51
|
Luo K, Li Y, Yin Y, Li L, Wu C, Chen Y, Nowsheen S, Hu Q, Zhang L, Lou Z, Yuan J. USP49 negatively regulates tumorigenesis and chemoresistance through FKBP51-AKT signaling. EMBO J 2017; 36:1434-1446. [PMID: 28363942 DOI: 10.15252/embj.201695669] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 02/24/2017] [Accepted: 03/08/2017] [Indexed: 12/21/2022] Open
Abstract
The AKT pathway is a fundamental signaling pathway that mediates multiple cellular processes, such as cell proliferation and survival, angiogenesis, and glucose metabolism. We recently reported that the immunophilin FKBP51 is a scaffolding protein that can enhance PHLPP-AKT interaction and facilitate PHLPP-mediated dephosphorylation of AKT at Ser473, negatively regulating AKT activation. However, the regulation of FKBP51-PHLPP-AKT pathway remains unclear. Here we report that a deubiquitinase, USP49, is a new regulator of the AKT pathway. Mechanistically, USP49 deubiquitinates and stabilizes FKBP51, which in turn enhances PHLPP's capability to dephosphorylate AKT Furthermore, USP49 inhibited pancreatic cancer cell proliferation and enhanced cellular response to gemcitabine in a FKBP51-AKT-dependent manner. Clinically, decreased expression of USP49 in patients with pancreatic cancer was associated with decreased FKBP51 expression and increased AKT phosphorylation. Overall, our findings establish USP49 as a novel regulator of AKT pathway with a critical role in tumorigenesis and chemo-response in pancreatic cancer.
Collapse
Affiliation(s)
- Kuntian Luo
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yujiao Yin
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lei Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chenming Wu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Somaira Nowsheen
- Medical Scientist Training Program, Mayo Clinic School of Medicine, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, USA
| | - Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Lizhi Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China .,Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Oncology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
52
|
Chen S, Jing Y, Kang X, Yang L, Wang DL, Zhang W, Zhang L, Chen P, Chang JF, Yang XM, Sun FL. Histone H2B monoubiquitination is a critical epigenetic switch for the regulation of autophagy. Nucleic Acids Res 2017; 45:1144-1158. [PMID: 28180298 PMCID: PMC5388390 DOI: 10.1093/nar/gkw1025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 10/08/2016] [Accepted: 10/19/2016] [Indexed: 12/16/2022] Open
Abstract
Autophagy is an evolutionarily conserved cellular process that primarily participates in lysosome-mediated protein degradation. Although autophagy is a cytoplasmic event, how epigenetic pathways are involved in the regulation of autophagy remains incompletely understood. Here, we found that H2B monoubiquitination (H2Bub1) is down-regulated in cells under starvation conditions and that the decrease in H2Bub1 results in the activation of autophagy. We also identified that the deubiquitinase USP44 is responsible for the starvation-induced decrease in H2Bub1. Furthermore, the changes in H2Bub1 affect the transcription of genes involved in the regulation of autophagy. Therefore, this study reveals a novel epigenetic pathway for the regulation of autophagy through H2Bub1.
Collapse
Affiliation(s)
- Su Chen
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
- School of Forensic Sciences, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi 710061, PR China
- Department of Science and Education, People's Hospital of Zunhua, Tangshan, Hebei 064200, PR China
| | - Yuanya Jing
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Xuan Kang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Lu Yang
- Research Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiao Tong University, Shaanxi 710061, PR China
| | - Da-Liang Wang
- School of Medicine, Tsinghua University, Beijing 100084, PR China
| | - Wei Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Lei Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Ping Chen
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Jian-Feng Chang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Xiao-Mei Yang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai 200092, PR China
| |
Collapse
|
53
|
Stegeman R, Spreacker PJ, Swanson SK, Stephenson R, Florens L, Washburn MP, Weake VM. The Spliceosomal Protein SF3B5 is a Novel Component of Drosophila SAGA that Functions in Gene Expression Independent of Splicing. J Mol Biol 2016; 428:3632-49. [PMID: 27185460 PMCID: PMC5011000 DOI: 10.1016/j.jmb.2016.05.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/19/2016] [Accepted: 05/08/2016] [Indexed: 12/16/2022]
Abstract
The interaction between splicing factors and the transcriptional machinery provides an intriguing link between the coupled processes of transcription and splicing. Here, we show that the two components of the SF3B complex, SF3B3 and SF3B5, that form part of the U2 small nuclear ribonucleoprotein particle (snRNP) are also subunits of the Spt-Ada-Gcn5 acetyltransferase (SAGA) transcriptional coactivator complex in Drosophila melanogaster. Whereas SF3B3 had previously been identified as a human SAGA subunit, SF3B5 had not been identified as a component of SAGA in any species. We show that SF3B3 and SF3B5 bind to SAGA independent of RNA and interact with multiple SAGA subunits including Sgf29 and Spt7 in a yeast two-hybrid assay. Through analysis of sf3b5 mutant flies, we show that SF3B5 is necessary for proper development and cell viability but not for histone acetylation. Although SF3B5 does not appear to function in SAGA's histone-modifying activities, SF3B5 is still required for expression of a subset of SAGA-regulated genes independent of splicing. Thus, our data support an independent function of SF3B5 in SAGA's transcription coactivator activity that is separate from its role in splicing.
