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Liu J, Jie W, Shi X, Ding Y, Ding C. Transcription elongation factors OsSPT4 and OsSPT5 are essential for rice growth and development and act with APO2. PLANT CELL REPORTS 2023:10.1007/s00299-023-03025-6. [PMID: 37148321 DOI: 10.1007/s00299-023-03025-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
KEY MESSAGE The transcription elongation factor SPT4/SPT5 complex is essential for rice vegetative and reproductive growth and that OsSPT5-1, with its interactor APO2, is involved in multiple phytohormone pathways. The SPT4/SPT5 complex is a transcription elongation factor that regulates the processivity of transcription elongation. However, our understanding of the role of SPT4/SPT5 complex in developmental regulation remains limited. Here, we identified three SPT4/SPT5 genes (OsSPT4, OsSPT5-1, and OsSPT5-2) in rice, and investigated their roles in vegetative and reproductive growth. These genes are highly conserved with their orthologs in other species. OsSPT4 and OsSPT5-1 are widely expressed in various tissues. By contrast, OsSPT5-2 is expressed at a relatively low level, which could cause osspt5-2 null mutants have no phenotypes. Loss-of-function mutants of OsSPT4 and OsSPT5-1 could not be obtained; their heterozygotes showed severe reproductive growth defects. An incomplete mutant line (osspt5-1#12) displayed gibberellin-related dwarfed defects and a weak root system at an early vegetative phase, and a short life cycle in different planting environments. Furthermore, OsSPT5-1 interacts with the transcription factor ABERRANT PANICLE ORGANIZATION 2 (APO2) and plays a similar role in regulating the growth of rice shoots. RNA sequencing analysis verified that OsSPT5-1 is involved in multiple phytohormone pathways, including gibberellin, auxin, and cytokinin. Therefore, the SPT4/SPT5 complex is essential for both vegetative and reproductive growth in rice.
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Affiliation(s)
- Jiajun Liu
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wanrong Jie
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xi'an Shi
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing, 210095, People's Republic of China
| | - Chengqiang Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing, 210095, People's Republic of China.
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2
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Soliman SH, Cisneros WJ, Iwanaszko M, Aoi Y, Ganesan S, Walter M, Zeidner JM, Mishra RK, Kim EY, Wolinsky SM, Hultquist JF, Shilatifard A. Enhancing HIV-1 latency reversal through regulating the elongating RNA Pol II pause-release by a small-molecule disruptor of PAF1C. SCIENCE ADVANCES 2023; 9:eadf2468. [PMID: 36888719 PMCID: PMC9995073 DOI: 10.1126/sciadv.adf2468] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/03/2023] [Indexed: 05/03/2023]
Abstract
The polymerase-associated factor 1 complex (PAF1C) is a key, post-initiation transcriptional regulator of both promoter-proximal pausing and productive elongation catalyzed by RNA Pol II and is also involved in transcriptional repression of viral gene expression during human immunodeficiency virus-1 (HIV-1) latency. Using a molecular docking-based compound screen in silico and global sequencing-based candidate evaluation in vivo, we identified a first-in-class, small-molecule inhibitor of PAF1C (iPAF1C) that disrupts PAF1 chromatin occupancy and induces global release of promoter-proximal paused RNA Pol II into gene bodies. Transcriptomic analysis revealed that iPAF1C treatment mimics acute PAF1 subunit depletion and impairs RNA Pol II pausing at heat shock-down-regulated genes. Furthermore, iPAF1C enhances the activity of diverse HIV-1 latency reversal agents both in cell line latency models and in primary cells from persons living with HIV-1. In sum, this study demonstrates that efficient disruption of PAF1C by a first-in-class, small-molecule inhibitor may have therapeutic potential for improving current HIV-1 latency reversal strategies.
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Affiliation(s)
- Shimaa H. A. Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - William J. Cisneros
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sheetal Ganesan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miriam Walter
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jacob M. Zeidner
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rama K. Mishra
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven M. Wolinsky
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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3
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Pal S, Yadav D, Biswas D. ATM-mediated ELL phosphorylation enhances its self-association through increased EAF1 interaction and inhibits global transcription during genotoxic stress. Nucleic Acids Res 2022; 50:10995-11012. [PMID: 36305813 PMCID: PMC9638944 DOI: 10.1093/nar/gkac943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/16/2022] [Accepted: 10/15/2022] [Indexed: 12/05/2022] Open
Abstract
Mammalian cells immediately inhibit transcription upon exposure to genotoxic stress to avoid fatal collision between ongoing transcription and newly recruited DNA repair machineries to protect genomic integrity. However, mechanisms of this early transcriptional inhibition are poorly understood. In this study, we decipher a novel role of human EAF1, a positive regulator of ELL-dependent RNA Polymerase II-mediated transcription in vitro, in regulation of temporal inhibition of transcription during genotoxic stress. Our results show that, besides Super Elongation Complex (SEC) and Little Elongation Complex (LEC), human ELL (aka ELL1) also forms a complex with EAF1 alone. Interestingly, contrary to the in vitro studies, EAF1 inhibits ELL-dependent RNA polymerase II-mediated transcription of diverse target genes. Mechanistically, we show that intrinsic self-association property of ELL leads to its reduced interaction with other SEC components. EAF1 enhances ELL self-association and thus reduces its interaction with other SEC components leading to transcriptional inhibition. Physiologically, we show that upon exposure to genotoxic stress, ATM-mediated ELL phosphorylation-dependent enhanced EAF1 association results in reduced ELL interaction with other SEC components that lead to global transcriptional inhibition. Thus, we describe an important mechanism of dynamic transcriptional regulation during genotoxic stress involving post-translational modification of a key elongation factor.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road , Kolkata - 32, India
- Academy of Scientific and Innovative Research (AcSIR) , Ghaziabad 201002, India
| | - Dipika Yadav
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road , Kolkata - 32, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road , Kolkata - 32, India
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4
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Li J, Tiwari M, Chen Y, Luanpitpong S, Sen GL. CDK12 Is Necessary to Promote Epidermal Differentiation Through Transcription Elongation. Stem Cells 2022; 40:435-445. [PMID: 35325240 PMCID: PMC9199850 DOI: 10.1093/stmcls/sxac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/17/2021] [Indexed: 01/30/2023]
Abstract
Proper differentiation of the epidermis is essential to prevent water loss and to protect the body from the outside environment. Perturbations in this process can lead to a variety of skin diseases that impacts 1 in 5 people. While transcription factors that control epidermal differentiation have been well characterized, other aspects of transcription control such as elongation are poorly understood. Here we show that of the two cyclin-dependent kinases (CDK12 and CDK13), that are known to regulate transcription elongation, only CDK12 is necessary for epidermal differentiation. Depletion of CDK12 led to loss of differentiation gene expression and absence of skin barrier formation in regenerated human epidermis. CDK12 binds to genes that code for differentiation promoting transcription factors (GRHL3, KLF4, and OVOL1) and is necessary for their elongation. CDK12 is necessary for elongation by promoting Ser2 phosphorylation on the C-terminal domain of RNA polymerase II and the stabilization of binding of the elongation factor SPT6 to target genes. Our results suggest that control of transcription elongation by CDK12 plays a prominent role in adult cell fate decisions.
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Affiliation(s)
- Jingting Li
- Institute of Precision Medicine, Department of Burns, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Manisha Tiwari
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Yifang Chen
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Sudjit Luanpitpong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, Thailand
| | - George L Sen
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
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5
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RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex. Cell Rep 2022; 39:110732. [PMID: 35476980 DOI: 10.1016/j.celrep.2022.110732] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/31/2021] [Accepted: 04/02/2022] [Indexed: 11/21/2022] Open
Abstract
RNA polymerase II (Pol II)-mediated transcription in metazoans requires precise regulation. RNA Pol II-associated protein 2 (RPAP2) was previously identified to transport Pol II from cytoplasm to nucleus and dephosphorylates Pol II C-terminal domain (CTD). Here, we show that RPAP2 binds hypo-/hyper-phosphorylated Pol II with undetectable phosphatase activity. The structure of RPAP2-Pol II shows mutually exclusive assembly of RPAP2-Pol II and pre-initiation complex (PIC) due to three steric clashes. RPAP2 prevents and disrupts Pol II-TFIIF interaction and impairs in vitro transcription initiation, suggesting a function in inhibiting PIC assembly. Loss of RPAP2 in cells leads to global accumulation of TFIIF and Pol II at promoters, indicating a critical role of RPAP2 in inhibiting PIC assembly independent of its putative phosphatase activity. Our study indicates that RPAP2 functions as a gatekeeper to inhibit PIC assembly and transcription initiation and suggests a transcription checkpoint.
