatal gynecological cancer. 15-61% of all cases metastasize and develop chemoresistance, reducing the 5-year survival of cervical cancer patients to as low as 17%. Therefore, unraveling the mechanisms contributing to metastasis is critical in developing better-targeted therapies against it. Here, we have identified a novel mechanism where nuclear Caspase-8 directly interacts with and inhibits the activity of CDK9, thereby modulating RNAPII-mediated global transcription, including those of cell-migration- and cell-invasion-associated genes. Crucially, low Caspase-8 expression in cervical cancer patients leads to poor prognosis, higher CDK9 phosphorylation at Thr186, and increased RNAPII activity in cervical cancer cell lines and patient biopsies. Caspase-8 knock-out cells were also more resistant to the small-molecule CDK9 inhibitor BAY1251152 in both 2D- and 3D-culture conditions. Combining BAY1251152 with Cisplatin synergistically overcame chemoresistance of Caspase-8-deficient cervical cancer cells. Therefore, Caspase-8 expression could be a marker in chemoresistant cervical tumors, suggesting CDK9 inhibitor treatment for their sensitization to Cisplatin-based chemotherapy.
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18
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Gachet-Castro C, Freitas-Castro F, Gonzáles-Córdova RA, da Fonseca CK, Gomes MD, Ishikawa-Ankerhold HC, Baqui MMA. Modulation of the Host Nuclear Compartment by Trypanosoma cruzi Uncovers Effects on Host Transcription and Splicing Machinery. Front Cell Infect Microbiol 2021; 11:718028. [PMID: 34737973 PMCID: PMC8560699 DOI: 10.3389/fcimb.2021.718028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/24/2021] [Indexed: 11/22/2022] Open
Abstract
Host manipulation is a common strategy for invading pathogens. Trypanosoma cruzi, the causative agent of Chagas Disease, lives intracellularly within host cells. During infection, parasite-associated modifications occur to the host cell metabolism and morphology. However, little is known about the effect of T. cruzi infection on the host cell nucleus and nuclear functionality. Here, we show that T. cruzi can modulate host transcription and splicing machinery in non-professional phagocytic cells during infection. We found that T. cruzi regulates host RNA polymerase II (RNAPII) in a time-dependent manner, resulting in a drastic decrease in RNAPII activity. Furthermore, host cell ribonucleoproteins associated with mRNA transcription (hnRNPA1 and AB2) are downregulated concurrently. We reasoned that T. cruzi may hijack the host U2AF35 auxiliary factor, a key regulator for RNA processing, as a strategy to affect the splicing machinery activities directly. In support of our hypothesis, we carried out in vivo splicing assays using an adenovirus E1A pre-mRNA splicing reporter, showing that intracellular T. cruzi directly modulates the host cells by appropriating U2AF35. For the first time, our results provide evidence of a complex and intimate molecular relationship between T. cruzi and the host cell nucleus during infection.
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Affiliation(s)
- Camila Gachet-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe Freitas-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Raul Alexander Gonzáles-Córdova
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Carol Kobori da Fonseca
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Marcelo Damário Gomes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Munira Muhammad Abdel Baqui
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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19
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Wiegard A, Kuzin V, Cameron DP, Grosser J, Ceribelli M, Mehmood R, Ballarino R, Valant F, Grochowski R, Karabogdan I, Crosetto N, Lindqvist A, Bizard AH, Kouzine F, Natsume T, Baranello L. Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1. Mol Cell 2021; 81:5007-5024.e9. [PMID: 34767771 DOI: 10.1016/j.molcel.2021.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/26/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
As cells enter mitosis, chromatin compacts to facilitate chromosome segregation yet remains transcribed. Transcription supercoils DNA to levels that can impede further progression of RNA polymerase II (RNAPII) unless it is removed by DNA topoisomerase 1 (TOP1). Using ChIP-seq on mitotic cells, we found that TOP1 is required for RNAPII translocation along genes. The stimulation of TOP1 activity by RNAPII during elongation allowed RNAPII clearance from genes in prometaphase and enabled chromosomal segregation. Disruption of the TOP1-RNAPII interaction impaired RNAPII spiking at promoters and triggered defects in the post-mitotic transcription program. This program includes factors necessary for cell growth, and cells with impaired TOP1-RNAPII interaction are more sensitive to inhibitors of mTOR signaling. We conclude that TOP1 is necessary for assisting transcription during mitosis with consequences for growth and gene expression long after mitosis is completed. In this sense, TOP1 ensures that cellular memory is preserved in subsequent generations.
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Affiliation(s)
- Anika Wiegard
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Vladislav Kuzin
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Donald P Cameron
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jan Grosser
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Michele Ceribelli
- Division of Pre-Clinical Innovation, NCATS, National Institutes of Health, Rockville, MD 20850, USA
| | - Rashid Mehmood
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden; Department of Software Engineering, University of Kotli, AJ&K, 45320 Kotli Azad Kashmir, Pakistan
| | - Roberto Ballarino
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Francesco Valant
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Radosław Grochowski
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | | | - Nicola Crosetto
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Anna Helene Bizard
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Fedor Kouzine
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Shizuoka 411-8540, Japan; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
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20
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Pfleiderer MM, Galej WP. Emerging insights into the function and structure of the Integrator complex. Transcription 2021; 12:251-265. [PMID: 35311473 PMCID: PMC9006982 DOI: 10.1080/21541264.2022.2047583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
The Integrator was originally discovered as a specialized 3'-end processing endonuclease complex required for maturation of RNA polymerase II (RNAPII)-dependent small nuclear RNAs (snRNAs). Since its discovery, Integrator's spectrum of substrates was significantly expanded to include non-polyadenylated long noncoding RNAs (lncRNA), enhancer RNAs (eRNAs), telomerase RNA (tertRNA), several Herpesvirus transcripts, and messenger RNAs (mRNAs). Recently emerging transcriptome-wide studies reveled an important role of the Integrator in protein-coding genes, where it contributes to gene expression regulation through promoter-proximal transcription attenuation. These new functional data are complemented by several structures of Integrator modules and higher-order complexes, providing mechanistic insights into Integrator-mediated processing events. In this work, we summarize recent progress in our understanding of the structure and function of the Integrator complex.
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21
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Uzun Ü, Brown T, Fischl H, Angel A, Mellor J. Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier. Cell Rep 2021; 36:109755. [PMID: 34592154 PMCID: PMC8492961 DOI: 10.1016/j.celrep.2021.109755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/18/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023] Open
Abstract
Spt4 is a transcription elongation factor with homologs in organisms with nucleosomes. Structural and in vitro studies implicate Spt4 in transcription through nucleosomes, and yet the in vivo function of Spt4 is unclear. Here, we assess the precise position of Spt4 during transcription and the consequences of the loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning in Saccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription, and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.
