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Zhang H, Li X, Song R, Zhan Z, Zhao F, Li Z, Jiang D. Cap-binding complex assists RNA polymerase II transcription in plant salt stress response. PLANT, CELL & ENVIRONMENT 2022; 45:2780-2793. [PMID: 35773782 DOI: 10.1111/pce.14388] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/14/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in messenger RNA (mRNA) production is crucial for maximized plant survival. Transcription and pre-mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap-binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II-associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 coregulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt-activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.
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Affiliation(s)
- Huairen Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyi Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruitian Song
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengyue Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zicong Li
- Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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2
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Wang Y, Miao C, Gao X. TCEB3 is Regulated by Circ-0000212/miR-140-3p Axis to Promote the Progression of Cervical Cancer. Onco Targets Ther 2021; 14:2853-2865. [PMID: 33953570 PMCID: PMC8091597 DOI: 10.2147/ott.s278710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 04/02/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Cervical cancer is a common female malignancy, which accounts for a large proportion of cancer-related mortality in the world. Therefore, exploring the mechanisms of cervical cancer progression and seeking new therapeutic targets are extraordinarily needful. The aim of this study was to explore the role of TCEB3 in cervical cancer progression. METHODS TCEB3 expression was detected in cervical cancer tissue and adjacent normal tissues using qRT-PCR and immunohistochemistry analysis. TCEB3 expression was measured in cells using Western blot and qRT-PCR assay. Flow cytometer, CCK-8, colony formation and transwell assays were used to detect cell apoptosis, viability, colony-forming ability and invasion of cervical cancer cells. The expression of Ki-67, MMP-2, and MMP-9 was detected using Western blot. Bioinformatics analysis was used to predict circRNA-miRNA and miRNA-mRNA interactions. RIP and luciferase reporter assay were used to determine the interaction relationship. RESULTS TCEB3 expression was up-regulated in both cervical cancer tissues and cells. Silencing of TCEB3 inhibited cell proliferation and invasion and promoted apoptosis of cervical cancer cells. Additionally, silencing of TCEB3 reduced the protein expression of Ki-67, MMP-2, and MMP-9 of cervical cancer cells. Mechanistically, we identified that TCEB3 was directly targeted gene of miR-140-3p, and circ-0000212 acted as a sponge of miR-140-3p. Moreover, TCEB3 was regulated by circ-0000212/miR-140-3p axis and played a tumor promotive role in cervical cancer. CONCLUSION Silencing of TCEB3 attenuated cell proliferation and invasion and promoted apoptosis of cervical cancer cells, and this effect was regulated by circ-0000212/miR-140-3p axis. Our findings may provide a novel promising target for cervical cancer treatment.
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Affiliation(s)
- Yufeng Wang
- Department of Gynecology, Jinan Second Maternal and Child Health Hospital, Jinan, Shandong, 271199, People’s Republic of China
| | - Chuanhui Miao
- Department of Obstetrics and Gynecology, Shizhong District People’s Hospital, Zaozhuang, Shandong, 277100, People’s Republic of China
| | - Xiang Gao
- Department of Geratology, The First Affiliated Hospital of Weifang Medical University (Weifang People’s Hospital), Weifang, Shandong, 261041, People’s Republic of China
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3
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The hunt for RNA polymerase II elongation factors: a historical perspective. Nat Struct Mol Biol 2019; 26:771-776. [PMID: 31439940 DOI: 10.1038/s41594-019-0283-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023]
Abstract
The discovery of the three eukaryotic nuclear RNA polymerases paved the way for serious biochemical investigations of eukaryotic transcription and the identification of eukaryotic transcription factors. Here we describe this adventure from our vantage point, with a focus on the hunt for factors that regulate elongation by RNA polymerase II.
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4
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Ørsted M, Rohde PD, Hoffmann AA, Sørensen P, Kristensen TN. Environmental variation partitioned into separate heritable components. Evolution 2017; 72:136-152. [DOI: 10.1111/evo.13391] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Michael Ørsted
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Parkville Victoria 3052 Australia
| | - Palle Duun Rohde
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; Blichers Allé 20 8830 Tjele Denmark
- i PSYCH; The Lundbeck Foundation Initiative for Integrative Psychiatric Research; 8000 Aarhus C Denmark
- i SEQ, Center for Integrative Sequencing; Aarhus University; Bartholins Allé 6 8000 Aarhus C Denmark
| | - Ary Anthony Hoffmann
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Parkville Victoria 3052 Australia
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; Blichers Allé 20 8830 Tjele Denmark
| | - Torsten Nygaard Kristensen
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- Section of Genetics, Ecology and Evolution, Department of Bioscience; Aarhus University; 8000 Aarhus C Denmark
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5
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Def1 interacts with TFIIH and modulates RNA polymerase II transcription. Proc Natl Acad Sci U S A 2017; 114:13230-13235. [PMID: 29180430 DOI: 10.1073/pnas.1707955114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The DNA damage response is an essential process for the survival of living cells. In a subset of stress-responsive genes in humans, Elongin controls transcription in response to multiple stimuli, such as DNA damage, oxidative stress, and heat shock. Yeast Elongin (Ela1-Elc1), along with Def1, is known to facilitate ubiquitylation and degradation of RNA polymerase II (pol II) in response to multiple stimuli, yet transcription activity has not been examined. We have found that Def1 copurifies from yeast whole-cell extract with TFIIH, the largest general transcription factor required for transcription initiation and nucleotide excision repair. The addition of recombinant Def1 and Ela1-Elc1 enhanced transcription initiation in an in vitro reconstituted system including pol II, the general transcription factors, and TFIIS. Def1 also enhanced transcription restart from TFIIS-induced cleavage in a pol II transcribing complex. In the Δdef1 strain, heat shock genes were misregulated, indicating that Def1 is required for induction of some stress-responsive genes in yeast. Taken together, our results extend the understanding of the molecular mechanism of transcription regulation on cellular stress and reveal functional similarities to the mammalian system.
