1
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Walker RL, Hornicek FJ, Duan Z. Transcriptional regulation and therapeutic potential of cyclin-dependent kinase 9 (CDK9) in sarcoma. Biochem Pharmacol 2024; 226:116342. [PMID: 38848777 DOI: 10.1016/j.bcp.2024.116342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Sarcomas include various subtypes comprising two significant groups - soft tissue and bone sarcomas. Although the survival rate for some sarcoma subtypes has improved over time, the current methods of treatment remain efficaciously limited, as recurrent, and metastatic diseases remain a major obstacle. There is a need for better options and therapeutic strategies in treating sarcoma. Cyclin dependent kinase 9 (CDK9) is a transcriptional kinase and has emerged as a promising target for treating various cancers. The aberrant expression and activation of CDK9 have been observed in several sarcoma subtypes, including rhabdomyosarcoma, synovial sarcoma, osteosarcoma, Ewing sarcoma, and chordoma. Enhanced CDK9 expression has also been correlated with poorer prognosis in sarcoma patients. As a master regulator of transcription, CDK9 promotes transcription elongation by phosphorylation and releasing RNA polymerase II (RNAPII) from its promoter proximal pause. Release of RNAPII from this pause induces transcription of critical genes in the tumor cell. Overexpression and activation of CDK9 have been observed to lead to the expression of oncogenes, including MYC and MCL-1, that aid sarcoma development and progression. Inhibition of CDK9 in sarcoma has been proven to reduce these oncogenes' expression and decrease proliferation and growth in different sarcoma cells. Currently, there are several CDK9 inhibitors in preclinical and clinical investigations. This review aims to highlight the recent discovery and results on the transcriptional role and therapeutic potential of CDK9 in sarcoma.
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Affiliation(s)
- Robert L Walker
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA
| | - Francis J Hornicek
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA
| | - Zhenfeng Duan
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA.
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2
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Han X, Xing L, Hong Y, Zhang X, Hao B, Lu JY, Huang M, Wang Z, Ma S, Zhan G, Li T, Hao X, Tao Y, Li G, Zhou S, Zheng Z, Shao W, Zeng Y, Ma D, Zhang W, Xie Z, Deng H, Yan J, Deng W, Shen X. Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence. Cell Stem Cell 2024; 31:694-716.e11. [PMID: 38631356 DOI: 10.1016/j.stem.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in a translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that the dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.
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Affiliation(s)
- Xue Han
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Linqing Xing
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xuechun Zhang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Hao
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - J Yuyang Lu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Mengyuan Huang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zuhui Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shaoqian Ma
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Ge Zhan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Tong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaowen Hao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yibing Tao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Guanwen Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuqin Zhou
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Zheng Zheng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Wen Shao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Yitian Zeng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Dacheng Ma
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and Systems Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiangwei Yan
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaohua Shen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi 030001, China.
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3
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [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] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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4
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Archuleta SR, Goodrich JA, Kugel JF. Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle. Biomolecules 2024; 14:176. [PMID: 38397413 PMCID: PMC10886972 DOI: 10.3390/biom14020176] [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: 12/21/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Central to the development and survival of all organisms is the regulation of gene expression, which begins with the process of transcription catalyzed by RNA polymerases. During transcription of protein-coding genes, the general transcription factors (GTFs) work alongside RNA polymerase II (Pol II) to assemble the preinitiation complex at the transcription start site, open the promoter DNA, initiate synthesis of the nascent messenger RNA, transition to productive elongation, and ultimately terminate transcription. Through these different stages of transcription, Pol II is dynamically phosphorylated at the C-terminal tail of its largest subunit, serving as a control mechanism for Pol II elongation and a signaling/binding platform for co-transcriptional factors. The large number of core protein factors participating in the fundamental steps of transcription add dense layers of regulation that contribute to the complexity of temporal and spatial control of gene expression within any given cell type. The Pol II transcription system is highly conserved across different levels of eukaryotes; however, most of the information here will focus on the human Pol II system. This review walks through various stages of transcription, from preinitiation complex assembly to termination, highlighting the functions and mechanisms of the core machinery that participates in each stage.
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Affiliation(s)
| | - James A. Goodrich
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
| | - Jennifer F. Kugel
- Department of Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309, USA;
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5
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Dunn LEM, Birkenheuer CH, Baines JD. A Revision of Herpes Simplex Virus Type 1 Transcription: First, Repress; Then, Express. Microorganisms 2024; 12:262. [PMID: 38399666 PMCID: PMC10892140 DOI: 10.3390/microorganisms12020262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The herpes virus genome bears more than 80 strong transcriptional promoters. Upon entry into the host cell nucleus, these genes are transcribed in an orderly manner, producing five immediate-early (IE) gene products, including ICP0, ICP4, and ICP22, while non-IE genes are mostly silent. The IE gene products are necessary for the transcription of temporal classes following sequentially as early, leaky late, and true late. A recent analysis using precision nuclear run-on followed by deep sequencing (PRO-seq) has revealed an important step preceding all HSV-1 transcription. Specifically, the immediate-early proteins ICP4 and ICP0 enter the cell with the incoming genome to help preclude the nascent antisense, intergenic, and sense transcription of all viral genes. VP16, which is also delivered into the nucleus upon entry, almost immediately reverses this repression on IE genes. The resulting de novo expression of ICP4 and ICP22 further repress antisense, intergenic, and early and late viral gene transcription through different mechanisms before the sequential de-repression of these gene classes later in infection. This early repression, termed transient immediate-early protein-mediated repression (TIEMR), precludes unproductive, antisense, intergenic, and late gene transcription early in infection to ensure the efficient and orderly progression of the viral cascade.
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Affiliation(s)
- Laura E M Dunn
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Claire H Birkenheuer
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Joel D Baines
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
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6
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics 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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7
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Ihashi S, Hamanaka M, Kaji M, Mori R, Nishizaki S, Mori M, Imasato Y, Inoue K, Matoba S, Ogonuki N, Takasu A, Nakamura M, Matsumoto K, Anzai M, Ogura A, Ikawa M, Miyamoto K. Incomplete activation of Alyref and Gabpb1 leads to preimplantation arrest in cloned mouse embryos. Life Sci Alliance 2023; 6:e202302296. [PMID: 37640449 PMCID: PMC10462978 DOI: 10.26508/lsa.202302296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023] Open
Abstract
Differentiated cell nuclei can be reprogrammed after nuclear transfer (NT) to oocytes and the produced NT embryos can give rise to cloned animals. However, development of NT embryos is often hampered by recurrent reprogramming failures, including the incomplete activation of developmental genes, yet specific genes responsible for the arrest of NT embryos are not well understood. Here, we searched for developmentally important genes among the reprogramming-resistant H3K9me3-repressed genes and identified Alyref and Gabpb1 by siRNA screening. Gene knockout of Alyref and Gabpb1 by the CRISPR/Cas9 system resulted in early developmental arrest in mice. Alyref was needed for the proper formation of inner cell mass by regulating Nanog, whereas Gabpb1 deficiency led to apoptosis. The supplement of Alyref and Gabpb1 mRNA supported efficient preimplantation development of cloned embryos. Alyref and Gabpb1 were silenced in NT embryos partially because of the repressed expression of Klf16 by H3K9me3. Thus, our study shows that the H3K9me3-repressed genes contain developmentally required genes, and the incomplete activation of such genes results in preimplantation arrest of cloned embryos.
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Affiliation(s)
- Shunya Ihashi
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Mizuto Hamanaka
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masaya Kaji
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Ryunosuke Mori
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Shuntaro Nishizaki
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Miki Mori
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Yuma Imasato
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Kimiko Inoue
- https://ror.org/00s05em53 Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shogo Matoba
- https://ror.org/00s05em53 Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Japan
- Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Narumi Ogonuki
- https://ror.org/00s05em53 Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Japan
| | - Atsushi Takasu
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Misaki Nakamura
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Kazuya Matsumoto
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masayuki Anzai
- Institute of Advanced Technology, Kindai University, Wakayama, Japan
| | - Atsuo Ogura
- https://ror.org/00s05em53 Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kei Miyamoto
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
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8
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Miller CLW, Warner JL, Winston F. Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability. Trends Genet 2023; 39:858-872. [PMID: 37481442 PMCID: PMC10592469 DOI: 10.1016/j.tig.2023.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/24/2023]
Abstract
Transcription elongation requires elaborate coordination between the transcriptional machinery and chromatin regulatory factors to successfully produce RNA while preserving the epigenetic landscape. Recent structural and genomic studies have highlighted that suppressor of Ty 6 (Spt6), a conserved histone chaperone and transcription elongation factor, sits at the crux of the transcription elongation process. Other recent studies have revealed that Spt6 also promotes DNA replication and genome integrity. Here, we review recent studies of Spt6 that have provided new insights into the mechanisms by which Spt6 controls transcription and have revealed the breadth of Spt6 functions in eukaryotic cells.