Collapse
Affiliation(s)
- Rachel Stegeman
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Peyton J Spreacker
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Selene K Swanson
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | - Robert Stephenson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
54
|
Pinto-Fernandez A, Kessler BM. DUBbing Cancer: Deubiquitylating Enzymes Involved in Epigenetics, DNA Damage and the Cell Cycle As Therapeutic Targets. Front Genet 2016; 7:133. [PMID: 27516771 PMCID: PMC4963401 DOI: 10.3389/fgene.2016.00133] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/12/2016] [Indexed: 12/21/2022] Open
Abstract
Controlling cell proliferation is one of the hallmarks of cancer. A number of critical checkpoints ascertain progression through the different stages of the cell cycle, which can be aborted when perturbed, for instance by errors in DNA replication and repair. These molecular checkpoints are regulated by a number of proteins that need to be present at the right time and quantity. The ubiquitin system has emerged as a central player controlling the fate and function of such molecules such as cyclins, oncogenes and components of the DNA repair machinery. In particular, proteases that cleave ubiquitin chains, referred to as deubiquitylating enzymes (DUBs), have attracted recent attention due to their accessibility to modulation by small molecules. In this review, we describe recent evidence of the critical role of DUBs in aspects of cell cycle checkpoint control, associated DNA repair mechanisms and regulation of transcription, representing pathways altered in cancer. Therefore, DUBs involved in these processes emerge as potentially critical targets for the treatment of not only hematological, but potentially also solid tumors.
Collapse
Affiliation(s)
- Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford, UK
| |
Collapse
|
55
|
Saldi T, Cortazar MA, Sheridan RM, Bentley DL. Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol 2016; 428:2623-2635. [PMID: 27107644 DOI: 10.1016/j.jmb.2016.04.017] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/27/2016] [Accepted: 04/12/2016] [Indexed: 01/07/2023]
Abstract
Pre-mRNA maturation frequently occurs at the same time and place as transcription by RNA polymerase II. The co-transcriptionality of mRNA processing has permitted the evolution of mechanisms that functionally couple transcription elongation with diverse events that occur on the nascent RNA. This review summarizes the current understanding of the relationship between transcriptional elongation through a chromatin template and co-transcriptional splicing including alternative splicing decisions that affect the expression of most human genes.
Collapse
Affiliation(s)
- Tassa Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - Michael A Cortazar
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - Ryan M Sheridan
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, P.O. Box 6511, Aurora, CO 80045, USA.
| |
Collapse
|
56
|
McClurg UL, Robson CN. Deubiquitinating enzymes as oncotargets. Oncotarget 2016; 6:9657-68. [PMID: 25962961 PMCID: PMC4496387 DOI: 10.18632/oncotarget.3922] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/08/2015] [Indexed: 12/19/2022] Open
Abstract
Carcinogenesis is a complex process tightly regulated at multiple levels by post-translational modifications. Epigenetics plays a major role in cancer development, all stable changes to the gene expression process that are not a result of a direct change in the DNA code are described as epigenetics. Epigenetic processes are regulated by post-translational modifications including ubiquitination which can directly affect either histones or transcription factors or may target their co-factors and interacting partners exerting an indirect effect. Deubiquitination of these target proteins is equally important and alterations in this pathway can also lead to cancer development, progression and metastasis. Only the correct, unaltered balance between ubiquitination and deubiquitination ensures healthy cellular homeostasis. In this review we focus on the role of deubiquitinating (DUB) enzymes in various aspects of epigenetics including the regulation of transcription factors, histone modifications, DNA damage repair pathways and cell cycle regulation. We discuss the impact of those processes on tumourigenesis and potential therapeutic applications of DUBs for cancer treatment.
Collapse
Affiliation(s)
- Urszula L McClurg
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Craig N Robson
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
57
|
Lim KH, Song MH, Baek KH. Decision for cell fate: deubiquitinating enzymes in cell cycle checkpoint. Cell Mol Life Sci 2016; 73:1439-55. [PMID: 26762302 PMCID: PMC11108577 DOI: 10.1007/s00018-015-2129-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 12/03/2015] [Accepted: 12/30/2015] [Indexed: 09/29/2022]
Abstract
All organs consisting of single cells are consistently maintaining homeostasis in response to stimuli such as free oxygen, DNA damage, inflammation, and microorganisms. The cell cycle of all mammalian cells is regulated by protein expression in the right phase to respond to proliferation and apoptosis signals. Post-translational modifications (PTMs) of proteins by several protein-editing enzymes are associated with cell cycle regulation by their enzymatic functions. Ubiquitination, one of the PTMs, is also strongly related to cell cycle regulation by protein degradation or signal transduction. The importance of deubiquitinating enzymes (DUBs), which have a reversible function for ubiquitination, has recently suggested that the function of DUBs is also important for determining the fate of proteins during cell cycle processing. This article reviews and summarizes the diverse roles of DUBs, including DNA damage, cell cycle processing, and regulation of histone proteins, and also suggests the possibility for therapeutic targets.
Collapse
Affiliation(s)
- Key-Hwan Lim
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 463-400, Republic of Korea
| | - Myoung-Hyun Song
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 463-400, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 463-400, Republic of Korea.
