201
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Ma H, Seebacher NA, Hornicek FJ, Duan Z. Cyclin-dependent kinase 9 (CDK9) is a novel prognostic marker and therapeutic target in osteosarcoma. EBioMedicine 2018; 39:182-193. [PMID: 30579871 PMCID: PMC6355967 DOI: 10.1016/j.ebiom.2018.12.022] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/07/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
Background Cyclin-dependent protein kinase 9 (CDK9) has been shown to play an important role in the pathogenesis of malignant tumors. However, the expression and function of CDK9 remain unknown in osteosarcomas. The purpose of this study is to assess the expression, function and clinical prognostic relationship of CDK9 in osteosarcomas. Methods A tissue microarray of 70 patient specimens was analyzed by immunohistochemistry to measure CDK9 expression, which was further investigated for correlation with patient clinical characteristics. CDK9 expression in osteosarcoma cell lines and patient tissues was also evaluated by Western blotting. CDK9-specific siRNA and the CDK9 inhibitor were applied to determine the effect of CDK9 inhibition on osteosarcoma cell proliferation and anti-apoptotic activity. The clonogenicity and migration activity were also examined using clonogenic and wound healing assays. A 3D cell culture model was performed to mimic the in vivo osteosarcoma environment to further validate the effect of CDK9 inhibition on osteosarcoma cells. Findings We demonstrated that higher CDK9-expression is associated with significantly shortened patient survival by immunohistochemistry. Expression of CDK9 is inversely correlated to the percent of tumor necrosis post-neoadjuvant chemotherapy, which is the most important predictive factor of disease outcome for osteosarcoma patients. Knockdown of CDK9 with siRNA and inhibition of CDK9 activity with inhibitor decreased cell proliferation and induced apoptosis in osteosarcoma. Interpretation High expression of CDK9 is an independent predictor of poor prognosis in osteosarcoma patients. Our results suggest that CDK9 is a novel prognostic marker and a promising therapeutic target for osteosarcomas.
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Affiliation(s)
- Hangzhan Ma
- Department of Orthopaedics, Panyu Hospital of Chinese Medicine, Guangzhou, Guangdong 511400, China; Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Nicole A Seebacher
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Francis J Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Zhenfeng Duan
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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202
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Probabilistic control of HIV latency and transactivation by the Tat gene circuit. Proc Natl Acad Sci U S A 2018; 115:12453-12458. [PMID: 30455316 DOI: 10.1073/pnas.1811195115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The reservoir of HIV latently infected cells is the major obstacle for eradication of HIV infection. The "shock-and-kill" strategy proposed earlier aims to reduce the reservoir by activating cells out of latency. While the intracellular HIV Tat gene circuit is known to play important roles in controlling latency and its transactivation in HIV-infected cells, the detailed control mechanisms are not well understood. Here we study the mechanism of probabilistic control of the latent and the transactivated cell phenotypes of HIV-infected cells. We reconstructed the probability landscape, which is the probability distribution of the Tat gene circuit states, by directly computing the exact solution of the underlying chemical master equation. Results show that the Tat circuit exhibits a clear bimodal probability landscape (i.e., there are two distinct probability peaks, one associated with the latent cell phenotype and the other with the transactivated cell phenotype). We explore potential modifications to reactions in the Tat gene circuit for more effective transactivation of latent cells (i.e., the shock-and-kill strategy). Our results suggest that enhancing Tat acetylation can dramatically increase Tat and viral production, while increasing the Tat-transactivation response binding affinity can transactivate latent cells more rapidly than other manipulations. Our results further explored the "block and lock" strategy toward a functional cure for HIV. Overall, our study demonstrates a general approach toward discovery of effective therapeutic strategies and druggable targets by examining control mechanisms of cell phenotype switching via exactly computed probability landscapes of reaction networks.
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203
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Abstract
Studies of RNA Polymerase II (Pol II) transcription of the HIV-1 genome are of clinical interest, as the insight gained may lead to strategies to selectively reactivate latent viruses in patients in whom viral replication is suppressed by antiviral drugs. Such a targeted reactivation may contribute to a functional cure of infection. This review discusses five Cyclin-dependent kinases - CDK7, CDK9, CDK11, CDK2, and CDK8 - involved in transcription and processing of HIV-1 RNA. CDK7 is required for Pol II promoter clearance of reactivated viruses; CDK7 also functions as an activating kinase for CDK9 when resting CD4+ T cells harboring latent HIV-1 are activated. CDK9 is targeted by the viral Tat protein and is essential for productive Pol II elongation of the HIV-1 genome. CDK11 is associated with the TREX/THOC complex and it functions in the 3' end processing and polyadenylation of HIV-1 transcripts. CDK2 phosphorylates Tat and CDK9 and this stimulates Tat activation of Pol II transcription. CDK8 may stimulate Pol II transcription of the HIV-1 genome through co-recruitment with NF-κB to the viral promoter. Some notable open questions are discussed concerning the roles of these CDKs in HIV-1 replication and viral latency.