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6
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Abstract
Omics-based technologies, which have developed rapidly over the last few decades, have generated increasing evidence demonstrating pervasive divergent transcription from RNA polymerase II (Pol II) promoters of eukaryotic genome, and indeed have raised considerable discussion as to their potential physiopathological function. Unlike many other long non-coding RNAs (lncRNAs), promoter antisense RNAs (PAS RNAs) were initially considered to be merely passive transcription by-products of active promoters. However, recent studies have begun to reveal their critical importance in a broad spectrum of biological processes. In this Review, I summarize recent technological advances that enable accurate detection of PAS RNA and discuss the mechanisms of PAS RNA biogenesis emphasizing the functional importance of its structure enabling the diverse functions of PAS RNA in transcription and chromatin regulation.
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Affiliation(s)
- Fan Yang
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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7
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The 7SK/P-TEFb snRNP controls ultraviolet radiation-induced transcriptional reprogramming. Cell Rep 2021; 35:108965. [PMID: 33852864 DOI: 10.1016/j.celrep.2021.108965] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/27/2021] [Accepted: 03/17/2021] [Indexed: 01/08/2023] Open
Abstract
Conversion of promoter-proximally paused RNA polymerase II (RNAPII) into elongating polymerase by the positive transcription elongation factor b (P-TEFb) is a central regulatory step of mRNA synthesis. The activity of P-TEFb is controlled mainly by the 7SK small nuclear ribonucleoprotein (snRNP), which sequesters active P-TEFb into inactive 7SK/P-TEFb snRNP. Here we demonstrate that under normal culture conditions, the lack of 7SK snRNP has only minor impacts on global RNAPII transcription without detectable consequences on cell proliferation. However, upon ultraviolet (UV)-light-induced DNA damage, cells lacking 7SK have a defective transcriptional response and reduced viability. Both UV-induced release of "lesion-scanning" polymerases and activation of key early-responsive genes are compromised in the absence of 7SK. Proper induction of 7SK-dependent UV-responsive genes requires P-TEFb activity directly mobilized from the nucleoplasmic 7SK/P-TEFb snRNP. Our data demonstrate that the primary function of the 7SK/P-TEFb snRNP is to orchestrate the proper transcriptional response to stress.
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8
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Li J, Xu X, Tiwari M, Chen Y, Fuller M, Bansal V, Tamayo P, Das S, Ghosh P, Sen GL. SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation. Nat Commun 2021; 12:784. [PMID: 33542242 PMCID: PMC7862286 DOI: 10.1038/s41467-021-21067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
In adult tissue, stem and progenitor cells must tightly regulate the balance between proliferation and differentiation to sustain homeostasis. How this exquisite balance is achieved is an area of active investigation. Here, we show that epidermal genes, including ~30% of induced differentiation genes already contain stalled Pol II at the promoters in epidermal stem and progenitor cells which is then released into productive transcription elongation upon differentiation. Central to this process are SPT6 and PAF1 which are necessary for the elongation of these differentiation genes. Upon SPT6 or PAF1 depletion there is a loss of human skin differentiation and stratification. Unexpectedly, loss of SPT6 also causes the spontaneous transdifferentiation of epidermal cells into an intestinal-like phenotype due to the stalled transcription of the master regulator of epidermal fate P63. Our findings suggest that control of transcription elongation through SPT6 plays a prominent role in adult somatic tissue differentiation and the inhibition of alternative cell fate choices.
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Affiliation(s)
- Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Xiaojun Xu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Mackenzie Fuller
- Departments of Medicine and Cellular and Molecular Medicine, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
- Department of Pathology, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - Varun Bansal
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Pablo Tamayo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
- Division of Medical Genetics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Soumita Das
- Department of Pathology, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.
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The ARF tumor suppressor targets PPM1G/PP2Cγ to counteract NF-κB transcription tuning cell survival and the inflammatory response. Proc Natl Acad Sci U S A 2020; 117:32594-32605. [PMID: 33288725 DOI: 10.1073/pnas.2004470117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Inducible transcriptional programs mediate the regulation of key biological processes and organismal functions. Despite their complexity, cells have evolved mechanisms to precisely control gene programs in response to environmental cues to regulate cell fate and maintain normal homeostasis. Upon stimulation with proinflammatory cytokines such as tumor necrosis factor-α (TNF), the master transcriptional regulator nuclear factor (NF)-κB utilizes the PPM1G/PP2Cγ phosphatase as a coactivator to normally induce inflammatory and cell survival programs. However, how PPM1G activity is precisely regulated to control NF-κB transcription magnitude and kinetics remains unknown. Here, we describe a mechanism by which the ARF tumor suppressor binds PPM1G to negatively regulate its coactivator function in the NF-κB circuit thereby promoting insult resolution. ARF becomes stabilized upon binding to PPM1G and forms a ternary protein complex with PPM1G and NF-κB at target gene promoters in a stimuli-dependent manner to provide tunable control of the NF-κB transcriptional program. Consistently, loss of ARF in colon epithelial cells leads to up-regulation of NF-κB antiapoptotic genes upon TNF stimulation and renders cells partially resistant to TNF-induced apoptosis in the presence of agents blocking the antiapoptotic program. Notably, patient tumor data analysis validates these findings by revealing that loss of ARF strongly correlates with sustained expression of inflammatory and cell survival programs. Collectively, we propose that PPM1G emerges as a therapeutic target in a variety of cancers arising from ARF epigenetic silencing, to loss of ARF function, as well as tumors bearing oncogenic NF-κB activation.
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10
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Fan Z, Devlin JR, Hogg SJ, Doyle MA, Harrison PF, Todorovski I, Cluse LA, Knight DA, Sandow JJ, Gregory G, Fox A, Beilharz TH, Kwiatkowski N, Scott NE, Vidakovic AT, Kelly GP, Svejstrup JQ, Geyer M, Gray NS, Vervoort SJ, Johnstone RW. CDK13 cooperates with CDK12 to control global RNA polymerase II processivity. SCIENCE ADVANCES 2020; 6:eaaz5041. [PMID: 32917631 PMCID: PMC7190357 DOI: 10.1126/sciadv.aaz5041] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/10/2020] [Indexed: 05/04/2023]
Abstract
The RNA polymerase II (POLII)-driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases (CDKs) and their cognate cyclins. The molecular events underpinning transcriptional elongation, processivity, and the CDK-cyclin pair(s) involved remain poorly understood. Using CRISPR-Cas9 homology-directed repair, we generated analog-sensitive kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with cellular growth signaling pathways and/or DNA damage, with minimal effects on cell viability. In contrast, dual kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including widespread use of alternative 3' polyadenylation sites. At the molecular level, dual kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define substantial redundancy between CDK12 and CDK13 and identify both as fundamental regulators of global POLII processivity and transcription elongation.
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Affiliation(s)
- Zheng Fan
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Jennifer R Devlin
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Simon J Hogg
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Maria A Doyle
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Paul F Harrison
- Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
- Monash Bioinformatics Platform, Monash University, Clayton, 3800 VIC, Australia
| | - Izabela Todorovski
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Leonie A Cluse
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Deborah A Knight
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, 3052 VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, 3052 VIC, Australia
| | - Gareth Gregory
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Andrew Fox
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia
| | - Traude H Beilharz
- Monash Biomedicine Discovery Institute, Monash University, Clayton, 3800 VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Parkville, 3052 VIC, Australia
| | | | - Gavin P Kelly
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephin J Vervoort
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, 3000 VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3052 VIC, Australia
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11
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Guo XJ, Yang D, Zhang XY. Epigenetics recording varied environment and complex cell events represents the origin of cellular aging. J Zhejiang Univ Sci B 2020; 20:550-562. [PMID: 31168969 DOI: 10.1631/jzus.b1800507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although a relationship between epigenetics and aging phenotypic changes has been established, a theoretical explanation of the intrinsic connection between the epigenetics and aging is lacking. In this essay, we propose that epigenetic recording of varied cell environment and complex history could be an origin of cellular aging. Through epigenetic modifications, the environment and historical events can induce the chromatin template into an activated or repressive accessible structure, thereby shaping the DNA template into a spectrum of chromatin states. The inner nature of diversity and conflicts born by the cell environment and its historical events are hence recorded into the chromatin template. This could result in a dissipated spectrum of the chromatin state and chaos in overall gene expression. An unavoidable degradation of epigenome entropy, similar to Shannon entropy, would be consequently induced. The resultant disorder in epigenome, characterized by corrosion of epigenome entropy as reflected in chromatin template, can be stably memorized and propagated through cell division. Furthermore, the hysteretic nature of epigenetics responding to the emerging environment could exacerbate the degradation of epigenome entropy. As well as stochastic errors, we propose that outside entropy (or chaos) derived from the varied environment and complex cell history, gradually input and imprinted into the chromatin via epigenetic modifications, would lead inevitably to cellular aging, the extent of which could be aggravated by hysteresis of epigenetics without error erasing and correction.
