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Schynkel T, Snippenberg WV, Verniers K, Jang GM, Krogan NJ, Mestdagh P, Vandekerckhove L, Trypsteen W. Interactome of the HIV-1 proteome and human host RNA. EMBO Rep 2024; 25:4078-4090. [PMID: 39122863 PMCID: PMC11387401 DOI: 10.1038/s44319-024-00222-6] [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: 11/09/2023] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
The human immunodeficiency virus (HIV-1) is highly dependent on a variety of host factors. Beside proteins, host RNA molecules are reported to aid HIV-1 replication and latency maintenance. Here, we implement multiple workflows of native RNA immunoprecipitation and sequencing (nRIPseq) to determine direct host RNA interaction partners of all 18 HIV-1 (poly)proteins. We identify 1,727 HIV-1 protein - human RNA interactions in the Jurkat cell line and 1,558 interactions in SupT1 cells for a subset of proteins, and discover distinct cellular pathways that seem to be used or controlled by HIV-1 on the RNA level: Tat binds mRNAs of proteins involved in the super elongation complex (AFF1-4, Cyclin-T1). Correlation of the interaction scores (based on binding abundancy) allows identifying the highest confidence interactions, for which we perform a small-scale knockdown screen that leads to the identification of three HIV-1 protein binding RNA interactors involved in HIV-1 replication (AFF2, H4C9 and RPLP0).
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Affiliation(s)
- Tinus Schynkel
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium
| | - Willem van Snippenberg
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium
| | - Kimberly Verniers
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Pieter Mestdagh
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium.
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University and Ghent University Hospital, Ghent, 9000, Belgium.
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, 9000, Belgium.
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2
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D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2024:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [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: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
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Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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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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Che Z, Liu X, Dai Q, Fang K, Guo C, Yue J, Fang H, Xie P, Luo Z, Lin C. Distinct roles of two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA polymerase II transcription elongation. J Mol Cell Biol 2024; 15:mjad049. [PMID: 37528066 PMCID: PMC11113081 DOI: 10.1093/jmcb/mjad049] [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: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
The super elongation complex (SEC) containing positive transcription elongation factor b plays a critical role in regulating transcription elongation. AFF1 and AFF4, two members of the AF4/FMR2 family, act as central scaffold proteins of SEC and are associated with various human diseases. However, their precise roles in transcriptional control remain unclear. Here, we investigate differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites (TSSs). AFF1 mainly binds upstream of the TSS, while AFF4 is enriched downstream of the TSS. Notably, disruption of AFF4 results in slow elongation and early termination in a subset of AFF4-bound active genes, whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same subset of genes. Additionally, AFF1 knockdown increases AFF4 levels at chromatin, and vice versa. In summary, these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate RNA polymerase II transcription.
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Affiliation(s)
- Zhuanzhuan Che
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Xiaoxu Liu
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Qian Dai
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Ke Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Chenghao Guo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Junjie Yue
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Haitong Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Peng Xie
- School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhuojuan Luo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Chengqi Lin
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
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Long Q, Xiang M, Xiao L, Wang J, Guan X, Liu J, Liao C. The Biological Significance of AFF4: Promoting Transcription Elongation, Osteogenic Differentiation and Tumor Progression. Comb Chem High Throughput Screen 2024; 27:1403-1412. [PMID: 37815186 DOI: 10.2174/0113862073241079230920082056] [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: 12/20/2022] [Revised: 06/23/2023] [Accepted: 07/27/2023] [Indexed: 10/11/2023]
Abstract
As a member of the AF4/FMR2 (AFF) family, AFF4 is a scaffold protein in the superelongation complex (SEC). In this mini-view, we discuss the role of AFF4 as a transcription elongation factor that mediates HIV activation and replication and stem cell osteogenic differentiation. AFF4 also promotes the progression of head and neck squamous cell carcinoma, leukemia, breast cancer, bladder cancer and other malignant tumors. The biological function of AFF4 is largely achieved through SEC assembly, regulates SRY-box transcription factor 2 (SOX2), MYC, estrogen receptor alpha (ESR1), inhibitor of differentiation 1 (ID1), c-Jun and noncanonical nuclear factor-κB (NF-κB) transcription and combines with fusion in sarcoma (FUS), unique regulatory cyclins (CycT1), or mixed lineage leukemia (MLL). We explore the prospects of using AFF4 as a therapeutic in Acquired immunodeficiency syndrome (AIDS) and malignant tumors and its potential as a stemness regulator.
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Affiliation(s)
- Qian Long
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Mingli Xiang
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Linlin Xiao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Jiajia Wang
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Xiaoyan Guan
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Jianguo Liu
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
| | - Chengcheng Liao
- Department of Orthodontics II, Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, 563000, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, 563006, China
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6
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Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
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Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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7
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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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8
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Camara MB, Sobeh AM, Eichhorn CD. Progress in 7SK ribonucleoprotein structural biology. Front Mol Biosci 2023; 10:1154622. [PMID: 37051324 PMCID: PMC10083321 DOI: 10.3389/fmolb.2023.1154622] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK RNP assembly and function. Here, we review progress in understanding the structural basis of 7SK RNA folding, biogenesis, and RNP assembly.
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Affiliation(s)
- Momodou B. Camara
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Amr M. Sobeh
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Catherine D. Eichhorn
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, United States
- *Correspondence: Catherine D. Eichhorn,
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9
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Lloyd SM, Leon DB, Brady MO, Rodriguez D, McReynolds MP, Kweon J, Neely AE, Blumensaadt LA, Ho PJ, Bao X. CDK9 activity switch associated with AFF1 and HEXIM1 controls differentiation initiation from epidermal progenitors. Nat Commun 2022; 13:4408. [PMID: 35906225 PMCID: PMC9338292 DOI: 10.1038/s41467-022-32098-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 07/15/2022] [Indexed: 11/24/2022] Open
Abstract
Progenitors in epithelial tissues, such as human skin epidermis, continuously make fate decisions between self-renewal and differentiation. Here we show that the Super Elongation Complex (SEC) controls progenitor fate decisions by directly suppressing a group of "rapid response" genes, which feature high enrichment of paused Pol II in the progenitor state and robust Pol II elongation in differentiation. SEC's repressive role is dependent on the AFF1 scaffold, but not AFF4. In the progenitor state, AFF1-SEC associates with the HEXIM1-containing inactive CDK9 to suppress these rapid-response genes. A key rapid-response SEC target is ATF3, which promotes the upregulation of differentiation-activating transcription factors (GRHL3, OVOL1, PRDM1, ZNF750) to advance terminal differentiation. SEC peptidomimetic inhibitors or PKC signaling activates CDK9 and rapidly induces these transcription factors within hours in keratinocytes. Thus, our data suggest that the activity switch of SEC-associated CDK9 underlies the initial processes bifurcating progenitor fates between self-renewal and differentiation.
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Affiliation(s)
- Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University, Chicago, IL, 60611, USA
| | - Daniel B Leon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Mari O Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Deborah Rodriguez
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Madison P McReynolds
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Junghun Kweon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Amy E Neely
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Laura A Blumensaadt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
- Simpson Querrey Institute for Epigenetics, Northwestern University, Chicago, IL, 60611, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA.
- Department of Dermatology, Northwestern University, Chicago, IL, 60611, USA.
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10
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Fang Y, Cao H, Gong X, Chen Y, Zhuang Y, Zhou S, Chen Y, Jiang Y, Ji X, Peng H, Jing X. AFF4 Predicts the Prognosis of Colorectal Cancer Patients and Suppresses Colorectal Cancer Metastasis via Promoting CDH1 Expression. Front Oncol 2022; 12:797392. [PMID: 35223479 PMCID: PMC8865618 DOI: 10.3389/fonc.2022.797392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION AF4/FMR2 family member 4 (AFF4) is a core component of super elongation complex (SEC) and regulates the transcription elongation of many genes. AFF4 depletion or amplification is associated with multiple cancers, but its role in colorectal cancer (CRC) has not been investigated so far. METHODS qRT-PCR and Western blot analyzed AFF4 expression in the paired clinical CRC tissues. The patients' overall survival curve was determined using the Kaplan-Meier plotter. In vitro experiments, such as cell proliferation, migration, and invasion, were used to preliminarily ascertain the role of AFF4 in CRC. A CRC cell liver metastasis animal model was well established. Livers were harvested and examined histologically by a series of indicators, such as tumor nodules, liver weight, ALT/AST activity, and tumor cell identification by hematoxylin-eosin (HE) staining. RESULTS We firstly examined the expression of AFF4 in colorectal cancer and normal tissues by collecting paired CRC tissues and adjacent normal tissues, revealing that AFF4 was significantly downregulated in CRC patients and lower expression of AFF4 was correlated with poor prognosis. Next, we observed that presence or absence of AFF4 in CRC cells had no effect on cancer cell proliferation, while AFF4 depletion significantly promoted the migration or invasion of CRC cells in vitro. Furthermore, we confirmed that AFF4 deficiency enhanced the metastatic capacity of CRC cells in vivo. Mechanistically, we found that AFF4 upregulated the transcription of CDH1 gene, which encodes E-cadherin and suppresses the epithelial-mesenchymal transition (EMT). Knockdown of AFF4 interfered with CDH1 transcription, resulting in downregulation of E-cadherin expression and the progression of CRC. Moreover, restored CDH1 expression could rescue the phenotype of CRC cells without AFF4. CONCLUSIONS Collectively, our data demonstrated that AFF4 served as a significant novel regulator of CRC via CDH1 transcriptional regulation and a potential effective therapy target for patients with CRC.