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Affiliation(s)
- Ülkü Uzun
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas Brown
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Harry Fischl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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22
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Wei Y, Li K, Lu DR, Zhu HX. Optimization of CUT&Tag product recovery and library construction method. Yi Chuan 2021; 43:362-374. [PMID: 33972210 DOI: 10.16288/j.yczz.21-016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The emerging cleavage under target and tagment (CUT&Tag) technology uses Tn5 transposase to cleavage near the DNA binding site of target protein and study the generated DNA fragments by the next-generation sequencing. It can quickly identify protein-DNA interactions, which greatly simplifies the experimental process of ChIP-Seq. After CUT&Tag tagment reaction, DNA recovery or other post-processing is required to perform library construction PCR. Different recovery methods have significant impact respectively. By establishing Streptavidin beads recovery CUT&Tag(srCUT&Tag), we can quickly and conveniently complete the product recovery of CUT&Tag. We carried out CUT&Tag assay of H3K4me3, RNA Polymerase II (RNA polymerase II, RNAPII), transcription factor CTCF and HMGA1 in K562 cells with different recovery methods, including ethanol precipitation, fragment separation magnetic beads (SPRI) Magnetic bead recovery, direct PCR method, as well as our srCUT&Tag recovery method. The results show that among the CUT&Tag results of four different targets, the SPRI magnetic bead recovery and our srCUT&Tag methods have higher recovery efficiency than the direct PCR method and ethanol precipitation method. All CUT&Tag results showed that the recovery of SPRI magnetic beads would lose most of the product fragments less than 150 bp. In the recovery of CTCF and HMGA1, direct PCR lost most of the fragments larger than 300 bp and has significant difference from result of other recovery method. This enables srCUT&Tag to provide more real and higher-resolution information than other recovery method. In summary, the newly established srCUT&Tag recovery method can improve the efficiency of CUT&Tag library construction and obtain better data quality compared with the existing CUT&Tag product recovery method, providing a better technical choice for epigenetics research.
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Affiliation(s)
- Ye Wei
- Statde Key Laboratory of Genetic Engineering School of Life Science, Fudan University, Shanghai 200438, China.,Novoprotein Scientific Inc., Wujiang 215200, China
| | - Ke Li
- Novoprotein Scientific Inc., Wujiang 215200, China
| | - Da Ru Lu
- Statde Key Laboratory of Genetic Engineering School of Life Science, Fudan University, Shanghai 200438, China
| | - Hua Xing Zhu
- Novoprotein Scientific Inc., Wujiang 215200, China
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23
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Batenburg NL, Cui S, Walker JR, Schellhorn HE, Zhu XD. The Winged Helix Domain of CSB Regulates RNAPII Occupancy at Promoter Proximal Pause Sites. Int J Mol Sci 2021; 22:ijms22073379. [PMID: 33806087 PMCID: PMC8037043 DOI: 10.3390/ijms22073379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/16/2022] Open
Abstract
Cockayne syndrome group B protein (CSB), a member of the SWI/SNF superfamily, resides in an elongating RNA polymerase II (RNAPII) complex and regulates transcription elongation. CSB contains a C-terminal winged helix domain (WHD) that binds to ubiquitin and plays an important role in DNA repair. However, little is known about the role of the CSB-WHD in transcription regulation. Here, we report that CSB is dependent upon its WHD to regulate RNAPII abundance at promoter proximal pause (PPP) sites of several actively transcribed genes, a key step in the regulation of transcription elongation. We show that two ubiquitin binding-defective mutations in the CSB-WHD, which impair CSB's ability to promote cell survival in response to treatment with cisplatin, have little impact on its ability to stimulate RNAPII occupancy at PPP sites. In addition, we demonstrate that two cancer-associated CSB mutations, which are located on the opposite side of the CSB-WHD away from its ubiquitin-binding pocket, impair CSB's ability to promote RNAPII occupancy at PPP sites. Taken together, these results suggest that CSB promotes RNAPII association with PPP sites in a manner requiring the CSB-WHD but independent of its ubiquitin-binding activity. These results further imply that CSB-mediated RNAPII occupancy at PPP sites is mechanistically separable from CSB-mediated repair of cisplatin-induced DNA damage.
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Affiliation(s)
| | | | | | | | - Xu-Dong Zhu
- Correspondence: ; Tel.: +1-905-525-9140 (ext. 27737)
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24
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Endres T, Solvie D, Heidelberger JB, Andrioletti V, Baluapuri A, Ade CP, Muhar M, Eilers U, Vos SM, Cramer P, Zuber J, Beli P, Popov N, Wolf E, Gallant P, Eilers M. Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Mol Cell 2021; 81:830-844.e13. [PMID: 33453168 DOI: 10.1016/j.molcel.2020.12.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 10/14/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
The MYC oncoprotein globally affects the function of RNA polymerase II (RNAPII). The ability of MYC to promote transcription elongation depends on its ubiquitylation. Here, we show that MYC and PAF1c (polymerase II-associated factor 1 complex) interact directly and mutually enhance each other's association with active promoters. PAF1c is rapidly transferred from MYC onto RNAPII. This transfer is driven by the HUWE1 ubiquitin ligase and is required for MYC-dependent transcription elongation. MYC and HUWE1 promote histone H2B ubiquitylation, which alters chromatin structure both for transcription elongation and double-strand break repair. Consistently, MYC suppresses double-strand break accumulation in active genes in a strictly PAF1c-dependent manner. Depletion of PAF1c causes transcription-dependent accumulation of double-strand breaks, despite widespread repair-associated DNA synthesis. Our data show that the transfer of PAF1c from MYC onto RNAPII efficiently couples transcription elongation with double-strand break repair to maintain the genomic integrity of MYC-driven tumor cells.
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25
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Maß L, Holtmannspötter M, Zachgo S. Dual-color 3D-dSTORM colocalization and quantification of ROXY1 and RNAPII variants throughout the transcription cycle in root meristem nuclei. Plant J 2020; 104:1423-1436. [PMID: 32896918 DOI: 10.1111/tpj.14986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/04/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
To unravel the function of a protein of interest, it is crucial to asses to what extent it associates via direct interactions or by overlapping expression with other proteins. ROXY1, a land plant-specific glutaredoxin, exerts a function in Arabidopsis flower development and interacts with TGA transcription factors in the nucleus. We detected a novel ROXY1 function in the root meristem. Root cells that lack chlorophyll reducing plant-specific background problems that can hamper colocalization 3D microscopy. Thus far, a super-resolution three-dimensional stochastic optical reconstruction microscopy (3D-dSTORM) approach has mainly been applied in animal studies. We established 3D-dSTORM using the roxy1 mutant complemented with green fluorescence protein-ROXY1 and investigated its colocalization with three distinct RNAPII isoforms. To quantify the colocalization results, 3D-dSTORM was coupled with the coordinate-based colocalization method. Interestingly, ROXY1 proteins colocalize with different RNA polymerase II (RNAPII) isoforms that are active at distinct transcription cycle steps. Our colocalization data provide new insights on nuclear glutaredoxin activities suggesting that ROXY1 is not only required in early transcription initiation events via interaction with transcription factors but likely also participates throughout further transcription processes until late termination steps. Furthermore, we showed the applicability of the combined approaches to detect and quantify responses to altered growth conditions, exemplified by analysis of H2 O2 treatment, causing a dissociation of ROXY1 and RNAPII isoforms. We envisage that the powerful dual-color 3D-dSTORM/coordinate-based colocalization combination offers plant cell biologists the opportunity to colocalize and quantify root meristem proteins at an increased, unprecedented resolution level <50 nm, which will enable the detection of novel subcellular protein associations and functions.