| |
Collapse
|
58
|
Li Z, Jiang D, Fu X, Luo X, Liu R, He Y. Coupling of histone methylation and RNA processing by the nuclear mRNA cap-binding complex. NATURE PLANTS 2016; 2:16015. [PMID: 27249350 DOI: 10.1038/nplants.2016.15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 01/14/2016] [Indexed: 05/08/2023]
Abstract
In eukaryotes, genes are transcribed into pre-mRNAs that are subsequently processed into mature mRNAs by adding a 5'-cap and a 3'-polyA tail and splicing introns. Pre-mRNA processing involves their binding proteins and processing factors, whereas gene transcription often involves chromatin modifiers. It has been unclear how the factors involved in chromatin modifications and RNA processing function in concert to control mRNA production. Here, we show that in Arabidopsis thaliana, the evolutionarily conserved nuclear mRNA cap-binding complex (CBC) forms multi-protein complexes with a conserved histone 3 lysine 4 (H3K4) methyltransferase complex called COMPASS-like and a histone 3 lysine 36 (H3K36) methyltransferase to integrate active histone methylations with co-transcriptional mRNA processing and cap preservation, leading to a high level of mature mRNA production. We further show that CBC is required for H3K4 and H3K36 trimethylation, and the histone methyltransferases are required for CBC-mediated mRNA cap preservation and efficient pre-mRNA splicing at their target loci, suggesting that these factors are functionally interdependent. Our study reveals novel roles for histone methyltransferases in RNA-processing-related events and provides mechanistic insights into how the 'downstream' RNA CBC controls eukaryotic gene transcription.
Collapse
Affiliation(s)
- Zicong Li
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543 Singapore, Singapore
| | - Danhua Jiang
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543 Singapore, Singapore
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Xiao Luo
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yuehui He
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543 Singapore, Singapore
| |
Collapse
|
59
|
Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
Collapse
Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
| | | | | | | |
Collapse
|
60
|
Amlie-Wolf A, Ryvkin P, Tong R, Dragomir I, Suh E, Xu Y, Van Deerlin VM, Gregory BD, Kwong LK, Trojanowski JQ, Lee VMY, Wang LS, Lee EB. Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin. PLoS One 2015; 10:e0141836. [PMID: 26510133 PMCID: PMC4624943 DOI: 10.1371/journal.pone.0141836] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/13/2015] [Indexed: 12/13/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is normally a nuclear RNA-binding protein that exhibits a range of functions including regulation of alternative splicing, RNA trafficking, and RNA stability. However, in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), TDP-43 is abnormally phosphorylated, ubiquitinated, and cleaved, and is mislocalized to the cytoplasm where it forms distinctive aggregates. We previously developed a mouse model expressing human TDP-43 with a mutation in its nuclear localization signal (ΔNLS-hTDP-43) so that the protein preferentially localizes to the cytoplasm. These mice did not exhibit a significant number of cytoplasmic aggregates, but did display dramatic changes in gene expression as measured by microarray, suggesting that cytoplasmic TDP-43 may be associated with a toxic gain-of-function. Here, we analyze new RNA-sequencing data from the ΔNLS-hTDP-43 mouse model, together with published RNA-sequencing data obtained previously from TDP-43 antisense oligonucleotide (ASO) knockdown mice to investigate further the dysregulation of gene expression in the ΔNLS model. This analysis reveals that the transcriptomic effects of the overexpression of the ΔNLS-hTDP-43 transgene are likely due to a gain of cytoplasmic function. Moreover, cytoplasmic TDP-43 expression alters transcripts that regulate chromatin assembly, the nucleolus, lysosomal function, and histone 3' untranslated region (UTR) processing. These transcriptomic alterations correlate with observed histologic abnormalities in heterochromatin structure and nuclear size in transgenic mouse and human brains.
Collapse
Affiliation(s)
- Alexandre Amlie-Wolf
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Paul Ryvkin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Rui Tong
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Isabelle Dragomir
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States of America
| | - EunRan Suh
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Yan Xu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Vivianna M. Van Deerlin
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Brian D. Gregory
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Linda K. Kwong
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - John Q. Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Virginia M.-Y. Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Edward B. Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- * E-mail:
| |
Collapse
|
61
|
Yao X, Tang Z, Fu X, Yin J, Liang Y, Li C, Li H, Tian Q, Roeder RG, Wang G. The Mediator subunit MED23 couples H2B mono-ubiquitination to transcriptional control and cell fate determination. EMBO J 2015; 34:2885-902. [PMID: 26330467 DOI: 10.15252/embj.201591279] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/10/2015] [Indexed: 01/18/2023] Open
Abstract
The Mediator complex orchestrates multiple transcription factors with the Pol II apparatus for precise transcriptional control. However, its interplay with the surrounding chromatin remains poorly understood. Here, we analyze differential histone modifications between WT and MED23(-/-) (KO) cells and identify H2B mono-ubiquitination at lysine 120 (H2Bub) as a MED23-dependent histone modification. Using tandem affinity purification and mass spectrometry, we find that MED23 associates with the RNF20/40 complex, the enzyme for H2Bub, and show that this association is critical for the recruitment of RNF20/40 to chromatin. In a cell-free system, Mediator directly and substantially increases H2Bub on recombinant chromatin through its cooperation with RNF20/40 and the PAF complex. Integrative genome-wide analyses show that MED23 depletion specifically reduces H2Bub on a subset of MED23-controlled genes. Importantly, MED23-coupled H2Bub levels are oppositely regulated during myogenesis and lung carcinogenesis. In sum, these results establish a mechanistic link between the Mediator complex and a critical chromatin modification in coordinating transcription with cell growth and differentiation.