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Affiliation(s)
- Catherine L W Miller
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Genome Maintenance, Rockefeller University, New York, NY 10065, USA
| | - James L Warner
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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9
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Wang Y, Zhang H, La Ferlita A, Sp N, Goryunova M, Sarchet P, Hu Z, Sorkin M, Kim A, Huang H, Zhu H, Tsung A, Pollock RE, Beane JD. Phosphorylation of IWS1 by AKT maintains liposarcoma tumor heterogeneity through preservation of cancer stem cell phenotypes and mesenchymal-epithelial plasticity. Oncogenesis 2023; 12:30. [PMID: 37237004 DOI: 10.1038/s41389-023-00469-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/07/2023] [Accepted: 04/17/2023] [Indexed: 05/28/2023] Open
Abstract
Chemotherapy remains the mainstay of treatment for patients with advanced liposarcoma (LPS), but response rates are only 25% and the overall survival at 5 years is dismal at 20-34%. Translation of other therapies have not been successful and there has been no significant improvement in prognosis for nearly 20 years. The aberrant activation of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway has been implicated in the aggressive clinical behavior LPS and in resistance to chemotherapy, but the precise mechanism remains elusive and efforts to target AKT clinically have failed. Here we show that the AKT-mediated phosphorylation of the transcription elongation factor IWS1, promotes the maintenance of cancer stem cells in both cell and xenograft models of LPS. In addition, phosphorylation of IWS1 by AKT contributes to a "metastable" cell phenotype, characterized by mesenchymal/epithelial plasticity. The expression of phosphorylated IWS1 also promotes anchorage-dependent and independent growth, cell migration, invasion, and tumor metastasis. In patients with LPS, IWS1 expression is associated with reduced overall survival, increased frequency of recurrence, and shorter time to relapse after resection. These findings indicate that IWS1-mediated transcription elongation is an important regulator of human LPS pathobiology in an AKT-dependent manner and implicate IWS1 as an important molecular target to treat LPS.
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Affiliation(s)
- Yu Wang
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Hongji Zhang
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alessandro La Ferlita
- Department of Cancer Biology and Genetics, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Nipin Sp
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Marina Goryunova
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Patricia Sarchet
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Zhiwei Hu
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Michael Sorkin
- Department of Plastic and Reconstructive Surgery, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alex Kim
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Hai Huang
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Hua Zhu
- Department of Surgery, Division of Cardiac Surgery, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Allan Tsung
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Raphael E Pollock
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Joal D Beane
- Department of Surgery, Division of Surgical Oncology, James Cancer Center, The Ohio State University, Columbus, OH, USA.
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10
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Suzuki H, Furugori K, Abe R, Ogawa S, Ito S, Akiyama T, Horiuchi K, Takahashi H. MED26-containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies. Bioessays 2023; 45:e2200178. [PMID: 36852638 DOI: 10.1002/bies.202200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
Mediator is a coregulatory complex that plays essential roles in multiple processes of transcription regulation. One of the human Mediator subunits, MED26, has a role in recruitment of the super elongation complex (SEC) to polyadenylated genes and little elongation complex (LEC) to non-polyadenylated genes, including small nuclear RNAs (snRNAs) and replication-dependent histone (RDH) genes. MED26-containing Mediator plays a role in 3' Pol II pausing at the proximal region of transcript end sites in RDH genes through recruitment of Cajal bodies (CBs) to histone locus bodies (HLBs). This finding suggests that Mediator is involved in the association of CBs with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing by supplying 3'-end processing factors from CBs. Thus, we argue the possibility that Mediator is involved in the organization of nuclear bodies to orchestrate multiple processes of gene transcription.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
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11
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Miller CLW, Winston F. The conserved histone chaperone Spt6 is strongly required for DNA replication and genome stability. Cell Rep 2023; 42:112264. [PMID: 36924499 PMCID: PMC10106089 DOI: 10.1016/j.celrep.2023.112264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 12/31/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Histone chaperones are an important class of proteins that regulate chromatin accessibility for DNA-templated processes. Spt6 is a conserved histone chaperone and key regulator of transcription and chromatin structure. However, its functions outside of these roles have been little explored. In this work, we demonstrate a requirement for S. cerevisiae Spt6 in DNA replication and, more broadly, as a regulator of genome stability. Depletion or mutation of Spt6 impairs DNA replication in vivo. Additionally, spt6 mutants are sensitive to DNA replication stress-inducing agents. Interestingly, this sensitivity is independent of the association of Spt6 with RNA polymerase II (RNAPII), suggesting that spt6 mutants have a transcription-independent impairment of DNA replication. Specifically, genomic studies reveal that spt6 mutants have decreased loading of the MCM replicative helicase at replication origins, suggesting that Spt6 promotes origin licensing. Our results identify Spt6 as a regulator of genome stability, at least in part through a role in DNA replication.
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Affiliation(s)
- Catherine L W Miller
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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12
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The TFIIS N-terminal domain (TND): a transcription assembly module at the interface of order and disorder. Biochem Soc Trans 2023; 51:125-135. [PMID: 36651856 PMCID: PMC9987994 DOI: 10.1042/bst20220342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
Interaction scaffolds that selectively recognize disordered protein strongly shape protein interactomes. An important scaffold of this type that contributes to transcription is the TFIIS N-terminal domain (TND). The TND is a five-helical bundle that has no known enzymatic activity, but instead selectively reads intrinsically disordered sequences of other proteins. Here, we review the structural and functional properties of TNDs and their cognate disordered ligands known as TND-interacting motifs (TIMs). TNDs or TIMs are found in prominent members of the transcription machinery, including TFIIS, super elongation complex, SWI/SNF, Mediator, IWS1, SPT6, PP1-PNUTS phosphatase, elongin, H3K36me3 readers, the transcription factor MYC, and others. We also review how the TND interactome contributes to the regulation of transcription. Because the TND is the most significantly enriched fold among transcription elongation regulators, TND- and TIM-driven interactions have widespread roles in the regulation of many transcriptional processes.
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13
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Shu J, Ding N, Liu J, Cui Y, Chen C. Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis. Nucleic Acids Res 2022; 50:12754-12767. [PMID: 36453990 PMCID: PMC9825159 DOI: 10.1093/nar/gkac1126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be restored mainly by SPT6LΔtSH2, which binds to TSS in a RNA polymerase II (Pol II)-independent manner. Furthermore, SPT6L and SYD/BRM are involved in regulating the nucleosome and Pol II occupancy around TSS. The presence of SPT6L is sufficient to restore the association of the chromatin remodeler SYD to chromatin and maintain normal nucleosome occupancy. Our findings suggest that the two chromatin remodelers can form protein complexes with the core subunit of the transcription machinery and regulate nucleosome occupancy in the early transcription stage.
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Affiliation(s)
- Jie Shu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Ning Ding
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Liu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Chen Chen
- To whom correspondence should be addressed. Tel: +86 20 37252711;
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14
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López-Rivera F, Chuang J, Spatt D, Gopalakrishnan R, Winston F. Suppressor mutations that make the essential transcription factor Spn1/Iws1 dispensable in Saccharomyces cerevisiae. Genetics 2022; 222:iyac125. [PMID: 35977387 PMCID: PMC9526074 DOI: 10.1093/genetics/iyac125] [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: 06/27/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022] Open
Abstract
Spn1/Iws1 is an essential eukaryotic transcription elongation factor that is conserved from yeast to humans as an integral member of the RNA polymerase II elongation complex. Several studies have shown that Spn1 functions as a histone chaperone to control transcription, RNA splicing, genome stability, and histone modifications. However, the precise role of Spn1 is not understood, and there is little understanding of why it is essential for viability. To address these issues, we have isolated 8 suppressor mutations that bypass the essential requirement for Spn1 in Saccharomyces cerevisiae. Unexpectedly, the suppressors identify several functionally distinct complexes and activities, including the histone chaperone FACT, the histone methyltransferase Set2, the Rpd3S histone deacetylase complex, the histone acetyltransferase Rtt109, the nucleosome remodeler Chd1, and a member of the SAGA coactivator complex, Sgf73. The identification of these distinct groups suggests that there are multiple ways in which Spn1 bypass can occur, including changes in histone acetylation and alterations in other histone chaperones. Thus, Spn1 may function to overcome repressive chromatin by multiple mechanisms during transcription. Our results suggest that bypassing a subset of these functions allows viability in the absence of Spn1.