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Affiliation(s)
- Xue-Jun Guo
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yuan Zhang
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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12
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Wang Y, Qiu T. Positive transcription elongation factor b and its regulators in development. ALL LIFE 2020. [DOI: 10.1080/21553769.2019.1663277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Yan Wang
- Department of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People’s Republic of China
| | - Tong Qiu
- Department of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People’s Republic of China
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13
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Promoter-proximal pausing mediated by the exon junction complex regulates splicing. Nat Commun 2019; 10:521. [PMID: 30705266 PMCID: PMC6355915 DOI: 10.1038/s41467-019-08381-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 01/04/2019] [Indexed: 02/08/2023] Open
Abstract
Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.
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14
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Chung CY, Berson A, Kennerdell JR, Sartoris A, Unger T, Porta S, Kim HJ, Smith ER, Shilatifard A, Van Deerlin V, Lee VMY, Chen-Plotkin A, Bonini NM. Aberrant activation of non-coding RNA targets of transcriptional elongation complexes contributes to TDP-43 toxicity. Nat Commun 2018; 9:4406. [PMID: 30353006 PMCID: PMC6199344 DOI: 10.1038/s41467-018-06543-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022] Open
Abstract
TDP-43 is the major disease protein associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitinated inclusions (FTLD-TDP). Here we identify the transcriptional elongation factor Ell—a shared component of little elongation complex (LEC) and super elongation complex (SEC)—as a strong modifier of TDP-43-mediated neurodegeneration. Our data indicate select targets of LEC and SEC become upregulated in the fly ALS/FTLD-TDP model. Among them, U12 snRNA and a stress-induced long non-coding RNA Hsrω, functionally contribute to TDP-43-mediated degeneration. We extend the findings of Hsrω, which we identify as a chromosomal target of TDP-43, to show that the human orthologue Sat III is elevated in a human cellular disease model and FTLD-TDP patient tissue. We further demonstrate an interaction between TDP-43 and human ELL2 by co-immunoprecipitation from human cells. These findings reveal important roles of Ell-complexes LEC and SEC in TDP-43-associated toxicity, providing potential therapeutic insight for TDP-43-associated neurodegeneration. TDP-43 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitinated inclusions (FTD-TDP). Here, the authors identify the transcriptional elongation factor Ell as a strong modifier of TDP-43-mediated neurodegeneration through the Ell transcriptional elongation complexes LEC and SEC.
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Affiliation(s)
- Chia-Yu Chung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Amit Berson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jason R Kennerdell
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ashley Sartoris
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Travis Unger
- Department of Neurology, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Sílvia Porta
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Hyung-Jun Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Neural Development and Disease, Korea Brain Research Institute (KBRI), Daegu, 41068, South Korea
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Vivianna Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Virginia M-Y Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Alice Chen-Plotkin
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, Philadelphia, PA, 19104, USA.,Department of Neurology, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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15
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Nassrallah A, Rougée M, Bourbousse C, Drevensek S, Fonseca S, Iniesto E, Ait-Mohamed O, Deton-Cabanillas AF, Zabulon G, Ahmed I, Stroebel D, Masson V, Lombard B, Eeckhout D, Gevaert K, Loew D, Genovesio A, Breyton C, De Jaeger G, Bowler C, Rubio V, Barneche F. DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis. eLife 2018; 7:37892. [PMID: 30192741 PMCID: PMC6128693 DOI: 10.7554/elife.37892] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.
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Affiliation(s)
- Amr Nassrallah
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Martin Rougée
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Clara Bourbousse
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Stephanie Drevensek
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sandra Fonseca
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Elisa Iniesto
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Ouardia Ait-Mohamed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Gerald Zabulon
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ikhlak Ahmed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - David Stroebel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vanessa Masson
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Berangere Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Dominique Eeckhout
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium.,VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Auguste Genovesio
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cecile Breyton
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
| | - Geert De Jaeger
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Fredy Barneche
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
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16
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Puttipanyalears C, Arayataweegool A, Chalertpet K, Rattanachayoto P, Mahattanasakul P, Tangjaturonsasme N, Kerekhanjanarong V, Mutirangura A, Kitkumthorn N. TRH site-specific methylation in oral and oropharyngeal squamous cell carcinoma. BMC Cancer 2018; 18:786. [PMID: 30081853 PMCID: PMC6080527 DOI: 10.1186/s12885-018-4706-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
Background The incidence of oral squamous cell carcinoma (OSCC) continues to increase each year. Clinical examination and biopsy usually detect OSCC at an advanced stage that is difficult to treat, leading to poor prognosis. DNA methylation pattern is tissue specific and has emerged as a biomarker for the detection of cancers of tissue origin. Herein, we aimed to discover a novel site-specific methylation marker for OSCC. Methods We selected OSCC datasets analyzed using the IlluminaHumanMethylation27 BeadChip from the Gene Expression Omnibus repository of the National Center for Biotechnology Information using a bioinformatics approach. From 27,578 CG dinucleotide (CpG) sites, the CpG site with the highest difference in methylation level between healthy and cancerous cells was selected for further validation. A total of 18 mucosal tissue samples were collected from nine healthy controls and nine from OSCC subjects and subjected to microdissection for cell purification, followed by DNA extraction, bisulfite conversion, and pyrosequencing. Additionally, epithelial cells were collected from 2 cohorts including oral rinse from healthy controls, oral rinse and oral swab from OSCC subjects and oral rinse from oropharyngeal squamous cell carcinoma (SCC) were examined for their methylation status using real-time polymerase chain reaction (PCR). Results Among the 27,578 differentially methylated CpG sites, cg01009664 of the thyrotropin-releasing hormone (TRH) gene showed the greatest difference in methylation level between healthy and cancerous cells. Validation of the TRH gene using pyrosequencing revealed a methylation percentage of 7% ± 3.43% in healthy cells in contrast to 63% ± 19.81% in cancerous cells. Screening of epithelial cells using real-time PCR showed that the DNA methylation level was significantly higher in oral swab and rinse samples collected from OSCC and oropharyngeal SCC subjects than those from healthy controls (p < 0.001). In addition, when using a cutoff at 3.31 ng/μL, the TRH methylation biomarker was able to distinguish OSCC and oropharyngeal SCC subjects from healthy controls with high level of area under the curve, sensitivity and specificity. Conclusion We demonstrated cg01009664 of TRH as a potential biomarker for OSCC and oropharyngeal SCC screening using oral rinse and swab techniques. Electronic supplementary material The online version of this article (10.1186/s12885-018-4706-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Puttipanyalears
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - A Arayataweegool
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - K Chalertpet
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - P Rattanachayoto
- Division of Medical Oncology, Department of Medicine, Chulalongkorn University and The King Chulalongkorn Memorial Hospital, Bangkok, 10330, Thailand
| | - P Mahattanasakul
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, Chulalongkorn University, Pathumwa, Bangkok, 10330, Thailand.,Department of Otolaryngology, Head and Neck Surgery, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Pathumwan, Bangkok, 10330, Thailand
| | - N Tangjaturonsasme
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, Chulalongkorn University, Pathumwa, Bangkok, 10330, Thailand
| | - V Kerekhanjanarong
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, Chulalongkorn University, Pathumwa, Bangkok, 10330, Thailand
| | - A Mutirangura
- Department of Anatomy, Faculty of Medicine, Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Chulalongkorn University, Bangkok, 10330, Thailand
| | - N Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, 6 Yothi Road, Ratchathewi, Bangkok, 10400, Thailand.
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17
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Rickels R, Shilatifard A. Enhancer Logic and Mechanics in Development and Disease. Trends Cell Biol 2018; 28:608-630. [PMID: 29759817 DOI: 10.1016/j.tcb.2018.04.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 12/31/2022]
Abstract
Enhancers are distally located genomic cis-regulatory elements that integrate spatiotemporal cues to coordinate gene expression in a tissue-specific manner during metazoan development. Enhancer function depends on a combination of bound transcription factors and cofactors that regulate local chromatin structure, as well as on the topological interactions that are necessary for their activity. Numerous genome-wide studies concur that the vast majority of disease-associated variations occur within non-coding genomic sequences, in other words the 'cis-regulome', and this underscores their relevance for human health. Advances in DNA sequencing and genome-editing technologies have dramatically expanded our ability to identify enhancers and investigate their properties in vivo, revealing an extraordinary level of interconnectivity underlying cis-regulatory networks. We discuss here these recently developed methodologies, as well as emerging trends and remaining questions in the field of enhancer biology, and how perturbation of enhancer activities/functions results in enhanceropathies.
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Affiliation(s)
- Ryan Rickels
- Simpson Querrey Center for Epigenetics, and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611, USA.
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18
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Abstract
A complete understanding of transcription and co-transcriptional RNA processing events by polymerase requires precise and robust approaches to visualize polymerase progress and quantify nascent transcripts on a genome-wide scale. Here, we present a transcriptome-wide method to measure the level of nascent transcribing RNA in a fast and unbiased manner.
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Affiliation(s)
- Fei Xavier Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Searle 6-510, 320 E. Superior St., Chicago, IL, 60611, USA.