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Affiliation(s)
- Andrew P Rice
- a Department of Molecular Virology and Microbiology , Baylor College of Medicine , Houston , TX , USA
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204
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Zeng M, Kwiatkowski NP, Zhang T, Nabet B, Xu M, Liang Y, Quan C, Wang J, Hao M, Palakurthi S, Zhou S, Zeng Q, Kirschmeier PT, Meghani K, Leggett AL, Qi J, Shapiro GI, Liu JF, Matulonis UA, Lin CY, Konstantinopoulos PA, Gray NS. Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13. eLife 2018; 7:39030. [PMID: 30422115 PMCID: PMC6251623 DOI: 10.7554/elife.39030] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/11/2018] [Indexed: 12/19/2022] Open
Abstract
High-grade serous ovarian cancer is characterized by extensive copy number alterations, among which the amplification of MYC oncogene occurs in nearly half of tumors. We demonstrate that ovarian cancer cells highly depend on MYC for maintaining their oncogenic growth, indicating MYC as a therapeutic target for this difficult-to-treat malignancy. However, targeting MYC directly has proven difficult. We screen small molecules targeting transcriptional and epigenetic regulation, and find that THZ1 - a chemical inhibiting CDK7, CDK12, and CDK13 - markedly downregulates MYC. Notably, abolishing MYC expression cannot be achieved by targeting CDK7 alone, but requires the combined inhibition of CDK7, CDK12, and CDK13. In 11 patient-derived xenografts models derived from heavily pre-treated ovarian cancer patients, administration of THZ1 induces significant tumor growth inhibition with concurrent abrogation of MYC expression. Our study indicates that targeting these transcriptional CDKs with agents such as THZ1 may be an effective approach for MYC-dependent ovarian malignancies.
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Affiliation(s)
- Mei Zeng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Nicholas P Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Mousheng Xu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Yanke Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Chunshan Quan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Mingfeng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Sangeetha Palakurthi
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, United States
| | - Shan Zhou
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, United States
| | - Qing Zeng
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, United States
| | - Paul T Kirschmeier
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, United States
| | - Khyati Meghani
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Alan L Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Geoffrey I Shapiro
- Early Drug Development Center, Dana-Farber Cancer Institute, Boston, United States
| | - Joyce F Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Charles Y Lin
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | | | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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205
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Abstract
The fact that many cancer types display transcriptional addiction driven by dysregulation of oncogenic enhancers and transcription factors has led to increased interest in a group of protein kinases, known as transcriptional cyclin dependent kinases (tCDKs), as potential therapeutic targets. Despite early reservations about targeting a process that is essential to healthy cell types, there is now evidence that targeting tCDKs could provide enough therapeutic window to be effective in the clinic. Here, we discuss recent developments in this field, with an emphasis on highly-selective inhibitors and the challenges to be addressed before these inhibitors could be used for therapeutic purposes. Abbreviations: CAK: CDK-activating kinase;CDK: cyclin-dependent kinase;CMGC group: CDK-, MAPK-, GSK3-, and CLK-like;CTD: C-terminal repeat domain of the RPB1 subunit of RNA polymerase II;DRB: 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole;mCRPC: metastatic castration-resistant prostate cancer;NSCLC: non-small cell lung cancer;P-TEFb: positive elongation factor b;RNAPII: RNA polymerase II;S2: serine-2 of CTD repeats;S5: serine-5 of CTD repeats;S7: serine-7 of CTD repeats;SEC: super elongation complex;tCDK: transcriptional cyclin-dependent kinase;TNBC: triple-negative breast cancer
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Affiliation(s)
- Matthew D Galbraith
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA
| | - Heather Bender
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA
| | - Joaquín M Espinosa
- a Linda Crnic Institute for Down Syndrome, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,b Department of Pharmacology, School of Medicine , University of Colorado Anschutz Medical Campus , Aurora , CO , USA.,c Department of Molecular, Cellular and Developmental Biology , University of Colorado Boulder , Boulder , CO , USA
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206
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Kalkat M, Resetca D, Lourenco C, Chan PK, Wei Y, Shiah YJ, Vitkin N, Tong Y, Sunnerhagen M, Done SJ, Boutros PC, Raught B, Penn LZ. MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis. Mol Cell 2018; 72:836-848.e7. [PMID: 30415952 DOI: 10.1016/j.molcel.2018.09.031] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/09/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
Transforming members of the MYC family (MYC, MYCL1, and MYCN) encode transcription factors containing six highly conserved regions, termed MYC homology boxes (MBs). By conducting proteomic profiling of the MB interactomes, we demonstrate that half of the MYC interactors require one or more MBs for binding. Comprehensive phenotypic analyses reveal that two MBs, MB0 and MBII, are universally required for transformation. MBII mediates interactions with acetyltransferase-containing complexes, enabling histone acetylation, and is essential for MYC-dependent tumor initiation. By contrast, MB0 mediates interactions with transcription elongation factors via direct binding to the general transcription factor TFIIF. MB0 is dispensable for tumor initiation but is a major accelerator of tumor growth. Notably, the full transforming activity of MYC can be restored by co-expression of the non-transforming MB0 and MBII deletion proteins, indicating that these two regions confer separate molecular functions, both of which are required for oncogenic MYC activity.