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6
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Sharma N. Regulation of RNA polymerase II-mediated transcriptional elongation: Implications in human disease. IUBMB Life 2016; 68:709-16. [DOI: 10.1002/iub.1538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/14/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University; Dwarka New Delhi 110078 India
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7
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Weems JC, Slaughter BD, Unruh JR, Hall SM, McLaird MB, Gilmore JM, Washburn MP, Florens L, Yasukawa T, Aso T, Conaway JW, Conaway RC. Assembly of the Elongin A Ubiquitin Ligase Is Regulated by Genotoxic and Other Stresses. J Biol Chem 2015; 290:15030-41. [PMID: 25878247 DOI: 10.1074/jbc.m114.632794] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Indexed: 11/06/2022] Open
Abstract
Elongin A performs dual functions in cells as a component of RNA polymerase II (Pol II) transcription elongation factor Elongin and as the substrate recognition subunit of a Cullin-RING E3 ubiquitin ligase that has been shown to target Pol II stalled at sites of DNA damage. Here we investigate the mechanism(s) governing conversion of the Elongin complex from its elongation factor to its ubiquitin ligase form. We report the discovery that assembly of the Elongin A ubiquitin ligase is a tightly regulated process. In unstressed cells, Elongin A is predominately present as part of Pol II elongation factor Elongin. Assembly of Elongin A into the ubiquitin ligase is strongly induced by genotoxic stress; by transcriptional stresses that lead to accumulation of stalled Pol II; and by other stimuli, including endoplasmic reticulum and nutrient stress and retinoic acid signaling, that activate Elongin A-dependent transcription. Taken together, our findings shed new light on mechanisms that control the Elongin A ubiquitin ligase and suggest that it may play a role in Elongin A-dependent transcription.
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Affiliation(s)
- Juston C Weems
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Brian D Slaughter
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Jay R Unruh
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Shawn M Hall
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Merry B McLaird
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Joshua M Gilmore
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Michael P Washburn
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, the Departments of Pathology and Laboratory Medicine and
| | - Laurence Florens
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Takashi Yasukawa
- the Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Teijiro Aso
- the Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Joan W Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
| | - Ronald C Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110, Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160, and
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8
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A novel approach for studying histone H1 function in vivo. Genetics 2015; 200:29-33. [PMID: 25805849 DOI: 10.1534/genetics.114.170514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
In this report, we investigate the mechanisms that regulate Drosophila histone H1 expression and its association with chromatin in vivo. We show that histone H1 is subject to negative autoregulation and exploit this result to examine the effects of mutations of the main phosphorylation site of histone H1.
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9
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Zhu M, Chen Y, Ding XS, Webb SL, Zhou T, Nelson RS, Fan Z. Maize Elongin C interacts with the viral genome-linked protein, VPg, of Sugarcane mosaic virus and facilitates virus infection. THE NEW PHYTOLOGIST 2014; 203:1291-1304. [PMID: 24954157 PMCID: PMC4143955 DOI: 10.1111/nph.12890] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/08/2014] [Indexed: 05/18/2023]
Abstract
The viral genome-linked protein, VPg, of potyviruses is involved in viral genome replication and translation. To determine host proteins that interact with Sugarcane mosaic virus (SCMV) VPg, a yeast two-hybrid screen was used and a maize (Zea mays) Elongin C (ZmElc) protein was identified. ZmELC transcript was observed in all maize organs, but most highly in leaves and pistil extracts, and ZmElc was present in the cytoplasm and nucleus of maize cells in the presence or absence of SCMV. ZmELC expression was increased in maize tissue at 4 and 6 d post SCMV inoculation. When ZmELC was transiently overexpressed in maize protoplasts the accumulation of SCMV RNA was approximately doubled compared with the amount of virus in control protoplasts. Silencing ZmELC expression using a Brome mosaic virus-based gene silencing vector (virus-induced gene silencing) did not influence maize plant growth and development, but did decrease RNA accumulation of two isolates of SCMV and host transcript encoding ZmeIF4E during SCMV infection. Interestingly, Maize chlorotic mottle virus, from outside the Potyviridae, was increased in accumulation after silencing ZmELC expression. Our results describe both the location of ZmElc expression in maize and a new activity associated with an Elc: support of potyvirus accumulation.