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Affiliation(s)
- Lucia Maß
- Botany Department, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
| | - Michael Holtmannspötter
- Integrated Bioimaging Facility iBiOs, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
- Center of Cellular Nanoanalytics Osnabrück, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
| | - Sabine Zachgo
- Botany Department, School of Biology and Chemistry, Osnabrück University, Osnabrück, 49076, Germany
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26
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Calvo O. RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression. Curr Genet 2020; 66:927-937. [PMID: 32508001 DOI: 10.1007/s00294-020-01084-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022]
Abstract
In eukaryotes, cellular RNAs are produced by three nuclear RNA polymerases (RNAPI, II, and III), which are multisubunit complexes. They share structural and functional features, although they are specialized in the synthesis of specific RNAs. RNAPII transcribes the vast majority of cellular RNAs, including mRNAs and a large number of noncoding RNAs. The structure of RNAPII is highly conserved in all eukaryotes, consisting of 12 subunits (Rpb1-12) organized into five structural modules, among which the Rpb4 and Rpb7 subunits form the stalk. Early studies suggested an accessory role for Rpb4, because is required for specific gene transcription pathways. Far from this initial hypothesis, it is now well established that the Rpb4/7 heterodimer plays much wider roles in gene expression regulation. It participates in nuclear and cytosolic processes ranging from transcription to translation and mRNA degradation in a cyclical process. For this reason, Rpb4/7 is considered a coordinator of gene expression. New functions have been added to the list of stalk functions during transcription, which will be reviewed herein: first, a role in the maintenance of proper RNAPII phosphorylation levels, and second, a role in the establishment of a looped gene architecture in actively transcribed genes.
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Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González 2, Salamanca, 37007, España.
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27
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Nakazawa Y, Hara Y, Oka Y, Komine O, van den Heuvel D, Guo C, Daigaku Y, Isono M, He Y, Shimada M, Kato K, Jia N, Hashimoto S, Kotani Y, Miyoshi Y, Tanaka M, Sobue A, Mitsutake N, Suganami T, Masuda A, Ohno K, Nakada S, Mashimo T, Yamanaka K, Luijsterburg MS, Ogi T. Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair. Cell 2020; 180:1228-1244.e24. [PMID: 32142649 DOI: 10.1016/j.cell.2020.02.010] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/16/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023]
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is initiated by the stalling of elongating RNA polymerase II (RNAPIIo) at DNA lesions. The ubiquitination of RNAPIIo in response to DNA damage is an evolutionarily conserved event, but its function in mammals is unknown. Here, we identified a single DNA damage-induced ubiquitination site in RNAPII at RPB1-K1268, which regulates transcription recovery and DNA damage resistance. Mechanistically, RPB1-K1268 ubiquitination stimulates the association of the core-TFIIH complex with stalled RNAPIIo through a transfer mechanism that also involves UVSSA-K414 ubiquitination. We developed a strand-specific ChIP-seq method, which revealed RPB1-K1268 ubiquitination is important for repair and the resolution of transcriptional bottlenecks at DNA lesions. Finally, RPB1-K1268R knockin mice displayed a short life-span, premature aging, and neurodegeneration. Our results reveal RNAPII ubiquitination provides a two-tier protection mechanism by activating TC-NER and, in parallel, the processing of DNA damage-stalled RNAPIIo, which together prevent prolonged transcription arrest and protect against neurodegeneration.
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Affiliation(s)
- Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichiro Hara
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Okiru Komine
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasukazu Daigaku
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan; Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Mayu Isono
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuxi He
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kana Kato
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nan Jia
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoru Hashimoto
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuko Kotani
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan; Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuka Miyoshi
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miyako Tanaka
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Immunometabolism, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Sobue
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norisato Mitsutake
- Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Takayoshi Suganami
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Immunometabolism, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, Japan; Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Tomoji Mashimo
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan; Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, Japan; Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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28
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Trizzino M, Barbieri E, Petracovici A, Wu S, Welsh SA, Owens TA, Licciulli S, Zhang R, Gardini A. The Tumor Suppressor ARID1A Controls Global Transcription via Pausing of RNA Polymerase II. Cell Rep 2019; 23:3933-3945. [PMID: 29949775 DOI: 10.1016/j.celrep.2018.05.097] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 05/30/2018] [Indexed: 12/17/2022] Open
Abstract
AT-rich interactive domain-containing proteins 1A and 1B (ARID1A and ARID1B) are mutually exclusive subunits of the chromatin remodeler SWI/SNF. ARID1A is the most frequently mutated chromatin regulator across all cancers, and ovarian clear cell carcinoma (OCCC) carries the highest prevalence of ARID1A mutations (∼57%). Despite evidence implicating ARID1A in tumorigenesis, the mechanism remains elusive. Here, we demonstrate that ARID1A binds active regulatory elements in OCCC. Depletion of ARID1A represses RNA polymerase II (RNAPII) transcription but results in modest changes to accessibility. Specifically, pausing of RNAPII is severely impaired after loss of ARID1A. Compromised pausing results in transcriptional dysregulation of active genes, which is compensated by upregulation of ARID1B. However, a subset of ARID1A-dependent genes is not rescued by ARID1B, including many p53 and estrogen receptor (ESR1) targets. Our results provide insight into ARID1A-mediated tumorigenesis and unveil functions of SWI/SNF in modulating RNAPII dynamics.