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Affiliation(s)
- Manpreet Kalkat
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Diana Resetca
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Corey Lourenco
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Pak-Kei Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yong Wei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, Toronto, ON M5G 1L7, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Natasha Vitkin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yufeng Tong
- Structural Genomics Consortium, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Susan J Done
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | - Linda Z Penn
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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207
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Defective transcription elongation in a subset of cancers confers immunotherapy resistance. Nat Commun 2018; 9:4410. [PMID: 30353012 PMCID: PMC6199328 DOI: 10.1038/s41467-018-06810-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 09/21/2018] [Indexed: 12/13/2022] Open
Abstract
The nature and role of global transcriptional deregulations in cancers are not fully understood. We report that a large proportion of cancers have widespread defects in mRNA transcription elongation (TE). Cancers with TE defects (TEdeff) display spurious transcription and defective mRNA processing of genes characterized by long genomic length, poised promoters and inducible expression. Signaling pathways regulated by such genes, such as pro-inflammatory response pathways, are consistently suppressed in TEdeff tumors. Remarkably, TEdeff correlates with the poor response and outcome in immunotherapy, but not chemo- or targeted therapy, -treated renal cell carcinoma and metastatic melanoma patients. Forced pharmacologic or genetic induction of TEdeff in tumor cells impairs pro-inflammatory response signaling, and imposes resistance to the innate and adaptive anti-tumor immune responses and checkpoint inhibitor therapy in vivo. Therefore, defective TE is a previously unknown mechanism of tumor immune resistance, and should be assessed in cancer patients undergoing immunotherapy. Transcription elongation (TE) is a key point of inducible gene expression regulation. Here, the authors report widespread TE defects (TEdeff) in a high proportion of cancers that correlate with poor immunotherapy response, highlighting TE defects as potential routes for immune resistance.
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208
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Liang K, Smith ER, Aoi Y, Stoltz KL, Katagi H, Woodfin AR, Rendleman EJ, Marshall SA, Murray DC, Wang L, Ozark PA, Mishra RK, Hashizume R, Schiltz GE, Shilatifard A. Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy. Cell 2018; 175:766-779.e17. [PMID: 30340042 PMCID: PMC6422358 DOI: 10.1016/j.cell.2018.09.027] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/02/2018] [Accepted: 09/13/2018] [Indexed: 11/15/2022]
Abstract
The super elongation complex (SEC) is required for robust and productive transcription through release of RNA polymerase II (Pol II) with its P-TEFb module and promoting transcriptional processivity with its ELL2 subunit. Malfunction of SEC contributes to multiple human diseases including cancer. Here, we identify peptidomimetic lead compounds, KL-1 and its structural homolog KL-2, which disrupt the interaction between the SEC scaffolding protein AFF4 and P-TEFb, resulting in impaired release of Pol II from promoter-proximal pause sites and a reduced average rate of processive transcription elongation. SEC is required for induction of heat-shock genes and treating cells with KL-1 and KL-2 attenuates the heat-shock response from Drosophila to human. SEC inhibition downregulates MYC and MYC-dependent transcriptional programs in mammalian cells and delays tumor progression in a mouse xenograft model of MYC-driven cancer, indicating that small-molecule disruptors of SEC could be used for targeted therapy of MYC-induced cancer.
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Affiliation(s)
- Kaiwei Liang
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Edwin R. Smith
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Yuki Aoi
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kristen L. Stoltz
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Hiroaki Katagi
- Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Ashley R. Woodfin
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily J. Rendleman
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stacy A. Marshall
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David C. Murray
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lu Wang
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Patrick A. Ozark
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rama K. Mishra
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA,Department of Pharmacology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Neurosurgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Gary E. Schiltz
- Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA,Department of Pharmacology, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 303 E. Superior St., Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg, School of Medicine, 303 E. Superior Street, Chicago, IL 60611, USA.