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Affiliation(s)
- Min Zhu
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Yuting Chen
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Xin Shun Ding
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Stephen L Webb
- Department of Computing Services, The Samuel Roberts Noble Foundation Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Tao Zhou
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
| | - Richard S Nelson
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc.2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Zaifeng Fan
- State Key Laboratory of Agro-biotechnology and Key Laboratory for Plant Pathology – Ministry of Agriculture, China Agricultural UniversityBeijing, 100193, China
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10
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Rougeot J, Renard M, Randsholt NB, Peronnet F, Mouchel-Vielh E. The elongin complex antagonizes the chromatin factor Corto for vein versus intervein cell identity in Drosophila wings. PLoS One 2013; 8:e77592. [PMID: 24204884 PMCID: PMC3804554 DOI: 10.1371/journal.pone.0077592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/10/2013] [Indexed: 01/08/2023] Open
Abstract
Drosophila wings mainly consist of two cell types, vein and intervein cells. Acquisition of either fate depends on specific expression of genes that are controlled by several signaling pathways. The nuclear mechanisms that translate signaling into regulation of gene expression are not completely understood, but they involve chromatin factors from the Trithorax (TrxG) and Enhancers of Trithorax and Polycomb (ETP) families. One of these is the ETP Corto that participates in intervein fate through interaction with the Drosophila EGF Receptor--MAP kinase ERK pathway. Precise mechanisms and molecular targets of Corto in this process are not known. We show here that Corto interacts with the Elongin transcription elongation complex. This complex, that consists of three subunits (Elongin A, B, C), increases RNA polymerase II elongation rate in vitro by suppressing transient pausing. Analysis of phenotypes induced by EloA, B, or C deregulation as well as genetic interactions suggest that the Elongin complex might participate in vein vs intervein specification, and antagonizes corto as well as several TrxG genes in this process. Chromatin immunoprecipitation experiments indicate that Elongin C and Corto bind the vein-promoting gene rhomboid in wing imaginal discs. We propose that Corto and the Elongin complex participate together in vein vs intervein fate, possibly through tissue-specific transcriptional regulation of rhomboid.
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Affiliation(s)
- Julien Rougeot
- Université Pierre et Marie Curie-Paris 6, UMR7622, Paris, France ; Centre National de la Recherche Scientifique, UMR7622, Laboratoire de Biologie du Développement, Paris, France
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11
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Smith E, Shilatifard A. Transcriptional elongation checkpoint control in development and disease. Genes Dev 2013; 27:1079-88. [PMID: 23699407 DOI: 10.1101/gad.215137.113] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transcriptional elongation control by RNA polymerase II and its associated factors has taken center stage as a process essential for the regulation of gene expression throughout development. In this review, we analyze recent findings on the identification of factors functioning in the regulation of the transcriptional elongation checkpoint control (TECC) stage of gene expression and how the factors' misregulation is associated with disease pathogenesis, including cancer.
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Affiliation(s)
- Edwin Smith
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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12
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Kawauchi J, Inoue M, Fukuda M, Uchida Y, Yasukawa T, Conaway RC, Conaway JW, Aso T, Kitajima S. Transcriptional properties of mammalian elongin A and its role in stress response. J Biol Chem 2013; 288:24302-15. [PMID: 23828199 DOI: 10.1074/jbc.m113.496703] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Elongin A was shown previously to be capable of potently activating the rate of RNA polymerase II (RNAPII) transcription elongation in vitro by suppressing transient pausing by the enzyme at many sites along DNA templates. The role of Elongin A in RNAPII transcription in mammalian cells, however, has not been clearly established. In this report, we investigate the function of Elongin A in RNAPII transcription. We present evidence that Elongin A associates with the IIO form of RNAPII at sites of newly transcribed RNA and is relocated to dotlike domains distinct from those containing RNAPII when cells are treated with the kinase inhibitor 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole. Significantly, Elongin A is required for maximal induction of transcription of the stress response genes ATF3 and p21 in response to several stimuli. Evidence from structure-function studies argues that Elongin A transcription elongation activity, but not its ubiquitination activity, is most important for its function in induction of transcription of ATF3 and p21. Taken together, our data provide new insights into the function of Elongin A in RNAPII transcription and bring to light a previously unrecognized role for Elongin A in the regulation of stress response genes.
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Affiliation(s)
- Junya Kawauchi
- Department of Biochemical Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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13
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Yasukawa T, Bhatt S, Takeuchi T, Kawauchi J, Takahashi H, Tsutsui A, Muraoka T, Inoue M, Tsuda M, Kitajima S, Conaway RC, Conaway JW, Trainor PA, Aso T. Transcriptional elongation factor elongin A regulates retinoic acid-induced gene expression during neuronal differentiation. Cell Rep 2012; 2:1129-36. [PMID: 23122963 DOI: 10.1016/j.celrep.2012.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 08/30/2012] [Accepted: 09/28/2012] [Indexed: 01/16/2023] Open
Abstract
Elongin A increases the rate of RNA polymerase II (pol II) transcript elongation by suppressing transient pausing by the enzyme. Elongin A also acts as a component of a cullin-RING ligase that can target stalled pol II for ubiquitylation and proteasome-dependent degradation. It is not known whether these activities of Elongin A are functionally interdependent in vivo. Here, we demonstrate that Elongin A-deficient (Elongin A(-/-)) embryos exhibit abnormalities in the formation of both cranial and spinal nerves and that Elongin A(-/-) embryonic stem cells (ESCs) show a markedly decreased capacity to differentiate into neurons. Moreover, we identify Elongin A mutations that selectively inactivate one or the other of the aforementioned activities and show that mutants that retain the elongation stimulatory, but not pol II ubiquitylation, activity of Elongin A rescue neuronal differentiation and support retinoic acid-induced upregulation of a subset of neurogenesis-related genes in Elongin A(-/-) ESCs.