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Affiliation(s)
- Yi Fang
- Emergency Department, Shanghai Tenth People's Hospital, Shanghai, China
| | - Hua Cao
- Emergency Department, Shanghai Tenth People's Hospital, Shanghai, China
| | - Xiaoyong Gong
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanqing Chen
- Emergency Department, Shanghai Tenth People's Hospital, Shanghai, China
| | - Yugang Zhuang
- Emergency Department, Shanghai Tenth People's Hospital, Shanghai, China
| | - Shuqin Zhou
- Emergency Department, Shanghai Tenth People's Hospital, Shanghai, China
| | - Yuanzhuo Chen
- Emergency Department, Shanghai Tenth People's Hospital, Shanghai, China
| | - Yimei Jiang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaopin Ji
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hu Peng
- Emergency Department, Shanghai Tenth People's Hospital, Shanghai, China
| | - Xiaoqian Jing
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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An effector index to predict target genes at GWAS loci. Hum Genet 2022; 141:1431-1447. [PMID: 35147782 DOI: 10.1007/s00439-022-02434-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/15/2022] [Indexed: 11/04/2022]
Abstract
Drug development and biological discovery require effective strategies to map existing genetic associations to causal genes. To approach this problem, we selected 12 common diseases and quantitative traits for which highly powered genome-wide association studies (GWAS) were available. For each disease or trait, we systematically curated positive control gene sets from Mendelian forms of the disease and from targets of medicines used for disease treatment. We found that these positive control genes were highly enriched in proximity of GWAS-associated single-nucleotide variants (SNVs). We then performed quantitative assessment of the contribution of commonly used genomic features, including open chromatin maps, expression quantitative trait loci (eQTL), and chromatin conformation data. Using these features, we trained and validated an Effector Index (Ei), to map target genes for these 12 common diseases and traits. Ei demonstrated high predictive performance, both with cross-validation on the training set, and an independently derived set for type 2 diabetes. Key predictive features included coding or transcript-altering SNVs, distance to gene, and open chromatin-based metrics. This work outlines a simple, understandable approach to prioritize genes at GWAS loci for functional follow-up and drug development, and provides a systematic strategy for prioritization of GWAS target genes.
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12
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Chen Y, Vos SM, Dienemann C, Ninov M, Urlaub H, Cramer P. Allosteric transcription stimulation by RNA polymerase II super elongation complex. Mol Cell 2021; 81:3386-3399.e10. [PMID: 34265249 DOI: 10.1016/j.molcel.2021.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/19/2021] [Accepted: 06/17/2021] [Indexed: 01/11/2023]
Abstract
The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.
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Affiliation(s)
- Ying Chen
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Seychelle M Vos
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Momchil Ninov
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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13
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Aso H, Nagaoka S, Kawakami E, Ito J, Islam S, Tan BJY, Nakaoka S, Ashizaki K, Shiroguchi K, Suzuki Y, Satou Y, Koyanagi Y, Sato K. Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In Vivo. Cell Rep 2021; 32:107887. [PMID: 32668246 DOI: 10.1016/j.celrep.2020.107887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
For eradication of HIV-1 infection, it is important to elucidate the detailed features and heterogeneity of HIV-1-infected cells in vivo. To reveal multiple characteristics of HIV-1-producing cells in vivo, we use a hematopoietic-stem-cell-transplanted humanized mouse model infected with GFP-encoding replication-competent HIV-1. We perform multiomics experiments using recently developed technology to identify the features of HIV-1-infected cells. Genome-wide HIV-1 integration-site analysis reveals that productive HIV-1 infection tends to occur in cells with viral integration into transcriptionally active genomic regions. Bulk transcriptome analysis reveals that a high level of viral mRNA is transcribed in HIV-1-infected cells. Moreover, single-cell transcriptome analysis shows the heterogeneity of HIV-1-infected cells, including CXCL13high cells and a subpopulation with low expression of interferon-stimulated genes, which can contribute to efficient viral spread in vivo. Our findings describe multiple characteristics of HIV-1-producing cells in vivo, which could provide clues for the development of an HIV-1 cure.
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Affiliation(s)
- Hirofumi Aso
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Shumpei Nagaoka
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Eiryo Kawakami
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan; Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba 2608670, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Saiful Islam
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Benjy Jek Yang Tan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 0600810, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Koichi Ashizaki
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan
| | - Katsuyuki Shiroguchi
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 5650874, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 2300045, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 2778561, Japan
| | - Yorifumi Satou
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan.
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14
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Yue J, Dai Q, Hao S, Zhu S, Liu X, Tang Z, Li M, Fang H, Lin C, Luo Z. Suppression of the NTS-CPS1 regulatory axis by AFF1 in lung adenocarcinoma cells. J Biol Chem 2021; 296:100319. [PMID: 33493519 PMCID: PMC7949158 DOI: 10.1016/j.jbc.2021.100319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/05/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Upregulation of the neuropeptide neurotensin (NTS) in a subgroup of lung cancers has been linked to poor prognosis. However, the regulatory pathway centered on NTS in lung cancer remains unclear. Here we identified the NTS-specific enhancer in lung adenocarcinoma cells. The AF4/FMR2 (AFF) family protein AFF1 occupies the NTS enhancer and inhibits NTS transcription. Clustering analysis of lung adenocarcinoma gene expression data demonstrated that NTS expression is highly positively correlated with the expression of the oncogenic factor CPS1. Detailed analyses demonstrated that the IL6 pathway antagonizes NTS in regulating CPS1. Thus, our analyses revealed a novel NTS-centered regulatory axis, consisting of AFF1 as a master transcription suppressor and IL6 as an antagonist in lung adenocarcinoma cells.
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Affiliation(s)
- Junjie Yue
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Qian Dai
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Shaohua Hao
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Shiqi Zhu
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Xiaoxu Liu
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zhiqun Tang
- Singapore Eye research Institute, Singapore, Singapore
| | - Meng Li
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Haitong Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chengqi Lin
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.
| | - Zhuojuan Luo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.
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15
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Tatum NJ, Endicott JA. Chatterboxes: the structural and functional diversity of cyclins. Semin Cell Dev Biol 2020; 107:4-20. [PMID: 32414682 DOI: 10.1016/j.semcdb.2020.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022]
Abstract
Proteins of the cyclin family have divergent sequences and execute diverse roles within the cell while sharing a common fold: the cyclin box domain. Structural studies of cyclins have played a key role in our characterization and understanding of cellular processes that they control, though to date only ten of the 29 CDK-activating cyclins have been structurally characterized by X-ray crystallography or cryo-electron microscopy with or without their cognate kinases. In this review, we survey the available structures of human cyclins, highlighting their molecular features in the context of their cellular roles. We pay particular attention to how cyclin activity is regulated through fine control of degradation motif recognition and ubiquitination. Finally, we discuss the emergent roles of cyclins independent of their roles as cyclin-dependent protein kinase activators, demonstrating the cyclin box domain to be a versatile and generalized scaffolding domain for protein-protein interactions across the cellular machinery.
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Affiliation(s)
- Natalie J Tatum
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Jane A Endicott
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.