Collapse
Affiliation(s)
- Xiao Yao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Zhanyun Tang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Xing Fu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Jingwen Yin
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Yan Liang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Chonghui Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Huayun Li
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Qing Tian
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Gang Wang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
62
|
Kumar P, Magala P, Geiger-Schuller KR, Majumdar A, Tolman JR, Wolberger C. Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity. Nucleic Acids Res 2015; 43:9039-50. [PMID: 26286193 PMCID: PMC4605308 DOI: 10.1093/nar/gkv845] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 08/07/2015] [Indexed: 11/15/2022] Open
Abstract
Rad6 is a yeast E2 ubiquitin conjugating enzyme that monoubiquitinates histone H2B in conjunction with the E3, Bre1, but can non-specifically modify histones on its own. We determined the crystal structure of a Rad6∼Ub thioester mimic, which revealed a network of interactions in the crystal in which the ubiquitin in one conjugate contacts Rad6 in another. The region of Rad6 contacted is located on the distal face of Rad6 opposite the active site, but differs from the canonical E2 backside that mediates free ubiquitin binding and polyubiquitination activity in other E2 enzymes. We find that free ubiquitin interacts weakly with both non-canonical and canonical backside residues of Rad6 and that mutations of non-canonical residues have deleterious effects on Rad6 activity comparable to those observed to mutations in the canonical E2 backside. The effect of non-canonical backside mutations is similar in the presence and absence of Bre1, indicating that contacts with non-canonical backside residues govern the intrinsic activity of Rad6. Our findings shed light on the determinants of intrinsic Rad6 activity and reveal new ways in which contacts with an E2 backside can regulate ubiquitin conjugating activity.
Collapse
Affiliation(s)
- Pankaj Kumar
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Pearl Magala
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Kathryn R Geiger-Schuller
- Department of Biophysics, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Ananya Majumdar
- Biomolecular NMR Center, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Joel R Tolman
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| |
Collapse
|
63
|
Wang P, Peng C, Liu X, Liu H, Chen Y, Zheng L, Han B, Pei H. OGT mediated histone H2B S112 GlcNAcylation regulates DNA damage response. J Genet Genomics 2015; 42:467-75. [PMID: 26408091 DOI: 10.1016/j.jgg.2015.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/01/2015] [Accepted: 07/14/2015] [Indexed: 01/18/2023]
Abstract
O-GlcNAcylation is an important post-translational modification and has been implicated in many fundamental cellular processes. Recent studies showed that O-linked N-acetylglucosamine (GlcNAc) transferase (OGT) mediated O-GlcNAcylation of histone H2B Ser 112 (H2B S112 GlcNAcylation) plays an important role in gene transcription. However, the role of this histone modification in DNA damage response has not been studied yet. In this study, we found that OGT and OGT mediated H2B S112 GlcNAcylation are involved in DNA damage response for maintaining genomic stability and are required for resistance to many DNA-damaging and replication stress-inducing agents. OGT mediated H2B S112 GlcNAcylation increased locally upon the induction of double-strand breaks (DSBs), and depletion of OGT or overexpression of H2B S112A mutant impaired homologous recombination (HR) and nonhomologous end-joining (NHEJ). Mechanistically, H2B S112 GlcNAcylation could bind Nijmegen breakage syndrome 1 (NBS1) and regulate NBS1 foci formation. Taken together, our results demonstrate a new function of histone O-GlcNAcylation in DNA damage response (DDR).
Collapse
Affiliation(s)
- Panfei Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China; School of Nursing and Medical Technology, Jianghan University, Wuhan 430056, China
| | - Changmin Peng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China; School of Nursing and Medical Technology, Jianghan University, Wuhan 430056, China
| | - Xia Liu
- Department of Radiotherapy, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, China; School of Nursing and Medical Technology, Jianghan University, Wuhan 430056, China
| | - Hailong Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yali Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Li Zheng
- School of Nursing and Medical Technology, Jianghan University, Wuhan 430056, China
| | - Baolin Han
- Department of Radiotherapy, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, China.
| | - Huadong Pei
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| |
Collapse
|
64
|
Kato A, Komatsu K. RNF20-SNF2H Pathway of Chromatin Relaxation in DNA Double-Strand Break Repair. Genes (Basel) 2015; 6:592-606. [PMID: 26184323 PMCID: PMC4584319 DOI: 10.3390/genes6030592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/25/2023] Open
Abstract
Rapid progress in the study on the association of histone modifications with chromatin remodeling factors has broadened our understanding of chromatin dynamics in DNA transactions. In DNA double-strand break (DSB) repair, the well-known mark of histones is the phosphorylation of the H2A variant, H2AX, which has been used as a surrogate marker of DSBs. The ubiquitylation of histone H2B by RNF20 E3 ligase was recently found to be a DNA damage-induced histone modification. This modification is required for DSB repair and regulated by a distinctive pathway from that of histone H2AX phosphorylation. Moreover, the connection between H2B ubiquitylation and the chromatin remodeling activity of SNF2H has been elucidated. In this review, we summarize the current knowledge of RNF20-mediated processes and the molecular link to H2AX-mediated processes during DSB repair.
Collapse
Affiliation(s)
- Akihiro Kato
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida-konoecho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kenshi Komatsu
- Division of Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida-konoecho, Sakyo-ku, Kyoto 606-8501, Japan.
| |
Collapse
|
65
|
Sen R, Bhaumik SR. Transcriptional stimulatory and repressive functions of histone H2B ubiquitin ligase. Transcription 2015; 4:221-6. [PMID: 24135701 DOI: 10.4161/trns.26623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
66
|
Abstract
Ubiquitination has traditionally been viewed in the context of polyubiquitination that is essential for marking proteins for degradation via the proteasome. Recent discoveries have shed light on key cellular roles for monoubiquitination, including as a post-translational modification (PTM) of histones such as histone H2B. Monoubiquitination plays a significant role as one of the largest histone PTMs, alongside smaller, better-studied modifications such as methylation, acetylation and phosphorylation. Monoubiquitination of histone H2B at lysine 120 (H2Bub1) has been shown to have key roles in transcription, the DNA damage response and stem cell differentiation. The H2Bub1 enzymatic cascade involves E3 RING finger ubiquitin ligases, with the main E3 generally accepted to be the RNF20-RNF40 complex, and deubiquitinases including ubiquitin-specific protease 7 (USP7), USP22 and USP44. H2Bub1 has been shown to physically disrupt chromatin strands, fostering a more open chromatin structure accessible to transcription factors and DNA repair proteins. It also acts as a recruiting signal, actively attracting proteins with roles in transcription and DNA damage. H2Bub1 also appears to play central roles in histone cross-talk, influencing methylation events on histone H3, including H3K4 and H3K79. Most significantly, global levels of H2Bub1 are low to absent in advanced cancers including breast, colorectal, lung and parathyroid, marking H2Bub1 and the enzymes that regulate it as key molecules of interest as possible new therapeutic targets for the treatment of cancer. This review offers an overview of current knowledge regarding H2Bub1 and highlights links between dysregulation of H2Bub1-associated enzymes, stem cells and malignancy.