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209
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Shiozaki Y, Okamura K, Kohno S, Keenan AL, Williams K, Zhao X, Chick WS, Miyazaki-Anzai S, Miyazaki M. The CDK9-cyclin T1 complex mediates saturated fatty acid-induced vascular calcification by inducing expression of the transcription factor CHOP. J Biol Chem 2018; 293:17008-17020. [PMID: 30209133 PMCID: PMC6222109 DOI: 10.1074/jbc.ra118.004706] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/07/2018] [Indexed: 11/06/2022] Open
Abstract
Vascular calcification (or mineralization) is a common complication of chronic kidney disease (CKD) and is closely associated with increased mortality and morbidity rates. We recently reported that activation of the activating transcription factor 4 (ATF4) pathway through the saturated fatty acid (SFA)-induced endoplasmic reticulum (ER) stress response plays a causative role in CKD-associated vascular calcification. Here, using mouse models of CKD, we 1) studied the contribution of the proapoptotic transcription factor CCAAT enhancer-binding protein homologous protein (CHOP) to CKD-dependent medial calcification, and 2) we identified an additional regulator of ER stress-mediated CHOP expression. Transgenic mice having smooth muscle cell (SMC)-specific CHOP expression developed severe vascular apoptosis and medial calcification under CKD. Screening of a protein kinase inhibitor library identified 16 compounds, including seven cyclin-dependent kinase (CDK) inhibitors, that significantly suppressed CHOP induction during ER stress. Moreover, selective CDK9 inhibitors and CRISPR/Cas9-mediated CDK9 reduction blocked SFA-mediated induction of CHOP expression, whereas inhibitors of other CDK isoforms did not. Cyclin T1 knockout inhibited SFA-mediated induction of CHOP and mineralization, whereas deletion of cyclin T2 and cyclin K promoted CHOP expression levels and mineralization. Of note, the CDK9-cyclin T1 complex directly phosphorylated and activated ATF4. These results demonstrate that the CDK9-cyclin T1 and CDK9-cyclin T2/K complexes have opposing roles in CHOP expression and CKD-induced vascular calcification. They further reveal that the CDK9-cyclin T1 complex mediates vascular calcification through CHOP induction and phosphorylation-mediated ATF4 activation.
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Affiliation(s)
- Yuji Shiozaki
- From the Division of Renal Diseases and Hypertension, Department of Medicine, and
| | - Kayo Okamura
- From the Division of Renal Diseases and Hypertension, Department of Medicine, and
| | - Shohei Kohno
- From the Division of Renal Diseases and Hypertension, Department of Medicine, and
| | - Audrey L Keenan
- From the Division of Renal Diseases and Hypertension, Department of Medicine, and
| | - Kristina Williams
- the Department of Cell and Developmental Biology, University of Colorado Denver, Aurora, Colorado 80045
| | - Xiaoyun Zhao
- the Department of Cell and Developmental Biology, University of Colorado Denver, Aurora, Colorado 80045
| | - Wallace S Chick
- the Department of Cell and Developmental Biology, University of Colorado Denver, Aurora, Colorado 80045
| | | | - Makoto Miyazaki
- From the Division of Renal Diseases and Hypertension, Department of Medicine, and
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210
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Erickson B, Sheridan RM, Cortazar M, Bentley DL. Dynamic turnover of paused Pol II complexes at human promoters. Genes Dev 2018; 32:1215-1225. [PMID: 30150253 PMCID: PMC6120720 DOI: 10.1101/gad.316810.118] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/11/2018] [Indexed: 12/30/2022]
Abstract
Paused RNA polymerase II (Pol II) that piles up near most human promoters is the target of mechanisms that control entry into productive elongation. Whether paused Pol II is a stable or dynamic target remains unresolved. We report that most 5' paused Pol II throughout the genome is turned over within 2 min. This process is revealed under hypertonic conditions that prevent Pol II recruitment to promoters. This turnover requires cell viability but is not prevented by inhibiting transcription elongation, suggesting that it is mediated at the level of termination. When initiation was prevented by triptolide during recovery from high salt, a novel preinitiated state of Pol II lacking the pausing factor Spt5 accumulated at transcription start sites. We propose that Pol II occupancy near 5' ends is governed by a cycle of ongoing assembly of preinitiated complexes that transition to pause sites followed by eviction from the DNA template. This model suggests that mechanisms regulating the transition to productive elongation at pause sites operate on a dynamic population of Pol II that is turning over at rates far higher than previously suspected. We suggest that a plausible alternative to elongation control via escape from a stable pause is by escape from premature termination.