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16
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Pinto DO, DeMarino C, Vo TT, Cowen M, Kim Y, Pleet ML, Barclay RA, Noren Hooten N, Evans MK, Heredia A, Batrakova EV, Iordanskiy S, Kashanchi F. Low-Level Ionizing Radiation Induces Selective Killing of HIV-1-Infected Cells with Reversal of Cytokine Induction Using mTOR Inhibitors. Viruses 2020; 12:E885. [PMID: 32823598 PMCID: PMC7472203 DOI: 10.3390/v12080885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
HIV-1 infects 39.5 million people worldwide, and cART is effective in preventing viral spread by reducing HIV-1 plasma viral loads to undetectable levels. However, viral reservoirs persist by mechanisms, including the inhibition of autophagy by HIV-1 proteins (i.e., Nef and Tat). HIV-1 reservoirs can be targeted by the "shock and kill" strategy, which utilizes latency-reversing agents (LRAs) to activate latent proviruses and immunotarget the virus-producing cells. Yet, limitations include reduced LRA permeability across anatomical barriers and immune hyper-activation. Ionizing radiation (IR) induces effective viral activation across anatomical barriers. Like other LRAs, IR may cause inflammation and modulate the secretion of extracellular vesicles (EVs). We and others have shown that cells may secrete cytokines and viral proteins in EVs and, therefore, LRAs may contribute to inflammatory EVs. In the present study, we mitigated the effects of IR-induced inflammatory EVs (i.e., TNF-α), through the use of mTOR inhibitors (mTORi; Rapamycin and INK128). Further, mTORi were found to enhance the selective killing of HIV-1-infected myeloid and T-cell reservoirs at the exclusion of uninfected cells, potentially via inhibition of viral transcription/translation and induction of autophagy. Collectively, the proposed regimen using cART, IR, and mTORi presents a novel approach allowing for the targeting of viral reservoirs, prevention of immune hyper-activation, and selectively killing latently infected HIV-1 cells.
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Affiliation(s)
- Daniel O. Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
| | - Thy T. Vo
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
| | - Yuriy Kim
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
| | - Michelle L. Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
| | - Robert A. Barclay
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (N.N.H.); (M.K.E.)
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (N.N.H.); (M.K.E.)
| | - Alonso Heredia
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Elena V. Batrakova
- Department of Medicine, University of North Carolina HIV Cure Center; University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA;
| | - Sergey Iordanskiy
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA;
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (D.O.P.); (C.D.); (T.T.V.); (M.C.); (Y.K.); (M.L.P.); (R.A.B.)
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17
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Walton SJ, Wang H, Quintero-Cadena P, Bateman A, Sternberg PW. Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression. Genetics 2020; 215:1039-1054. [PMID: 32518061 PMCID: PMC7404228 DOI: 10.1534/genetics.120.302923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/27/2020] [Indexed: 02/08/2023] Open
Abstract
To mitigate the deleterious effects of temperature increases on cellular organization and proteotoxicity, organisms have developed mechanisms to respond to heat stress. In eukaryotes, HSF1 is the master regulator of the heat shock transcriptional response, but the heat shock response pathway is not yet fully understood. From a forward genetic screen for suppressors of heat-shock-induced gene expression in Caenorhabditis elegans, we found a new allele of hsf-1 that alters its DNA-binding domain, and we found three additional alleles of sup-45, a previously molecularly uncharacterized genetic locus. We identified sup-45 as one of the two hitherto unknown C. elegans orthologs of the human AF4/FMR2 family proteins, which are involved in regulation of transcriptional elongation rate. We thus renamed sup-45 as affl-2 (AF4/FMR2-Like). Through RNA-seq, we demonstrated that affl-2 mutants are deficient in heat-shock-induced transcription. Additionally, affl-2 mutants have herniated intestines, while worms lacking its sole paralog (affl-1) appear wild type. AFFL-2 is a broadly expressed nuclear protein, and nuclear localization of AFFL-2 is necessary for its role in heat shock response. affl-2 and its paralog are not essential for proper HSF-1 expression and localization after heat shock, which suggests that affl-2 may function downstream of, or parallel to, hsf-1 Our characterization of affl-2 provides insights into the regulation of heat-shock-induced gene expression to protect against heat stress.
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Affiliation(s)
- Sophie J Walton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Han Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Porfirio Quintero-Cadena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute, (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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18
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Shao H, Zhu Q, Lu H, Chang A, Gao C, Zhou Q, Luo K. HEXIM1 controls P-TEFb processing and regulates drug sensitivity in triple-negative breast cancer. Mol Biol Cell 2020; 31:1867-1878. [PMID: 32520633 PMCID: PMC7525814 DOI: 10.1091/mbc.e19-12-0704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
The positive transcription elongation factor b (P-TEFb), composed of CDK9 and cyclin T, stimulates transcriptional elongation by RNA polymerase (Pol) II and regulates cell growth and differentiation. Recently, we demonstrated that P-TEFb also controls the expression of EMT regulators to promote breast cancer progression. In the nucleus, more than half of P-TEFb are sequestered in the inactive-state 7SK snRNP complex. Here, we show that the assembly of the 7SK snRNP is preceded by an intermediate complex between HEXIM1 and P-TEFb that allows transfer of the kinase active P-TEFb from Hsp90 to 7SK snRNP for its suppression. Down-regulation of HEXIM1 locks P-TEFb in the Hsp90 complex, keeping it in the active state to enhance breast cancer progression, but also rendering the cells highly sensitive to Hsp90 inhibition. Because HEXIM1 is often down-regulated in human triple-negative breast cancer (TNBC), these cells are particularly sensitive to Hsp90 inhibition. Our study provides a mechanistic explanation for the increased sensitivity of TNBC to Hsp90 inhibition.
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Affiliation(s)
- Hengyi Shao
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Qingwei Zhu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Huasong Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Amanda Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Carol Gao
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Kunxin Luo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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19
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Wu J, Xue Y, Gao X, Zhou Q. Host cell factors stimulate HIV-1 transcription by antagonizing substrate-binding function of Siah1 ubiquitin ligase to stabilize transcription elongation factor ELL2. Nucleic Acids Res 2020; 48:7321-7332. [PMID: 32479599 PMCID: PMC7367184 DOI: 10.1093/nar/gkaa461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022] Open
Abstract
The Siah1 and Siah2 ubiquitin ligases are implicated in diverse biological processes ranging from cellular stress responses, signaling to transcriptional regulation. A key substrate of Siah1 is ELL2, which undergoes proteolysis upon polyubiquitination. ELL2 stimulates transcriptional elongation and is a subunit of the Super Elongation Complex (SEC) essential for HIV-1 transactivation. Previously, multiple transcriptional and post-translational mechanisms are reported to control Siah's expression and activity. Here we show that the activity of Siah1/2 can also be suppressed by host cell factor 1 (HCF1), and the hitherto poorly characterized HCF2, which themselves are not degraded but can bind and block the substrate-binding domain (SBD) of Siah1/2 to prevent their autoubiquitination and trans-ubiquitination of downstream targets including ELL2. This effect stabilizes ELL2 and enhances the ELL2-SEC formation for robust HIV-1 transactivation. Thus, our study not only identifies HCF1/2 as novel activators of HIV-1 transcription through inhibiting Siah1 to stabilize ELL2, but also reveals the SBD of Siah1/2 as a previously unrecognized new target for HCF1/2 to exert this inhibition.
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Affiliation(s)
- Jun Wu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Yuhua Xue
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiang Gao
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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20
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Chen Y, Wang Y, Lin W, Sheng R, Wu Y, Xu R, Zhou C, Yuan Q. AFF1 inhibits adipogenic differentiation via targeting TGM2 transcription. Cell Prolif 2020; 53:e12831. [PMID: 32441391 PMCID: PMC7309944 DOI: 10.1111/cpr.12831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/16/2020] [Accepted: 04/28/2020] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES AF4/FMR2 family member 1 (AFF1), known as a central scaffolding protein of super elongation complex (SEC), regulates gene transcription. We previously reported that AFF1 inhibited osteogenic differentiation of human mesenchymal stromal/stem cells (hMSCs). However, its role in adipogenic differentiation has not been elucidated. MATERIALS AND METHODS hMSCs and 3T3-L1 pre-adipocytes were cultured and induced for adipogenic differentiation. Small interfering RNAs (siRNAs) were applied to deplete AFF1 while lentiviruses expressing HA-Aff1 were used for overexpression. Oil Red O staining, triglyceride (TAG) quantification, quantitative real-time PCR (qPCR), Western blot analysis, immunofluorescence staining, RNA sequencing (RNA-seq) analysis and ChIP-qPCR were performed. To evaluate the adipogenesis in vivo, BALB/c nude mice were subcutaneously injected with Aff1-overexpressed 3T3-L1 pre-adipocytes. RESULTS AFF1 depletion leads to an enhanced adipogenesis in both hMSCs and 3T3-L1 pre-adipocytes. Overexpression of Aff1 in 3T3-L1 cells results in the reduction of adipogenic differentiation and less adipose tissue formation in vivo. Mechanistically, AFF1 binds to the promoter region of Tgm2 gene and regulates its transcription. Overexpression of Tgm2 largely rescues adipogenic differentiation of Aff1-deficient cells. CONCLUSIONS Our data indicate that AFF1 inhibits adipogenic differentiation by regulating the transcription of TGM2.