Collapse
Affiliation(s)
- Alexander J Cole
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Roderick Clifton-Bligh
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Deborah J Marsh
- Hormones and Cancer GroupKolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney, New South Wales 2065, Australia
| |
Collapse
|
67
|
Joo HY, Dai Q, Jones AE, Zhai L, Wang H. In vitro and in vivo assays for studying histone ubiquitination and deubiquitination. Methods Mol Biol 2015; 1288:213-30. [PMID: 25827882 DOI: 10.1007/978-1-4939-2474-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Posttranslational histone modifications play important roles in regulating chromatin structure and function (Rando, Curr Opin Genet Dev 22:148-155, 2012; Zentner and Henikoff, Nat Struct Mol Biol 20:259-266, 2013). One example of such modifications is histone ubiquitination, which occurs predominately on H2A and H2B. Recent studies have highlighted important regulatory roles of H2A ubiquitination in Polycomb group protein-mediated gene silencing and DNA damage repair (de Napoles et al., Dev Cell 7:663-676, 2004; Wang et al., Nature 431:873-878, 2004; Doil et al., Cell 136:435-446, 2009; Gatti et al., Cell Cycle 11:2538-2544, 2012; Mattiroli et al., Cell 150:1182-1195, 2012; Stewart et al., Cell 136:420-434, 2009; Bergink et al., Genes Dev 20:1343-1352, 2006; Facchino et al., J Neurosci 30:10096-10111, 2010; Ginjala et al., Mol Cell Biol 31:1972-1982, 2011; Ismail et al., J Cell Biol 191:45-60, 2010), H2B ubiquitination in transcription initiation and elongation (Xiao et al., Mol Cell Biol 25:637-651, 2005; Kao et al., Genes Dev 18:184-195, 2004; Pavri et al., Cell 125:703-717, 2006; Kim et al., Cell 137:459-471, 2009), pre-mRNA splicing (Jung et al. Genome Res 22:1026-1035, 2012; Shieh et al., BMC Genomics 12:627, 2011; Zhang et al., Genes Dev 27:1581-1595, 2013), nucleosome stabilities (Fleming et al., Mol Cell 31:57-66, 2008; Chandrasekharan et al., Proc Natl Acad Sci U S A 106:16686-16691, 2009), H3 methylation (Sun and Allis, Nature 418:104-108, 2002; Briggs et al., Nature 418:498, 2002; Dover et al., J Biol Chem 277:28368-28371, 2002; Ng et al., J Biol Chem 277:34655-34657, 2002), and DNA methylation (Sridhar et al., Nature 447:735-738, 2007). Here we describe methods for in vitro histone ubiquitination and deubiquitination assays. We also describe approaches to investigate the in vivo function of putative histone ubiquitin ligase(s) and deubiquitinase(s). These experimental procedures are largely based on our studies in mammalian cells. These methods should provide useful tools for studying this bulky histone modification.
Collapse
Affiliation(s)
- Heui-Yun Joo
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Kaul Human Genetics Building 402A, 720 20th Street South, Birmingham, 35294, AL, USA
| | | | | | | | | |
Collapse
|
68
|
Huang Y, Yao X, Wang G. 'Mediator-ing' messenger RNA processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:257-69. [PMID: 25515410 DOI: 10.1002/wrna.1273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/29/2014] [Accepted: 10/17/2014] [Indexed: 12/27/2022]
Abstract
Pre-messenger RNA (mRNA) processing, generally including capping, mRNA splicing, and cleavage-polyadenylation, is physically and functionally associated with transcription. The reciprocal coupling between transcription and mRNA processing ensures the efficient and regulated gene expression and editing. Multiple transcription factors/cofactors and mRNA processing factors are involved in the coupling process. This review focuses on several classic examples and recent advances that enlarge our understanding of how the transcriptional factors or cofactors, especially the Mediator complex, contribute to the RNA Pol II elongation, mRNA splicing, and polyadenylation.