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Affiliation(s)
| | - James Chuang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dan Spatt
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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15
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Aoi Y, Shah AP, Ganesan S, Soliman SHA, Cho BK, Goo YA, Kelleher NL, Shilatifard A. SPT6 functions in transcriptional pause/release via PAF1C recruitment. Mol Cell 2022; 82:3412-3423.e5. [PMID: 35973425 PMCID: PMC9714687 DOI: 10.1016/j.molcel.2022.06.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/11/2022] [Accepted: 06/29/2022] [Indexed: 01/24/2023]
Abstract
It is unclear how various factors functioning in the transcriptional elongation by RNA polymerase II (RNA Pol II) cooperatively regulate pause/release and productive elongation in living cells. Using an acute protein-depletion approach, we report that SPT6 depletion results in the release of paused RNA Pol II into gene bodies through an impaired recruitment of PAF1C. Short genes demonstrate a release with increased mature transcripts, whereas long genes are released but fail to yield mature transcripts, due to a reduced processivity resulting from both SPT6 and PAF1C loss. Unexpectedly, SPT6 depletion causes an association of NELF with the elongating RNA Pol II on gene bodies, without any observed functional significance on transcriptional elongation pattern, arguing against a role for NELF in keeping RNA Pol II in the paused state. Furthermore, SPT6 depletion impairs heat-shock-induced pausing, pointing to a role for SPT6 in regulating RNA Pol II pause/release through PAF1C recruitment.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avani P Shah
- 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
| | - 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
| | - Byoung-Kyu Cho
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Young Ah Goo
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Neil L Kelleher
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, 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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16
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The Mis6 inner kinetochore subcomplex maintains CENP-A nucleosomes against centromeric non-coding transcription during mitosis. Commun Biol 2022; 5:818. [PMID: 35970865 PMCID: PMC9378642 DOI: 10.1038/s42003-022-03786-y] [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: 10/28/2021] [Accepted: 08/02/2022] [Indexed: 11/29/2022] Open
Abstract
Centromeres are established by nucleosomes containing the histone H3 variant CENP-A. CENP-A is recruited to centromeres by the Mis18–HJURP machinery. During mitosis, CENP-A recruitment ceases, implying the necessity of CENP-A maintenance at centromeres, although the exact underlying mechanism remains elusive. Herein, we show that the inner kinetochore protein Mis6 (CENP-I) and Mis15 (CENP-N) retain CENP-A during mitosis in fission yeast. Eliminating Mis6 or Mis15 during mitosis caused immediate loss of pre-existing CENP-A at centromeres. CENP-A loss occurred due to the transcriptional upregulation of non-coding RNAs at the central core region of centromeres, as confirmed by the observation RNA polymerase II inhibition preventing CENP-A loss from centromeres in the mis6 mutant. Thus, we concluded that the inner kinetochore complex containing Mis6–Mis15 blocks the indiscriminate transcription of non-coding RNAs at the core centromere, thereby retaining the epigenetic inheritance of CENP-A during mitosis. The kinetochore protein Mis6 (CENP-I) plays an important role in CENP-A maintenance during mitosis in fission yeast and blocks the indiscriminate transcription of non-coding RNAs at the core centromere to retain CENP-A during mitosis.
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17
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Molenaar TM, van Leeuwen F. SETD2: from chromatin modifier to multipronged regulator of the genome and beyond. Cell Mol Life Sci 2022; 79:346. [PMID: 35661267 PMCID: PMC9167812 DOI: 10.1007/s00018-022-04352-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022]
Abstract
Histone modifying enzymes play critical roles in many key cellular processes and are appealing proteins for targeting by small molecules in disease. However, while the functions of histone modifying enzymes are often linked to epigenetic regulation of the genome, an emerging theme is that these enzymes often also act by non-catalytic and/or non-epigenetic mechanisms. SETD2 (Set2 in yeast) is best known for associating with the transcription machinery and methylating histone H3 on lysine 36 (H3K36) during transcription. This well-characterized molecular function of SETD2 plays a role in fine-tuning transcription, maintaining chromatin integrity, and mRNA processing. Here we give an overview of the various molecular functions and mechanisms of regulation of H3K36 methylation by Set2/SETD2. These fundamental insights are important to understand SETD2’s role in disease, most notably in cancer in which SETD2 is frequently inactivated. SETD2 also methylates non-histone substrates such as α-tubulin which may promote genome stability and contribute to the tumor-suppressor function of SETD2. Thus, to understand its role in disease, it is important to understand and dissect the multiple roles of SETD2 within the cell. In this review we discuss how histone methylation by Set2/SETD2 has led the way in connecting histone modifications in active regions of the genome to chromatin functions and how SETD2 is leading the way to showing that we also have to look beyond histones to truly understand the physiological role of an ‘epigenetic’ writer enzyme in normal cells and in disease.
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18
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Kasiliauskaite A, Kubicek K, Klumpler T, Zanova M, Zapletal D, Koutna E, Novacek J, Stefl R. Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic Acids Res 2022; 50:5961-5973. [PMID: 35640611 PMCID: PMC9177984 DOI: 10.1093/nar/gkac451] [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: 04/15/2021] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/14/2022] Open
Abstract
Transcription elongation factor Spt6 associates with RNA polymerase II (Pol II) and acts as a histone chaperone, which promotes the reassembly of nucleosomes following the passage of Pol II. The precise mechanism of nucleosome reassembly mediated by Spt6 remains unclear. In this study, we used a hybrid approach combining cryo-electron microscopy and small-angle X-ray scattering to visualize the architecture of Spt6 from Saccharomyces cerevisiae. The reconstructed overall architecture of Spt6 reveals not only the core of Spt6, but also its flexible N- and C-termini, which are critical for Spt6's function. We found that the acidic N-terminal region of Spt6 prevents the binding of Spt6 not only to the Pol II CTD and Pol II CTD-linker, but also to pre-formed intact nucleosomes and nucleosomal DNA. The N-terminal region of Spt6 self-associates with the tSH2 domain and the core of Spt6 and thus controls binding to Pol II and nucleosomes. Furthermore, we found that Spt6 promotes the assembly of nucleosomes in vitro. These data indicate that the cooperation between the intrinsically disordered and structured regions of Spt6 regulates nucleosome and Pol II CTD binding, and also nucleosome assembly.
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Affiliation(s)
- Aiste Kasiliauskaite
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - Tomas Klumpler
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic
| | - Martina Zanova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno CZ-61137, Czech Republic
| | - David Zapletal
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Eliska Koutna
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Novacek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno CZ-62500, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
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19
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Li S, Edwards G, Radebaugh CA, Luger K, A Stargell L. Spn1 and its dynamic interactions with Spt6, histones and nucleosomes. J Mol Biol 2022; 434:167630. [PMID: 35595162 DOI: 10.1016/j.jmb.2022.167630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
Abstract
Histone chaperones facilitate the assembly and disassembly of nucleosomes and regulate DNA accessibility for critical cellular processes. Spn1 is an essential, highly conserved histone chaperone that functions in transcription initiation and elongation in a chromatin context. Here we demonstrate that Spn1 binds H3-H4 with low nanomolar affinity, residues 85-99 within the acidic N-terminal region of Spn1 are required for H3-H4 binding, and Spn1 binding to H3-H4 dimers does not impede (H3-H4)2 tetramer formation. Previous work has shown the central region of Spn1 (residues 141-305) is important for interaction with Spt6, another conserved and essential histone chaperone. We show that the C-terminal region of Spn1 also contributes to Spt6 binding and is critical for Spn1 binding to nucleosomes. We also show Spt6 preferentially binds H3-H4 tetramers and Spt6 competes with nucleosomes for Spn1 binding. Combined with previous results, this indicates the Spn1-Spt6 complex does not bind nucleosomes. In contrast to nucleosome binding, we found that the Spn1-Spt6 complex can bind H3-H4 dimers and tetramers and H2A-H2B to form ternary complexes. These important results provide new information about the functions of Spn1, Spt6, and the Spn1-Spt6 complex, two essential and highly conserved histone chaperones.
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Affiliation(s)
- Sha Li
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA; Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Garrett Edwards
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Catherine A Radebaugh
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Laurie A Stargell
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA
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20
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Thomas A, Rehfeld F, Zhang H, Chang TC, Goodarzi M, Gillet F, Mendell JT. RBM33 directs the nuclear export of transcripts containing GC-rich elements. Genes Dev 2022; 36:550-565. [PMID: 35589130 PMCID: PMC9186391 DOI: 10.1101/gad.349456.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/03/2022] [Indexed: 12/13/2022]
Abstract
Although splicing is a major driver of RNA nuclear export, many intronless RNAs are efficiently exported to the cytoplasm through poorly characterized mechanisms. For example, GC-rich sequences promote nuclear export in a splicing-independent manner, but how GC content is recognized and coupled to nuclear export is unknown. Here, we developed a genome-wide screening strategy to investigate the mechanism of export of NORAD, an intronless cytoplasmic long noncoding RNA (lncRNA). This screen revealed an RNA binding protein, RBM33, that directs the nuclear export of NORAD and numerous other transcripts. RBM33 directly binds substrate transcripts and recruits components of the TREX-NXF1/NXT1 RNA export pathway. Interestingly, high GC content emerged as the feature that specifies RBM33-dependent nuclear export. Accordingly, RBM33 directly binds GC-rich elements in target transcripts. These results provide a broadly applicable strategy for the genetic dissection of nuclear export mechanisms and reveal a long-sought nuclear export pathway for transcripts with GC-rich sequences.
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Affiliation(s)
- Anu Thomas
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Frederick Rehfeld
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Tsung-Cheng Chang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Mohammad Goodarzi
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Frank Gillet
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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21
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The ins and outs of CENP-A: Chromatin dynamics of the centromere-specific histone. Semin Cell Dev Biol 2022; 135:24-34. [PMID: 35422390 DOI: 10.1016/j.semcdb.2022.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 01/08/2023]
Abstract
Centromeres are highly specialised chromosome domains defined by the presence of an epigenetic mark, the specific histone H3 variant called CENP-A (centromere protein A). They constitute the genomic regions on which kinetochores form and when defective cause segregation defects that can lead to aneuploidy and cancer. Here, we discuss how CENP-A is established and maintained to propagate centromere identity while subjected to dynamic chromatin remodelling during essential cellular processes like DNA repair, replication, and transcription. We highlight parallels and identify conserved mechanisms between different model organism with a particular focus on 1) the establishment of CENP-A at centromeres, 2) CENP-A maintenance during transcription and replication, and 3) the mechanisms that help preventing CENP-A localization at non-centromeric sites. We then give examples of how timely loading of new CENP-A to the centromere, maintenance of old CENP-A during S-phase and transcription, and removal of CENP-A at non-centromeric sites are coordinated and controlled by an intricate network of factors whose identity is slowly being unravelled.