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Affiliation(s)
- Yaqian Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuan Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rui Sheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yunshu Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ruoshi Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenchen Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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21
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Shukla A, Ramirez NGP, D’Orso I. HIV-1 Proviral Transcription and Latency in the New Era. Viruses 2020; 12:v12050555. [PMID: 32443452 PMCID: PMC7291205 DOI: 10.3390/v12050555] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Three decades of extensive work in the HIV field have revealed key viral and host cell factors controlling proviral transcription. Various models of transcriptional regulation have emerged based on the collective information from in vitro assays and work in both immortalized and primary cell-based models. Here, we provide a recount of the past and current literature, highlight key regulatory aspects, and further describe potential limitations of previous studies. We particularly delve into critical steps of HIV gene expression including the role of the integration site, nucleosome positioning and epigenomics, and the transition from initiation to pausing and pause release. We also discuss open questions in the field concerning the generality of previous regulatory models to the control of HIV transcription in patients under suppressive therapy, including the role of the heterogeneous integration landscape, clonal expansion, and bottlenecks to eradicate viral persistence. Finally, we propose that building upon previous discoveries and improved or yet-to-be discovered technologies will unravel molecular mechanisms of latency establishment and reactivation in a “new era”.
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22
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Basu S, Nandy A, Biswas D. Keeping RNA polymerase II on the run: Functions of MLL fusion partners in transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194563. [PMID: 32348849 DOI: 10.1016/j.bbagrm.2020.194563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/13/2020] [Accepted: 04/13/2020] [Indexed: 12/21/2022]
Abstract
Since the identification of key MLL fusion partners as transcription elongation factors regulating expression of HOX cluster genes during hematopoiesis, extensive work from the last decade has resulted in significant progress in our overall mechanistic understanding of role of MLL fusion partner proteins in transcriptional regulation of diverse set of genes beyond just the HOX cluster. In this review, we are going to detail overall understanding of role of MLL fusion partner proteins in transcriptional regulation and thus provide mechanistic insights into possible MLL fusion protein-mediated transcriptional misregulation leading to aberrant hematopoiesis and leukemogenesis.
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Affiliation(s)
- Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 32, India.
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ELL-associated factors EAF1/2 negatively regulate HIV-1 transcription through inhibition of Super Elongation Complex formation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194508. [PMID: 32087315 DOI: 10.1016/j.bbagrm.2020.194508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 01/03/2023]
Abstract
The ELL (ELL1 and ELL2)-containing Super Elongation Complex (SEC) is required for efficient HIV-1 transactivation by the viral-encoded Tat protein. EAF1 and EAF2 are ELL-associated factors and considered as positive regulators of ELL. However, their role in HIV-1 transcriptional control is unknown. In this study, we show that EAF1/2 inhibit the SEC-dependent and Tat-activated HIV-1 transcription. EAF1/2 are found to interact with the SEC components in an ELL1/2-dependent manner. Surprisingly, the depletion of EAF1/2 increases the SEC formation and occupancy on the HIV-1 proviral DNA, thereby stimulating Tat transactivation of HIV-1. Although EAF1/2 interact with members of the SEC in a ELL-dependent manner, this interaction competes with the binding of the scaffolding subunit AFF1 with ELL, thus reducing the SEC formation. Together, these data reveal how EAF1/2 regulate the SEC formation to control HIV-1 transcription.
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Tang D, Chen C, Liao G, Liu J, Liao B, Huang Q, Chen Q, Zhao J, Jiang H, Duan J, Huang J, Wang K, Wang J, Zhou C, Chu W, Li W, Sun B, Li Z, Dai L, Fu X, Cheng W, Xue Y, Qi S. Structural and functional insight into the effect of AFF4 dimerization on activation of HIV-1 proviral transcription. Cell Discov 2020; 6:7. [PMID: 32128251 PMCID: PMC7026398 DOI: 10.1038/s41421-020-0142-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/23/2019] [Indexed: 02/05/2023] Open
Abstract
Super elongation complex (SEC) is a positive regulator of RNA polymerase II, which is required for HIV-1 proviral transcription. AFF1/4 is the scaffold protein that recruits other components of SEC and forms dimer depending on its THD domain (TPRL with Handle Region Dimerization Domain). Here we report the crystal structure of the human AFF4-THD at the resolution of 2.4 Å. The α4, α5, and α6 of one AFF4-THD mediate the formation of a dimer and pack tightly against the equivalent part of the second molecule in the dimer of AFF-THD. Mutagenesis analysis revealed that single mutations of either Phe1014 or Tyr1096 of AFF4 to alanine impair the formation of the AFF4 dimer. In addition, transactivation assay also indicated that Phe1014 and Tyr1096 of AFF4 are critical to the transactivation activity of AFF4. Interestingly, the corresponding residues Phe1063 and Tyr1145 in AFF1 have an effect on the transactivation of HIV-1 provirus. However, such mutations of AFF1/4 have no effect on the interaction of AFF1/4 with other subunits of the SEC. Together, our data demonstrated that the dimerization of AFF1/4 is essential to transactivation of HIV-1 provirus.
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Affiliation(s)
- Dan Tang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Chunjing Chen
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102 China
| | - Ga Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041 China
| | - Jiaming Liu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Banghua Liao
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - QingQing Huang
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102 China
| | - Qianqian Chen
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Jiahui Zhao
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Hui Jiang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Jinsong Duan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Jin Huang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Kunjie Wang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Cuiyan Zhou
- School of Biomedicine in Tsinghua University, National Protein Science Facility, Beijing, 100084 China
| | - Wendan Chu
- School of Biomedicine in Tsinghua University, National Protein Science Facility, Beijing, 100084 China
| | - Wenqi Li
- School of Biomedicine in Tsinghua University, National Protein Science Facility, Beijing, 100084 China
| | - Bo Sun
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204 China
| | - Zhonghan Li
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Lunzhi Dai
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Xianghui Fu
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Wei Cheng
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
| | - Yuhua Xue
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian 361102 China
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041 China
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P-TEFb as A Promising Therapeutic Target. Molecules 2020; 25:molecules25040838. [PMID: 32075058 PMCID: PMC7070488 DOI: 10.3390/molecules25040838] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) was first identified as a general factor that stimulates transcription elongation by RNA polymerase II (RNAPII), but soon afterwards it turned out to be an essential cellular co-factor of human immunodeficiency virus (HIV) transcription mediated by viral Tat proteins. Studies on the mechanisms of Tat-dependent HIV transcription have led to radical advances in our knowledge regarding the mechanism of eukaryotic transcription, including the discoveries that P-TEFb-mediated elongation control of cellular transcription is a main regulatory step of gene expression in eukaryotes, and deregulation of P-TEFb activity plays critical roles in many human diseases and conditions in addition to HIV/AIDS. P-TEFb is now recognized as an attractive and promising therapeutic target for inflammation/autoimmune diseases, cardiac hypertrophy, cancer, infectious diseases, etc. In this review article, I will summarize our knowledge about basic P-TEFb functions, the regulatory mechanism of P-TEFb-dependent transcription, P-TEFb’s involvement in biological processes and diseases, and current approaches to manipulating P-TEFb functions for the treatment of these diseases.