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Searle 6-510, 320 E. Superior St., Chicago, IL, 60611, USA
| | - Yu Deng
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Searle 6-510, 320 E. Superior St., Chicago, IL, 60611, USA
| | - Sun Tianjiao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Searle 6-510, 320 E. Superior St., Chicago, IL, 60611, USA
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19
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Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate. Nat Commun 2017; 8:2076. [PMID: 29233992 PMCID: PMC5727188 DOI: 10.1038/s41467-017-02145-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/08/2017] [Indexed: 01/11/2023] Open
Abstract
Complex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV irradiation, RNA polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions into elongation to promote uniform and accelerated surveillance of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased damage-sensing, as confirmed by RNAPII progressive accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. In turn, this transcription elongation ‘safe’ mode guarantees efficient DNA repair regardless of damage location, gene size and transcription level. Accordingly, we detect low and homogenous rates of mutational signatures associated with UV exposure or cigarette smoke across all active genes. Our study reveals a novel advantage for transcription regulation at the promoter-proximal level and provides unanticipated insights into how active transcription shapes the mutagenic landscape of cancer genomes. Precise orchestration of gene expression regulation upon DNA damage is essential for genome integrity. Here the authors identify a novel widespread stress-triggered defence mechanism that promotes rapid transcription-driven genomic surveillance thus limiting mutagenesis and shaping cancer genomes.
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20
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Grasser M, Grasser KD. The plant RNA polymerase II elongation complex: A hub coordinating transcript elongation and mRNA processing. Transcription 2017; 9:117-122. [PMID: 28886274 DOI: 10.1080/21541264.2017.1356902] [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: 12/20/2022] Open
Abstract
Characterisation of the Arabidopsis RNA polymerase II (RNAPII) elongation complex revealed an assembly of a conserved set of transcript elongation factors associated with chromatin remodellers, histone modifiers as well as with various pre-mRNA splicing and polyadenylation factors. Therefore, transcribing RNAPII streamlines the processes of mRNA synthesis and processing in plants.
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Affiliation(s)
- Marion Grasser
- a Department of Cell Biology & Plant Biochemistry, Biochemistry Centre , University of Regensburg , Regensburg , Germany
| | - Klaus D Grasser
- a Department of Cell Biology & Plant Biochemistry, Biochemistry Centre , University of Regensburg , Regensburg , Germany
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21
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Abstract
In this review, Hu and Shilatifard summarize recent advances in our understanding of the role of chromatin modifiers in normal hematopoiesis and their contributions in hematopoietic transformation. Hematological malignancies comprise a diverse set of lymphoid and myeloid neoplasms in which normal hematopoiesis has gone awry and together account for ∼10% of all new cancer cases diagnosed in the United States in 2016. Recent intensive genomic sequencing of hematopoietic malignancies has identified recurrent mutations in genes that encode regulators of chromatin structure and function, highlighting the central role that aberrant epigenetic regulation plays in the pathogenesis of these neoplasms. Deciphering the molecular mechanisms for how alterations in epigenetic modifiers, specifically histone and DNA methylases and demethylases, drive hematopoietic cancer could provide new avenues for developing novel targeted epigenetic therapies for treating hematological malignancies. Just as past studies of blood cancers led to pioneering discoveries relevant to other cancers, determining the contribution of epigenetic modifiers in hematologic cancers could also have a broader impact on our understanding of the pathogenesis of solid tumors in which these factors are mutated.
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Affiliation(s)
- Deqing Hu
- Department of Biochemistry and Molecular Genetics
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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22
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Yang H, Basquin D, Pauli D, Oliver B. Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. BMC Genomics 2017; 18:384. [PMID: 28521739 PMCID: PMC5436443 DOI: 10.1186/s12864-017-3755-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/03/2017] [Indexed: 11/22/2022] Open
Abstract
Background Transcriptional elongation is a generic function, but is also regulated to allow rapid transcription responses. Following relatively long initiation and promoter clearance, RNA polymerase II can pause and then rapidly elongate following recruitment of positive elongation factors. Multiple elongation complexes exist, but the role of specific components in adult Drosophila is underexplored. Results We conducted RNA-seq experiments to analyze the effect of RNAi knockdown of Suppressor of Triplolethal and lilliputian. We similarly analyzed the effect of expressing a dominant negative Cyclin-dependent kinase 9 allele. We observed that almost half of the genes expressed in adults showed reduced expression, supporting a broad role for the three tested genes in steady-state transcript abundance. Expression profiles following lilliputian and Suppressor of Triplolethal RNAi were nearly identical raising the possibility that they are obligatory co-factors. Genes showing reduced expression due to these RNAi treatments were short and enriched for genes encoding metabolic or enzymatic functions. The dominant-negative Cyclin-dependent kinase 9 profiles showed both overlapping and specific differential expression, suggesting involvement in multiple complexes. We also observed hundreds of genes with sex-biased differential expression following treatment. Conclusion Transcriptional profiles suggest that Lilliputian and Suppressor of Triplolethal are obligatory cofactors in the adult and that they can also function with Cyclin-dependent kinase 9 at a subset of loci. Our results suggest that transcriptional elongation control is especially important for rapidly expressed genes to support digestion and metabolism, many of which have sex-biased function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3755-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haiwang Yang
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA.
| | - Denis Basquin
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Daniel Pauli
- Department of Genetics & Evolution, Sciences III, University of Geneva, Boulevard d'Yvoy 4, CH 1205, Geneva, Switzerland
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA
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23
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Egloff S, Vitali P, Tellier M, Raffel R, Murphy S, Kiss T. The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression. EMBO J 2017; 36:934-948. [PMID: 28254838 DOI: 10.15252/embj.201695740] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/26/2017] [Accepted: 01/27/2017] [Indexed: 11/09/2022] Open
Abstract
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, regulates the mRNA elongation capacity of RNA polymerase II (RNAPII) through controlling the nuclear activity of positive transcription elongation factor b (P-TEFb). Here, we demonstrate that the human 7SK snRNP also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes. The 7SK snRNA specifically associates with a fraction of RNAPII hyperphosphorylated at Ser5 and Ser7, which is a hallmark of RNAPII engaged in snRNA synthesis. Chromatin immunoprecipitation (ChIP) and chromatin isolation by RNA purification (ChIRP) experiments revealed enrichments for all components of the 7SK snRNP on RNAPII-specific sn/snoRNA genes. Depletion of 7SK snRNA or Larp7 disrupts LEC integrity, inhibits RNAPII recruitment to RNAPII-specific sn/snoRNA genes, and reduces nascent snRNA and snoRNA synthesis. Thus, through controlling both mRNA elongation and sn/snoRNA synthesis, the 7SK snRNP is a key regulator of nuclear RNA production by RNAPII.
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Affiliation(s)
- Sylvain Egloff
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Patrice Vitali
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Raoul Raffel
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Tamás Kiss
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse Cedex 9, France .,Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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24
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Kuzmina A, Krasnopolsky S, Taube R. Super elongation complex promotes early HIV transcription and its function is modulated by P-TEFb. Transcription 2017; 8:133-149. [PMID: 28340332 DOI: 10.1080/21541264.2017.1295831] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear. Here we revisit the contribution of SEC in early steps of HIV gene transcription. In the absence of Tat, the AF4/FMR2 Family member 4 (AFF4) of SEC efficiently activates HIV transcription, while gene activation by its homolog AFF1 is substantially lower. Differential recruitment to the HIV promoter and association with Human Polymerase-Associated Factor complex (PAFc) play key role in this functional distinction between AFF4 and AFF1. Moreover, while depletion of cyclin T1 expression has subtle effects on HIV gene transcription in the absence of Tat, knockout (KO) of AFF1, AFF4, or both proteins slightly repress this early step of viral transcription. Upon Tat expression, HIV transcription reaches optimal levels despite KO of AFF1 or AFF4 expression. However, double AFF1/AFF4 KO completely diminishes Tat trans-activation. Significantly, our results show that P-TEFb phosphorylates AFF4 and modulates SEC assembly, AFF1/4 dimerization and recruitment to the viral promoter. We conclude that SEC promotes both early steps of HIV transcription in the absence of Tat, as well as elongation of transcription, when Tat is expressed. Significantly, SEC functions are modulated by P-TEFb.
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Affiliation(s)
- Alona Kuzmina
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Simona Krasnopolsky
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Ran Taube
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
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25
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Abstract
Cohesin is a large ring-shaped protein complex, conserved from yeast to human, which participates in most DNA transactions that take place in the nucleus. It mediates sister chromatid cohesion, which is essential for chromosome segregation and homologous recombination (HR)-mediated DNA repair. Together with architectural proteins and transcriptional regulators, such as CTCF and Mediator, respectively, it contributes to genome organization at different scales and thereby affects transcription, DNA replication, and locus rearrangement. Although cohesin is essential for cell viability, partial loss of function can affect these processes differently in distinct cell types. Mutations in genes encoding cohesin subunits and regulators of the complex have been identified in several cancers. Understanding the functional significance of these alterations may have relevant implications for patient classification, risk prediction, and choice of treatment. Moreover, identification of vulnerabilities in cancer cells harboring cohesin mutations may provide new therapeutic opportunities and guide the design of personalized treatments.