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Affiliation(s)
- Takashi Yasukawa
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
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14
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Fasulo B, Deuring R, Murawska M, Gause M, Dorighi KM, Schaaf CA, Dorsett D, Brehm A, Tamkun JW. The Drosophila MI-2 chromatin-remodeling factor regulates higher-order chromatin structure and cohesin dynamics in vivo. PLoS Genet 2012; 8:e1002878. [PMID: 22912596 PMCID: PMC3415455 DOI: 10.1371/journal.pgen.1002878] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/17/2012] [Indexed: 11/24/2022] Open
Abstract
dMi-2 is a highly conserved ATP-dependent chromatin-remodeling factor that regulates transcription and cell fates by altering the structure or positioning of nucleosomes. Here we report an unanticipated role for dMi-2 in the regulation of higher-order chromatin structure in Drosophila. Loss of dMi-2 function causes salivary gland polytene chromosomes to lose their characteristic banding pattern and appear more condensed than normal. Conversely, increased expression of dMi-2 triggers decondensation of polytene chromosomes accompanied by a significant increase in nuclear volume; this effect is relatively rapid and is dependent on the ATPase activity of dMi-2. Live analysis revealed that dMi-2 disrupts interactions between the aligned chromatids of salivary gland polytene chromosomes. dMi-2 and the cohesin complex are enriched at sites of active transcription; fluorescence-recovery after photobleaching (FRAP) assays showed that dMi-2 decreases stable association of cohesin with polytene chromosomes. These findings demonstrate that dMi-2 is an important regulator of both chromosome condensation and cohesin binding in interphase cells.
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Affiliation(s)
- Barbara Fasulo
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Renate Deuring
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Magdalena Murawska
- Institute for Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Maria Gause
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Kristel M. Dorighi
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Cheri A. Schaaf
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Alexander Brehm
- Institute for Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - John W. Tamkun
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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15
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Guergnon J, Dalmasso C, Broet P, Meyer L, Westrop SJ, Imami N, Vicenzi E, Morsica G, Tinelli M, Zanone Poma B, Goujard C, Potard V, Gotch FM, Casoli C, Cossarizza A, Macciardi F, Debré P, Delfraissy JF, Galli M, Autran B, Costagliola D, Poli G, Theodorou I, Riva A. Single-nucleotide polymorphism-defined class I and class III major histocompatibility complex genetic subregions contribute to natural long-term nonprogression in HIV infection. J Infect Dis 2012; 205:718-24. [PMID: 22238471 DOI: 10.1093/infdis/jir833] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We performed a genome-wide association study comparing a cohort of 144 human immunodeficiency virus (HIV type 1-infected, untreated white long-term nonprogressors (LTNPs) with a cohort of 605 HIV-1-infected white seroconverters. Forty-seven single-nucleotide polymorphisms (SNPs), located from class I to class III major histocompatibility complex (MHC) subregions, show statistical association (false discovery rate, <0.05) with the LTNP condition, among which 5 reached genome-wide significance after Bonferonni correction. The MHC LTNP-associated SNPs are ordered in ≥4 linkage disequilibrium blocks; interestingly, an MHC class III linkage disequilibrium block (defined by the rs9368699 SNP) seems specific to the LTNP phenotype.
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16
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Cummins TD, Mendenhall MD, Lowry MN, Korte EA, Barati MT, Khundmiri SJ, Salyer SA, Klein JB, Powell DW. Elongin C is a mediator of Notch4 activity in human renal tubule cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1748-57. [PMID: 22001063 DOI: 10.1016/j.bbapap.2011.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/12/2011] [Accepted: 09/23/2011] [Indexed: 10/17/2022]
Abstract
Notch proteins (Notch 1-4) are a family of trans-membrane cell surface receptors that are converted into transcriptional regulators when activated by interactions with cell surface ligands on adjacent cells. Ligand-binding stimulates proteolytic cleavage of the trans-membrane domain, releasing an active intracellular domain (ICD) that translocates to the nucleus and impacts transcription. In transit, the ICD may interact with regulatory proteins that modulate the expression and transcriptional activity. We have found that Notch4(ICD) expression is enhanced in the tubule cells of fibrotic kidneys from diabetic mice and humans and identified Notch4(ICD) interacting proteins that could be pertinent to normal and pathological functions. Using proteomic techniques, several components of the Elongin C complex were identified as candidate Notch4(ICD) interactors. Elongin C complexes can function as ubiquitin ligases capable of regulating proteasomal degradation of specific protein substrates. Our studies indicate that ectopic Elongin C expression stimulates Notch4(ICD) degradation and inhibits its transcriptional activity in human kidney tubule HK11 cells. Blocking Elongin C mediated degradation by MG132 indicates the potential for ubiquitin-mediated Elongin C regulation of Notch4(ICD). Functional interaction of Notch4(ICD) and Elongin C provides novel insight into regulation of Notch signaling in epithelial cell biology and disease.