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Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2019; 19:464-478. [PMID: 29740129 DOI: 10.1038/s41580-018-0010-5] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dynamic regulation of transcription elongation by RNA polymerase II (Pol II) is an integral part of the implementation of gene expression programmes during development. In most metazoans, the majority of transcribed genes exhibit transient pausing of Pol II at promoter-proximal regions, and the release of Pol II into gene bodies is controlled by many regulatory factors that respond to environmental and developmental cues. Misregulation of the elongation stage of transcription is implicated in cancer and other human diseases, suggesting that mechanistic understanding of transcription elongation control is therapeutically relevant. In this Review, we discuss the features, establishment and maintenance of Pol II pausing, the transition into productive elongation, the control of transcription elongation by enhancers and by factors of other cellular processes, such as topoisomerases and poly(ADP-ribose) polymerases (PARPs), and the potential of therapeutic targeting of the elongation stage of transcription by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Chen Y, Cramer P. Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization. J Biol Chem 2019; 294:10663-10673. [PMID: 31147444 PMCID: PMC6615702 DOI: 10.1074/jbc.ra119.008577] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/27/2019] [Indexed: 12/12/2022] Open
Abstract
AF4/FMR2 family member 4 (AFF4) is the scaffold protein of the multisubunit super-elongation complex, which plays key roles in the release of RNA polymerase II from promoter-proximal pausing and in the transactivation of HIV-1 transcription. AFF4 consists of an intrinsically disordered N-terminal region that interacts with other super-elongation complex subunits and a C-terminal homology domain (CHD) that is conserved among AF4/FMR2 family proteins, including AFF1, AFF2, AFF3, and AFF4. Here, we solved the X-ray crystal structure of the CHD in human AFF4 (AFF4-CHD) to 2.2 Å resolution and characterized its biochemical properties. The structure disclosed that AFF4-CHD folds into a novel domain that consists of eight helices and is distantly related to tetratrico peptide repeat motifs. Our analyses further revealed that AFF4-CHD mediates the formation of an AFF4 homodimer or an AFF1-AFF4 heterodimer. Results from fluorescence anisotropy experiments suggested that AFF4-CHD interacts with both RNA and DNA in vitro Furthermore, we identified a surface loop region in AFF4-CHD as a substrate for the P-TEFb kinase cyclin-dependent kinase 9, which triggers release of polymerase II from promoter-proximal pausing sites. In conclusion, the AFF-CHD structure and biochemical analyses reported here reveal the molecular basis for the homo- and heterodimerization of AFF proteins and implicate the AFF4-CHD in nucleic acid interactions. The high conservation of the CHD among several other proteins suggests that our results are also relevant for understanding other CHD-containing proteins and their dimerization behavior.
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Affiliation(s)
- Ying Chen
- From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick Cramer
- From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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28
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Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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29
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Metabolome-based signature of disease pathology in MS. Mult Scler Relat Disord 2019; 31:12-21. [PMID: 30877925 DOI: 10.1016/j.msard.2019.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/06/2019] [Accepted: 03/05/2019] [Indexed: 11/21/2022]
Abstract
BACKGROUND Diagnostic delays are common for multiple sclerosis (MS) since diagnosis typically depends on the presentation of nonspecific clinical symptoms together with radiologically-determined central nervous system (CNS) lesions. It is important to reduce diagnostic delays as earlier initiation of disease modifying therapies mitigates long-term disability. Developing a metabolomic blood-based MS biomarker is attractive, but prior efforts have largely focused on specific subsets of metabolite classes or analytical platforms. Thus, there are opportunities to interrogate metabolite profiles using more expansive and comprehensive approaches for developing MS biomarkers and for advancing our understanding of MS pathogenesis. METHODS To identify putative blood-based MS biomarkers, we comprehensively interrogated the metabolite profiles in 12 non-Hispanic white, non-smoking, male MS cases who were drug naïve for 3 months prior to biospecimen collection and 13 non-Hispanic white, non-smoking male controls who were frequency matched to cases by age and body mass index. We performed untargeted two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS) and targeted lipidomic and amino acid analysis on serum. 325 metabolites met quality control and supervised machine learning was used to identify metabolites most informative for MS status. The discrimination potential of these select metabolites were assessed using receiver operator characteristic curves based on logistic models; top candidate metabolites were defined as having area under the curves (AUC) >80%. The associations between whole-genome expression data and the top candidate metabolites were examined, followed by pathway enrichment analyses. Similar associations were examined for 175 putative MS risk variants and the top candidate metabolites. RESULTS 12 metabolites were determined to be informative for MS status, of which 6 had AUCs >80%: pyroglutamate, laurate, acylcarnitine C14:1, N-methylmaleimide, and 2 phosphatidylcholines (PC ae 40:5, PC ae 42:5). These metabolites participate in glutathione metabolism, fatty acid metabolism/oxidation, cellular membrane composition, and transient receptor potential channel signaling. Pathway analyses based on the gene expression association for each metabolite suggested enrichment for pathways associated with apoptosis and mitochondrial dysfunction. Interestingly, the predominant MS genetic risk allele HLA-DRB1×15:01 was associated with one of the 6 top metabolites. CONCLUSION Our analysis represents the most comprehensive description of metabolic changes associated with MS in serum, to date, with the inclusion of genomic and genetic information. We identified atypical metabolic processes that differed between MS patients and controls, which may enable the development of biological targets for diagnosis and treatment.
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Zhu X, Liu Y, Yu J, Du J, Guo R, Feng Y, Zhong G, Jiang Y, Lin J. LncRNA HOXA-AS2 represses endothelium inflammation by regulating the activity of NF-κB signaling. Atherosclerosis 2019; 281:38-46. [DOI: 10.1016/j.atherosclerosis.2018.12.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 12/06/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022]
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31
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Li Z, Wu J, Chavez L, Hoh R, Deeks SG, Pillai SK, Zhou Q. Reiterative Enrichment and Authentication of CRISPRi Targets (REACT) identifies the proteasome as a key contributor to HIV-1 latency. PLoS Pathog 2019; 15:e1007498. [PMID: 30645648 PMCID: PMC6333332 DOI: 10.1371/journal.ppat.1007498] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023] Open
Abstract
The establishment of HIV-1 latency gives rise to persistent chronic infection that requires life-long treatment. To reverse latency for viral eradiation, the HIV-1 Tat protein and its associated ELL2-containing Super Elongation Complexes (ELL2-SECs) are essential to activate HIV-1 transcription. Despite efforts to identify effective latency-reversing agents (LRA), avenues for exposing latent HIV-1 remain inadequate, prompting the need to identify novel LRA targets. Here, by conducting a CRISPR interference-based screen to reiteratively enrich loss-of-function genotypes that increase HIV-1 transcription in latently infected CD4+ T cells, we have discovered a key role of the proteasome in maintaining viral latency. Downregulating or inhibiting the proteasome promotes Tat-transactivation in cell line models. Furthermore, the FDA-approved proteasome inhibitors bortezomib and carfilzomib strongly synergize with existing LRAs to reactivate HIV-1 in CD4+ T cells from antiretroviral therapy-suppressed individuals without inducing cell activation or proliferation. Mechanistically, downregulating/inhibiting the proteasome elevates the levels of ELL2 and ELL2-SECs to enable Tat-transactivation, indicating the proteasome-ELL2 axis as a key regulator of HIV-1 latency and promising target for therapeutic intervention. To cure chronic HIV-1 infection requires reversal of HIV-1 latency from latently infected CD4+ T cells. A key step in HIV latency reversal is the recruitment of Super Elongation Complexes (SECs) that contain ELL2 by an HIV-encoded protein, Tat, to activate proviral transcription. To identify novel drug targets, we conducted a CRISPRi-based screen to enrich the sgRNAs that increase HIV transcription in latently infected CD4+ T cells. Three of the six most prominent hits in our screen are proteasome subunits. We further proved that antagonizing the proteasome promotes Tat-induced HIV-1 transcription in cell line-based latency models. Furthermore, we found that two FDA-approved proteasome inhibitors strongly synergize with existing LRAs ex vivo without inducing cell activation or proliferation. We further found that antagonizing the proteasome elevates the levels of ELL2 and ELL2-containing SECs in the cells, thus enabling Tat-transactivation. These results indicate that the proteasome-ELL2 axis is a key regulator of HIV-1 latency could potentially be targeted for therapeutic interventions.
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Affiliation(s)
- Zichong Li
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Jun Wu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Leonard Chavez
- Vitalant Research Institute, San Francisco, California, United States of America
- University of California, San Francisco, California, United States of America
| | - Rebecca Hoh
- University of California, San Francisco, California, United States of America
| | - Steven G. Deeks
- University of California, San Francisco, California, United States of America
| | - Satish K. Pillai
- Vitalant Research Institute, San Francisco, California, United States of America
- University of California, San Francisco, California, United States of America
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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Ghosh K, Tang M, Kumari N, Nandy A, Basu S, Mall DP, Rai K, Biswas D. Positive Regulation of Transcription by Human ZMYND8 through Its Association with P-TEFb Complex. Cell Rep 2018; 24:2141-2154.e6. [PMID: 30134174 PMCID: PMC6152903 DOI: 10.1016/j.celrep.2018.07.064] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 07/02/2018] [Accepted: 07/18/2018] [Indexed: 11/25/2022] Open
Abstract
Although human ZMYND8 has been implicated as a transcriptional co-repressor of multiple targets, global association of ZMYND8 with active genes and enhancer regions predicts otherwise. Here, we report an additional function of ZMYND8 in transcriptional activation through its association with the P-TEFb complex. Biochemical reconstitution analyses show that human ZMYND8, through direct association with CylcinT1, forms a minimal ZMYND8-P-TEFb complex. The importance of ZMYND8 in target gene activation, through P-TEFb complex recruitment, is demonstrated on chromosomally integrated reporter gene as well as native target genes in vivo. Physiologically, we further show that the ZMYND8-P-TEFb complex-mediated transcriptional activation is required for all-trans retinoic acid (ATRA)-mediated differentiation of neuronal precursor cells. Finally, to detail the dual activator and repressor nature, mechanistically we show that, through its putative coiled-coil domain, ZMYND8 forms a homodimer that preferentially associates with the activator P-TEFb complex, whereas the monomer associates with the CHD4 subunit of repressor NuRD complex.