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Affiliation(s)
- Magali De Koninck
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid E-28029, Spain
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26
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Zhang Y, Najmi SM, Schneider DA. Transcription factors that influence RNA polymerases I and II: To what extent is mechanism of action conserved? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:246-255. [PMID: 27989933 DOI: 10.1016/j.bbagrm.2016.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023]
Abstract
In eukaryotic cells, nuclear RNA synthesis is accomplished by at least three unique, multisubunit RNA polymerases. The roles of these enzymes are generally partitioned into the synthesis of the three major classes of RNA: rRNA, mRNA, and tRNA for RNA polymerases I, II, and III respectively. Consistent with their unique cellular roles, each enzyme has a complement of specialized transcription factors and enzymatic properties. However, not all transcription factors have evolved to affect only one eukaryotic RNA polymerase. In fact, many factors have been shown to influence the activities of multiple nuclear RNA polymerases. This review focuses on a subset of these factors, specifically addressing the mechanisms by which these proteins influence RNA polymerases I and II.
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Affiliation(s)
- Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Saman M Najmi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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27
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Strikoudis A, Lazaris C, Trimarchi T, Galvao Neto AL, Yang Y, Ntziachristos P, Rothbart S, Buckley S, Dolgalev I, Stadtfeld M, Strahl BD, Dynlacht BD, Tsirigos A, Aifantis I. Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a. Nat Cell Biol 2016; 18:1127-1138. [PMID: 27749823 PMCID: PMC5083132 DOI: 10.1038/ncb3424] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 09/15/2016] [Indexed: 12/12/2022]
Abstract
Pluripotent embryonic stem cells (ESCs) self-renew or differentiate into all tissues of the developing embryo and cell-specification factors are necessary to balance gene expression. Here we delineate the function of the PHD-finger protein 5a (Phf5a) in ESC self-renewal and ascribe its role in regulating pluripotency, cellular reprogramming, and myoblast specification. We demonstrate that Phf5a is essential for maintaining pluripotency, since depleted ESCs exhibit hallmarks of differentiation. Mechanistically, we attribute Phf5a function to the stabilization of the Paf1 transcriptional complex and control of RNA polymerase II elongation on pluripotency loci. Apart from an ESC-specific factor, we demonstrate that Phf5a controls differentiation of adult myoblasts. Our findings suggest a potent mode of regulation by the Phf5a in stem cells, which directs their transcriptional program ultimately regulating maintenance of pluripotency and cellular reprogramming.
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Affiliation(s)
- Alexandros Strikoudis
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Charalampos Lazaris
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA
| | - Thomas Trimarchi
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Antonio L Galvao Neto
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York 10016, USA
| | - Yan Yang
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA
| | - Panagiotis Ntziachristos
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Scott Rothbart
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599, USA
| | - Shannon Buckley
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Igor Dolgalev
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA.,Genome Technology Center, Office of Collaborative Science, NYU School of Medicine, New York, New York 10016, USA
| | - Matthias Stadtfeld
- Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599, USA
| | - Brian D Dynlacht
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
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28
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Gilan O, Lam EYN, Becher I, Lugo D, Cannizzaro E, Joberty G, Ward A, Wiese M, Fong CY, Ftouni S, Tyler D, Stanley K, MacPherson L, Weng CF, Chan YC, Ghisi M, Smil D, Carpenter C, Brown P, Garton N, Blewitt ME, Bannister AJ, Kouzarides T, Huntly BJP, Johnstone RW, Drewes G, Dawson SJ, Arrowsmith CH, Grandi P, Prinjha RK, Dawson MA. Functional interdependence of BRD4 and DOT1L in MLL leukemia. Nat Struct Mol Biol 2016; 23:673-81. [PMID: 27294782 DOI: 10.1038/nsmb.3249] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/19/2016] [Indexed: 02/06/2023]
Abstract
Targeted therapies against disruptor of telomeric silencing 1-like (DOT1L) and bromodomain-containing protein 4 (BRD4) are currently being evaluated in clinical trials. However, the mechanisms by which BRD4 and DOT1L regulate leukemogenic transcription programs remain unclear. Using quantitative proteomics, chemoproteomics and biochemical fractionation, we found that native BRD4 and DOT1L exist in separate protein complexes. Genetic disruption or small-molecule inhibition of BRD4 and DOT1L showed marked synergistic activity against MLL leukemia cell lines, primary human leukemia cells and mouse leukemia models. Mechanistically, we found a previously unrecognized functional collaboration between DOT1L and BRD4 that is especially important at highly transcribed genes in proximity to superenhancers. DOT1L, via dimethylated histone H3 K79, facilitates histone H4 acetylation, which in turn regulates the binding of BRD4 to chromatin. These data provide new insights into the regulation of transcription and specify a molecular framework for therapeutic intervention in this disease with poor prognosis.
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MESH Headings
- Acetylation
- Animals
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Cycle Proteins
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Clinical Trials as Topic
- Disease Models, Animal
- Female
- Gene Expression Regulation, Leukemic
- Histone-Lysine N-Methyltransferase
- Histones/genetics
- Histones/metabolism
- Humans
- Leukemia, Biphenotypic, Acute/genetics
- Leukemia, Biphenotypic, Acute/metabolism
- Leukemia, Biphenotypic, Acute/pathology
- Male
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mice
- Mice, Inbred C57BL
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Primary Cell Culture
- Protein Binding
- Proteomics/methods
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Signal Transduction
- T-Lymphocytes/metabolism
- T-Lymphocytes/pathology
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Isabelle Becher
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Dave Lugo
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | | | - Gerard Joberty
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Aoife Ward
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Meike Wiese
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Chun Yew Fong
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sarah Ftouni
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dean Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kym Stanley
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Chen-Fang Weng
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Margherita Ghisi
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Peter Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Neil Garton
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Brian J P Huntly
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge, UK
- Cambridge Stem Cell Institute, Cambridge, UK
| | - Ricky W Johnstone
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Paola Grandi
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Heidelberg, Germany
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
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29
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D'Urso A, Takahashi YH, Xiong B, Marone J, Coukos R, Randise-Hinchliff C, Wang JP, Shilatifard A, Brickner JH. Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. eLife 2016; 5:e16691. [PMID: 27336723 DOI: 10.7554/elife.16691.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/22/2016] [Indexed: 05/21/2023] Open
Abstract
In yeast and humans, previous experiences can lead to epigenetic transcriptional memory: repressed genes that exhibit mitotically heritable changes in chromatin structure and promoter recruitment of poised RNA polymerase II preinitiation complex (RNAPII PIC), which enhances future reactivation. Here, we show that INO1 memory in yeast is initiated by binding of the Sfl1 transcription factor to the cis-acting Memory Recruitment Sequence, targeting INO1 to the nuclear periphery. Memory requires a remodeled form of the Set1/COMPASS methyltransferase lacking Spp1, which dimethylates histone H3 lysine 4 (H3K4me2). H3K4me2 recruits the SET3C complex, which plays an essential role in maintaining this mark. Finally, while active INO1 is associated with Cdk8(-) Mediator, during memory, Cdk8(+) Mediator recruits poised RNAPII PIC lacking the Kin28 CTD kinase. Aspects of this mechanism are generalizable to yeast and conserved in human cells. Thus, COMPASS and Mediator are repurposed to promote epigenetic transcriptional poising by a highly conserved mechanism.