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22
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Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, Srb P, Hexnerova R, Fabry M, Madlikova M, Horejsi M, De Rijck J, Debyser Z, Adelman K, Hodges HC, Veverka V. A ubiquitous disordered protein interaction module orchestrates transcription elongation. Science 2021; 374:1113-1121. [PMID: 34822292 DOI: 10.1126/science.abe2913] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Katerina Cermakova
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Vanda Lux
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Monika Nedomova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Seth R Goldman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric A Smith
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rozalie Hexnerova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Milan Fabry
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Marcela Madlikova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Magdalena Horejsi
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan De Rijck
- Molecular Virology and Gene Therapy, KU Leuven, Leuven, Flanders, Belgium
| | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Leuven, Flanders, Belgium
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - H Courtney Hodges
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, and Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
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23
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Gopalakrishnan R, Winston F. The histone chaperone Spt6 is required for normal recruitment of the capping enzyme Abd1 to transcribed regions. J Biol Chem 2021; 297:101205. [PMID: 34543624 PMCID: PMC8511950 DOI: 10.1016/j.jbc.2021.101205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/20/2021] [Accepted: 09/15/2021] [Indexed: 10/29/2022] Open
Abstract
The histone chaperone Spt6 is involved in promoting elongation of RNA polymerase II (RNAPII), maintaining chromatin structure, regulating cotranscriptional histone modifications, and controlling mRNA processing. These diverse functions of Spt6 are partly mediated through its interactions with RNAPII and other factors in the transcription elongation complex. In this study, we used mass spectrometry to characterize the differences in RNAPII-interacting factors between wildtype cells and those depleted for Spt6, leading to the identification of proteins that depend on Spt6 for their interaction with RNAPII. The altered association of some of these factors could be attributed to changes in steady-state protein levels. However, Abd1, the mRNA cap methyltransferase, had decreased association with RNAPII after Spt6 depletion despite unchanged Abd1 protein levels, showing a requirement for Spt6 in mediating the Abd1-RNAPII interaction. Genome-wide studies showed that Spt6 is required for maintaining the level of Abd1 over transcribed regions, as well as the level of Spt5, another protein known to recruit Abd1 to chromatin. Abd1 levels were particularly decreased at the 5' ends of genes after Spt6 depletion, suggesting a greater need for Spt6 in Abd1 recruitment over these regions. Together, our results show that Spt6 is important in regulating the composition of the transcription elongation complex and reveal a previously unknown function for Spt6 in the recruitment of Abd1.
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Affiliation(s)
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.
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LeBlanc BM, Moreno RY, Escobar EE, Venkat Ramani MK, Brodbelt JS, Zhang Y. What's all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry. RSC Chem Biol 2021; 2:1084-1095. [PMID: 34458825 PMCID: PMC8341212 DOI: 10.1039/d1cb00083g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and its phosphorylation state are critically important in regulating transcription in vivo. Early methods of identifying phosphorylation on the CTD heptad were plagued by issues of low specificity and ambiguous signals. However, advancements in the field of mass spectrometry (MS) have presented the opportunity to gain new insights into well-studied processes as well as explore new frontiers in transcription. By using MS, residues which are modified within the CTD heptad and across repeats are now able to be pinpointed. Likewise, identification of kinase and phosphatase specificity towards residues of the CTD has reached a new level of accuracy. Now, MS is being used to investigate the crosstalk between modified residues of the CTD and may be a critical technique for understanding how phosphorylation plays a role in the new LLPS model of transcription. Herein, we discuss the development of various MS techniques and evaluate their capabilities. By highlighting the pros and cons of each technique, we aim to provide future investigators with a comprehensive overview of how MS can be used to investigate the complexities of RNAP-II mediated transcription.
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Affiliation(s)
- Blase M LeBlanc
- Department of Molecular Biosciences, University of Texas Austin USA
| | - R Yvette Moreno
- Department of Molecular Biosciences, University of Texas Austin USA
| | | | | | | | - Yan Zhang
- Department of Molecular Biosciences, University of Texas Austin USA
- Institute of Cellular and Molecular Biology, University of Texas Austin USA
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25
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Importance of tyrosine phosphorylation for transmembrane signaling in plants. Biochem J 2021; 478:2759-2774. [PMID: 34297043 PMCID: PMC8331091 DOI: 10.1042/bcj20210202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022]
Abstract
Reversible protein phosphorylation is a widespread post-translational modification fundamental for signaling across all domains of life. Tyrosine (Tyr) phosphorylation has recently emerged as being important for plant receptor kinase (RK)-mediated signaling, particularly during plant immunity. How Tyr phosphorylation regulates RK function is however largely unknown. Notably, the expansion of protein Tyr phosphatase and SH2 domain-containing protein families, which are the core of regulatory phospho-Tyr (pTyr) networks in choanozoans, did not occur in plants. Here, we summarize the current understanding of plant RK Tyr phosphorylation focusing on the critical role of a pTyr site (‘VIa-Tyr’) conserved in several plant RKs. Furthermore, we discuss the possibility of metazoan-like pTyr signaling modules in plants based on atypical components with convergent biochemical functions.
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Narain A, Bhandare P, Adhikari B, Backes S, Eilers M, Dölken L, Schlosser A, Erhard F, Baluapuri A, Wolf E. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Mol Cell 2021; 81:3110-3127.e14. [PMID: 34233157 PMCID: PMC8354102 DOI: 10.1016/j.molcel.2021.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/24/2021] [Accepted: 06/11/2021] [Indexed: 01/22/2023]
Abstract
SPT6 is a histone chaperone that tightly binds RNA polymerase II (RNAPII) during transcription elongation. However, its primary role in transcription is uncertain. We used targeted protein degradation to rapidly deplete SPT6 in human cells and analyzed defects in RNAPII behavior by a multi-omics approach and mathematical modeling. Our data indicate that SPT6 is a crucial factor for RNAPII processivity and is therefore required for the productive transcription of protein-coding genes. Unexpectedly, SPT6 also has a vital role in RNAPII termination, as acute depletion induced readthrough transcription for thousands of genes. Long-term depletion of SPT6 induced cryptic intragenic transcription, as observed earlier in yeast. However, this phenotype was not observed upon acute SPT6 depletion and therefore can be attributed to accumulated epigenetic perturbations in the prolonged absence of SPT6. In conclusion, targeted degradation of SPT6 allowed the temporal discrimination of its function as an epigenetic safeguard and RNAPII elongation factor. Auxin-inducible degradation discriminates direct roles of human SPT6 in transcription Acute loss of SPT6 globally impairs RNAPII processivity and speed SPT6 is required for efficient transcription termination on protein-coding genes Long-term loss of SPT6 ultimately results in cryptic intragenic transcription
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Affiliation(s)
- Ashwin Narain
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Bikash Adhikari
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Simone Backes
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Florian Erhard
- Computational Systems Virology and Bioinformatics, Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University of Würzburg, Beethovenstraße 1A, 97080 Würzburg, Germany.
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27
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Kearns S, Mason FM, Rathmell WK, Park IY, Walker C, Verhey KJ, Cianfrocco MA. Molecular determinants for α-tubulin methylation by SETD2. J Biol Chem 2021; 297:100898. [PMID: 34157286 PMCID: PMC8294582 DOI: 10.1016/j.jbc.2021.100898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/28/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Post-translational modifications to tubulin are important for many microtubule-based functions inside cells. It was recently shown that methylation of tubulin by the histone methyltransferase SETD2 occurs on mitotic spindle microtubules during cell division, with its absence resulting in mitotic defects. However, the catalytic mechanism of methyl addition to tubulin is unclear. We used a truncated version of human wild type SETD2 (tSETD2) containing the catalytic SET and C-terminal Set2-Rpb1-interacting (SRI) domains to investigate the biochemical mechanism of tubulin methylation. We found that recombinant tSETD2 had a higher activity toward tubulin dimers than polymerized microtubules. Using recombinant single-isotype tubulin, we demonstrated that methylation was restricted to lysine 40 of α-tubulin. We then introduced pathogenic mutations into tSETD2 to probe the recognition of histone and tubulin substrates. A mutation in the catalytic domain (R1625C) allowed tSETD2 to bind to tubulin but not methylate it, whereas a mutation in the SRI domain (R2510H) caused loss of both tubulin binding and methylation. Further investigation of the role of the SRI domain in substrate binding found that mutations within this region had differential effects on the ability of tSETD2 to bind to tubulin versus the binding partner RNA polymerase II for methylating histones in vivo, suggesting distinct mechanisms for tubulin and histone methylation by SETD2. Finally, we found that substrate recognition also requires the negatively charged C-terminal tail of α-tubulin. Together, this study provides a framework for understanding how SETD2 serves as a dual methyltransferase for both histone and tubulin methylation.
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Affiliation(s)
- Sarah Kearns
- Program of Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank M Mason
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci 2021; 78:5543-5567. [PMID: 34146121 PMCID: PMC8257543 DOI: 10.1007/s00018-021-03878-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), the kinase component of positive transcription elongation factor b (P-TEFb), is essential for transcription of most protein-coding genes by RNA polymerase II (RNAPII). By releasing promoter-proximally paused RNAPII into gene bodies, CDK9 controls the entry of RNAPII into productive elongation and is, therefore, critical for efficient synthesis of full-length messenger (m)RNAs. In recent years, new players involved in P-TEFb-dependent processes have been identified and an important function of CDK9 in coordinating elongation with transcription initiation and termination has been unveiled. As the regulatory functions of CDK9 in gene expression continue to expand, a number of human pathologies, including cancers, have been associated with aberrant CDK9 activity, underscoring the need to properly regulate CDK9. Here, I provide an overview of CDK9 function and regulation, with an emphasis on CDK9 dysregulation in human diseases.