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Affiliation(s)
- Marco Trizzino
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ana Petracovici
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Shuai Wu
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Sarah A Welsh
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Tori A Owens
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Silvia Licciulli
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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29
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Hsieh MC, Peng HY, Ho YC, Lai CY, Cheng JK, Chen GD, Lin TB. Transcription Repressor Hes1 Contributes to Neuropathic Pain Development by Modifying CDK9/ RNAPII-Dependent Spinal mGluR5 Transcription. Int J Mol Sci 2019; 20:E4177. [PMID: 31454988 DOI: 10.3390/ijms20174177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/23/2019] [Accepted: 08/25/2019] [Indexed: 11/18/2022] Open
Abstract
Diverse transcriptional controls in the dorsal horn have been observed in pain hypersensitivity. However, the understanding of the exact causes and mechanisms of neuropathic pain development is still fragmentary. Here, the results demonstrated nerve injury decreased the expression of spinal hairy and enhancer of split 1 (Hes1), a transcriptional repressor, and enhanced metabotropic glutamate receptor subtype 5 (mGluR5) transcription/expression, which was accompanied with behavioral allodynia. Moreover, nerve injury decreased Hes1 levels and reciprocally increased cyclin dependent kinase-9 (CDK9) levels and recruited CDK9 to phosphorylate RNA polymerase II (RNAPII) in the promoter fragments of mGluR5, thereby enhancing mGluR5 transcription/expression in the dorsal horn. These effects were also induced by intrathecally administering naïve rats with Hes1 small interfering RNA (siRNA). Conversely, Hes1 overexpression using intrathecal lentiviral vectors in nerve injury rats produced reversal of pain behavior and reversed protein expressions, phosphorylation, and coupling to the promoter segments in the dorsal horn. Collectively, the results in this study indicated nerve injury diminishes spinal Hes1-dependent suppression of CDK9-dependent RNAPII phosphorylation on the mGluR5 promoter that possibly enhances mGluR5 transcription/expression for neuropathic pain development.
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30
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Caron P, van der Linden J, van Attikum H. Bon voyage: A transcriptional journey around DNA breaks. DNA Repair (Amst) 2019; 82:102686. [PMID: 31476573 DOI: 10.1016/j.dnarep.2019.102686] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/20/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023]
Abstract
DNA double-strand breaks (DSBs) affect chromatin integrity and impact DNA-dependent processes such as transcription. Several studies revealed that the transcription of genes located in close proximity to DSBs is transiently repressed. This is achieved through the establishment of either a transient repressive chromatin context or eviction of the RNA polymerase II complex from the damaged chromatin. While these mechanisms of transcription repression have been shown to affect the efficiency and accuracy of DSB repair, it became evident that the transcriptional state of chromatin before DSB formation also influences this process. Moreover, transcription can be initiated from DSB ends, generating long non-coding (lnc)RNAs that will be processed into sequence-specific double-stranded RNAs. These so-called DNA damage-induced (dd)RNAs dictate DSB repair by regulating the accumulation of DNA repair proteins at DSBs. Thus, a complex interplay between mechanisms of transcription activation and repression occurs at DSBs and affects their repair. Here we review our current understanding of the mechanisms that coordinate transcription and DSB repair to prevent genome instability arising from DNA breaks in transcribed regions.
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Affiliation(s)
- Pierre Caron
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands
| | - Janette van der Linden
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333ZC, Leiden, the Netherlands.
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31
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Zheng N, Wang T, Wei A, Chen W, Zhao C, Li H, Wang L. High-content analysis boosts identification of the initial cause of triptolide-induced hepatotoxicity. J Appl Toxicol 2019; 39:1337-1347. [PMID: 31218727 DOI: 10.1002/jat.3821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/21/2022]
Abstract
Triptolide (TP) has been widely used in China for more than 40 years as an immunosuppressive agent. Recently, serious concerns have been raised over TP-induced liver injury, though the real hepatotoxic mechanism is still unclear, particularly in terms of the initial cause. To our knowledge, this study is the first to screen systematically the mechanism of TP-induced toxicity through a global cytotoxicity profile high-content analysis using three independent cytotoxic assay panels with multiple endpoints of cytotoxicity, including cell loss, mitochondrial membrane potential, nuclear membrane permeability, manganese superoxide dismutase, phosphorylated gamma-H2AX, light chain 3B, lysosome, reactive oxygen species and glutathione. We assessed nine parameters and four stress response pathway models by labeling nuclear factor erythroid 2-related factor 2, activating transcription factor 6, hypoxia inducible factor 1α and nuclear factor κB and found that all testing parameters except glutathione and manganese superoxide dismutase showed concentration- and time-dependent changes, as well as increased cell loss after TP treatment. Considering that RNA polymerase II is the molecular target of TP, we quantified transcription from inducible genes, bromodeoxyuridine incorporation, and expression from transiently transfected green fluorescence protein plasmids in HepG2 cells. The results show that inhibition of global transcription by TP took place at earlier times and at lower concentrations than those observed for cell death. Therefore, global transcriptional suppression and the cell dysfunction it drives play a central role in TP-induced hepatotoxicity. This provides valuable information for the safe use of TP in the clinic.
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Affiliation(s)
- Nan Zheng
- Institute of Pharmacology and Toxicology, Beijing, China
| | - Tiantian Wang
- Institute of Pharmacology and Toxicology, Beijing, China.,Key Laboratory of Cell Proliferation and Regulation Biology, Beijing Normal University, Beijing, China
| | - Aili Wei
- Institute of Pharmacology and Toxicology, Beijing, China
| | - Wei Chen
- Institute of Pharmacology and Toxicology, Beijing, China
| | - Changqi Zhao
- Key Laboratory of Cell Proliferation and Regulation Biology, Beijing Normal University, Beijing, China
| | - Hua Li
- Institute of Pharmacology and Toxicology, Beijing, China
| | - Lili Wang
- Institute of Pharmacology and Toxicology, Beijing, China.,State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, China
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32
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Jiang H, Wolgast M, Beebe LM, Reese JC. Ccr4-Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII. Genes Dev 2019; 33:705-17. [PMID: 30948432 DOI: 10.1101/gad.322453.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/14/2019] [Indexed: 12/23/2022]
Abstract
The Ccr4-Not complex regulates essentially every aspect of gene expression, from mRNA synthesis to protein destruction. The Not4 subunit of the complex contains an E3 RING domain and targets proteins for ubiquitin-dependent proteolysis. Ccr4-Not associates with elongating RNA polymerase II (RNAPII), which raises the possibility that it controls the degradation of elongation complex components. Here, we demonstrate that Ccr4-Not controls the ubiquitylation and turnover of Rpb1, the largest subunit of RNAPII, during transcription arrest. Deleting NOT4 or mutating its RING domain strongly reduced the DNA damage-dependent ubiquitylation and destruction of Rpb1. Surprisingly, in vitro ubiquitylation assays indicate that Ccr4-Not does not directly ubiquitylate Rpb1 but instead promotes Rpb1 ubiquitylation by the HECT domain-containing ligase Rsp5. Genetic analyses suggest that Ccr4-Not acts upstream of RSP5, where it acts to initiate the destruction process. Ccr4-Not binds Rsp5 and forms a ternary complex with it and the RNAPII elongation complex. Analysis of mutant Ccr4-Not lacking the RING domain of Not4 suggests that it both recruits Rsp5 and delivers the E2 Ubc4/5 to RNAPII. Our work reveals a previously unknown function of Ccr4-Not and identifies an essential new regulator of RNAPII turnover during genotoxic stress.