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Affiliation(s)
- Agustina D'Urso
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Bin Xiong
- Department of Statistics, Northwestern University, Evanston, United States
| | - Jessica Marone
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | | | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, United States
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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30
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D'Urso A, Takahashi YH, Xiong B, Marone J, Coukos R, Randise-Hinchliff C, Wang JP, Shilatifard A, Brickner JH. Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. eLife 2016; 5. [PMID: 27336723 PMCID: PMC4951200 DOI: 10.7554/elife.16691] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/22/2016] [Indexed: 12/17/2022] Open
Abstract
In yeast and humans, previous experiences can lead to epigenetic transcriptional memory: repressed genes that exhibit mitotically heritable changes in chromatin structure and promoter recruitment of poised RNA polymerase II preinitiation complex (RNAPII PIC), which enhances future reactivation. Here, we show that INO1 memory in yeast is initiated by binding of the Sfl1 transcription factor to the cis-acting Memory Recruitment Sequence, targeting INO1 to the nuclear periphery. Memory requires a remodeled form of the Set1/COMPASS methyltransferase lacking Spp1, which dimethylates histone H3 lysine 4 (H3K4me2). H3K4me2 recruits the SET3C complex, which plays an essential role in maintaining this mark. Finally, while active INO1 is associated with Cdk8- Mediator, during memory, Cdk8+ Mediator recruits poised RNAPII PIC lacking the Kin28 CTD kinase. Aspects of this mechanism are generalizable to yeast and conserved in human cells. Thus, COMPASS and Mediator are repurposed to promote epigenetic transcriptional poising by a highly conserved mechanism. DOI:http://dx.doi.org/10.7554/eLife.16691.001 Cells respond to stressful conditions by changing which of their genes are switched on. Such stress-specific genes are typically switched off again when the conditions improve, but can remain primed and ready to be switched on again when needed. This phenomenon is known as “epigenetic transcriptional memory” and allows for a faster or stronger response to the same stress in the future. In fact, these memories can last for a long time, even after the cell divides many times. Inside cells, most of the DNA is wrapped tightly around proteins called histones. To activate – or transcribe – a gene, the DNA must be re-packaged to allow better access for specific proteins including the enzyme called RNA polymerase II. This repackaging involves a number of changes including chemical modification of the histone proteins. Genes that have been previously transcribed under stress are packaged in a different way so that they are poised and ready for the next time they are needed. However, the details of this process were not clear. Using yeast as a model, D'Urso et al. have dissected the changes that are responsible for priming genes to respond to future events. The yeast gene INO1, which shows transcriptional memory, was studied in cells by characterizing the proteins bound at and around the gene and the histone modifications in the region. D'Urso et al. found that a protein called SfI1 bound to this gene only during transcriptional memory and that this binding was critical to start the phenomenon. Further experiments showed that transcriptional memory also required altering two protein complexes that normally bind to genes when they are switched on. One complex, which includes an enzyme that modifies histones, was altered so that the histones at the INO1 gene were marked in a unique way. The other complex was responsible for recruiting an inactive, poised form of RNA polymerase II to the gene, which allowed the gene to be activated when needed. In addition, D'Urso found that other genes that show transcriptional memory in yeast, as well as such genes in human cells, were also marked in the same ways. A future challenge will be to understand how different conditions in different organisms can lead to transcriptional memory. Further studies could also explore how this memory phenomenon is inherited and how it influences an organism’s fitness. DOI:http://dx.doi.org/10.7554/eLife.16691.002
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Affiliation(s)
- Agustina D'Urso
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Bin Xiong
- Department of Statistics, Northwestern University, Evanston, United States
| | - Jessica Marone
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | | | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, United States
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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31
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Liu J, Xiao Y, Zhang T, Ma J. Time to move on: Modeling transcription dynamics during an embryonic transition away from maternal control. Fly (Austin) 2016; 10:101-7. [PMID: 27172244 DOI: 10.1080/19336934.2016.1188231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In a recent study, we investigated the regulation of hunchback (hb) transcription dynamics in Drosophila embryos. Our results suggest that shutdown of hb transcription at early nuclear cycle (nc) 14 is an event associated with the global changes taking place during the mid-blastula transition (MBT). Here we have developed a simple model of hb transcription dynamics during this transition time. With kinetic parameters estimated from our published experimental data, the model describes the dynamical processes of hb gene transcription and hb mRNA accumulation. With two steps, transcription onset upon exiting the previous mitosis followed by a sudden impact that blocks gene activation, the model recapitulates the observed dynamics of hb transcription during the nc14 interphase. The timing of gene inactivation is essential, as its alterations lead to changes in both hb transcription dynamics and hb mRNA levels. Our model provides a clear dynamical picture of hb transcription regulation as one of the many, actively regulated events concurrently taking place during the MBT.
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Affiliation(s)
- Junbo Liu
- a Division of Biomedical Informatics, Cincinnati Children's Research Foundation , Cincinnati , OH
| | - Yanyu Xiao
- b Department of Mathematical Sciences , University of Cincinnati , Cincinnati , OH
| | - Tongli Zhang
- c Department of Molecular and Cellular Physiology , University of Cincinnati College of Medicine , Cincinnati , OH
| | - Jun Ma
- a Division of Biomedical Informatics, Cincinnati Children's Research Foundation , Cincinnati , OH.,d Division of Developmental Biology, Cincinnati Children's Research Foundation , Cincinnati , OH
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32
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Abstract
RNA polymerase II (Pol II) pausing at promoter-proximal regions is a highly regulated step in the transcription cycle. Pause release is facilitated by the P-TEFb kinase, which phosphorylates Pol II and negative elongation factors. Recent studies suggest that P-TEFb (as part of the inhibitory 7SK snRNP) is recruited to promoter-proximal regions through interaction with KAP1/TRIM28/TIF1β to facilitate 'on-site' kinase activation and transcription elongation. Here, I discuss features of this model and future challenges to further hone our understanding of transcriptional regulation including Pol II pausing and pause release.
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Affiliation(s)
- Iván D'Orso
- a Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
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33
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Chen Y, Zhou C, Ji W, Mei Z, Hu B, Zhang W, Zhang D, Wang J, Liu X, Ouyang G, Zhou J, Xiao W. ELL targets c-Myc for proteasomal degradation and suppresses tumour growth. Nat Commun 2016; 7:11057. [PMID: 27009366 PMCID: PMC4820845 DOI: 10.1038/ncomms11057] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/16/2016] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence supports that ELL (eleven-nineteen lysine-rich leukaemia) is a key regulator of transcriptional elongation, but the physiological function of Ell in mammals remains elusive. Here we show that ELL functions as an E3 ubiquitin ligase and targets c-Myc for proteasomal degradation. In addition, we identify that UbcH8 serves as a ubiquitin-conjugating enzyme in this pathway. Cysteine 595 of ELL is an active site of the enzyme; its mutation to alanine (C595A) renders the protein unable to promote the ubiquitination and degradation of c-Myc. ELL-mediated c-Myc degradation inhibits c-Myc-dependent transcriptional activity and cell proliferation, and also suppresses c-Myc-dependent xenograft tumour growth. In contrast, the ELL(C595A) mutant not only loses the ability to inhibit cell proliferation and xenograft tumour growth, but also promotes tumour metastasis. Thus, our work reveals a previously unrecognized function for ELL as an E3 ubiquitin ligase for c-Myc and a potential tumour suppressor.
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Affiliation(s)
- Yu Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Chi Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Wei Ji
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Zhichao Mei
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Bo Hu
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Wei Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Dawei Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Jing Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Xing Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Gang Ouyang
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Jiangang Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
| | - Wuhan Xiao
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072 Wuhan, China
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34
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Liang K, Woodfin AR, Slaughter BD, Unruh JR, Box AC, Rickels RA, Gao X, Haug JS, Jaspersen SL, Shilatifard A. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis. Mol Cell 2016; 60:435-45. [PMID: 26527278 DOI: 10.1016/j.molcel.2015.09.021] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/04/2015] [Accepted: 09/22/2015] [Indexed: 12/14/2022]
Abstract
Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division.
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Affiliation(s)
- Kaiwei Liang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Brian D Slaughter
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Andrew C Box
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Jeffrey S Haug
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
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35
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Tellier M, Ferrer-Vicens I, Murphy S. The point of no return: The poly(A)-associated elongation checkpoint. RNA Biol 2016; 13:265-71. [PMID: 26853452 DOI: 10.1080/15476286.2016.1142037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Cyclin-dependent kinases play critical roles in transcription by RNA polymerase II (pol II) and processing of the transcripts. For example, CDK9 regulates transcription of protein-coding genes, splicing, and 3' end formation of the transcripts. Accordingly, CDK9 inhibitors have a drastic effect on the production of mRNA in human cells. Recent analyses indicate that CDK9 regulates transcription at the early-elongation checkpoint of the vast majority of pol II-transcribed genes. Our recent discovery of an additional CDK9-regulated elongation checkpoint close to poly(A) sites adds a new layer to the control of transcription by this critical cellular kinase. This novel poly(A)-associated checkpoint has the potential to powerfully regulate gene expression just before a functional polyadenylated mRNA is produced: the point of no return. However, many questions remain to be answered before the role of this checkpoint becomes clear. Here we speculate on the possible biological significance of this novel mechanism of gene regulation and the players that may be involved.
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Affiliation(s)
- Michael Tellier
- a Sir William Dunn School of Pathology, University of Oxford , Oxford OX1 3RE , UK
| | - Ivan Ferrer-Vicens
- a Sir William Dunn School of Pathology, University of Oxford , Oxford OX1 3RE , UK
| | - Shona Murphy
- a Sir William Dunn School of Pathology, University of Oxford , Oxford OX1 3RE , UK
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36
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Gudipaty SA, D’Orso I. Functional interplay between PPM1G and the transcription elongation machinery. RNA & DISEASE 2016; 3:e1215. [PMID: 27088130 PMCID: PMC4830430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transcription elongation is a critical regulatory step in the gene expression cycle. One key regulator of the switch between transcription initiation and elongation is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) and several negative elongation factors to relieve the elongation block at paused promoters to facilitate productive elongation. Here, we highlight recent findings signifying the role of the PPM1G/PP2Cγ phosphatase in activating and maintaining the active transcription elongation state by regulating the availability of P-TEFb and blocking its assembly into the catalytic inactive 7SK small nuclear ribonucleoprotein (snRNP) complex.