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Affiliation(s)
- Timothy D Cummins
- Departments of Biochemistry and Molecular Biology, University of Kentucky, KY, USA
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17
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Abstract
Until recently, it was generally assumed that essentially all regulation of transcription takes place via regions adjacent to the coding region of a gene--namely promoters and enhancers--and that, after recruitment to the promoter, the polymerase simply behaves like a machine, quickly "reading the gene." However, over the past decade a revolution in this thinking has occurred, culminating in the idea that transcript elongation is extremely complex and highly regulated and, moreover, that this process significantly affects both the organization and integrity of the genome. This review addresses basic aspects of transcript elongation by RNA polymerase II (RNAPII) and how it relates to other DNA-related processes.
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Affiliation(s)
- Luke A Selth
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, Hertfordshire EN6 3LD, United Kingdom
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18
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Drosophila ISWI regulates the association of histone H1 with interphase chromosomes in vivo. Genetics 2009; 182:661-9. [PMID: 19380479 DOI: 10.1534/genetics.109.102053] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although tremendous progress has been made toward identifying factors that regulate nucleosome structure and positioning, the mechanisms that regulate higher-order chromatin structure remain poorly understood. Recent studies suggest that the ISWI chromatin-remodeling factor plays a key role in this process by promoting the assembly of chromatin containing histone H1. To test this hypothesis, we investigated the function of H1 in Drosophila. The association of H1 with salivary gland polytene chromosomes is regulated by a dynamic, ATP-dependent process. Reducing cellular ATP levels triggers the dissociation of H1 from polytene chromosomes and causes chromosome defects similar to those resulting from the loss of ISWI function. H1 knockdown causes even more severe defects in chromosome structure and a reduction in nucleosome repeat length, presumably due to the failure to incorporate H1 during replication-dependent chromatin assembly. Our findings suggest that ISWI regulates higher-order chromatin structure by modulating the interaction of H1 with interphase chromosomes.
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19
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Spt6 enhances the elongation rate of RNA polymerase II in vivo. EMBO J 2009; 28:1067-77. [PMID: 19279664 DOI: 10.1038/emboj.2009.56] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Accepted: 02/06/2009] [Indexed: 12/20/2022] Open
Abstract
Several eukaryotic transcription factors have been shown to modulate the elongation rate of RNA polymerase II (Pol II) on naked or chromatin-reconstituted templates in vitro. However, none of the tested factors have been shown to directly affect the elongation rate of Pol II in vivo. We performed a directed RNAi knock-down (KD) screen targeting 141 candidate transcription factors and identified multiple factors, including Spt6, that alter the induced Hsp70 transcript levels in Drosophila S2 cells. Spt6 is known to interact with both nucleosome structure and Pol II, and it has properties consistent with having a role in elongation. Here, ChIP assays of the first wave of Pol II after heat shock in S2 cells show that KD of Spt6 reduces the rate of Pol II elongation. Also, fluorescence recovery after photobleaching assays of GFP-Pol II in salivary gland cells show that this Spt6-dependent effect on elongation rate persists during steady-state-induced transcription, reducing the elongation rate from approximately 1100 to 500 bp/min. Furthermore, RNAi depletion of Spt6 reveals its broad requirement during different stages of development.
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20
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Grasser M, Kane CM, Merkle T, Melzer M, Emmersen J, Grasser KD. Transcript elongation factor TFIIS is involved in arabidopsis seed dormancy. J Mol Biol 2009; 386:598-611. [PMID: 19150360 DOI: 10.1016/j.jmb.2008.12.066] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 12/13/2008] [Accepted: 12/22/2008] [Indexed: 01/12/2023]
Abstract
Transcript elongation factor TFIIS promotes efficient transcription by RNA polymerase II, since it assists in bypassing blocks during mRNA synthesis. While yeast cells lacking TFIIS are viable, inactivation of mouse TFIIS causes embryonic lethality. Here, we have identified a protein encoded in the Arabidopsis genome that displays a marked sequence similarity to TFIIS of other organisms, primarily within domains II and III in the C-terminal part of the protein. TFIIS is widely expressed in Arabidopsis, and a green fluorescent protein-TFIIS fusion protein localises specifically to the cell nucleus. When expressed in yeast cells lacking the endogenous TFIIS, Arabidopsis TFIIS partially complements the sensitivity of mutant cells to the nucleotide analog 6-azauridine, which is a typical characteristic of transcript elongation factors. We have characterised Arabidopsis lines harbouring T-DNA insertions in the coding sequence of TFIIS. Plants homozygous for T-DNA insertions are viable, and genomewide transcript profiling revealed that compared to control plants, a relatively small number of genes are differentially expressed in mutant plants. TFIIS(-/-) plants display essentially normal development, but they flower slightly earlier than control plants and show clearly reduced seed dormancy. Plants with RNAi-mediated knockdown of TFIIS expression also are affected in seed dormancy. Therefore, TFIIS plays a critical role in Arabidopsis seed development.