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29
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Žumer K, Maier KC, Farnung L, Jaeger MG, Rus P, Winter G, Cramer P. Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo. Mol Cell 2021; 81:3096-3109.e8. [PMID: 34146481 DOI: 10.1016/j.molcel.2021.05.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/16/2021] [Accepted: 05/26/2021] [Indexed: 12/27/2022]
Abstract
Transcription by RNA polymerase II (RNA Pol II) relies on the elongation factors PAF1 complex (PAF), RTF1, and SPT6. Here, we use rapid factor depletion and multi-omics analysis to investigate how these elongation factors influence RNA Pol II elongation activity in human cells. Whereas depletion of PAF subunits PAF1 and CTR9 has little effect on cellular RNA synthesis, depletion of RTF1 or SPT6 strongly compromises RNA Pol II activity, albeit in fundamentally different ways. RTF1 depletion decreases RNA Pol II velocity, whereas SPT6 depletion impairs RNA Pol II progression through nucleosomes. These results show that distinct elongation factors stimulate either RNA Pol II velocity or RNA Pol II progression through chromatin in vivo. Further analysis provides evidence for two distinct barriers to early elongation: the promoter-proximal pause site and the +1 nucleosome. It emerges that the first barrier enables loading of elongation factors that are required to overcome the second and subsequent barriers to transcription.
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Affiliation(s)
- Kristina Žumer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kerstin C Maier
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faßberg 11, 37077 Göttingen, Germany
| | - Lucas Farnung
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faßberg 11, 37077 Göttingen, Germany
| | - Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria
| | - Petra Rus
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faßberg 11, 37077 Göttingen, Germany
| | - Georg Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faßberg 11, 37077 Göttingen, Germany.
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30
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Pipkin ME. Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development. Immunol Rev 2021; 300:100-124. [PMID: 33682165 DOI: 10.1111/imr.12954] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Adaptive immunity to intracellular pathogens and tumors is mediated by antigen-experienced CD8 T cells. Individual naive CD8 T cells have the potential to differentiate into a diverse array of antigen-experienced subsets that exhibit distinct effector functions, life spans, anatomic positioning, and potential for regenerating an entirely new immune response during iterative pathogenic exposures. The developmental process by which activated naive cells undergo diversification involves regulation of chromatin structure and transcription but is not entirely understood. This review examines how alterations in chromatin structure, transcription factor binding, extracellular signals, and single-cell gene expression explain the differential development of distinct effector (TEFF ) and memory (TMEM ) CD8 T cell subsets. Special emphasis is placed on how Runx proteins function with additional transcription factors to pioneer changes in chromatin accessibility and drive transcriptional programs that establish the core attributes of cytotoxic T lymphocytes, subdivide circulating and non-circulating TMEM cell subsets, and govern terminal differentiation. The discussion integrates the roles of specific cytokine signals, transcriptional circuits and how regulation of individual nucleosomes and RNA polymerase II activity can contribute to the process of differentiation. A model that integrates many of these features is discussed to conceptualize how activated CD8 T cells arrive at their fates.
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Affiliation(s)
- Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute - FL, Jupiter, FL, USA
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31
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Role of promoters in regulating alternative splicing. Gene 2021; 782:145523. [PMID: 33667606 DOI: 10.1016/j.gene.2021.145523] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/31/2020] [Accepted: 02/09/2021] [Indexed: 01/19/2023]
Abstract
Alternative splicing (AS) plays a critical role in enhancing proteome complexity in higher eukaryotes. Almost all the multi intron-containing genes undergo AS in humans. Splicing mainly occurs co-transcriptionally, where RNA polymerase II (RNA pol II) plays a crucial role in coordinating transcription and pre-mRNA splicing. Aberrant AS leads to non-functional proteins causative in various pathophysiological conditions such as cancers, neurodegenerative diseases, and muscular dystrophies. Transcription and pre-mRNA splicing are deeply interconnected and can influence each other's functions. Several studies evinced that specific promoters employed by RNA pol II dictate the RNA processing decisions. Promoter-specific recruitment of certain transcriptional factors or transcriptional coactivators influences splicing, and the extent to which these factors affect splicing has not been discussed in detail. Here, in this review, various DNA-binding proteins and their influence on promoter-specific AS are extensively discussed. Besides, this review highlights how the promoter-specific epigenetic changes might regulate AS.
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Rosales M, Rodríguez-Ulloa A, Besada V, Ramón AC, Pérez GV, Ramos Y, Guirola O, González LJ, Zettl K, Wiśniewski JR, Perera Y, Perea SE. Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945. Cells 2021; 10:cells10020338. [PMID: 33562780 PMCID: PMC7915770 DOI: 10.3390/cells10020338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/30/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Casein kinase 2 (CK2) regulates a plethora of proteins with pivotal roles in solid and hematological neoplasia. Particularly, in acute myeloid leukemia (AML) CK2 has been pointed as an attractive therapeutic target and prognostic marker. Here, we explored the impact of CK2 inhibition over the phosphoproteome of two cell lines representing major AML subtypes. Quantitative phosphoproteomic analysis was conducted to evaluate changes in phosphorylation levels after incubation with the ATP-competitive CK2 inhibitor CX-4945. Functional enrichment, network analysis, and database mining were performed to identify biological processes, signaling pathways, and CK2 substrates that are responsive to CX-4945. A total of 273 and 1310 phosphopeptides were found differentially modulated in HL-60 and OCI-AML3 cells, respectively. Despite regulated phosphopeptides belong to proteins involved in multiple biological processes and signaling pathways, most of these perturbations can be explain by direct CK2 inhibition rather than off-target effects. Furthermore, CK2 substrates regulated by CX-4945 are mainly related to mRNA processing, translation, DNA repair, and cell cycle. Overall, we evidenced that CK2 inhibitor CX-4945 impinge on mediators of signaling pathways and biological processes essential for primary AML cells survival and chemosensitivity, reinforcing the rationale behind the pharmacologic blockade of protein kinase CK2 for AML targeted therapy.
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Affiliation(s)
- Mauro Rosales
- Department of Animal and Human Biology, Faculty of Biology, University of Havana (UH), Havana 10400, Cuba;
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - Arielis Rodríguez-Ulloa
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Vladimir Besada
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Ailyn C. Ramón
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - George V. Pérez
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
| | - Yassel Ramos
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Osmany Guirola
- Bioinformatics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba;
| | - Luis J. González
- Mass Spectrometry Laboratory, Proteomics Group, Department of Systems Biology, Biomedical Research Division, CIGB, Havana 10600, Cuba; (A.R.-U.); (V.B.); (Y.R.); (L.J.G.)
| | - Katharina Zettl
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Munich, Germany; (K.Z.); (J.R.W.)
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, 82152 Munich, Germany; (K.Z.); (J.R.W.)
| | - Yasser Perera
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
- China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Lengshuitan District, Yongzhou 425000, China
- Correspondence: (Y.P.); (S.E.P.)
| | - Silvio E. Perea
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering and Biotechnology (CIGB), Havana 10600, Cuba; (A.C.R.); (G.V.P.)
- Correspondence: (Y.P.); (S.E.P.)
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The XPB Subunit of the TFIIH Complex Plays a Critical Role in HIV-1 Transcription and XPB Inhibition by Spironolactone Prevents HIV-1 Reactivation from Latency. J Virol 2021; 95:JVI.01247-20. [PMID: 33239456 PMCID: PMC7851559 DOI: 10.1128/jvi.01247-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
HIV transcription requires assembly of cellular transcription factors at the HIV-1promoter. The TFIIH general transcription factor facilitates transcription initiation by opening the DNA strands around the transcription start site and phosphorylating the C-terminal domain for RNA polymerase II (RNAPII) for activation. Spironolactone (SP), an FDA approved aldosterone antagonist, triggers the proteasomal degradation of the XPB subunit of TFIIH, and concurrently suppresses acute HIV infection in vitro Here we investigated SP as a possible block-and-lock agent for a functional cure aimed at the transcriptional silencing of the viral reservoir. The long-term activity of SP was investigated in primary and cell line models of HIV-1 latency and reactivation. We show that SP rapidly inhibits HIV-1 transcription by reducing RNAPII recruitment to the HIV-1 genome. shRNA knockdown of XPB confirmed XPB degradation as the mechanism of action. Unfortunately, long-term pre-treatment with SP does not result in epigenetic suppression of HIV upon SP treatment interruption, since virus rapidly rebounds when XPB reemerges; however, SP alone without ART maintains the transcriptional suppression. Importantly, SP inhibits HIV reactivation from latency in both cell line models and resting CD4+T cells isolated from aviremic infected individuals upon cell stimulation with latency reversing agents. Furthermore, long-term treatment with concentrations of SP that potently degrade XPB does not lead to global dysregulation of cellular mRNA expression. Overall, these results suggest that XPB plays a key role in HIV transcriptional regulation and XPB degradation by SP strengthens the potential of HIV transcriptional inhibitors in block-and-lock HIV cure approaches.IMPORTANCE Antiretroviral therapy (ART) effectively reduces an individual's HIV loads to below the detection limit, nevertheless rapid viral rebound immediately ensues upon treatment interruption. Furthermore, virally suppressed individuals experience chronic immune activation from ongoing low-level virus expression. Thus, the importance of identifying novel therapeutics to explore in block-and-lock HIV functional cure approaches, aimed at the transcriptional and epigenetic silencing of the viral reservoir to block reactivation from latency. We investigated the potential of repurposing the FDA-approved spironolactone (SP), as one such drug. SP treatment rapidly degrades a host transcription factor subunit, XPB, inhibiting HIV transcription and blocking reactivation from latency. Long-term SP treatment does not affect cellular viability, cell cycle progression or global cellular transcription. SP alone blocks HIV transcription in the absence of ART but does not delay rebound upon drug removal as XPB rapidly reemerges. This study highlights XPB as a novel drug target in block-and-lock therapeutic approaches.