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Affiliation(s)
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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37
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Gudipaty SA, McNamara RP, Morton EL, D'Orso I. PPM1G Binds 7SK RNA and Hexim1 To Block P-TEFb Assembly into the 7SK snRNP and Sustain Transcription Elongation. Mol Cell Biol 2015; 35:3810-28. [PMID: 26324325 PMCID: PMC4609742 DOI: 10.1128/mcb.00226-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/11/2015] [Accepted: 08/19/2015] [Indexed: 12/31/2022] Open
Abstract
Transcription elongation programs are vital for the precise regulation of several biological processes. One key regulator of such programs is the P-TEFb kinase, which phosphorylates RNA polymerase II (Pol II) once released from the inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex. Although mechanisms of P-TEFb release from the snRNP are becoming clearer, how P-TEFb remains in the 7SK-unbound state to sustain transcription elongation programs remains unknown. Here we report that the PPM1G phosphatase (inducibly recruited by nuclear factor κB [NF-κB] to target promoters) directly binds 7SK RNA and the kinase inhibitor Hexim1 once P-TEFb has been released from the 7SK snRNP. This dual binding activity of PPM1G blocks P-TEFb reassembly onto the snRNP to sustain NF-κB-mediated Pol II transcription in response to DNA damage. Notably, the PPM1G-7SK RNA interaction is direct, kinetically follows the recruitment of PPM1G to promoters to activate NF-κB transcription, and is reversible, since the complex disassembles before resolution of the program. Strikingly, we found that the ataxia telangiectasia mutated (ATM) kinase regulates the interaction between PPM1G and the 7SK snRNP through site-specific PPM1G phosphorylation. The precise and temporally regulated interaction of a cellular enzyme and a noncoding RNA provides a new paradigm for simultaneously controlling the activation and maintenance of inducible transcription elongation programs.
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Affiliation(s)
- Swapna Aravind Gudipaty
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ryan P McNamara
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Emily L Morton
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Iván D'Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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38
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Rosso M, Polotskaia A, Bargonetti J. Homozygous mdm2 SNP309 cancer cells with compromised transcriptional elongation at p53 target genes are sensitive to induction of p53-independent cell death. Oncotarget 2015; 6:34573-91. [PMID: 26416444 PMCID: PMC4741474 DOI: 10.18632/oncotarget.5312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/07/2015] [Indexed: 11/25/2022] Open
Abstract
A single nucleotide polymorphism (T to G) in the mdm2 P2 promoter, mdm2 SNP309, leads to MDM2 overexpression promoting chemotherapy resistant cancers. Two mdm2 G/G SNP309 cancer cell lines, MANCA and A875, have compromised wild-type p53 that co-localizes with MDM2 on chromatin. We hypothesized that MDM2 in these cells inhibited transcription initiation at the p53 target genes p21 and puma. Surprisingly, following etoposide treatment transcription initiation occurred at the compromised target genes in MANCA and A875 cells similar to the T/T ML-1 cell line. In all cell lines tested there was equally robust recruitment of total and initiated RNA polymerase II (Pol II). We found that knockdown of MDM2 in G/G cells moderately increased expression of subsets of p53 target genes without increasing p53 stability. Importantly, etoposide and actinomycin D treatments increased histone H3K36 trimethylation in T/T, but not G/G cells, suggesting a G/G correlated inhibition of transcription elongation. We therefore tested a chemotherapeutic agent (8-amino-adenosine) that induces p53-independent cell death for higher clinically relevant cytotoxicity. We demonstrated that T/T and G/G mdm2 SNP309 cells were equally sensitive to 8-amino-adenosine induced cell death. In conclusion for cancer cells overexpressing MDM2, targeting MDM2 may be less effective than inducing p53-independent cell death.
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Affiliation(s)
- Melissa Rosso
- The Department of Biological Sciences Hunter College at The Belfer Research Building and The Graduate Center Biology PhD Program, CUNY, New York, NY 10021, USA
| | - Alla Polotskaia
- The Department of Biological Sciences Hunter College at The Belfer Research Building and The Graduate Center Biology PhD Program, CUNY, New York, NY 10021, USA
| | - Jill Bargonetti
- The Department of Biological Sciences Hunter College at The Belfer Research Building and The Graduate Center Biology PhD Program, CUNY, New York, NY 10021, USA
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39
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Reeder JE, Kwak YT, McNamara RP, Forst CV, D'Orso I. HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells. eLife 2015; 4. [PMID: 26488441 PMCID: PMC4733046 DOI: 10.7554/elife.08955] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/20/2015] [Indexed: 12/22/2022] Open
Abstract
HIV encodes Tat, a small protein that facilitates viral transcription by binding an RNA structure (trans-activating RNA [TAR]) formed on nascent viral pre-messenger RNAs. Besides this well-characterized mechanism, Tat appears to modulate cellular transcription, but the target genes and molecular mechanisms remain poorly understood. We report here that Tat uses unexpected regulatory mechanisms to reprogram target immune cells to promote viral replication and rewire pathways beneficial for the virus. Tat functions through master transcriptional regulators bound at promoters and enhancers, rather than through cellular ‘TAR-like’ motifs, to both activate and repress gene sets sharing common functional annotations. Despite the complexity of transcriptional regulatory mechanisms in the cell, Tat precisely controls RNA polymerase II recruitment and pause release to fine-tune the initiation and elongation steps in target genes. We propose that a virus with a limited coding capacity has optimized its genome by evolving a small but ‘multitasking’ protein to simultaneously control viral and cellular transcription. DOI:http://dx.doi.org/10.7554/eLife.08955.001 The human immunodeficiency virus (HIV) reproduces and spreads throughout the body by hijacking human immune cells and causing them to copy the virus’s genetic information. As the virus multiplies, it also causes the death of the immune system cells that help the human body recognize and eliminate viruses. This allows the virus to multiply unchecked. Studies of the genetic material of HIV – which is in the form of single-stranded RNA molecules and contains only a handful of genes – have begun to reveal how the virus can wreak such havoc to the human immune system. A small protein encoded by the virus, called Tat, boosts the expression of HIV genes in infected immune cells by binding to a structure that forms on newly synthesized viral RNAs. Recent evidence suggests that HIV also changes the expression of human genes to make immune cells more hospitable to the virus. However, it was not known exactly which specific genes are targeted, or how the virus alters their expression. Now, Reeder, Kwak et al. reveal how the Tat protein alters the expression of more than 400 human genes. Rather than bind to the same structure seen in newly forming HIV RNAs, Tat turns on or off the expression of its human target genes by interacting with proteins that regulate human gene expression. In doing so, Tat is able to precisely control the activity of an enzyme called RNA Polymerase II that is necessary for the early steps of gene expression. Tat’s multitasking ability – boosting HIV gene expression at the same time as reprogramming human gene expression – helps explain how a virus with so little genetic material of its own can perform such a wide range of activities in infected cells. The work of Reeder, Kwak et al. suggests that Tat reshapes the human genome to position target genes in ways that allow them to be efficiently turned on or off. Future studies will further reveal how Tat accomplishes this genome remodeling during different stages of infection. In addition, further research is also necessary to look closely into the sets of genes targeted by Tat to find patterns of genes that work together to alter cell behavior, and investigate how these new behaviors allow HIV to thrive. DOI:http://dx.doi.org/10.7554/eLife.08955.002
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Affiliation(s)
- Jonathan E Reeder
- Department of Biological Sciences, University of Texas at Dallas, Richardson, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Youn-Tae Kwak
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ryan P McNamara
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Iván D'Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
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40
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Chen FX, Woodfin AR, Gardini A, Rickels RA, Marshall SA, Smith ER, Shiekhattar R, Shilatifard A. PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II. Cell 2015; 162:1003-15. [PMID: 26279188 DOI: 10.1016/j.cell.2015.07.042] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 05/16/2015] [Accepted: 07/02/2015] [Indexed: 10/25/2022]
Abstract
The control of promoter-proximal pausing and the release of RNA polymerase II (Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify that Pol-II-associated factor 1 (PAF1) possesses an evolutionarily conserved function in metazoans in the regulation of promoter-proximal pausing. Reduction in PAF1 levels leads to an increased release of paused Pol II into gene bodies at thousands of genes. PAF1 depletion results in increased nascent and mature transcripts and increased levels of phosphorylation of Pol II's C-terminal domain on serine 2 (Ser2P). These changes can be explained by the recruitment of the Ser2P kinase super elongation complex (SEC) effecting increased release of paused Pol II into productive elongation, thus establishing PAF1 as a regulator of promoter-proximal pausing by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Alessandro Gardini
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
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41
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Abstract
Transcriptional regulation of thousands of genes instructs complex morphogenetic and molecular events for heart development. Cardiac transcription factors choreograph gene expression at each stage of differentiation by interacting with cofactors, including chromatin-modifying enzymes, and by binding to a constellation of regulatory DNA elements. Here, we present salient examples relevant to cardiovascular development and heart disease, and review techniques that can sharpen our understanding of cardiovascular biology. We discuss the interplay between cardiac transcription factors, cis-regulatory elements, and chromatin as dynamic regulatory networks, to orchestrate sequential deployment of the cardiac gene expression program.