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Affiliation(s)
- Marion Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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21
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Regulation of the transcriptional activity of poised RNA polymerase II by the elongation factor ELL. Proc Natl Acad Sci U S A 2008; 105:8575-9. [PMID: 18562276 DOI: 10.1073/pnas.0804379105] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Many developmentally regulated genes contain a poised RNA polymerase II (Pol II) at their promoters under conditions where full-length transcripts are undetectable. It has been proposed that the transcriptional activity of such promoters is regulated at the elongation stage of Pol II transcription. In Drosophila, the heat-shock loci expressing the Hsp70 genes have been used as a model for the regulation of the transcriptional activity of poised Pol II. Drosophila ELL (dELL) is a Pol II elongation factor capable of stimulating the rate of transcription both in vivo and in vitro. Although ELL and the elongation factor Elongin A have indistinguishable effects on RNA polymerase in vitro, the loss-of-function studies indicate that these proteins are not redundant in vivo. In this article, we use RNAi to investigate the physiological properties of dELL and a dELL-associated factor (dEaf) in a living organism. Both ELL and Eaf are essential for fly development. dELL is recruited to heat shock loci upon induction, and its presence with Pol II at such loci is required for proper heat-shock gene expression. Consistent with a role in elongation, dELL knockdown reduces the levels of phosphorylated Pol II at heat-shock loci. This study implicates dELL in the expression of loci regulated by Pol II elongation.
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22
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Corona DFV, Siriaco G, Armstrong JA, Snarskaya N, McClymont SA, Scott MP, Tamkun JW. ISWI regulates higher-order chromatin structure and histone H1 assembly in vivo. PLoS Biol 2007; 5:e232. [PMID: 17760505 PMCID: PMC1951781 DOI: 10.1371/journal.pbio.0050232] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 06/29/2007] [Indexed: 12/17/2022] Open
Abstract
Imitation SWI (ISWI) and other ATP-dependent chromatin-remodeling factors play key roles in transcription and other processes by altering the structure and positioning of nucleosomes. Recent studies have also implicated ISWI in the regulation of higher-order chromatin structure, but its role in this process remains poorly understood. To clarify the role of ISWI in vivo, we examined defects in chromosome structure and gene expression resulting from the loss of Iswi function in Drosophila. Consistent with a broad role in transcriptional regulation, the expression of a large number of genes is altered in Iswi mutant larvae. The expression of a dominant-negative form of ISWI leads to dramatic alterations in higher-order chromatin structure, including the apparent decondensation of both mitotic and polytene chromosomes. The loss of ISWI function does not cause obvious defects in nucleosome assembly, but results in a significant reduction in the level of histone H1 associated with chromatin in vivo. These findings suggest that ISWI plays a global role in chromatin compaction in vivo by promoting the association of the linker histone H1 with chromatin. Chromatin-remodeling factors such as ISWI play a role in transcription and other nuclear processes by altering the structure and positioning of nucleosomes (the protein–DNA complexes that organize chromatin). Recent studies have suggested that chromatin-remodeling factors can also influence higher-order chromatin structure, but how they do this is not well understood. Using Drosophila melanogaster as a model organism, we investigated the role of ISWI in gene expression and the regulation of chromosome structure in higher eukaryotes. Loss of ISWI alters the expression of a large number of genes. The loss of ISWI function also causes dramatic alterations in higher-order chromatin structure—including the decondensation of mitotic and polytene chromosomes—accompanied by a striking reduction in the amount of the linker histone H1 associated with chromatin. Based on these findings, we propose that ISWI plays a global role in chromosome compaction by promoting the association of a linker histone with chromatin. ISWI is a chromatin-remodeling factor that recruits linker histone H1 into chromatin, thus altering the structure and positioning of nucleosomes and the degree of chromatin compaction.
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Affiliation(s)
- Davide F. V Corona
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Giorgia Siriaco
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennifer A Armstrong
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Natalia Snarskaya
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stephanie A McClymont
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matthew P Scott
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - John W Tamkun
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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23
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Miyata K, Yasukawa T, Fukuda M, Takeuchi T, Yamazaki K, Sakumi K, Tamamori-Adachi M, Ohnishi Y, Ohtsuki Y, Nakabeppu Y, Kitajima S, Onishi S, Aso T. Induction of apoptosis and cellular senescence in mice lacking transcription elongation factor, Elongin A. Cell Death Differ 2006; 14:716-26. [PMID: 17170753 DOI: 10.1038/sj.cdd.4402067] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Elongin A is a transcription elongation factor that increases the overall rate of mRNA chain elongation by RNA polymerase II. To gain more insight into the physiological functions of Elongin A, we generated Elongin A-deficient mice. Elongin A homozygous mutant (Elongin A(-/-)) embryos demonstrated a severely retarded development and died at between days 10.5 and 12.5 of gestation, most likely due to extensive apoptosis. Moreover, mouse embryonic fibroblasts (MEFs) derived from Elongin A(-/-) embryos exhibited not only increased apoptosis but also senescence-like growth defects accompanied by the activation of p38 MAPK and p53. Knockdown of Elongin A in MEFs by RNA interference also dramatically induced the senescent phenotype. A study using inhibitors of p38 MAPK and p53 and the generation of Elongin A-deficient mice with p53-null background suggests that both the p38 MAPK and p53 pathways are responsible for the induction of senescence-like phenotypes, whereas additional signaling pathways appear to be involved in the mediation of apoptosis in Elongin A(-/-) cells. Taken together, our results suggest that Elongin A is required for the transcription of genes essential for early embryonic development and downregulation of its activity is tightly associated with cellular senescence.