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Affiliation(s)
- Koushik Ghosh
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 32, India
| | - Ming Tang
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Nidhi Kumari
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 32, India
| | - Arijit Nandy
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 32, India
| | - Subham Basu
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 32, India
| | - Dheerendra Pratap Mall
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 32, India
| | - Kunal Rai
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 32, India.
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Eichhorn CD, Yang Y, Repeta L, Feigon J. Structural basis for recognition of human 7SK long noncoding RNA by the La-related protein Larp7. Proc Natl Acad Sci U S A 2018; 115:E6457-E6466. [PMID: 29946027 PMCID: PMC6048529 DOI: 10.1073/pnas.1806276115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The La and the La-related protein (LARP) superfamily is a diverse class of RNA binding proteins involved in RNA processing, folding, and function. Larp7 binds to the abundant long noncoding 7SK RNA and is required for 7SK ribonucleoprotein (RNP) assembly and function. The 7SK RNP sequesters a pool of the positive transcription elongation factor b (P-TEFb) in an inactive state; on release, P-TEFb phosphorylates RNA Polymerase II to stimulate transcription elongation. Despite its essential role in transcription, limited structural information is available for the 7SK RNP, particularly for protein-RNA interactions. Larp7 contains an N-terminal La module that binds UUU-3'OH and a C-terminal atypical RNA recognition motif (xRRM) required for specific binding to 7SK and P-TEFb assembly. Deletion of the xRRM is linked to gastric cancer in humans. We report the 2.2-Å X-ray crystal structure of the human La-related protein group 7 (hLarp7) xRRM bound to the 7SK stem-loop 4, revealing a unique binding interface. Contributions of observed interactions to binding affinity were investigated by mutagenesis and isothermal titration calorimetry. NMR 13C spin relaxation data and comparison of free xRRM, RNA, and xRRM-RNA structures show that the xRRM is preordered to bind a flexible loop 4. Combining structures of the hLarp7 La module and the xRRM-7SK complex presented here, we propose a structural model for Larp7 binding to the 7SK 3' end and mechanism for 7SK RNP assembly. This work provides insight into how this domain contributes to 7SK recognition and assembly of the core 7SK RNP.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Yuan Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Lucas Repeta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569
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Abstract
BACKGROUND The viral transactivator Tat protein is a key modulator of HIV-1 replication, as it regulates transcriptional elongation from the integrated proviral genome. Tat recruits the human transcription elongation factor b, and other host proteins, such as the super elongation complex, to activate the cellular RNA polymerase II, normally stalled shortly after transcription initiation at the HIV promoter. By means of a complex set of interactions with host cellular factors, Tat determines the fate of viral activity within the infected cell. The virus will either actively replicate to promote dissemination in blood and tissues, or become dormant mostly in memory CD4+ T cells, as part of a small but long-living latent reservoir, the main obstacle for HIV eradication. OBJECTIVE In this review, we summarize recent advances in the understanding of the multi-step mechanism that regulates Tat-mediated HIV-1 transcription and RNA polymerase II release, to promote viral transcription elongation. Early events of the human transcription elongation factor b release from the inhibitory 7SK small nuclear ribonucleoprotein complex and its recruitment to the HIV promoter will be discussed. Specific roles of the super elongation complex subunits during transcription elongation, and insight on recently identified cellular factors and mechanisms regulating HIV latency will be detailed. CONCLUSION Understanding the complexity of HIV transcriptional regulation by host factors may open the door for development of novel strategies to eradicate the resilient latent reservoir.
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Affiliation(s)
- Guillaume Mousseau
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
| | - Susana T Valente
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
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35
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Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD. The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation. eLife 2018; 7:31879. [PMID: 29845934 PMCID: PMC5999396 DOI: 10.7554/elife.31879] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 05/26/2018] [Indexed: 12/12/2022] Open
Abstract
The HIV-1 Tat protein hijacks P-TEFb kinase to activate paused RNA polymerase II (RNAP II) at the viral promoter. Tat binds additional host factors, but it is unclear how they regulate RNAP II elongation. Here, we identify the cytoplasmic ubiquitin ligase UBE2O as critical for Tat transcriptional activity. Tat hijacks UBE2O to ubiquitinate the P-TEFb kinase inhibitor HEXIM1 of the 7SK snRNP, a fraction of which also resides in the cytoplasm bound to P-TEFb. HEXIM1 ubiquitination sequesters it in the cytoplasm and releases P-TEFb from the inhibitory 7SK complex. Free P-TEFb then becomes enriched in chromatin, a process that is also stimulated by treating cells with a CDK9 inhibitor. Finally, we demonstrate that UBE2O is critical for P-TEFb recruitment to the HIV-1 promoter. Together, the data support a unique model of elongation control where non-degradative ubiquitination of nuclear and cytoplasmic 7SK snRNP pools increases P-TEFb levels for transcriptional activation.
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Affiliation(s)
- Tyler B Faust
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Yang Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Curtis W Bacon
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,J David Gladstone Institutes, San Francisco, United States
| | - Amit Weiss
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,J David Gladstone Institutes, San Francisco, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,J David Gladstone Institutes, San Francisco, United States
| | - Iván D'Orso
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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36
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Brogie JE, Price DH. Reconstitution of a functional 7SK snRNP. Nucleic Acids Res 2017; 45:6864-6880. [PMID: 28431135 PMCID: PMC5499737 DOI: 10.1093/nar/gkx262] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 01/29/2023] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) plays a central role in RNA polymerase II elongation control by regulating the availability of active P-TEFb. We optimized conditions for analyzing 7SK RNA by SHAPE and demonstrated a hysteretic effect of magnesium on 7SK folding dynamics including a 7SK GAUC motif switch. We also found evidence that the 5΄ end pairs alternatively with two different regions of 7SK giving rise to open and closed forms that dictate the state of the 7SK motif. We then used recombinant P-TEFb, HEXIM1, LARP7 and MEPCE to reconstruct a functional 7SK snRNP in vitro. Stably associated P-TEFb was highly inhibited, but could still be released and activated by HIV-1 Tat. Notably, P-TEFb association with both in vitro-reconstituted and cellular snRNPs led to similar changes in SHAPE reactivities, confirming that 7SK undergoes a P-TEFb-dependent structural change. We determined that the xRRM of LARP7 binds to the 3΄ stem loop of 7SK and inhibits the methyltransferase activity of MEPCE through a C-terminal MEPCE interaction domain (MID). Inhibition of MEPCE is dependent on the structure of the 3΄ stem loop and the closed form of 7SK RNA. This study provides important insights into intramolecular interactions within the 7SK snRNP.
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Affiliation(s)
- John E Brogie
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
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38
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Faust TB, Binning JM, Gross JD, Frankel AD. Making Sense of Multifunctional Proteins: Human Immunodeficiency Virus Type 1 Accessory and Regulatory Proteins and Connections to Transcription. Annu Rev Virol 2017; 4:241-260. [PMID: 28961413 DOI: 10.1146/annurev-virology-101416-041654] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Viruses are completely dependent upon cellular machinery to support replication and have therefore developed strategies to co-opt cellular processes to optimize infection and counter host immune defenses. Many viruses, including human immunodeficiency virus type 1 (HIV-1), encode a relatively small number of genes. Viruses with limited genetic content often encode multifunctional proteins that function at multiple stages of the viral replication cycle. In this review, we discuss the functions of HIV-1 regulatory (Tat and Rev) and accessory (Vif, Vpr, Vpu, and Nef) proteins. Each of these proteins has a highly conserved primary activity; however, numerous additional activities have been attributed to these viral proteins. We explore the possibility that HIV-1 proteins leverage their multifunctional nature to alter host transcriptional networks to elicit a diverse set of cellular responses. Although these transcriptional effects appear to benefit the virus, it is not yet clear whether they are strongly selected for during viral evolution or are a ripple effect from the primary function. As our detailed knowledge of these viral proteins improves, we will undoubtedly uncover how the multifunctional nature of these HIV-1 regulatory and accessory proteins, and in particular their transcriptional functions, work to drive viral pathogenesis.