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Affiliation(s)
- Irfan S Kathiriya
- From the Gladstone Institute of Cardiovascular Disease and the Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (I.S.K., E.P.N., B.G.B.); and Department of Anesthesia and Perioperative Care (I.S.K.), Department of Pediatrics (B.G.B.), Cardiovascular Research Institute (B.G.B.), and Institute for Regeneration Medicine (B.G.B.), University of California, San Francisco.
| | - Elphège P Nora
- From the Gladstone Institute of Cardiovascular Disease and the Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (I.S.K., E.P.N., B.G.B.); and Department of Anesthesia and Perioperative Care (I.S.K.), Department of Pediatrics (B.G.B.), Cardiovascular Research Institute (B.G.B.), and Institute for Regeneration Medicine (B.G.B.), University of California, San Francisco.
| | - Benoit G Bruneau
- From the Gladstone Institute of Cardiovascular Disease and the Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (I.S.K., E.P.N., B.G.B.); and Department of Anesthesia and Perioperative Care (I.S.K.), Department of Pediatrics (B.G.B.), Cardiovascular Research Institute (B.G.B.), and Institute for Regeneration Medicine (B.G.B.), University of California, San Francisco.
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42
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Chen F, Gao X, Shilatifard A. Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide. Genes Dev 2015; 29:39-47. [PMID: 25561494 PMCID: PMC4281563 DOI: 10.1101/gad.246173.114] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genome-wide studies have demonstrated that the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved in developmental and stimulus-responsive pathways. Here, Chen et al. used the small molecule triptolide (TPL), an XPB/TFIIH inhibitor, to block transcriptional initiation and then measured Pol II occupancy by ChIP-seq. This revealed that most genes with paused Pol II show significant clearance of Pol II during the period of TPL treatment. They also identified a group of genes with unexpectedly stably paused Pol II, with unchanged Pol II occupancy during 1 h of inhibition of initiation. Transcription by RNA polymerase II (Pol II) in metazoans is regulated in several steps, including preinitiation complex (PIC) formation, initiation, Pol II escape, productive elongation, cotranscriptional RNA processing, and termination. Genome-wide studies have demonstrated that the phenomenon of promoter-bound Pol II pausing is widespread, especially for genes involved in developmental and stimulus-responsive pathways. However, a mechanistic understanding of the paused Pol II state at promoters is limited. For example, at a global level, it is unclear to what extent the engaged paused Pol II is stably tethered to the promoter or undergoes rapid cycles of initiation and termination. Here we used the small molecule triptolide (TPL), an XPB/TFIIH inhibitor, to block transcriptional initiation and then measured Pol II occupancy by chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq). This inhibition of initiation enabled us to investigate different states of paused Pol II. Specifically, our global analysis revealed that most genes with paused Pol II, as defined by a pausing index, show significant clearance of Pol II during the period of TPL treatment. Our study further identified a group of genes with unexpectedly stably paused Pol II, with unchanged Pol II occupancy even after 1 h of inhibition of initiation. This group of genes constitutes a small portion of all paused genes defined by the conventional criterion of pausing index. These findings could pave the way for evaluating the contribution of different elongation/pausing factors on different states of Pol II pausing in developmental and other stimulus-responsive pathways.
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Affiliation(s)
- Fei Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Xin Gao
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Ali Shilatifard
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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43
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7SK small nuclear RNA inhibits cancer cell proliferation through apoptosis induction. Tumour Biol 2014; 36:2809-14. [DOI: 10.1007/s13277-014-2907-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/27/2014] [Indexed: 12/20/2022] Open
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44
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Analysis of methylation microarray for tissue specific detection. Gene 2014; 553:31-41. [DOI: 10.1016/j.gene.2014.09.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/08/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
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45
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Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming. Cell Stem Cell 2014; 15:574-88. [DOI: 10.1016/j.stem.2014.09.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 08/07/2014] [Accepted: 09/26/2014] [Indexed: 02/07/2023]
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46
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Kireeva ML, Kashlev M, Burton ZF. RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression. Chem Rev 2014; 113:8325-30. [PMID: 24219496 DOI: 10.1021/cr400436m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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47
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Abstract
Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity.
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48
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Lijsebettens MV, Dürr J, Woloszynska M, Grasser KD. Elongator and SPT4/SPT5 complexes as proxy to study RNA polymerase II transcript elongation control of plant development. Proteomics 2014; 14:2109-14. [DOI: 10.1002/pmic.201400024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 02/27/2014] [Accepted: 03/27/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Mieke Van Lijsebettens
- Department of Plant Systems Biology; VIB; Ghent Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent Belgium
| | - Julius Dürr
- Department of Cell Biology and Plant Biochemistry; Biochemie-Zentrum Regensburg (BZR); University of Regensburg; Regensburg Germany
| | - Magdalena Woloszynska
- Department of Plant Systems Biology; VIB; Ghent Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent Belgium
| | - Klaus D. Grasser
- Department of Cell Biology and Plant Biochemistry; Biochemie-Zentrum Regensburg (BZR); University of Regensburg; Regensburg Germany
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49
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Dürr J, Lolas IB, Sørensen BB, Schubert V, Houben A, Melzer M, Deutzmann R, Grasser M, Grasser KD. The transcript elongation factor SPT4/SPT5 is involved in auxin-related gene expression in Arabidopsis. Nucleic Acids Res 2014; 42:4332-47. [PMID: 24497194 PMCID: PMC3985667 DOI: 10.1093/nar/gku096] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/21/2013] [Accepted: 01/09/2014] [Indexed: 11/28/2022] Open
Abstract
The heterodimeric complex SPT4/SPT5 is a transcript elongation factor (TEF) that directly interacts with RNA polymerase II (RNAPII) to regulate messenger RNA synthesis in the chromatin context. We provide biochemical evidence that in Arabidopsis, SPT4 occurs in a complex with SPT5, demonstrating that the SPT4/SPT5 complex is conserved in plants. Each subunit is encoded by two genes SPT4-1/2 and SPT5-1/2. A mutant affected in the tissue-specifically expressed SPT5-1 is viable, whereas inactivation of the generally expressed SPT5-2 is homozygous lethal. RNAi-mediated downregulation of SPT4 decreases cell proliferation and causes growth reduction and developmental defects. These plants display especially auxin signalling phenotypes. Consistently, auxin-related genes, most strikingly AUX/IAA genes, are downregulated in SPT4-RNAi plants that exhibit an enhanced auxin response. In Arabidopsis nuclei, SPT5 clearly localizes to the transcriptionally active euchromatin, and essentially co-localizes with transcribing RNAPII. Typical for TEFs, SPT5 is found over the entire transcription unit of RNAPII-transcribed genes. In SPT4-RNAi plants, elevated levels of RNAPII and SPT5 are detected within transcribed regions (including those of downregulated genes), indicating transcript elongation defects in these plants. Therefore, SPT4/SPT5 acts as a TEF in Arabidopsis, regulating transcription during the elongation stage with particular impact on the expression of certain auxin-related genes.
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Affiliation(s)
- Julius Dürr
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Ihab B. Lolas
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Brian B. Sørensen
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Veit Schubert
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Andreas Houben
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Michael Melzer
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Rainer Deutzmann
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Marion Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Klaus D. Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany and Institute for Biochemistry I, Biochemie-Zentrum Regensburg (BZR), University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Transcription factors mediate the enzymatic disassembly of promoter-bound 7SK snRNP to locally recruit P-TEFb for transcription elongation. Cell Rep 2013; 5:1256-68. [PMID: 24316072 DOI: 10.1016/j.celrep.2013.11.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/02/2013] [Accepted: 11/02/2013] [Indexed: 12/19/2022] Open
Abstract
The transition from transcription initiation into elongation is controlled by transcription factors, which recruit positive transcription elongation factor b (P-TEFb) to promoters to phosphorylate RNA polymerase II. A fraction of P-TEFb is recruited as part of the inhibitory 7SK small nuclear ribonucleoprotein particle (snRNP), which inactivates the kinase and prevents elongation. However, it is unclear how P-TEFb is captured from the promoter-bound 7SK snRNP to activate elongation. Here, we describe a mechanism by which transcription factors mediate the enzymatic release of P-TEFb from the 7SK snRNP at promoters to trigger activation in a gene-specific manner. We demonstrate that Tat recruits PPM1G/PP2Cγ to locally disassemble P-TEFb from the 7SK snRNP at the HIV promoter via dephosphorylation of the kinase T loop. Similar to Tat, nuclear factor (NF)-κB recruits PPM1G in a stimulus-dependent manner to activate elongation at inflammatory-responsive genes. Recruitment of PPM1G to promoter-assembled 7SK snRNP provides a paradigm for rapid gene activation through transcriptional pause release.
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