Collapse
Affiliation(s)
- Yan Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | | |
Collapse
|
69
|
Sako-Kubota K, Tanaka N, Nagae S, Meng W, Takeichi M. Minus end-directed motor KIFC3 suppresses E-cadherin degradation by recruiting USP47 to adherens junctions. Mol Biol Cell 2014; 25:3851-60. [PMID: 25253721 PMCID: PMC4244195 DOI: 10.1091/mbc.e14-07-1245] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
KIFC3, a minus end–directed kinesin motor, recruits the ubiquitin-specific protease USP47, a protease that removes ubiquitin chains from substrates, to epithelial adherens junctions. This process suppresses the ubiquitination and resultant degradation of E-cadherin, thereby maintaining stable cell–cell adhesion in epithelial sheets. The adherens junction (AJ) plays a crucial role in maintaining cell–cell adhesion in epithelial tissues. Previous studies show that KIFC3, a minus end–directed kinesin motor, moves into AJs via microtubules that grow from clusters of CAMSAP3 (also known as Nezha), a protein that binds microtubule minus ends. The function of junction-associated KIFC3, however, remains to be elucidated. Here we find that KIFC3 binds the ubiquitin-specific protease USP47, a protease that removes ubiquitin chains from substrates and hence inhibits proteasome-mediated proteolysis, and recruits it to AJs. Depletion of KIFC3 or USP47 promotes cleavage of E-cadherin at a juxtamembrane region of the cytoplasmic domain, resulting in the production of a 90-kDa fragment and the internalization of E-cadherin. This cleavage depends on the E3 ubiquitin protein ligase Hakai and is inhibited by proteasome inhibitors. E-cadherin ubiquitination consistently increases after depletion of KIFC3 or USP47. These findings suggest that KIFC3 suppresses the ubiquitination and resultant degradation of E-cadherin by recruiting USP47 to AJs, a process that may be involved in maintaining stable cell–cell adhesion in epithelial sheets.
Collapse
Affiliation(s)
| | | | - Shigenori Nagae
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Wenxiang Meng
- RIKEN Center for Developmental Biology, Kobe 650-0047, Japan State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | | |
Collapse
|
70
|
Balamurugan K, Bombardi R, Duncan G, McCord B. Identification of spermatozoa by tissue-specific differential DNA methylation using bisulfite modification and pyrosequencing. Electrophoresis 2014; 35:3079-86. [DOI: 10.1002/elps.201400175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/15/2014] [Accepted: 05/15/2014] [Indexed: 11/12/2022]
Affiliation(s)
| | - Robin Bombardi
- School of Criminal Justice; The University of Southern Mississippi; Hattiesburg MS USA
| | - George Duncan
- DNA Unit; Broward County Sheriff's Office; Fort Lauderdale FL USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| |
Collapse
|
71
|
Fuchs G, Hollander D, Voichek Y, Ast G, Oren M. Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate. Genome Res 2014; 24:1572-83. [PMID: 25049226 PMCID: PMC4199367 DOI: 10.1101/gr.176487.114] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Various histone modifications decorate nucleosomes within transcribed genes. Among these, monoubiquitylation of histone H2B (H2Bub1) and methylation of histone H3 on lysines 36 (H3K36me2/3) and 79 (H3K79me2/3) correlate positively with gene expression. By measuring the progression of the transcriptional machinery along genes within live cells, we now report that H2B monoubiquitylation occurs cotranscriptionally and accurately reflects the advance of RNA polymerase II (Pol II). In contrast, H3K36me3 and H3K79me2 are less dynamic and represent Pol II movement less faithfully. High-resolution ChIP-seq reveals that H2Bub1 levels are selectively reduced at exons and decrease in an exon-dependent stepwise manner toward the 3' end of genes. Exonic depletion of H2Bub1 in gene bodies is highly correlated with Pol II pausing at exons, suggesting elongation rate changes associated with intron-exon structure. In support of this notion, H2Bub1 levels were found to be significantly correlated with transcription elongation rates measured in various cell lines. Overall, our data shed light on the organization of H2Bub1 within transcribed genes and single out H2Bub1 as a reliable marker for ongoing transcription elongation.
Collapse
Affiliation(s)
- Gilad Fuchs
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dror Hollander
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel;
| |
Collapse
|
72
|
Yoshikawa Y, Sato A, Tsujimura T, Otsuki T, Fukuoka K, Hasegawa S, Nakano T, Hashimoto-Tamaoki T. Biallelic germline and somatic mutations in malignant mesothelioma: multiple mutations in transcription regulators including mSWI/SNF genes. Int J Cancer 2014; 136:560-71. [PMID: 24916674 DOI: 10.1002/ijc.29015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 04/22/2014] [Accepted: 05/26/2014] [Indexed: 12/22/2022]
Abstract
We detected low levels of acetylation for histone H3 tail lysines in malignant mesothelioma (MM) cell lines resistant to histone deacetylase inhibitors. To identify the possible genetic causes related to the low histone acetylation levels, whole-exome sequencing was conducted with MM cell lines established from eight patients. A mono-allelic variant of BRD1 was common to two MM cell lines with very low acetylation levels. We identified 318 homozygous protein-damaging variants/mutations (18-78 variants/mutations per patient); annotation analysis showed enrichment of the molecules associated with mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes and co-activators that facilitate initiation of transcription. In seven of the patients, we detected a combination of variants in histone modifiers or transcription factors/co-factors, in addition to variants in mSWI/SNF. Direct sequencing showed that homozygous mutations in SMARCA4, PBRM1 and ARID2 were somatic. In one patient, homozygous germline variants were observed for SMARCC1 and SETD2 in chr3p22.1-3p14.2. These exhibited extended germline homozygosity and were in regions containing somatic mutations, leading to a loss of BAP1 and PBRM1 expression in MM cell line. Most protein-damaging variants were heterozygous in normal tissues. Heterozygous germline variants were often converted into hemizygous variants by mono-allelic deletion, and were rarely homozygous because of acquired uniparental disomy. Our findings imply that MM might develop through the somatic inactivation of mSWI/SNF complex subunits and/or histone modifiers, including BAP1, in subjects that have rare germline variants of these transcription regulators and/or transcription factors/co-factors, and in regions prone to mono-allelic deletion during oncogenesis.