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Affiliation(s)
- Tyler B Faust
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158; ,
| | - Jennifer M Binning
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158; ,
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158; ,
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158; ,
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39
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
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40
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AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs. Bone Res 2017; 5:17044. [PMID: 28955517 PMCID: PMC5613922 DOI: 10.1038/boneres.2017.44] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/18/2017] [Accepted: 06/18/2017] [Indexed: 02/05/2023] Open
Abstract
AFF1 and AFF4 belong to the AFF (AF4/FMR2) family of proteins, which function as scaffolding proteins linking two different transcription elongation factors, positive elongation factor b (P-TEFb) and ELL1/2, in super elongation complexes (SECs). Both AFF1 and AFF4 regulate gene transcription through elongation and chromatin remodeling. However, their function in the osteogenic differentiation of mesenchymal stem cells (MSCs) is unknown. In this study, we show that small interfering RNA (siRNA)-mediated depletion of AFF1 in human MSCs leads to increased alkaline phosphatase (ALP) activity, enhanced mineralization and upregulated expression of osteogenic-related genes. On the contrary, depletion of AFF4 significantly inhibits the osteogenic potential of MSCs. In addition, we confirm that overexpression of AFF1 and AFF4 differentially affects osteogenic differentiation in vitro and MSC-mediated bone formation in vivo. Mechanistically, we find that AFF1 regulates the expression of DKK1 via binding to its promoter region. Depletion of DKK1 in HA-AFF1-overexpressing MSCs abrogates the impairment of osteogenic differentiation. Moreover, we detect that AFF4 is enriched in the promoter region of ID1. AFF4 knockdown blunts the BRE luciferase activity, SP7 expression and ALP activity induced by BMP2 treatment. In conclusion, our data indicate that AFF1 and AFF4 differentially regulate the osteogenic differentiation of human MSCs.
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41
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A chalcone derivative reactivates latent HIV-1 transcription through activating P-TEFb and promoting Tat-SEC interaction on viral promoter. Sci Rep 2017; 7:10657. [PMID: 28878233 PMCID: PMC5587564 DOI: 10.1038/s41598-017-10728-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/14/2017] [Indexed: 12/12/2022] Open
Abstract
The principal barrier to the eradication of HIV/AIDS is the existence of latent viral reservoirs. One strategy to overcome this barrier is to use latency-reversing agents (LRAs) to reactivate the latent proviruses, which can then be eliminated by effective anti-retroviral therapy. Although a number of LRAs have been found to reactivate latent HIV, they have not been used clinically due to high toxicity and poor efficacy. In this study, we report the identification of a chalcone analogue called Amt-87 that can significantly reactivate the transcription of latent HIV provirses and act synergistically with known LRAs such as prostratin and JQ1 to reverse latency. Amt-87 works by activating the human transcriptional elongation factor P-TEFb, a CDK9-cyclin T1 heterodimer that is part of the super elongation complex (SEC) used by the viral encoded Tat protein to activate HIV transcription. Amt-87 does so by promoting the phosphorylation of CDK9 at the T-loop, liberating P-TEFb from the inactive 7SK snRNP, and inducing the formation of the Tat-SEC complex at the viral promoter. Together, our data reveal chalcones as a promising category of compounds that should be further explored to identify effective LRAs for targeted reversal of HIV latency.
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42
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Kuzmina A, Krasnopolsky S, Taube R. Super elongation complex promotes early HIV transcription and its function is modulated by P-TEFb. Transcription 2017; 8:133-149. [PMID: 28340332 DOI: 10.1080/21541264.2017.1295831] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear. Here we revisit the contribution of SEC in early steps of HIV gene transcription. In the absence of Tat, the AF4/FMR2 Family member 4 (AFF4) of SEC efficiently activates HIV transcription, while gene activation by its homolog AFF1 is substantially lower. Differential recruitment to the HIV promoter and association with Human Polymerase-Associated Factor complex (PAFc) play key role in this functional distinction between AFF4 and AFF1. Moreover, while depletion of cyclin T1 expression has subtle effects on HIV gene transcription in the absence of Tat, knockout (KO) of AFF1, AFF4, or both proteins slightly repress this early step of viral transcription. Upon Tat expression, HIV transcription reaches optimal levels despite KO of AFF1 or AFF4 expression. However, double AFF1/AFF4 KO completely diminishes Tat trans-activation. Significantly, our results show that P-TEFb phosphorylates AFF4 and modulates SEC assembly, AFF1/4 dimerization and recruitment to the viral promoter. We conclude that SEC promotes both early steps of HIV transcription in the absence of Tat, as well as elongation of transcription, when Tat is expressed. Significantly, SEC functions are modulated by P-TEFb.
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Affiliation(s)
- Alona Kuzmina
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Simona Krasnopolsky
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
| | - Ran Taube
- a The Shraga Segal Department of Microbiology Immunology and Genetics Faculty of Health Sciences , Ben-Gurion University of the Negev , Israel
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43
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Structural basis for ELL2 and AFF4 activation of HIV-1 proviral transcription. Nat Commun 2017; 8:14076. [PMID: 28134250 PMCID: PMC5290273 DOI: 10.1038/ncomms14076] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/28/2016] [Indexed: 02/05/2023] Open
Abstract
The intrinsically disordered scaffold proteins AFF1/4 and the transcription elongation factors ELL1/2 are core components of the super elongation complex required for HIV-1 proviral transcription. Here we report the 2.0-Å resolution crystal structure of the human ELL2 C-terminal domain bound to its 50-residue binding site on AFF4, the ELLBow. The ELL2 domain has the same arch-shaped fold as the tight junction protein occludin. The ELLBow consists of an N-terminal helix followed by an extended hairpin that we refer to as the elbow joint, and occupies most of the concave surface of ELL2. This surface is important for the ability of ELL2 to promote HIV-1 Tat-mediated proviral transcription. The AFF4–ELL2 interface is imperfectly packed, leaving a cavity suggestive of a potential binding site for transcription-promoting small molecules. The host super elongation complex (SEC) is hijacked by HIV-1 for viral transcription. Here the authors present the structure of RNA polymerase elongation factor ELL2 bound to the intrinsically disordered scaffold protein AFF4, identifying an ELL2 surface important for HIV-1 transcription.
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44
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Chen HS, De Leo A, Wang Z, Kerekovic A, Hills R, Lieberman PM. BET-Inhibitors Disrupt Rad21-Dependent Conformational Control of KSHV Latency. PLoS Pathog 2017; 13:e1006100. [PMID: 28107481 PMCID: PMC5287475 DOI: 10.1371/journal.ppat.1006100] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 02/01/2017] [Accepted: 11/29/2016] [Indexed: 12/11/2022] Open
Abstract
Kaposi’s Sarcoma-associated Herpesvirus (KSHV) establishes stable latent infection in B-lymphocytes and pleural effusion lymphomas (PELs). During latency, the viral genome persists as an epigenetically constrained episome with restricted gene expression programs. To identify epigenetic regulators of KSHV latency, we screened a focused small molecule library containing known inhibitors of epigenetic factors. We identified JQ1, a Bromodomain and Extended Terminal (BET) protein inhibitor, as a potent activator of KSHV lytic reactivation from B-cells carrying episomal KSHV. We validated that JQ1 and other BET inhibitors efficiently stimulated reactivation of KSHV from latently infected PEL cells. We found that BET proteins BRD2 and BRD4 localize to several regions of the viral genome, including the LANA binding sites within the terminal repeats (TR), as well as at CTCF-cohesin sites in the latent and lytic control regions. JQ1 did not disrupt the interaction of BRD4 or BRD2 with LANA, but did reduce the binding of LANA with KSHV TR. We have previously demonstrated a cohesin-dependent DNA-loop interaction between the latent and lytic control regions that restrict expression of ORF50/RTA and ORF45 immediate early gene transcripts. JQ1 reduced binding of cohesin subunit Rad21 with the CTCF binding sites in the latency and lytic control regions. JQ1 also reduced DNA-loop interaction between latent and lytic control regions. These findings implicate BET proteins BRD2 and BRD4 in the maintenance of KSHV chromatin architecture during latency and reveal BET inhibitors as potent activators of KSHV reactivation from latency. KSHV is an oncogenic human herpesvirus implicated as the causative agent of KS and cofactor in pleural effusion lymphomas (PELs). The latent virus persists in PELs as an epigenetically regulated episome. We found that small molecule inhibitors of BET family have potent activity in triggering the lytic switch during latent infection in PELs. The BET family inhibitor JQ1 disrupted the latent virus from maintaining a closed DNA loop conformation. These findings have implications for treatment of KSHV-associated malignancies with epigenetic modulators of the BET inhibitor family.