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Affiliation(s)
- K Miyata
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi, Japan
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24
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Schneider J, Bajwa P, Johnson FC, Bhaumik SR, Shilatifard A. Rtt109 Is Required for Proper H3K56 Acetylation. J Biol Chem 2006; 281:37270-4. [PMID: 17046836 DOI: 10.1074/jbc.c600265200] [Citation(s) in RCA: 175] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Histone acetylation has been shown to be required for the proper regulation of many cellular processes including transcription, DNA repair, and chromatin assembly. Acetylation of histone H3 on lysine 56 (H3K56) occurs both during the premeiotic and mitotic S phase and persists throughout DNA damage repair. To learn more about the molecular mechanism of H3K56 acetylation and factors required for this process, we surveyed the genome of the yeast Saccharomyces cerevisiae to identify genes necessary for this process. A comparative global proteomic screen identified several factors required for global H3K56 acetylation, which included histone chaperone Asf1 and a protein of an unknown function Rtt109 but not Spt10. Our results indicate that the loss of Rtt109 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin, similar to that of asf1Delta or the K56Q mutation. RTT109 deletion exhibits sensitivity to DNA damaging agents similar to that of asf1Delta and H3K56Q mutants. Furthermore, Rtt109 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of polymerase II in yeast. This histone modification is also associated with some of the transcriptionally active puff sites in Drosophila. Our results indicate a new role for the Rtt109 protein in the proper regulation of H3K56 acetylation.
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Affiliation(s)
- Jessica Schneider
- Department of Biochemistry, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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25
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Eissenberg JC, Shilatifard A, Dorokhov N, Michener DE. Cdk9 is an essential kinase in Drosophila that is required for heat shock gene expression, histone methylation and elongation factor recruitment. Mol Genet Genomics 2006; 277:101-14. [PMID: 17001490 DOI: 10.1007/s00438-006-0164-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 08/30/2006] [Indexed: 12/11/2022]
Abstract
Phosphorylation of the large RNA Polymerase II subunit C-terminal domain (CTD) is believed to be important in promoter clearance and for recruiting protein factors that function in messenger RNA synthesis and processing. P-TEFb is a protein kinase that targets the (CTD). The goal of this study was to identify chromatin modifications and associations that require P-TEFb activity in vivo. We knocked down the catalytic subunit of P-TEFb, Cdk9, in Drosophila melanogaster using RNA interference. Cdk9 knockdown flies die during metamorphosis. Phosphorylation at serine 2 and serine 5 of the CTD heptad repeat were both dramatically reduced in knockdown larvae. Hsp 70 mRNA induction by heat shock was attenuated in Cdk9 knockdown larvae. Both mono- and trimethylation of histone H3 at lysine 4 were dramatically reduced, suggesting a link between CTD phosphorylation and histone methylation in transcribed chromatin in vivo. Levels of the chromo helicase protein CHD1 were reduced in Cdk9 knockdown chromosomes, suggesting that CHD1 is targeted to chromosomes through P-TEFb-dependent histone methylation. Dimethylation of histone H3 at lysine 36 was significantly reduced in knockdown larvae, implicating CTD phosphorylation in the regulation of this chromatin modification. Binding of the RNA Polymerase II elongation factor ELL was reduced in knockdown chromosomes, suggesting that ELL is recruited to active polymerase via CTD phosphorylation.
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Affiliation(s)
- Joel C Eissenberg
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Blvd, St. Louis, MO 63104, USA.
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26
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Tenney K, Gerber M, Ilvarsonn A, Schneider J, Gause M, Dorsett D, Eissenberg JC, Shilatifard A. Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling. Proc Natl Acad Sci U S A 2006; 103:11970-4. [PMID: 16882721 PMCID: PMC1567682 DOI: 10.1073/pnas.0603620103] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Rtf1 subunit of the Paf1 complex is required for proper monoubiquitination of histone H2B and methylation of histone H3 on lysines 4 (H3K4) and 79 in yeast Saccharomyces cerevisiae. Using RNAi, we examined the role of Rtf1 in histone methylation and gene expression in Drosophila melanogaster. We show that Drosophila Rtf1 (dRtf1) is required for proper gene expression and development. Furthermore, we show that RNAi-mediated reduction of dRtf1 results in a reduction in histone H3K4 trimethylation levels on bulk histones and chromosomes in vivo, indicating that the histone modification pathway via Rtf1 is conserved among yeast, Drosophila, and human. Recently, it was demonstrated that histone H3K4 methylation mediated via the E3 ligase Bre1 is critical for transcription of Notch target genes in Drosophila. Here we demonstrate that the dRtf1 component of the Paf1 complex functions in Notch signaling.