Collapse
Affiliation(s)
- Yoshie Yoshikawa
- Department of Genetics, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | | | | | | | | | | | | | | |
Collapse
|
73
|
Moehle EA, Braberg H, Krogan NJ, Guthrie C. Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate. RNA Biol 2014; 11:313-9. [PMID: 24717535 PMCID: PMC4075515 DOI: 10.4161/rna.28646] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Control of pre-mRNA splicing is a critical part of the eukaryotic gene expression process. Extensive evidence indicates that transcription and splicing are spatiotemporally coordinated and that most splicing events occur co-transcriptionally. A kinetic coupling model has been proposed in metazoans to describe how changing RNA Polymerase II (RNAPII) elongation rate can impact which alternative splice sites are used. In Saccharomyces cerevisiae, in which most spliced genes have only a single intron and splice sites adhere to a strong consensus sequence, we recently observed that splicing efficiency was sensitive to mutations in RNAPII that increase or decrease its elongation rate. Our data revealed that RNAPII speed and splicing efficiency are generally anti-correlated: at many genes, increased elongation rate caused decreased splicing efficiency, while decreased elongation rate increased splicing efficiency. An improved splicing phenotype was also observed upon deletion of SUB1, a condition in which elongation rate is slowed. We discuss these data in the context of a growing field and expand the kinetic coupling model to apply to both alternative splicing and splicing efficiency.
Collapse
Affiliation(s)
- Erica A Moehle
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA; California Institute for Quantitative Biosciences; QB3; San Francisco, CA USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA; California Institute for Quantitative Biosciences; QB3; San Francisco, CA USA; J. David Gladstone Institutes; San Francisco, CA USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics; University of California; San Francisco, CA USA
| |
Collapse
|
74
|
Xu Q, Yang C, Du Y, Chen Y, Liu H, Deng M, Zhang H, Zhang L, Liu T, Liu Q, Wang L, Lou Z, Pei H. AMPK regulates histone H2B O-GlcNAcylation. Nucleic Acids Res 2014; 42:5594-604. [PMID: 24692660 PMCID: PMC4027166 DOI: 10.1093/nar/gku236] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Histone H2B O-GlcNAcylation is an important post-translational modification of chromatin during gene transcription. However, how this epigenetic modification is regulated remains unclear. Here we found that the energy-sensing adenosine-monophosphate-activated protein kinase (AMPK) could suppress histone H2B O-GlcNAcylation. AMPK directly phosphorylates O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT). Although this phosphorylation does not regulate the enzymatic activity of OGT, it inhibits OGT-chromatin association, histone O-GlcNAcylation and gene transcription. Conversely, OGT also O-GlcNAcylates AMPK and positively regulates AMPK activity, creating a feedback loop. Taken together, these results reveal a crosstalk between the LKB1-AMPK and the hexosamine biosynthesis (HBP)-OGT pathways, which coordinate together for the sensing of nutrient state and regulation of gene transcription.
Collapse
Affiliation(s)
- Qiuran Xu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Caihong Yang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Du
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yali Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hailong Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Min Deng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Haoxing Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Lei Zhang
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Tongzheng Liu
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Qingguang Liu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Liewei Wang
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Huadong Pei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| |
Collapse
|
75
|
Vitting-Seerup K, Porse BT, Sandelin A, Waage J. spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 2014; 15:81. [PMID: 24655717 PMCID: PMC3998036 DOI: 10.1186/1471-2105-15-81] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/17/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing and prediction of coding potential. RESULTS spliceR uses the full-length transcript output from RNA-seq assemblers to detect single or multiple exon skipping, alternative donor and acceptor sites, intron retention, alternative first or last exon usage, and mutually exclusive exon events. For each of these events spliceR also annotates the genomic coordinates of the differentially spliced elements, facilitating downstream sequence analysis. For each transcript isoform fraction values are calculated to identify transcript switching between conditions. Lastly, spliceR predicts the coding potential, as well as the potential nonsense mediated decay (NMD) sensitivity of each transcript. CONCLUSIONS spliceR is an easy-to-use tool that extends the usability of RNA-seq and assembly technologies by allowing greater depth of annotation of RNA-seq data. spliceR is implemented as an R package and is freely available from the Bioconductor repository ( http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html).
Collapse
Affiliation(s)
| | | | - Albin Sandelin
- Department of Biology, The Bioinformatics Centre, University of Copenhagen, Ole Maaloes Vej 5, Copenhagen, DK2200, Denmark.
| | | |
Collapse
|
76
|
Hérissant L, Moehle EA, Bertaccini D, Van Dorsselaer A, Schaeffer-Reiss C, Guthrie C, Dargemont C. H2B ubiquitylation modulates spliceosome assembly and function in budding yeast. Biol Cell 2014; 106:126-38. [PMID: 24476359 DOI: 10.1111/boc.201400003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND INFORMATION Commitment to splicing occurs co-transcriptionally, but a major unanswered question is the extent to which various modifications of chromatin, the template for transcription in vivo, contribute to the regulation of splicing. RESULTS Here, we perform genome-wide analyses showing that inhibition of specific marks - H2B ubiquitylation, H3K4 methylation and H3K36 methylation - perturbs splicing in budding yeast, with each modification exerting gene-specific effects. Furthermore, semi-quantitative mass spectrometry on purified nuclear mRNPs and chromatin immunoprecipitation analysis on intron-containing genes indicated that H2B ubiquitylation, but not Set1-, Set2- or Dot1-dependent H3 methylation, stimulates recruitment of the early splicing factors, namely U1 and U2 snRNPs, onto nascent RNAs. CONCLUSIONS These results suggest that histone modifications impact splicing of distinct subsets of genes using distinct pathways.