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Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. Wiley Interdiscip Rev RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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Godoy Herz MA, Kornblihtt AR. Alternative Splicing and Transcription Elongation in Plants. Front Plant Sci 2019; 10:309. [PMID: 30972082 PMCID: PMC6443983 DOI: 10.3389/fpls.2019.00309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/26/2019] [Indexed: 05/19/2023]
Abstract
Alternative splicing and transcription elongation by RNA polymerase II (RNAPII) are two processes which are tightly connected. Splicing is a co-transcriptional process, and different experimental approaches show that splicing is coupled to transcription in Drosophila, yeast and mammals. However, little is known about coupling of transcription and alternative splicing in plants. The kinetic coupling explains how changes in RNAPII elongation rate influence alternative splicing choices. Recent work in Arabidopsis shows that expression of a dominant negative transcription elongation factor, TFIIS, enhances exon inclusion. Furthermore, the Arabidopsis transcription elongation complex has been recently described, providing new information about elongation factors that interact with elongating RNAPII. Light regulates alternative splicing in plants through a chloroplast retrograde signaling. We have recently shown that light promotes RNAPII elongation in the affected genes, while in darkness elongation is lower. These changes in transcription are consistent with elongation causing the observed changes in alternative splicing. Altogether, these findings provide evidence that coupling between transcription and alternative splicing is an important layer of gene expression regulation in plants.
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Affiliation(s)
- Micaela A. Godoy Herz
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Alberto R. Kornblihtt
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
- *Correspondence: Alberto R. Kornblihtt,
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35
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Shukla M, Tong P, White SA, Singh PP, Reid AM, Catania S, Pidoux AL, Allshire RC. Centromere DNA Destabilizes H3 Nucleosomes to Promote CENP-A Deposition during the Cell Cycle. Curr Biol 2018; 28:3924-3936.e4. [PMID: 30503616 PMCID: PMC6303189 DOI: 10.1016/j.cub.2018.10.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 09/12/2018] [Accepted: 10/22/2018] [Indexed: 12/31/2022]
Abstract
Active centromeres are defined by the presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location, CENP-A chromatin and kinetochores are maintained at that location through a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication. Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences. Intrinsic properties of centromeric DNA may favor the assembly of CENP-A rather than H3 nucleosomes. Here we investigate histone dynamics on centromere DNA. We show that during S phase, histone H3 is deposited as a placeholder at fission yeast centromeres and is subsequently evicted in G2, when we detect deposition of the majority of new CENP-ACnp1. We also find that centromere DNA has an innate property of driving high rates of turnover of H3-containing nucleosomes, resulting in low nucleosome occupancy. When placed at an ectopic chromosomal location in the absence of any CENP-ACnp1 assembly, centromere DNA appears to retain its ability to impose S phase deposition and G2 eviction of H3, suggesting that features within centromere DNA program H3 dynamics. Because RNA polymerase II (RNAPII) occupancy on this centromere DNA coincides with H3 eviction in G2, we propose a model in which RNAPII-coupled chromatin remodeling promotes replacement of H3 with CENP-ACnp1 nucleosomes.
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Affiliation(s)
- Manu Shukla
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Pin Tong
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sharon A White
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Puneet P Singh
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Angus M Reid
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sandra Catania
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alison L Pidoux
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Robin C Allshire
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK.
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36
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Boureau L, Constantinof A, Moisiadis VG, Matthews SG, Szyf M. The DNA methylation landscape of enhancers in the guinea pig hippocampus. Epigenomics 2018; 10:349-365. [PMID: 29616589 DOI: 10.2217/epi-2017-0064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM To determine the state of methylation of DNA molecules in the guinea pig hippocampus that are associated with either poised or active enhancers. METHODS We used sequential chromatin immunoprecipitation-bisulfite-sequencing with an antibody to H3K4me1 to map the state of methylation of DNA that is found within enhancers. Actively transcribing transcription start sites were mapped by chromatin immunoprecipitation-sequencing with an antibody to RNApolII-PS5. Total DNA methylation was mapped using reduced representation bisulfite sequencing. RESULTS DNA that overlaps with H3K4me1 binding regions in the genome is heavily methylated. However, DNA molecules that are found in H3K4me1 chromatin are hypomethylated, while DNA found in enhancers that are associated with active transcription is further demethylated. Differential methylation in enhancers is spotted in single CGs, bimodal and corresponds to transcription factor binding sites. CONCLUSION Our study delineates the DNA methylation status of H3K4 me1-bound regions in the hippocampus in active and inactive genes.
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Affiliation(s)
- Lisa Boureau
- Department of Pharmacology & Therapeutics, Sackler Program for Epigenetics & Psychobiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Andrea Constantinof
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Vasilis G Moisiadis
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Stephen G Matthews
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Obstetrics & Gynecology, University of Toronto, Toronto, Ontario M5G 1E2, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5G 2C4, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, Sackler Program for Epigenetics & Psychobiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
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37
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Wong VCL. Nuclear EGFR and Integrator/Super Elongation Complex concurrently binds to Immediate Early Genes for gene transactivation. J Cancer 2018; 9:108-116. [PMID: 29290775 PMCID: PMC5743717 DOI: 10.7150/jca.21925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/06/2017] [Indexed: 12/14/2022] Open
Abstract
The gene transactivation function of nuclear EGFR (nEGFR) has been studied by investigating the genomic co-occupancies of nEGFR and RNA Polymerase II (RNAPII). However, due to RNAPII pausing, the co-recruitment of RNAPII and nEGFR does not necessarily represent productive transactivation. In this study, we integrated gatekeepers of productive transcriptional elongation such as Integrator and Super Elongation Complex (SEC) to interrogate the function of nEGFR. By analyzing publicly available ChIP-seq and RNA-seq data, we aims to 1) explore the function of nEGFR, 2) unravel nEGFR target genes, and 3) discuss potential mechanisms of nEGFR chromatin recruitment. EGF treatment in HeLa cells instigated chromatin recruitment of nEGFR, ERK, RNAPII, Integrator, and SEC in a cluster of 61 EGF-responsive genes. The function of nEGFR was identified as gene-activating rather than gene-repressing. Within the cluster of EGF-responsive genes, nEGFR targeted eleven Immediate Early Genes (IEGs) — JUN, EGR1, JUNB, IER2, KLF2, FOS, FOSL1, RHOB, CCNL1, DUSP2, and DUSP5, which up-regulated >2-fold after EGF stimulation. The promoter of these target genes commonly harbors AT-rich minimal consensus sequences for nEGFR binding. In addition, TCGA data analysis demonstrated positive correlations between EGFR and JUN/FOSL1/RHOB expressions, as well as clinical correlations in specific cancer types. To our knowledge, this is the first study to compare the genome-wide distribution of nEGFR versus Integrator and SEC, providing novel insight into supporting the gene-activating function of nEGFR. We revealed a panel of eleven nEGFR target genes, which concurrently recruited nEGFR, RNAPII, Integrator, and SEC for productive transcriptional elongation.