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Affiliation(s)
- Benjamin Erickson
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Ryan M Sheridan
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Michael Cortazar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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211
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Chen X, Zhang JX, Luo JH, Wu S, Yuan GJ, Ma NF, Feng Y, Cai MY, Chen RX, Lu J, Jiang LJ, Chen JW, Jin XH, Liu HL, Chen W, Guan XY, Kang TB, Zhou FJ, Xie D. CSTF2-induced shortening of the RAC1 3'UTR promotes the pathogenesis of urothelial carcinoma of the bladder. Cancer Res 2018; 78:5848-5862. [PMID: 30143523 DOI: 10.1158/0008-5472.can-18-0822] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/06/2018] [Accepted: 08/15/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Xin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Xing Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Oncology, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jun-Hang Luo
- Department of Urology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Song Wu
- The Affiliated Luohu Hospital of Shenzhen University, Shenzhen Luohu Hospital Group, Shenzhen, China
| | - Gang-Jun Yuan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ning-Fang Ma
- Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China.
| | - Yong Feng
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Mu-Yan Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ri-Xin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun Lu
- Department of Urology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Li-Juan Jiang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jie-Wei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Han Jin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hai-Liang Liu
- CapitalBio Genomics Co., Ltd, Dongguan, Guangdong, China
| | - Wei Chen
- Department of Urology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tie-Bang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fang-Jian Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
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212
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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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213
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Rice AP. The HIV-1 Tat Protein: Mechanism of Action and Target for HIV-1 Cure Strategies. Curr Pharm Des 2018; 23:4098-4102. [PMID: 28677507 DOI: 10.2174/1381612823666170704130635] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023]
Abstract
The general mechanism involved in Tat activation of RNA Polymerase II (RNAP II) elongation of the integrated HIV-1 was elucidated over 20 years ago. This mechanism involves Tat binding to the TAR RNA element that forms at the 5' end of viral transcripts and recruiting a general RNAP II elongation factor termed as PTEFb. This elongation factor consists of CDK9 and Cyclin T1, and when recruited by Tat to TAR RNA, CDK9 was proposed to phosphorylate the carboxyl terminal domain of RNAP II and thereby activate elongation. Research in the past two decades has shown that the mechanism of Tat action is considerably more complicated than this simple model. In metabolically active cells, CDK9 and Cyclin T1 are now known to be largely sequestered in a RNA-protein complex termed the 7SK RNP. CDK9 and Cyclin T1 are released from the 7SK RNP by mechanisms not yet fully elucidated and along with Tat, bind to TAR RNA and orchestrate the assembly of a Super Elongation Complex (SEC) containing several additional proteins. CDK9 in the SEC then phosphorylates multiple substrates in the RNAP II complex to activate elongation. Importantly for therapeutic strategies, CDK9 and Cyclin T1 functions are down-regulated in resting CD4+ T cells that harbor latent HIV-1, and their up-regulation is required for reactivation of latent virus. Current strategies for a functional cure of HIV-1 infection therefore are likely to require development of latency reversal agents that up-regulate CDK9 and Cyclin T1 function in resting CD4+ T cells.
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Affiliation(s)
- Andrew P Rice
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030. United States
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214
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Quintero-Ronderos P, Laissue P. The multisystemic functions of FOXD1 in development and disease. J Mol Med (Berl) 2018; 96:725-739. [PMID: 29959475 DOI: 10.1007/s00109-018-1665-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/18/2018] [Accepted: 06/21/2018] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) participate in a wide range of cellular processes due to their inherent function as essential regulatory proteins. Their dysfunction has been linked to numerous human diseases. The forkhead box (FOX) family of TFs belongs to the "winged helix" superfamily, consisting of proteins sharing a related winged helix-turn-helix DNA-binding motif. FOX genes have been extensively present during vertebrates and invertebrates' evolution, participating in numerous molecular cascades and biological functions, such as embryonic development and organogenesis, cell cycle regulation, metabolism control, stem cell niche maintenance, signal transduction, and many others. FOXD1, a forkhead TF, has been related to different key biological processes such as kidney and retina development and embryo implantation. FOXD1 dysfunction has been linked to different pathologies, thereby constituting a diagnostic biomarker and a promising target for future therapies. This paper aims to present, for the first time, a comprehensive review of FOXD1's role in mouse development and human disease. Molecular, structural, and functional aspects of FOXD1 are presented in light of physiological and pathogenic conditions, including its role in human disease aetiology, such as cancer and recurrent pregnancy loss. Taken together, the information given here should enable a better understanding of FOXD1 function for basic science researchers and clinicians.
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Affiliation(s)
- Paula Quintero-Ronderos
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá, Colombia
| | - Paul Laissue
- Center For Research in Genetics and Genomics-CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 No. 63C-69, Bogotá, Colombia.