Collapse
Affiliation(s)
- Lucas Hérissant
- Pathologie Cellulaire, University Paris Diderot, Sorbonne Paris Cité, INSERM U944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, Hôpital Saint Louis, Paris, Cedex 10, France
| | | | | | | | | | | | | |
Collapse
|
77
|
Long L, Thelen JP, Furgason M, Haj-Yahya M, Brik A, Cheng D, Peng J, Yao T. The U4/U6 recycling factor SART3 has histone chaperone activity and associates with USP15 to regulate H2B deubiquitination. J Biol Chem 2014; 289:8916-30. [PMID: 24526689 DOI: 10.1074/jbc.m114.551754] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications of histone proteins produce dynamic signals that regulate the structure and function of chromatin. Mono-ubiquitination of H2B in the histone tail (at Lys-123 in yeast or Lys-120 in humans) is a conserved modification that has been implicated in the regulation of transcription, replication, and DNA repair processes. In a search for direct effectors of ubH2B, we identified a deubiquitinating enzyme, Usp15, through affinity purification with a nonhydrolyzable ubH2B mimic. In the nucleus, Usp15 indirectly associates with the ubH2B E3 ligase, RNF20/RNF40, and directly associates with a component of the splicing machinery, SART3 (also known as TIP110 or p110). These physical interactions place Usp15 in the vicinity of actively transcribed DNA. Importantly we found that SART3 has previously unrecognized histone chaperone activities. SART3, but not the well-characterized histone chaperone Nap1, enhances Usp15 binding to ubH2B and facilitates deubiquitination of ubH2B in free histones but not in nucleosomes. These results suggest that SART3 recruits ubH2B, which may be evicted from DNA during transcription, for deubiquitination by Usp15. In light of the function played by SART3 in U4/U6 di-snRNP formation, our discovery points to a direct link between eviction-coupled erasure of the ubiquitin mark from ubH2B and co-transcriptional pre-mRNA splicing.
Collapse
Affiliation(s)
- Lindsey Long
- From the Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | | | | | | | | | | | | | | |
Collapse
|
78
|
Fuchs G, Oren M. Writing and reading H2B monoubiquitylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:694-701. [PMID: 24412854 DOI: 10.1016/j.bbagrm.2014.01.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/01/2014] [Accepted: 01/02/2014] [Indexed: 01/27/2023]
Abstract
Monoubiquitylation of histone H2B (H2Bub1), catalyzed by the heterodimeric ubiquitin ligase complex RNF20/40, regulates multiple molecular and biological processes. The addition of a large ubiquitin moiety to the small H2B is believed to change the biochemical features of the chromatin. H2B monoubiquitylation alters nucleosome stability, nucleosome reassembly and higher order compaction of the chromatin. While these effects explain some of the direct roles of H2Bub1, there is growing evidence that H2Bub1 can also regulate multiple DNA-templated processes indirectly, by recruitment of specific factors ("readers") to the chromatin. H2Bub1 readers mediate much of the effect of H2Bub1 on histone crosstalk, transcriptional outcome and probably other chromatin-related activities. Here we summarize the current knowledge about H2Bub1-specific readers and their role in various biological processes. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
Collapse
Affiliation(s)
- Gilad Fuchs
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
79
|
Wang ZJ, Yang JL, Wang YP, Lou JY, Chen J, Liu C, Guo LD. Decreased histone H2B monoubiquitination in malignant gastric carcinoma. World J Gastroenterol 2013; 19:8099-8107. [PMID: 24307806 PMCID: PMC3848160 DOI: 10.3748/wjg.v19.i44.8099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 09/23/2013] [Accepted: 10/22/2013] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate H2B monoubiquitination (uH2B) and H3K4 di- and tri-methylation (H3K4-2me, H3K4-3me) levels and their clinical significance in gastric cancer (GC).
METHODS: Immunohistochemistry (IGC) was used to detect the differential levels of uH2B, H3K4-2me and H3K4-3me modifications in GC specimens from chemo/radiotherapy-naïve patients who underwent potentially curative surgical resection (n = 159) and in a random sampling of non-tumor gastric epithelium specimens (normal controls, n = 20). The immunohistochemistry (IHC)-detected modifications were classified as negative, low-level, or high-level using a dual-rated (staining intensity and percentage of positively-stained cells) semi-quantitative method. The relationships between uH2B modification levels and clinicopathological parameters of GC were assessed by a Wilcoxon rank sum test (pairwise comparisons) and the Kruskal-Wallis H test (multiple comparisons). The correlation between uH2B modification and survival was estimated by Kaplan-Meier analysis, and the role of uH2B as an independent prognostic factor for survival was assessed by multivariate Cox regression analysis.
RESULTS: The presence and level of H3K4-2me and H3K4-3me IHC staining was similar between the normal controls and GC specimens. In contrast, the level of uH2B was significantly lower in the malignant gastric tissues (vs normal control tissues) and decreased along with increases in dedifferentiation (well differentiated > moderately differentiated > poorly differentiated). The level of uH2B correlated with tumor differentiation (P < 0.001), Lauren’s diffuse- and intestinal-type classification (P < 0.001), lymph node metastasis (P = 0.049) and tumor-node-metastasis stage (P = 0.005). Patients with uH2B+ staining had higher 5-year survival rates than patients with uH2B-staining (52.692 ± 2.452 vs 23.739 ± 5.207, P < 0.001). The uH2B level was an independent prognostic factor for cancer-specific survival (95%CI: 0.237-0.677, P = 0.001).
CONCLUSION: uH2B displays differential IHC staining patterns corresponding to progressive stages of GC. uH2B may contribute to tumorigenesis and could be a potential therapeutic target.
Collapse
|