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Affiliation(s)
- Victor Chun-Lam Wong
- OncoSeek Limited, Hong Kong Science and Technology Parks, Hong Kong Special Administrative Region
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38
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Ma C, Karwacki-Neisius V, Tang H, Li W, Shi Z, Hu H, Xu W, Wang Z, Kong L, Lv R, Fan Z, Zhou W, Yang P, Wu F, Diao J, Tan L, Shi YG, Lan F, Shi Y. Nono, a Bivalent Domain Factor, Regulates Erk Signaling and Mouse Embryonic Stem Cell Pluripotency. Cell Rep 2017; 17:997-1007. [PMID: 27760330 DOI: 10.1016/j.celrep.2016.09.078] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 08/29/2016] [Accepted: 09/22/2016] [Indexed: 10/20/2022] Open
Abstract
Nono is a component of the para-speckle, which stores and processes RNA. Mouse embryonic stem cells (mESCs) lack para-speckles, leaving the function of Nono in mESCs unclear. Here, we find that Nono functions as a chromatin regulator cooperating with Erk to regulate mESC pluripotency. We report that Nono loss results in robust self-renewing mESCs with epigenomic and transcriptomic features resembling the 2i (GSK and Erk inhibitors)-induced "ground state." Erk interacts with and is required for Nono localization to a subset of bivalent genes that have high levels of poised RNA polymerase. Nono loss compromises Erk activation and RNA polymerase poising at its target bivalent genes in undifferentiated mESCs, thus disrupting target gene activation and differentiation. These findings argue that Nono collaborates with Erk signaling to regulate the integrity of bivalent domains and mESC pluripotency.
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Affiliation(s)
- Chun Ma
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Violetta Karwacki-Neisius
- Newborn Medicine Division, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Haoran Tang
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenjing Li
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhennan Shi
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Haolin Hu
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenqi Xu
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhentian Wang
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lingchun Kong
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ruitu Lv
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zheng Fan
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wenhao Zhou
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China
| | - Pengyuan Yang
- Department of Systems Biology, Institutes of Biomedical Sciences, Fudan University, 138 Yixue Yuan Road, Shanghai 200032, China
| | - Feizhen Wu
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianbo Diao
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Li Tan
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yujiang Geno Shi
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fei Lan
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Yang Shi
- Key Laboratory of Birth Defects, Children's Hospital and Key Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 201102, China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Newborn Medicine Division, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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Dejure FR, Eilers M. MYC and tumor metabolism: chicken and egg. EMBO J 2017; 36:3409-3420. [PMID: 29127156 DOI: 10.15252/embj.201796438] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 09/16/2017] [Accepted: 09/28/2017] [Indexed: 12/17/2022] Open
Abstract
Transcription factors of the MYC family are deregulated in the majority of all human cancers. Oncogenic levels of MYC reprogram cellular metabolism, a hallmark of cancer development, to sustain the high rate of proliferation of cancer cells. Conversely, cells need to modulate MYC function according to the availability of nutrients, in order to avoid a metabolic collapse. Here, we review recent evidence that the multiple interactions of MYC with cell metabolism are mutual and review mechanisms that control MYC levels and function in response to metabolic stress situations. The main hypothesis we put forward is that regulation of MYC levels is an integral part of the adaptation of cells to nutrient deprivation. Since such mechanisms would be particularly relevant in tumor cells, we propose that-in contrast to growth factor-dependent controls-they are not disrupted during tumorigenesis and that maintaining flexibility of expression is integral to MYC's oncogenic function.
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Affiliation(s)
- Francesca R Dejure
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Würzburg, Germany
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40
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Slobodin B, Han R, Calderone V, Vrielink JAFO, Loayza-Puch F, Elkon R, Agami R. Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation. Cell 2017; 169:326-337.e12. [PMID: 28388414 PMCID: PMC5388891 DOI: 10.1016/j.cell.2017.03.031] [Citation(s) in RCA: 318] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 01/23/2017] [Accepted: 03/21/2017] [Indexed: 01/15/2023]
Abstract
Transcription and translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these processes are mainly regarded as distinct and generally uncoupled, despite serving a common purpose. Here, we sought for a possible connection between transcription and translation. Employing an unbiased screen of multiple human promoters, we identified a positive effect of TATA box on translation and a general coupling between mRNA expression and translational efficiency. Using a CRISPR-Cas9-mediated approach, genome-wide analyses, and in vitro experiments, we show that the rate of transcription regulates the efficiency of translation. Furthermore, we demonstrate that m6A modification of mRNAs is co-transcriptional and depends upon the dynamics of the transcribing RNAPII. Suboptimal transcription rates lead to elevated m6A content, which may result in reduced translation. This study uncovers a general and widespread link between transcription and translation that is governed by epigenetic modification of mRNAs. Transcription rates of mRNAs positively correlate with rates of their translation Dynamics of RNA polymerase II impact the deposition of m6A on mRNAs Suboptimal transcription enhances m6A modification of mRNAs Excessive m6A modification is detrimental for the translation process
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Affiliation(s)
- Boris Slobodin
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
| | - Ruiqi Han
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Vittorio Calderone
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joachim A F Oude Vrielink
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Fabricio Loayza-Puch
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Reuven Agami
- Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands.
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41
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Cheishvili D, Christiansen S, Stochinsky R, Pepin AS, Sapozhnikov DM, Zhou R, Schmeltzer L, Dymov S, Szyf M. DNA methylation controls unmethylated transcription start sites in the genome in trans. Epigenomics 2017; 9:611-633. [PMID: 28470094 DOI: 10.2217/epi-2016-0141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM DNA methylation downregulates transcription. However, a large number of genes, which are unmethylated in the promoter region, are inactive. We tested the hypothesis that these genes are regulated by DNA methylation of upstream regulators. METHODS We inhibited DNMT1 with 5-aza-2'-deoxycytidine or depleted it with shRNA to map the transcription initiation positions controlled by DNMT1 using ChIPseq with RNApolIIser5 antibody. Ingenuity pathway analysis identified potential methylated upstream regulators. Their functional role in controlling unmethylated promoters was determined by CRISPR/Cas9 gene editing. RESULTS We show that a large group of unmethylated promoters is regulated by DNMT1 through DNA methylation dependent silencing of upstream regulators such as transcription factor HNF4A. CONCLUSION The landscape of genes regulated by DNA methylation is more wide-ranging than genes downregulated by methylation of their own cis-regulatory sequences; regulation of unmethylated promoters is dependent on the methylation state of upstream trans regulators.