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215
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216
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Lu H, Yu D, Hansen AS, Ganguly S, Liu R, Heckert A, Darzacq X, Zhou Q. Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. Nature 2018; 558:318-323. [PMID: 29849146 PMCID: PMC6475116 DOI: 10.1038/s41586-018-0174-3] [Citation(s) in RCA: 362] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 05/02/2018] [Indexed: 12/15/2022]
Abstract
Hyperphosphorylation of the C-terminal domain (CTD) of the RPB1 subunit of human RNA polymerase (Pol) II is essential for transcriptional elongation and mRNA processing1-3. The CTD contains 52 heptapeptide repeats of the consensus sequence YSPTSPS. The highly repetitive nature and abundant possible phosphorylation sites of the CTD exert special constraints on the kinases that catalyse its hyperphosphorylation. Positive transcription elongation factor b (P-TEFb)-which consists of CDK9 and cyclin T1-is known to hyperphosphorylate the CTD and negative elongation factors to stimulate Pol II elongation1,4,5. The sequence determinant on P-TEFb that facilitates this action is currently unknown. Here we identify a histidine-rich domain in cyclin T1 that promotes the hyperphosphorylation of the CTD and stimulation of transcription by CDK9. The histidine-rich domain markedly enhances the binding of P-TEFb to the CTD and functional engagement with target genes in cells. In addition to cyclin T1, at least one other kinase-DYRK1A 6 -also uses a histidine-rich domain to target and hyperphosphorylate the CTD. As a low-complexity domain, the histidine-rich domain also promotes the formation of phase-separated liquid droplets in vitro, and the localization of P-TEFb to nuclear speckles that display dynamic liquid properties and are sensitive to the disruption of weak hydrophobic interactions. The CTD-which in isolation does not phase separate, despite being a low-complexity domain-is trapped within the cyclin T1 droplets, and this process is enhanced upon pre-phosphorylation by CDK7 of transcription initiation factor TFIIH1-3. By using multivalent interactions to create a phase-separated functional compartment, the histidine-rich domain in kinases targets the CTD into this environment to ensure hyperphosphorylation and efficient elongation of Pol II.
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Affiliation(s)
- Huasong Lu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dan Yu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sourav Ganguly
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rongdiao Liu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Alec Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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217
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Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR, Jones KA. SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy. PLoS Pathog 2018; 14:e1007071. [PMID: 29791506 PMCID: PMC5988312 DOI: 10.1371/journal.ppat.1007071] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/05/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
HIV-1 Tat is a key regulator of viral transcription, however little is known about the mechanisms that control its turnover in T cells. Here we use a novel proteomics technique, called DiffPOP, to identify the molecular target of JIB-04, a small molecule compound that potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines. Mass-spectrometry analysis of whole-cell extracts from 2D10 Jurkat T cells revealed that JIB-04 targets Serine Hydroxymethyltransferase 2 (SHMT2), a regulator of glycine biosynthesis and an adaptor for the BRCC36 K63Ub-specific deubiquitinase in the BRISC complex. Importantly, knockdown of SHMT1,2 or BRCC36, or exposure of cells to JIB-04, strongly increased Tat K63Ub-dependent destruction via autophagy. Moreover, point mutation of multiple lysines in Tat, or knockdown of BRCC36 or SHMT1,2, was sufficient to prevent destruction of Tat by JIB-04. We conclude that HIV-1 Tat levels are regulated through K63Ub-selective autophagy mediated through SHMT1,2 and the BRCC36 deubiquitinase.
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Affiliation(s)
- Muyu Xu
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - James J. Moresco
- Mass Spectrometry Core for Proteomics and Metabolomics, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Max Chang
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Amey Mukim
- Division of Infectious Diseases, University of California San Diego School of Medicine, La Jolla, CA, United States of America
| | - Davey Smith
- Division of Infectious Diseases, University of California San Diego School of Medicine, La Jolla, CA, United States of America
| | - Jolene K. Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, United States of America
| | - John R. Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, United States of America
| | - Katherine A. Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
- * E-mail:
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218
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Sadasivam DA, Huang DH. Feedback regulation by antagonistic epigenetic factors potentially maintains developmental homeostasis in Drosophila. J Cell Sci 2018; 131:jcs.210179. [PMID: 29661849 DOI: 10.1242/jcs.210179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 04/04/2018] [Indexed: 01/09/2023] Open
Abstract
Drosophila Polycomb group (PcG) repressors confer epigenetically heritable silencing on key regulatory genes through histone H3 trimethylation on lysine 27 (H3K27me3). How the silencing state withstands antagonistic activities from co-expressed trithorax group (trxG) activators is unclear. Upon overexpression of Trx H3K4 methylase, to perturb the silenced state, we find a dynamic process triggered in a stepwise fashion to neutralize the inductive impacts from excess Trx. Shortly after Trx overexpression, there are global increases in H3K4 trimethylation and RNA polymerase II phosphorylation, marking active transcription. Subsequently, these patterns diminish at the same time as the levels of Set1, an abundant H3K4 methylase involved in productive transcription, reduce. Concomitantly, the global H3K27me3 level is markedly reduced, corresponding to an increase in the amount of Utx demethylase. Finally, excess Pc repressive complex 1 (PRC1) is induced and located to numerous ectopic chromosomal sites independently of H3K27me3 and several key recruitment factors. The observation that PRC1 becomes almost completely colocalized with Trx suggests new aspects of recruitment and antagonistic interaction. We propose that these events represent a feedback circuitry ensuring the stability of the silenced state.