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Affiliation(s)
- Kristen Tenney
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
| | - Mark Gerber
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
| | - Anne Ilvarsonn
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
| | - Jessica Schneider
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
| | - Maria Gause
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
| | - Dale Dorsett
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
- Saint Louis University Cancer Center, Saint Louis University School of Medicine, St. Louis, MO 63104
| | - Joel C. Eissenberg
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
- Saint Louis University Cancer Center, Saint Louis University School of Medicine, St. Louis, MO 63104
| | - Ali Shilatifard
- *Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 South Grand Boulevard, St. Louis, MO 63104; and
- Saint Louis University Cancer Center, Saint Louis University School of Medicine, St. Louis, MO 63104
- To whom correspondence should be sent at the ∗ address. E-mail:
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27
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Ito T, Arimitsu N, Takeuchi M, Kawamura N, Nagata M, Saso K, Akimitsu N, Hamamoto H, Natori S, Miyajima A, Sekimizu K. Transcription elongation factor S-II is required for definitive hematopoiesis. Mol Cell Biol 2006; 26:3194-203. [PMID: 16581793 PMCID: PMC1446961 DOI: 10.1128/mcb.26.8.3194-3203.2006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Transcription elongation factor S-II/TFIIS promotes readthrough of transcriptional blocks by stimulating nascent RNA cleavage activity of RNA polymerase II in vitro. The biologic significance of S-II function in higher eukaryotes, however, remains unclear. To determine its role in mammalian development, we generated S-II-deficient mice through targeted gene disruption. Homozygous null mutants died at midgestation with marked pallor, suggesting severe anemia. S-II(-/-) embryos had a decreased number of definitive erythrocytes in the peripheral blood and disturbed erythroblast differentiation in fetal liver. There was a dramatic increase in apoptotic cells in S-II(-/-) fetal liver, which was consistent with a reduction in Bcl-x(L) gene expression. The presence of phenotypically defined hematopoietic stem cells and in vitro colony-forming hematopoietic progenitors in S-II(-/-) fetal liver indicates that S-II is dispensable for the generation and differentiation of hematopoietic stem cells. S-II-deficient fetal liver cells, however, exhibited a loss of long-term repopulating potential when transplanted into lethally irradiated adult mice, indicating that S-II deficiency causes an intrinsic defect in the self-renewal of hematopoietic stem cells. Thus, S-II has critical and nonredundant roles in definitive hematopoiesis.
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Affiliation(s)
- Takahiro Ito
- Division of Developmental Biochemistry, Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033
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28
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Eissenberg JC, Shilatifard A. Leaving a mark: the many footprints of the elongating RNA polymerase II. Curr Opin Genet Dev 2006; 16:184-90. [PMID: 16503129 DOI: 10.1016/j.gde.2006.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Accepted: 02/13/2006] [Indexed: 01/08/2023]
Abstract
The elongation phase of transcription by RNA polymerase II involves a complex choreography of events besides the polymerization of RNA. In addition to coordinating the processing of the nascent transcript, elongating RNA polymerase II recruits histone methyltransferases to methylate lysines 4 and 36 of histone H3 in nucleosomes in the body of actively transcribed genes. Methylation at these sites is genetically implicated in marking actively transcribed genes. Recent studies link transcriptional elongation by RNA polymerase II to H3K9 methylation and the recruitment of the HP1 family protein HP1gamma. These findings expand the role for RNA polymerase II elongation in targeting chromatin modifications to include a histone methyl mark more commonly associated with gene silencing.
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Affiliation(s)
- Joel C Eissenberg
- Edward A Doisy Department of Biochemistry and Molecular Biology and the Cancer Center, St Louis University School of Medicine, 1402 South Grand Boulevard, St Louis, MO 63104, USA
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29
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Grasser KD. Emerging role for transcript elongation in plant development. TRENDS IN PLANT SCIENCE 2005; 10:484-90. [PMID: 16150628 DOI: 10.1016/j.tplants.2005.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 08/04/2005] [Accepted: 08/24/2005] [Indexed: 05/04/2023]
Abstract
Transcript elongation by RNA polymerase II (RNAPII), once regarded as the simple extension of the initiated mRNA, is a complex and highly regulated phase of the transcription cycle. Many factors have been identified that contribute to the dynamic control of the elongation stage of transcription. There are elongation factors that modulate the activity of RNAPII and other factors that facilitate the transcription through chromatin. Recent studies of mutants defective in elongation factors have revealed the importance of proper transcript elongation for the development of higher eukaryotes. Here, the essentials of transcript elongation are briefly summarized to discuss its role in developmental processes.
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Affiliation(s)
- Klaus D Grasser
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
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30
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Gerber M, Tenney K, Conaway JW, Conaway RC, Eissenberg JC, Shilatifard A. Regulation of Heat Shock Gene Expression by RNA Polymerase II Elongation Factor, Elongin A. J Biol Chem 2005; 280:4017-20. [PMID: 15611125 DOI: 10.1074/jbc.c400487200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The elongation stage of transcription by RNA polymerase II (Pol II) has emerged as an essential regulated step. Elongin A (EloA) is the largest subunit of the Elongin complex that can increase the catalytic rate of mRNA synthesis by Pol II. We recently demonstrated that the Elongin A homologue in Drosophila, dEloA, is essential and has properties consistent with those of a Pol II elongation factor in vivo. The goal of this study was to test whether dEloA is required for heat shock gene transcription, since heat shock gene expression is thought to be controlled at the level of Pol II elongation. Here, we demonstrate that dEloA is rapidly recruited to heat shock loci with Pol II in response to heat shock. Furthermore, through the use of RNA interference in vivo, we show that dEloA is required for the proper expression of one of these genes, HSP70, and that its requirement for heat shock gene expression is exerted after the initiation of transcription at heat shock loci. Our data represent the first demonstration of an essential role for an RNA polymerase II elongation factor in the regulation of heat shock gene expression in an animal model.
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Affiliation(s)
- Mark Gerber
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University Health Sciences Center, Saint Louis, Missouri 63104, USA
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