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Diao C, Guo P, Yang W, Sun Y, Liao Y, Yan Y, Zhao A, Cai X, Hao J, Hu S, Yu W, Chen M, Wang R, Li W, Zuo Y, Pan J, Hua C, Lu X, Fan W, Zheng Z, Deng W, Luo G, Guo W. SPT6 recruits SND1 to co-activate human telomerase reverse transcriptase to promote colon cancer progression. Mol Oncol 2021; 15:1180-1202. [PMID: 33305480 PMCID: PMC8024721 DOI: 10.1002/1878-0261.12878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/06/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022] Open
Abstract
Human telomerase reverse transcriptase (hTERT) plays an extremely important role in cancer initiation and development, including colorectal cancer (CRC). However, the precise upstream regulatory mechanisms of hTERT in different cancer types remain poorly understood. Here, we uncovered the candidate transcriptional factor of hTERT in CRC and explored its role and the corresponding molecular mechanisms in regulating hTERT expression and CRC survival with an aim of developing mechanism-based combinational targeting therapy. The possible binding proteins at the hTERT promoter were uncovered using pull-down/mass spectrometry analysis. The regulation of SPT6 on hTERT expression and CRC survival was evaluated in human CRC cell lines and mouse models. Mechanistic studies focusing on the synergy between SPT6 and staphylococcal nuclease and Tudor domain containing 1 (SND1) in controlling hTERT expression and CRC progression were conducted also in the above two levels. The expression correlation and clinical significance of SPT6, SND1, and hTERT were investigated in tumor tissues from murine models and patients with CRC in situ. SPT6 was identified as a possible transcriptional factor to bind to the hTERT promoter. SPT6 knockdown decreased the activity of hTERT promoter, downregulated the protein expression level of hTERT, suppressed proliferation, invasion, and stem-like properties, promoted apoptosis induction, and enhanced chemotherapeutic drug sensitivity in vitro. SPT6 silencing also led to the delay of tumor growth and metastasis in mice carrying xenografts of human-derived colon cancer cells. Mechanistically, SND1 interacted with SPT6 to co-control hTERT expression and CRC cell proliferation, stemness, and growth in vitro and in vivo. SPT6, SND1, and hTERT were highly expressed simultaneously in CRC tissues, both from the murine model and patients with CRC in situ, and pairwise expression among these three factors showed a significant positive correlation. In brief, our research demonstrated that SPT6 synergized with SND1 to promote CRC development by targeting hTERT and put forward that inhibiting the SPT6-SND1-hTERT axis may create a therapeutic vulnerability in CRC.
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Affiliation(s)
- Chaoliang Diao
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Ping Guo
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Wenjing Yang
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Yao Sun
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Yina Liao
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Yue Yan
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Anshi Zhao
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Xin Cai
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Jiaojiao Hao
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Sheng Hu
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Wendan Yu
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Manyu Chen
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Ruozhu Wang
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Wenyang Li
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Yan Zuo
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Jinjin Pan
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Chunyu Hua
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Xiaona Lu
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
| | - Wenhua Fan
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Zongheng Zheng
- The Third Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Wuguo Deng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Guangyu Luo
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Wei Guo
- Institute of Cancer Stem Cells and the First Affiliated HospitalDalian Medical UniversityChina
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35
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Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:10241-10258. [PMID: 32941642 PMCID: PMC7544207 DOI: 10.1093/nar/gkaa745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.
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Affiliation(s)
- Natalia I Reim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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36
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Decker TM. Mechanisms of Transcription Elongation Factor DSIF (Spt4-Spt5). J Mol Biol 2020; 433:166657. [PMID: 32987031 DOI: 10.1016/j.jmb.2020.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/16/2020] [Accepted: 09/20/2020] [Indexed: 12/19/2022]
Abstract
The transcription elongation factor Spt5 is conserved from bacteria to humans. In eukaryotes, Spt5 forms a complex with Spt4 and regulates processive transcription elongation. Recent studies on transcription elongation suggest different mechanistic roles in yeast versus mammals. Higher eukaryotes utilize Spt4-Spt5 (DSIF) to regulate promoter-proximal pausing, a transcription-regulatory mechanism that connects initiation to productive elongation. DSIF is a versatile transcription factor and has been implicated in both gene-specific regulation and transcription through nucleosomes. Future studies will further elucidate the role of DSIF in transcriptional dynamics and disentangle its inhibitory and enhancing activities in transcription.
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Affiliation(s)
- Tim-Michael Decker
- Department of Biochemistry, University of Colorado, 3415 Colorado Ave, Boulder, CO 80303, USA.
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37
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Jeronimo C, Poitras C, Robert F. Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications. Cell Rep 2020; 28:1206-1218.e8. [PMID: 31365865 DOI: 10.1016/j.celrep.2019.06.097] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/28/2019] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
Genomic DNA is framed by additional layers of information, referred to as the epigenome. Epigenomic marks such as DNA methylation, histone modifications, and histone variants are concentrated on specific genomic sites, where they can both instruct and reflect gene expression. How this information is maintained, notably in the face of transcription, is not completely understood. Specifically, the extent to which modified histones themselves are retained through RNA polymerase II passage is unclear. Here, we show that several histone modifications are mislocalized when the transcription-coupled histone chaperones FACT or Spt6 are disrupted in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates nucleosome loss, which is partially compensated for by the increased activity of non-transcription-coupled histone chaperones. The random incorporation of transcription-evicted modified histones scrambles epigenomic information. Our work highlights the importance of local recycling of modified histones by FACT and Spt6 during transcription in the maintenance of the epigenomic landscape.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, Canada.
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38
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Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro. J Mol Biol 2020; 432:4092-4107. [PMID: 32439331 PMCID: PMC7327521 DOI: 10.1016/j.jmb.2020.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/21/2022]
Abstract
Transcription elongation factor Spt6 associates with RNA polymerase II (RNAP II) via a tandem SH2 (tSH2) domain. The mechanism and significance of the RNAP II–Spt6 interaction is still unclear. Recently, it was proposed that Spt6-tSH2 is recruited via a newly described phosphorylated linker between the Rpb1 core and its C-terminal domain (CTD). Here, we report binding studies with isolated tSH2 of Spt6 (Spt6-tSH2) and Spt6 lacking the first unstructured 297 residues (Spt6ΔN) with a minimal CTD substrate of two repetitive heptads phosphorylated at different sites. The data demonstrate that Spt6 also binds the phosphorylated CTD, a site that was originally proposed as a recognition epitope. We also show that an extended CTD substrate harboring 13 repetitive heptads of the tyrosine-phosphorylated CTD binds Spt6-tSH2 and Spt6ΔN with tighter affinity than the minimal CTD substrate. The enhanced binding is achieved by avidity originating from multiple phosphorylation marks present in the CTD. Interestingly, we found that the steric effects of additional domains in the Spt6ΔN construct partially obscure the binding of the tSH2 domain to the multivalent ligand. We show that Spt6-tSH2 binds various phosphorylation patterns in the CTD and found that the studied combinations of phospho-CTD marks (1,2; 1,5; 2,4; and 2,7) all facilitate the interaction of CTD with Spt6. Our structural studies reveal a plasticity of the tSH2 binding pockets that enables the accommodation of CTDs with phosphorylation marks in different registers. High-affinity Pol II CTD-binding by Spt6 is achieved by avidity originating from multiple phosphorylation marks presented in the CTD, suggesting how phosphorylation levels fine-tune the CTD interactome. Structure of RNAP II CTD bound with tandem SH2 domain of Spt6 reveals how phosphorylated CTD is recognized. Isolated tSH2 of Spt6 binds the extended CTD substrate with tighter affinity than nearly full-length Spt6, suggesting that the steric effects of additional domains in Spt6 influence the binding of the tSH2 domain to the multivalent CTD ligand.
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39
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Lyons DE, McMahon S, Ott M. A combinatorial view of old and new RNA polymerase II modifications. Transcription 2020; 11:66-82. [PMID: 32401151 DOI: 10.1080/21541264.2020.1762468] [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: 12/26/2022] Open
Abstract
The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.