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Affiliation(s)
| | - Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529
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219
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Rimel JK, Taatjes DJ. The essential and multifunctional TFIIH complex. Protein Sci 2018; 27:1018-1037. [PMID: 29664212 PMCID: PMC5980561 DOI: 10.1002/pro.3424] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022]
Abstract
TFIIH is a 10‐subunit complex that regulates RNA polymerase II (pol II) transcription but also serves other important biological roles. Although much remains unknown about TFIIH function in eukaryotic cells, much progress has been made even in just the past few years, due in part to technological advances (e.g. cryoEM and single molecule methods) and the development of chemical inhibitors of TFIIH enzymes. This review focuses on the major cellular roles for TFIIH, with an emphasis on TFIIH function as a regulator of pol II transcription. We describe the structure of TFIIH and its roles in pol II initiation, promoter‐proximal pausing, elongation, and termination. We also discuss cellular roles for TFIIH beyond transcription (e.g. DNA repair, cell cycle regulation) and summarize small molecule inhibitors of TFIIH and diseases associated with defects in TFIIH structure and function.
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Affiliation(s)
- Jenna K Rimel
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
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220
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Liu J, Wu X, Zhang H, Pfeifer GP, Lu Q. Dynamics of RNA Polymerase II Pausing and Bivalent Histone H3 Methylation during Neuronal Differentiation in Brain Development. Cell Rep 2018; 20:1307-1318. [PMID: 28793256 DOI: 10.1016/j.celrep.2017.07.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/17/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022] Open
Abstract
During cellular differentiation, genes important for differentiation are expected to be silent in stem/progenitor cells yet can be readily activated. RNA polymerase II (Pol II) pausing and bivalent chromatin marks are two paradigms suited for establishing such a poised state of gene expression; however, their specific contributions in development are not well understood. Here we characterized Pol II pausing and H3K4me3/H3K27me3 marks in neural progenitor cells (NPCs) and their daughter neurons purified from the developing mouse cortex. We show that genes paused in NPCs or neurons are characteristic of respective cellular functions important for each cell type, although pausing and pause release were not correlated with gene activation. Bivalent chromatin marks poised the marked genes in NPCs for activation in neurons. Interestingly, we observed a positive correlation between H3K27me3 and paused Pol II. This study thus reveals cell type-specific Pol II pausing and gene activation-associated bivalency during mammalian neuronal differentiation.
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Affiliation(s)
- Jiancheng Liu
- Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Heying Zhang
- Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Gerd P Pfeifer
- Department of Cancer Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Qiang Lu
- Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
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221
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Yu F, Shi G, Cheng S, Chen J, Wu SY, Wang Z, Xia N, Zhai Y, Wang Z, Peng Y, Wang D, Du JX, Liao L, Duan SZ, Shi T, Cheng J, Chiang CM, Li J, Wong J. SUMO suppresses and MYC amplifies transcription globally by regulating CDK9 sumoylation. Cell Res 2018; 28:670-685. [PMID: 29588524 DOI: 10.1038/s41422-018-0023-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/28/2018] [Accepted: 02/11/2018] [Indexed: 01/21/2023] Open
Abstract
Regulation of transcription is fundamental to the control of cellular gene expression and function. Although recent studies have revealed a role for the oncoprotein MYC in amplifying global transcription, little is known as to how the global transcription is suppressed. Here we report that SUMO and MYC mediate opposite effects upon global transcription by controlling the level of CDK9 sumoylation. On one hand, SUMO suppresses global transcription via sumoylation of CDK9, the catalytic subunit of P-TEFb kinase essential for productive transcriptional elongation. On the other hand, MYC amplifies global transcription by antagonizing CDK9 sumoylation. Sumoylation of CDK9 blocks its interaction with Cyclin T1 and thus the formation of active P-TEFb complex. Transcription profiling analyses reveal that SUMO represses global transcription, particularly of moderately to highly expressed genes and by generating a sumoylation-resistant CDK9 mutant, we confirm that sumoylation of CDK9 inhibits global transcription. Together, our data reveal that SUMO and MYC oppositely control global gene expression by regulating the dynamic sumoylation and desumoylation of CDK9.