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Affiliation(s)
- David Cheishvili
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Steffan Christiansen
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Rebecca Stochinsky
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Anne-Sophie Pepin
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Daniel M Sapozhnikov
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Rudy Zhou
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Lauren Schmeltzer
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Sergey Dymov
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada.,Department of Pharmacology & Therapeutics, Sackler Program for Epigenetics & Developmental Psychobiology, McGill University Medical School, Montreal, Quebec, Canada.,Department of Pharmacology & Therapeutics, Canadian Institute for Advanced Research, Montreal, Quebec, Canada
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42
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Sánchez-Hernández N, Boireau S, Schmidt U, Muñoz-Cobo JP, Hernández-Munain C, Bertrand E, Suñé C. The in vivo dynamics of TCERG1, a factor that couples transcriptional elongation with splicing. RNA 2016; 22:571-582. [PMID: 26873599 PMCID: PMC4793212 DOI: 10.1261/rna.052795.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/23/2015] [Indexed: 06/05/2023]
Abstract
Coupling between transcription and RNA processing is key for gene regulation. Using live-cell photobleaching techniques, we investigated the factor TCERG1, which coordinates transcriptional elongation with splicing. We demonstrate that TCERG1 is highly mobile in the nucleoplasm and that this mobility is slightly decreased when it is associated with speckles. Dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) but not α-amanitin treatment reduced the mobility of TCERG1, which suggests interaction with paused transcription elongation complexes. We found that TCERG1 mobility is rapid at the transcription site (TS) of a reporter that splices post-transcriptionally and that TCERG1 is recruited to the active TS independent of the CTD of RNAPII, thus excluding phosphorylated CTD as a requirement for recruiting this factor to the TS. Importantly, the mobility of TCERG1 is reduced when the reporter splices cotranscriptionally, which suggests that TCERG1 forms new macromolecular complexes when splicing occurs cotranscriptionally. In this condition, spliceostatin A has no effect, indicating that TCERG1 rapidly binds and dissociates from stalled spliceosomal complexes and that the mobility properties of TCERG1 do not depend on events occurring after the initial spliceosome formation. Taken together, these data suggest that TCERG1 binds independently to elongation and splicing complexes, thus performing their coupling by transient interactions rather than by stable association with one or the other complexes. This finding has conceptual implications for understanding the coupling between transcription and RNA processing.
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Affiliation(s)
- Noemí Sánchez-Hernández
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Stéphanie Boireau
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Ute Schmidt
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Juan Pablo Muñoz-Cobo
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier, France
| | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), PTS, Granada 18016, Spain
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43
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Wang B, Sun J, Shi J, Guo Q, Tong X, Zhang J, Hu N, Hu Y. Small-Activating RNA Can Change Nucleosome Positioning in Human Fibroblasts. ACTA ACUST UNITED AC 2016; 21:634-42. [PMID: 26993320 DOI: 10.1177/1087057116637562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/15/2016] [Indexed: 11/16/2022]
Abstract
RNA activation (RNAa) is a mechanism of positive gene expression regulation mediated by small-activating RNAs (saRNAs), which target gene promoters and have been used as tools to manipulate gene expression. Studies have shown that RNAa is associated with epigenetic modifications at promoter regions; however, it is unclear whether these modifications are the cause or a consequence of RNAa. In this study, we examined changes in nucleosome repositioning and the involvement of RNA polymerase II (RNAPII) in this process. We screened saRNAs for OCT4 (POU5F1), SOX2, and NANOG, and identified several novel saRNAs. We found that nucleosome positioning was altered after saRNA treatment and that the formation of nucleosome-depleted regions (NDRs) contributed to RNAa at sites of RNAPII binding, such as the TATA box, CpG islands (CGIs), proximal enhancers, and proximal promoters. Moreover, RNAPII appeared to be bound specifically to NDRs. These results suggested that changes in nucleosome positions resulted from RNAa. We thus propose a hypothesis that targeting promoter regions using exogenous saRNAs can induce the formation of NDRs, exposing regulatory binding sites to recruit RNAPII, a key component of preinitiation complex, and leading to increased initiation of transcription.
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Affiliation(s)
- Bin Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China Department of Biology, Kunming University, Kunming, China
| | - Jing Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jiandong Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Qing Guo
- Department of Biology, Kunming University, Kunming, China
| | - Xiangrong Tong
- Department of Biology, Kunming University, Kunming, China
| | - Jin Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Ningzhu Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - YunZhang Hu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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Abstract
The RNAPII-CTD functions as a binding platform for coordinating the recruitment of transcription associated factors. Altering CTD function results in gene expression defects, although mounting evidence suggests that these effects likely vary among species and loci. Here we highlight emerging evidence of species- and loci-specific functions for the RNAPII-CTD.
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Affiliation(s)
- Maria J Aristizabal
- a Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver , British Columbia , Canada
| | - Michael S Kobor
- a Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver , British Columbia , Canada
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45
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Poli J, Gerhold CB, Tosi A, Hustedt N, Seeber A, Sack R, Herzog F, Pasero P, Shimada K, Hopfner KP, Gasser SM. Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress. Genes Dev 2016; 30:337-54. [PMID: 26798134 PMCID: PMC4743062 DOI: 10.1101/gad.273813.115] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/21/2015] [Indexed: 12/11/2022]
Abstract
Poli et al. present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C, and the transcription complex PAF1C. A subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea. Little is known about how cells ensure DNA replication in the face of RNA polymerase II (RNAPII)-mediated transcription, especially under conditions of replicative stress. Here we present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C (INO80 complex), and the transcription complex PAF1C (PAF1 complex). We found that a subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea (HU). On HU, Mec1 triggers the efficient removal of PAF1C and RNAPII from transcribed genes near early firing origins. Failure to evict RNAPII correlates inversely with recovery from replication stress: paf1Δ cells, like ino80 and mec1 mutants, fail to restart forks efficiently after stalling. Our data reveal unexpected synergies between INO80C, Mec1, and PAF1C in the maintenance of genome integrity and suggest a mechanism of RNAPII degradation that reduces transcription–replication fork collision.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | | | - Alessandro Tosi
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Nicole Hustedt
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Franz Herzog
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Philippe Pasero
- UPR 1142, Institut de Génétique Humaine, Centre National de la Recherche Scientifique, 30396 Montpellier, France
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Karl-Peter Hopfner
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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Abstract
The circadian oscillator is based on transcription-translation feedback loops that generate 24 h oscillations in gene expression. Although circadian regulation of mRNA expression at the transcriptional level is one of the most important steps for the generation of circadian rhythms within the cell, multiple lines of evidence point to a disconnect between transcript oscillation and protein oscillation. This can be explained by regulatory RNA-binding proteins acting on the nascent transcripts to modulate their processing, export, translation and degradation rates. In this chapter we will review what is known about the different steps involved in circadian gene expression from transcription initiation to mRNA stability and translation efficiency. The role of ribonucleoprotein particles in the generation of rhythmic gene expression is only starting to be elucidated, but it is likely that they cooperate with the basal transcriptional machinery to help to maintain the precision of the clock under diverse cellular and environmental conditions.
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Affiliation(s)
- Giorgia Benegiamo
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.,Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Satchidananda Panda
- Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA.