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Affiliation(s)
- Danielle E Lyons
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Sarah McMahon
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
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40
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Key Players in HIV-1 Transcriptional Regulation: Targets for a Functional Cure. Viruses 2020; 12:v12050529. [PMID: 32403278 PMCID: PMC7291152 DOI: 10.3390/v12050529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 establishes a life-long infection when proviral DNA integrates into the host genome. The provirus can then either actively transcribe RNA or enter a latent state, without viral production. The switch between these two states is governed in great part by the viral protein, Tat, which promotes RNA transcript elongation. Latency is also influenced by the availability of host transcription factors, integration site, and the surrounding chromatin environment. The latent reservoir is established in the first few days of infection and serves as the source of viral rebound upon treatment interruption. Despite effective suppression of HIV-1 replication by antiretroviral therapy (ART), to below the detection limit, ART is ineffective at reducing the latent reservoir size. Elimination of this reservoir has become a major goal of the HIV-1 cure field. However, aside from the ideal total HIV-1 eradication from the host genome, an HIV-1 remission or functional cure is probably more realistic. The “block-and-lock” approach aims at the transcriptional silencing of the viral reservoir, to render suppressed HIV-1 promoters extremely difficult to reactivate from latency. There are unfortunately no clinically available HIV-1 specific transcriptional inhibitors. Understanding the mechanisms that regulate latency is expected to provide novel targets to be explored in cure approaches.
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41
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Chen C, Shu J, Li C, Thapa RK, Nguyen V, Yu K, Yuan ZC, Kohalmi SE, Liu J, Marsolais F, Huang S, Cui Y. RNA polymerase II-independent recruitment of SPT6L at transcription start sites in Arabidopsis. Nucleic Acids Res 2020; 47:6714-6725. [PMID: 31127286 PMCID: PMC6648355 DOI: 10.1093/nar/gkz465] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 01/20/2023] Open
Abstract
SPT6 is a conserved elongation factor that is associated with phosphorylated RNA polymerase II (RNAPII) during transcription. Recent transcriptome analysis in yeast mutants revealed its potential role in the control of transcription initiation at genic promoters. However, the mechanism by which this is achieved and how this is linked to elongation remains to be elucidated. Here, we present the genome-wide occupancy of Arabidopsis SPT6-like (SPT6L) and demonstrate its conserved role in facilitating RNAPII occupancy across transcribed genes. We also further demonstrate that SPT6L enrichment is unexpectedly shifted, from gene body to transcription start site (TSS), when its association with RNAPII is disrupted. Protein domains, required for proper function and enrichment of SPT6L on chromatin, are subsequently identified. Finally, our results suggest that recruitment of SPT6L at TSS is indispensable for its spreading along the gene body during transcription. These findings provide new insights into the mechanisms underlying SPT6L recruitment in transcription and shed light on the coordination between transcription initiation and elongation.
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Affiliation(s)
- Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Jie Shu
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Chenlong Li
- School of Life Sciences, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Raj K Thapa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada
| | - Kangfu Yu
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, Ontario N0R 1G0, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada
| | - Susanne E Kohalmi
- Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Jun Liu
- Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
| | - Shangzhi Huang
- School of Life Sciences, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario N5V 4T3, Canada.,Department of Biology, Western University, London, Ontario N6A 5B7, Canada
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42
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Fan H, Quan S, Qi S, Xu N, Wang Y. Novel Aspects of Nitrate Regulation in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:574246. [PMID: 33362808 PMCID: PMC7758431 DOI: 10.3389/fpls.2020.574246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is one of the most essential macronutrients for plant growth and development. Nitrate (NO3 -), the major form of N that plants uptake from the soil, acts as an important signaling molecule in addition to its nutritional function. Over the past decade, significant progress has been made in identifying new components involved in NO3 - regulation and starting to unravel the NO3 - regulatory network. Great reviews have been made recently by scientists on the key regulators in NO3 - signaling, NO3 - effects on plant development, and its crosstalk with phosphorus (P), potassium (K), hormones, and calcium signaling. However, several novel aspects of NO3 - regulation have not been previously reviewed in detail. Here, we mainly focused on the recent advances of post-transcriptional regulation and non-coding RNA (ncRNAs) in NO3 - signaling, and NO3 - regulation on leaf senescence and the circadian clock. It will help us to extend the general picture of NO3 - regulation and provide a basis for further exploration of NO3 - regulatory network.
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Affiliation(s)
- Hongmei Fan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yong Wang,
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43
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Scott DD, Aguilar LC, Kramar M, Oeffinger M. It's Not the Destination, It's the Journey: Heterogeneity in mRNA Export Mechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:33-81. [PMID: 31811630 DOI: 10.1007/978-3-030-31434-7_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The process of creating a translation-competent mRNA is highly complex and involves numerous steps including transcription, splicing, addition of modifications, and, finally, export to the cytoplasm. Historically, much of the research on regulation of gene expression at the level of the mRNA has been focused on either the regulation of mRNA synthesis (transcription and splicing) or metabolism (translation and degradation). However, in recent years, the advent of new experimental techniques has revealed the export of mRNA to be a major node in the regulation of gene expression, and numerous large-scale and specific mRNA export pathways have been defined. In this chapter, we will begin by outlining the mechanism by which most mRNAs are homeostatically exported ("bulk mRNA export"), involving the recruitment of the NXF1/TAP export receptor by the Aly/REF and THOC5 components of the TREX complex. We will then examine various mechanisms by which this pathway may be controlled, modified, or bypassed in order to promote the export of subset(s) of cellular mRNAs, which include the use of metazoan-specific orthologs of bulk mRNA export factors, specific cis RNA motifs which recruit mRNA export machinery via specific trans-acting-binding factors, posttranscriptional mRNA modifications that act as "inducible" export cis elements, the use of the atypical mRNA export receptor, CRM1, and the manipulation or bypass of the nuclear pore itself. Finally, we will discuss major outstanding questions in the field of mRNA export heterogeneity and outline how cutting-edge experimental techniques are providing new insights into and tools for investigating the intriguing field of mRNA export heterogeneity.
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Affiliation(s)
- Daniel D Scott
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | | | - Mathew Kramar
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Marlene Oeffinger
- Institut de recherches cliniques de Montréal, Montréal, QC, Canada. .,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada. .,Faculté de Médecine, Département de Biochimie, Université de Montréal, Montréal, QC, Canada.
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44
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Decker TM, Forné I, Straub T, Elsaman H, Ma G, Shah N, Imhof A, Eick D. Analog-sensitive cell line identifies cellular substrates of CDK9. Oncotarget 2019; 10:6934-6943. [PMID: 31857848 PMCID: PMC6916755 DOI: 10.18632/oncotarget.27334] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/07/2019] [Indexed: 11/25/2022] Open
Abstract
Transcriptional cyclin-dependent kinases regulate all phases of transcription. Cyclin-dependent kinase 9 (CDK9) has been implicated in the regulation of promoter-proximal pausing of RNA polymerase II and more recently in transcription termination. Study of the substrates of CDK9 has mostly been limited to in vitro approaches that lack a quantitative assessment of CDK9 activity. Here we analyzed the cellular phosphoproteome upon inhibition of CDK9 by combining analog-sensitive kinase technology with quantitative phosphoproteomics in Raji B-cells. Our analysis revealed the activity of CDK9 on 1102 phosphosites quantitatively, and we identified 120 potential cellular substrates. Furthermore, a substantial number of CDK9 substrates were described as splicing factors, highlighting the role of CDK9 in transcription-coupled splicing events. Based on comparison to in vitro data, our findings suggest that cellular context fundamentally impacts the activity of CDK9 and specific selection of its substrates.
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Affiliation(s)
- Tim-Michael Decker
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Germany.,Present address: Department of Biochemistry, University of Colorado, Boulder, USA
| | - Ignasi Forné
- Biomedical Center Munich, ZFP, Ludwig-Maximilian University Munich, Germany
| | - Tobias Straub
- Bioinformatic Unit, Biomedical Center Munich, Ludwig-Maximilian University Munich, Planegg-Martinsried, Germany
| | - Hesham Elsaman
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Germany
| | - Guoli Ma
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Germany
| | - Nilay Shah
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Germany.,Present address: Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Axel Imhof
- Biomedical Center Munich, ZFP, Ludwig-Maximilian University Munich, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Germany
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45
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Dronamraju R, Kerschner JL, Peck SA, Hepperla AJ, Adams AT, Hughes KD, Aslam S, Yoblinski AR, Davis IJ, Mosley AL, Strahl BD. Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction. Cell Rep 2019; 25:3476-3489.e5. [PMID: 30566871 PMCID: PMC6347388 DOI: 10.1016/j.celrep.2018.11.089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 10/22/2018] [Accepted: 11/21/2018] [Indexed: 02/07/2023] Open
Abstract
Spt6 is a histone chaperone that associates with RNA polymerase II and deposits nucleosomes in the wake of transcription. Although Spt6 has an essential function in nucleosome deposition, it is not known whether this function is influenced by post-translational modification. Here, we report that casein kinase II (CKII) phosphorylation of Spt6 is required for nucleosome occupancy at the 5′ ends of genes to prevent aberrant antisense transcription and enforce transcriptional directionality. Mechanistically, we show that CKII phosphorylation of Spt6 promotes the interaction of Spt6 with Spn1, a binding partner required for chromatin reassembly and full recruitment of Spt6 to genes. Our study defines a function for CKII phosphorylation in transcription and highlights the importance of post-translational modification in histone chaperone function. Dronamraju et al. show that the N terminus of Spt6 is phosphorylated by casein kinase II, which is required for proper Spt6-Spn1 interaction. CKII phosphorylation of Spt6 is pivotal to maintain nucleosome occupancy at the 5′ ends of genes, suppression of antisense transcription from the 5′ ends, and resistance to genotoxic agents.