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MESH Headings
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Azepines/pharmacology
- B-Lymphocytes/virology
- Binding Sites/drug effects
- Cell Cycle Proteins
- Cell Line, Tumor
- DNA-Binding Proteins
- Gene Expression Regulation, Viral
- HEK293 Cells
- Herpesvirus 8, Human/drug effects
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/physiology
- Humans
- Immediate-Early Proteins/biosynthesis
- Immediate-Early Proteins/genetics
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphoproteins/metabolism
- Pleural Effusion, Malignant/virology
- Protein Binding/drug effects
- Protein Serine-Threonine Kinases/antagonists & inhibitors
- Protein Serine-Threonine Kinases/metabolism
- RNA Interference
- RNA, Small Interfering
- Sarcoma, Kaposi/virology
- Trans-Activators/biosynthesis
- Trans-Activators/genetics
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/metabolism
- Triazoles/pharmacology
- Virus Activation/drug effects
- Virus Latency/drug effects
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Affiliation(s)
- Horng-Shen Chen
- The Wistar Institute, Philadelphia, PA, United States of America
| | | | - Zhuo Wang
- The Wistar Institute, Philadelphia, PA, United States of America
| | - Andrew Kerekovic
- The Wistar Institute, Philadelphia, PA, United States of America
| | - Robert Hills
- The Wistar Institute, Philadelphia, PA, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, PA, United States of America
- * E-mail:
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45
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Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. eLife 2016; 5. [PMID: 27731797 PMCID: PMC5072841 DOI: 10.7554/elife.15910] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/07/2016] [Indexed: 01/04/2023] Open
Abstract
HIV-1 Tat hijacks the human superelongation complex (SEC) to promote proviral transcription. Here we report the 5.9 Å structure of HIV-1 TAR in complex with HIV-1 Tat and human AFF4, CDK9, and CycT1. The TAR central loop contacts the CycT1 Tat-TAR recognition motif (TRM) and the second Tat Zn2+-binding loop. Hydrogen-deuterium exchange (HDX) shows that AFF4 helix 2 is stabilized in the TAR complex despite not touching the RNA, explaining how it enhances TAR binding to the SEC 50-fold. RNA SHAPE and SAXS data were used to help model the extended (Tat Arginine-Rich Motif) ARM, which enters the TAR major groove between the bulge and the central loop. The structure and functional assays collectively support an integrative structure and a bipartite binding model, wherein the TAR central loop engages the CycT1 TRM and compact core of Tat, while the TAR major groove interacts with the extended Tat ARM. DOI:http://dx.doi.org/10.7554/eLife.15910.001
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Affiliation(s)
- Ursula Schulze-Gahmen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Yun Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Huasong Lu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,California Institute of Quantitative Biosciences, University of California San, Francisco, San Francisco, United States
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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46
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Eichhorn CD, Chug R, Feigon J. hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA. Nucleic Acids Res 2016; 44:9977-9989. [PMID: 27679474 PMCID: PMC5175362 DOI: 10.1093/nar/gkw833] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/21/2022] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal La module binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear. We report the solution NMR structure of the hLARP7 CTD and show that this domain contains an xRRM, a class of atypical RRM first identified in the Tetrahymena thermophila telomerase LARP7 protein p65. The xRRM binds the 3' end of 7SK RNA at the top of stem-loop 4 (SL4) and interacts with both unpaired and base-paired nucleotides. This study confirms that the xRRM is general to the LARP7 family of proteins and defines the binding site for hLARP7 on the 7SK RNA, providing insight into function.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Rahul Chug
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
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47
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Zhao Y, Karijolich J, Glaunsinger B, Zhou Q. Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV-1 transcription and escape from latency. EMBO Rep 2016; 17:1441-1451. [PMID: 27558685 DOI: 10.15252/embr.201642682] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/28/2016] [Indexed: 12/16/2022] Open
Abstract
The 7SK snRNA sequesters P-TEFb, a general transcription elongation factor and human co-factor for HIV-1 Tat protein, into the catalytically inactive 7SK snRNP Little is known about how 7SK RNA is regulated to perform this function. Here, we show that most of 7SK is pseudouridylated at position U250 by the predominant cellular pseudouridine synthase machinery, the DKC1-box H/ACA RNP Pseudouridylation is critical to stabilize 7SK snRNP, as its abolishment by either mutation at or around U250 or depletion of DKC1, the catalytic component of the box H/ACA RNP, disrupts 7SK snRNP and releases P-TEFb to form the super elongation complex (SEC) and the Brd4-P-TEFb complex. The SEC is then recruited by Tat to the HIV-1 promoter to stimulate viral transcription and escape from latency. Thus, although 7SK RNA levels remain mostly unchanged, its function is modulated by pseudouridylation, which in turn controls transcription of both HIV-1 and cellular genes.
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Affiliation(s)
- Yang Zhao
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - John Karijolich
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Britt Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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48
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Sharma N. Regulation of RNA polymerase II-mediated transcriptional elongation: Implications in human disease. IUBMB Life 2016; 68:709-16. [DOI: 10.1002/iub.1538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/14/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University; Dwarka New Delhi 110078 India
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49
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C Quaresma AJ, Bugai A, Barboric M. Cracking the control of RNA polymerase II elongation by 7SK snRNP and P-TEFb. Nucleic Acids Res 2016; 44:7527-39. [PMID: 27369380 PMCID: PMC5027500 DOI: 10.1093/nar/gkw585] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/17/2016] [Indexed: 01/01/2023] Open
Abstract
Release of RNA polymerase II (Pol II) from promoter-proximal pausing has emerged as a critical step regulating gene expression in multicellular organisms. The transition of Pol II into productive elongation requires the kinase activity of positive transcription elongation factor b (P-TEFb), which is itself under a stringent control by the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP) complex. Here, we provide an overview on stimulating Pol II pause release by P-TEFb and on sequestering P-TEFb into 7SK snRNP. Furthermore, we highlight mechanisms that govern anchoring of 7SK snRNP to chromatin as well as means that release P-TEFb from the inhibitory complex, and propose a unifying model of P-TEFb activation on chromatin. Collectively, these studies shine a spotlight on the central role of RNA binding proteins (RBPs) in directing the inhibition and activation of P-TEFb, providing a compelling paradigm for controlling Pol II transcription with a non-coding RNA.
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Affiliation(s)
- Alexandre J C Quaresma
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Andrii Bugai
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Matjaz Barboric
- Medicum, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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50
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Le Douce V, Ait-Amar A, Forouzan Far F, Fahmi F, Quiel J, El Mekdad H, Daouad F, Marban C, Rohr O, Schwartz C. Improving combination antiretroviral therapy by targeting HIV-1 gene transcription. Expert Opin Ther Targets 2016; 20:1311-1324. [PMID: 27266557 DOI: 10.1080/14728222.2016.1198777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Combination Antiretroviral Therapy (cART) has not allowed the cure of HIV. The main obstacle to HIV eradication is the existence of quiescent reservoirs. Several other limitations of cART have been described, such as strict life-long treatment and high costs, restricting it to Western countries, as well as the development of multidrug resistance. Given these limitations and the impetus to find a cure, the development of new treatments is necessary. Areas covered: In this review, we discuss the current status of several efficient molecules able to suppress HIV gene transcription, including NF-kB and Tat inhibitors. We also assess the potential of new proteins belonging to the intriguing DING family, which have been reported to have potential anti-HIV-1 activity by inhibiting HIV gene transcription. Expert opinion: Targeting HIV-1 gene transcription is an alternative approach, which could overcome cART-related issues, such as the emergence of multidrug resistance. Improving cART will rely on the identification and characterization of new actors inhibiting HIV-1 transcription. Combining such efforts with the use of new technologies, the development of new models for preclinical studies, and improvement in drug delivery will considerably reduce drug toxicity and thus increase patient adherence.
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Affiliation(s)
- Valentin Le Douce
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France.,c UCD Centre for Research in Infectious Diseases (CRID) School of Medicine and Medical Science , University College Dublin , Dublin 4 , Ireland
| | - Amina Ait-Amar
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Faezeh Forouzan Far
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Faiza Fahmi
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Jose Quiel
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Hala El Mekdad
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Fadoua Daouad
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France
| | - Céline Marban
- d Faculté de Chirurgie Dentaire , Inserm UMR 1121 , Strasbourg , France
| | - Olivier Rohr
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France.,e Institut Universitaire de France , Paris , France
| | - Christian Schwartz
- a Institut de Parasitologie et de Pathologie Tropicale, EA7292 , Université de Strasbourg , Strasbourg , France.,b IUT de Schiltigheim , Schiltigheim , France
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