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Felipe-Abrio I, Lafuente-Barquero J, García-Rubio ML, Aguilera A. RNA polymerase II contributes to preventing transcription-mediated replication fork stalls. EMBO J 2014; 34:236-50. [PMID: 25452497 DOI: 10.15252/embj.201488544] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. However, we know little of the possible role, if any, of the RNA polymerase (RNAP) in this process. Here, we analyzed 4 specific yeast RNAPII mutants that show different phenotypes of genetic instability including hyper-recombination, DNA damage sensitivity and/or a strong dependency on double-strand break repair functions for viability. Three specific alleles of the RNAPII core, rpb1-1, rpb1-S751F and rpb9∆, cause a defect in replication fork progression, compensated for by additional origin firing, as the main action responsible for instability. The transcription elongation defects of rpb1-S751F and rpb9∆ plus our observation that rpb1-1 causes RNAPII retention on chromatin suggest that RNAPII could participate in facilitating fork progression upon a transcription-replication encounter. Our results imply that the RNAPII or ancillary factors actively help prevent transcription-associated genome instability.
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Affiliation(s)
- Irene Felipe-Abrio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - Juan Lafuente-Barquero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
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Watanabe Y, Onodera A, Kanai U, Ichikawa T, Obata-Ninomiya K, Wada T, Kiuchi M, Iwamura C, Tumes DJ, Shinoda K, Yagi R, Motohashi S, Hirahara K, Nakayama T. Trithorax complex component Menin controls differentiation and maintenance of T helper 17 cells. Proc Natl Acad Sci U S A 2014; 111:12829-34. [PMID: 25136117 DOI: 10.1073/pnas.1321245111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modifications, such as posttranslational modifications of histones, play an important role in gene expression and regulation. These modifications are in part mediated by the Trithorax group (TrxG) complex and the Polycomb group (PcG) complex, which activate and repress transcription, respectively. We herein investigate the role of Menin, a component of the TrxG complex in T helper (Th) cell differentiation and show a critical role for Menin in differentiation and maintenance of Th17 cells. Menin(-/-) T cells do not efficiently differentiate into Th17 cells, leaving Th1 and Th2 cell differentiation intact in in vitro cultures. Menin deficiency resulted in the attenuation of Th17-induced airway inflammation. In differentiating Th17 cells, Menin directly bound to the Il17a gene locus and was required for the deposition of permissive histone modifications and recruitment of the RNA polymerase II transcriptional complex. Interestingly, although Menin bound to the Rorc locus, Menin was dispensable for the induction of Rorc expression and permissive histone modifications in differentiating Th17 cells. In contrast, Menin was required to maintain expression of Rorc in differentiated Th17 cells, indicating that Menin is essential to stabilize expression of the Rorc gene. Thus, Menin orchestrates Th17 cell differentiation and function by regulating both the induction and maintenance of target gene expression.
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49
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Hwang JS, Hwang SY, Han IO. Basal transcription is regulated by lipopolysaccharide and glucosamine via the regulation of DNA binding of RNA polymerase II in RAW264.7 cells. Life Sci 2014; 110:93-8. [PMID: 24968300 DOI: 10.1016/j.lfs.2014.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 11/30/2022]
Abstract
AIMS The objective of this study is to investigate glucosamine (GlcN) as a transcriptional regulator of iNOS and other genes in association with the dynamic O-GlcNAcylation of RNA polymerase II (RNAPII). MAIN METHODS The LPS- and/or GlcN-stimulated transcriptional activities of various Gal4-binding site/TATA-box-containing reporter constructs were measured. KEY FINDINGS Basal transcriptional activities of nuclear factor-κB (NF-κB) and nitric oxide synthase (iNOS) reporter plasmids are inhibited by GlcN in RAW264.7 cells. Furthermore, GlcN suppressed whereas lipopolysaccharide (LPS) stimulated the basal activity of Gal4-binding site/TATA-box-containing reporter constructs. LPS reduced the O-linked N-acetylglucosamine modification (O-GlcNAcylation) of RNAPII, but enhanced the binding of this enzyme to the iNOS promoter. In contrast, GlcN enhanced RNAPII O-GlcNAcylation, but inhibited iNOS promoter binding. Furthermore, the basal activities of reporter plasmids containing activator protein 1 (AP1), E2F, or cyclic AMP response element (CRE) binding sites were consistently inhibited by GlcN in a dose-dependent manner. However, GlcN did not inhibit the phorbol 12-myristate 13-acetate- (PMA-) or forskolin-induced transcriptional activities of AP1 and CRE. The transcriptional activity of transforming growth factor alpha (TGF-α) was slightly increased by both LPS and GlcN. SIGNIFICANCE In conclusion, our data demonstrate that LPS activates, whereas GlcN suppresses, basal activities of transcription through the regulation of RNAPII O-GlcNAcylation and DNA binding.
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Affiliation(s)
- Ji-Sun Hwang
- Department of Physiology and Biophysics, College of Medicine, Inha University, Incheon, Republic of Korea
| | - So-Young Hwang
- Department of Physiology and Biophysics, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Inn-Oc Han
- Department of Physiology and Biophysics, College of Medicine, Inha University, Incheon, Republic of Korea.
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50
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Marsman J, O'Neill AC, Kao BRY, Rhodes JM, Meier M, Antony J, Mönnich M, Horsfield JA. Cohesin and CTCF differentially regulate spatiotemporal runx1 expression during zebrafish development. Biochim Biophys Acta 2014; 1839:50-61. [PMID: 24321385 DOI: 10.1016/j.bbagrm.2013.11.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/19/2013] [Accepted: 11/25/2013] [Indexed: 11/23/2022]
Abstract
Runx1 is a transcription factor essential for definitive hematopoiesis. In all vertebrates, the Runx1 gene is transcribed from two promoters: a proximal promoter (P2), and a distal promoter (P1). We previously found that runx1 expression in a specific hematopoietic cell population in zebrafish embryos depends on cohesin. Here we show that zebrafish runx1 is directly bound by cohesin and CCCTC binding factor (CTCF) at the P1 and P2 promoters, and within the intron between P1 and P2. Cohesin initiates expression of runx1 in the posterior lateral mesoderm and influences promoter use, while CTCF represses its expression in the newly emerging cells of the tail bud. The intronic binding sites for cohesin and CTCF coincide with histone modifications that confer enhancer-like properties, and two of the cohesin/CTCF sites behaved as insulators in an in vivo assay. The identified cohesin and CTCF binding sites are likely to be cis-regulatory elements (CREs) for runx1 since they also recruit RNA polymerase II (RNAPII). CTCF depletion excluded RNAPII from two intronic CREs but not the promoters of runx1. We propose that cohesin and CTCF have distinct functions in the regulation of runx1 during zebrafish embryogenesis, and that these regulatory functions are likely to involve runx1 intronic CREs. Cohesin (but not CTCF) depletion enhanced RUNX1 expression in a human leukemia cell line, suggesting conservation of RUNX1 regulation through evolution.
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Affiliation(s)
- Judith Marsman
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Adam C O'Neill
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Betty Rui-Yun Kao
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Jenny M Rhodes
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Michael Meier
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Jisha Antony
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Maren Mönnich
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, The University of Otago, P.O. Box 913, Dunedin, New Zealand.
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