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Affiliation(s)
- Raghuvar Dronamraju
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jenny L Kerschner
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Austin J Hepperla
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexander T Adams
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sadia Aslam
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Andrew R Yoblinski
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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46
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Gopalakrishnan R, Marr SK, Kingston RE, Winston F. A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation. Nucleic Acids Res 2019; 47:3888-3903. [PMID: 30793188 PMCID: PMC6486648 DOI: 10.1093/nar/gkz119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/05/2019] [Accepted: 02/13/2019] [Indexed: 12/28/2022] Open
Abstract
The transcription elongation factor Spt6 and the H3K36 methyltransferase Set2 are both required for H3K36 methylation and transcriptional fidelity in Saccharomyces cerevisiae. However, the nature of the requirement for Spt6 has remained elusive. By selecting for suppressors of a transcriptional defect in an spt6 mutant, we have isolated several highly clustered, dominant SET2 mutations (SET2sup mutations) in a region encoding a proposed autoinhibitory domain. SET2sup mutations suppress the H3K36 methylation defect in the spt6 mutant, as well as in other mutants that impair H3K36 methylation. We also show that SET2sup mutations overcome the requirement for certain Set2 domains for H3K36 methylation. In vivo, SET2sup mutants have elevated levels of H3K36 methylation and the purified Set2sup mutant protein has greater enzymatic activityin vitro. ChIP-seq studies demonstrate that the H3K36 methylation defect in the spt6 mutant, as well as its suppression by a SET2sup mutation, occurs at a step following the recruitment of Set2 to chromatin. Other experiments show that a similar genetic relationship between Spt6 and Set2 exists in Schizosaccharomyces pombe. Taken together, our results suggest a conserved mechanism by which the Set2 autoinhibitory domain requires multiple Set2 interactions to ensure that H3K36 methylation occurs specifically on actively transcribed chromatin.
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Affiliation(s)
| | - Sharon K Marr
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert E Kingston
- Department of Genetics, Harvard Medical School, Boston, MA, USA 02115.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA, USA 02115
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47
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Kneuss E, Munafò M, Eastwood EL, Deumer US, Preall JB, Hannon GJ, Czech B. Specialization of the Drosophila nuclear export family protein Nxf3 for piRNA precursor export. Genes Dev 2019; 33:1208-1220. [PMID: 31416967 PMCID: PMC6719614 DOI: 10.1101/gad.328690.119] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/15/2019] [Indexed: 12/29/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved small RNA-based immune system that protects animal germ cell genomes from the harmful effects of transposon mobilization. In Drosophila ovaries, most piRNAs originate from dual-strand clusters, which generate piRNAs from both genomic strands. Dual-strand clusters use noncanonical transcription mechanisms. Although transcribed by RNA polymerase II, cluster transcripts lack splicing signatures and poly(A) tails. mRNA processing is important for general mRNA export mediated by nuclear export factor 1 (Nxf1). Although UAP56, a component of the transcription and export complex, has been implicated in piRNA precursor export, it remains unknown how dual-strand cluster transcripts are specifically targeted for piRNA biogenesis by export from the nucleus to cytoplasmic processing centers. Here we report that dual-strand cluster transcript export requires CG13741/Bootlegger and the Drosophila nuclear export factor family protein Nxf3. Bootlegger is specifically recruited to piRNA clusters and in turn brings Nxf3. We found that Nxf3 specifically binds to piRNA precursors and is essential for their export to piRNA biogenesis sites, a process that is critical for germline transposon silencing. Our data shed light on how dual-strand clusters compensate for a lack of canonical features of mature mRNAs to be specifically exported via Nxf3, ensuring proper piRNA production.
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Affiliation(s)
- Emma Kneuss
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Undine-Sophie Deumer
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Jonathan B Preall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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48
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Chirackal Manavalan AP, Pilarova K, Kluge M, Bartholomeeusen K, Rajecky M, Oppelt J, Khirsariya P, Paruch K, Krejci L, Friedel CC, Blazek D. CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes. EMBO Rep 2019; 20:e47592. [PMID: 31347271 PMCID: PMC6727028 DOI: 10.15252/embr.201847592] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/09/2019] [Accepted: 06/24/2019] [Indexed: 12/31/2022] Open
Abstract
CDK12 is a kinase associated with elongating RNA polymerase II (RNAPII) and is frequently mutated in cancer. CDK12 depletion reduces the expression of homologous recombination (HR) DNA repair genes, but comprehensive insight into its target genes and cellular processes is lacking. We use a chemical genetic approach to inhibit analog‐sensitive CDK12, and find that CDK12 kinase activity is required for transcription of core DNA replication genes and thus for G1/S progression. RNA‐seq and ChIP‐seq reveal that CDK12 inhibition triggers an RNAPII processivity defect characterized by a loss of mapped reads from 3′ends of predominantly long, poly(A)‐signal‐rich genes. CDK12 inhibition does not globally reduce levels of RNAPII‐Ser2 phosphorylation. However, individual CDK12‐dependent genes show a shift of P‐Ser2 peaks into the gene body approximately to the positions where RNAPII occupancy and transcription were lost. Thus, CDK12 catalytic activity represents a novel link between regulation of transcription and cell cycle progression. We propose that DNA replication and HR DNA repair defects as a consequence of CDK12 inactivation underlie the genome instability phenotype observed in many cancers.
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Affiliation(s)
| | - Kveta Pilarova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Koen Bartholomeeusen
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Michal Rajecky
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Prashant Khirsariya
- Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic.,Center of Biomolecular and Cellular Engineering, International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Kamil Paruch
- Department of Chemistry, CZ Openscreen, Faculty of Science, Masaryk University, Brno, Czech Republic.,Center of Biomolecular and Cellular Engineering, International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- Center of Biomolecular and Cellular Engineering, International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic.,Department of Biology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
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49
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Li S, Almeida AR, Radebaugh CA, Zhang L, Chen X, Huang L, Thurston AK, Kalashnikova AA, Hansen JC, Luger K, Stargell LA. The elongation factor Spn1 is a multi-functional chromatin binding protein. Nucleic Acids Res 2019; 46:2321-2334. [PMID: 29300974 PMCID: PMC5861400 DOI: 10.1093/nar/gkx1305] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/19/2017] [Indexed: 12/17/2022] Open
Abstract
The process of transcriptional elongation by RNA polymerase II (RNAPII) in a chromatin context involves a large number of crucial factors. Spn1 is a highly conserved protein encoded by an essential gene and is known to interact with RNAPII and the histone chaperone Spt6. Spn1 negatively regulates the ability of Spt6 to interact with nucleosomes, but the chromatin binding properties of Spn1 are largely unknown. Here, we demonstrate that full length Spn1 (amino acids 1–410) binds DNA, histones H3–H4, mononucleosomes and nucleosomal arrays, and has weak nucleosome assembly activity. The core domain of Spn1 (amino acids 141–305), which is necessary and sufficient in Saccharomyces cerevisiae for growth under ideal growth conditions, is unable to optimally interact with histones, nucleosomes and/or DNA and fails to assemble nucleosomes in vitro. Although competent for binding with Spt6 and RNAPII, the core domain derivative is not stably recruited to the CYC1 promoter, indicating chromatin interactions are an important aspect of normal Spn1 functions in vivo. Moreover, strong synthetic genetic interactions are observed with Spn1 mutants and deletions of histone chaperone genes. Taken together, these results indicate that Spn1 is a histone binding factor with histone chaperone functions.
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Affiliation(s)
- Sha Li
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Adam R Almeida
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Catherine A Radebaugh
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ling Zhang
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Xu Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Liangqun Huang
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Alison K Thurston
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Anna A Kalashnikova
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Karolin Luger
- Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA.,Howard Hughes Medical Institute
| | - Laurie A Stargell
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.,Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523-1870, USA
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50
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The elongation factor Elof1 is required for mammalian gastrulation. PLoS One 2019; 14:e0219410. [PMID: 31276560 PMCID: PMC6611630 DOI: 10.1371/journal.pone.0219410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/21/2019] [Indexed: 01/07/2023] Open
Abstract
Despite having been sequenced over a decade ago, the functional significance of much of the mammalian genome remains unknown. The mouse has become the preeminent mammalian model for identifying endogenous gene function in vivo. Here we characterize the phenotype of a loss-of function allele for the evolutionarily conserved transcription factor, Elongation Factor Homolog 1 (Elof1). Recent work utilizing the yeast homolog, Elf1, has demonstrated that Elf1 associates with the RNA polymerase II complex to promote elongation by relieving the association of the template DNA strand with bound histones. Loss of Elof1 results in developmental delay and morphological defects during early mouse development resulting in peri-gastrulation lethality. Although Elof1 is highly conserved we observe tissue specific expression during gastrulation and in adult murine tissues, suggesting there may be other genes with similar function in diverse tissues or that mElof1 has adopted lineage specific functions. To better understand its function in mammalian transcription, we examined splice variants and find that Elof1 regulates mutually exclusive exon use in vivo. Distinct from what has been demonstrated in yeast, we demonstrate that Elof1 is essential for viability during mammalian gastrulation which may be due to a role mediating tissue specific exclusive exon use, a regulatory function unique to higher eukaryotes.
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