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Affiliation(s)
- Fang Yu
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Guang Shi
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.,Key Laboratory of Gene Engineering of the Ministry of Education and Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shimeng Cheng
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jiwei Chen
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, Department of Biochemistry, and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Zhiqiang Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Nansong Xia
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yunhao Zhai
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Zhenxing Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yu Peng
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dong Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - James X Du
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Sheng-Zhong Duan
- Laboratory of Oral Microbiology, Shanghai Research Institute of Stomatology, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital, School of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Tieliu Shi
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Jinke Cheng
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Biochemistry, and Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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222
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RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia. Nat Commun 2018; 9:1163. [PMID: 29563491 PMCID: PMC5862959 DOI: 10.1038/s41467-018-03513-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 01/26/2018] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
The roles of RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) in lineage-associated chromatin organization and drug response/resistance are unclear. Here we demonstrate that the RCMTs, namely NSUN3 and DNMT2, directly bind hnRNPK, a conserved RNA-binding protein. hnRNPK interacts with the lineage-determining transcription factors (TFs), GATA1 and SPI1/PU.1, and with CDK9/P-TEFb to recruit RNA-polymerase-II at nascent RNA, leading to formation of 5-Azacitidine (5-AZA)-sensitive chromatin structure. In contrast, NSUN1 binds BRD4 and RNA-polymerase-II to form an active chromatin structure that is insensitive to 5-AZA, but hypersensitive to the BRD4 inhibitor JQ1 and to the downregulation of NSUN1 by siRNAs. Both 5-AZA-resistant leukaemia cell lines and clinically 5-AZA-resistant myelodysplastic syndrome and acute myeloid leukaemia specimens have a significant increase in RNA:m5C and NSUN1-/BRD4-associated active chromatin. This study reveals novel RNA:m5C/RCMT-mediated chromatin structures that modulate 5-AZA response/resistance in leukaemia cells, and hence provides a new insight into treatment of leukaemia. Resistance to chemotherapy is a serious issue that can be influenced by RNA epigenetics and chromatin structure. Here, the authors show in leukaemia cells that RNA 5-methylcytosine (RNA:m5C) and RNA:m5C methyltransferases (RCMTs) mediate chromatin structures that can modulate 5-Azacitidine response and resistance.
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223
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Borisova ME, Voigt A, Tollenaere MAX, Sahu SK, Juretschke T, Kreim N, Mailand N, Choudhary C, Bekker-Jensen S, Akutsu M, Wagner SA, Beli P. p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. Nat Commun 2018. [PMID: 29523821 PMCID: PMC5845016 DOI: 10.1038/s41467-018-03417-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ultraviolet (UV) light radiation induces the formation of bulky photoproducts in the DNA that globally affect transcription and splicing. However, the signaling pathways and mechanisms that link UV-light-induced DNA damage to changes in RNA metabolism remain poorly understood. Here we employ quantitative phosphoproteomics and protein kinase inhibition to provide a systems view on protein phosphorylation patterns induced by UV light and uncover the dependencies of phosphorylation events on the canonical DNA damage signaling by ATM/ATR and the p38 MAP kinase pathway. We identify RNA-binding proteins as primary substrates and 14-3-3 as direct readers of p38-MK2-dependent phosphorylation induced by UV light. Mechanistically, we show that MK2 phosphorylates the RNA-binding subunit of the NELF complex NELFE on Serine 115. NELFE phosphorylation promotes the recruitment of 14-3-3 and rapid dissociation of the NELF complex from chromatin, which is accompanied by RNA polymerase II elongation. UV-light-induced DNA damage affects RNA metabolism but the underlying signalling pathways are largely unexplored. Here, the authors show that UV light triggers p38-MK2-mediated phosphorylation of the NELF complex, promoting its release from chromatin and concurrent transcriptional elongation.
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Affiliation(s)
- Marina E Borisova
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Maxim A X Tollenaere
- Cellular Stress Signaling Group, Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen, Denmark
| | - Sanjeeb Kumar Sahu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Thomas Juretschke
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Nastasja Kreim
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Niels Mailand
- Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics and Cell Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Cellular Stress Signaling Group, Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen, Denmark
| | - Masato Akutsu
- Institute of Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von Laue-Strasse 15, 60438, Frankfurt, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.,German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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224
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hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons. Proc Natl Acad Sci U S A 2018; 115:E2859-E2868. [PMID: 29507242 PMCID: PMC5866599 DOI: 10.1073/pnas.1721670115] [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] [Indexed: 02/08/2023] Open
Abstract
Neurons are highly polarized cells. RNA-binding proteins contribute to this polarization by generating diverse subcellular transcriptomes. The RNA-binding protein hnRNP R is essential for axon growth in motoneurons. This study reports the RNA interactome for hnRNP R. The main interacting RNA of hnRNP R was the noncoding RNA 7SK. Depletion of 7SK from primary motoneurons disturbed axon growth. This effect was dependent on the interaction of 7SK with hnRNP R. Both hnRNP R and 7SK localize to axons. Loss of 7SK led to a similar depletion of axonal transcripts as loss of hnRNP R. Our data suggest that 7SK, in addition to its role in transcriptional regulation, acts in concert with hnRNP R to sort specific transcripts into axons. Disturbed RNA processing and subcellular transport contribute to the pathomechanisms of motoneuron diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. RNA-binding proteins are involved in these processes, but the mechanisms by which they regulate the subcellular diversity of transcriptomes, particularly in axons, are not understood. Heterogeneous nuclear ribonucleoprotein R (hnRNP R) interacts with several proteins involved in motoneuron diseases. It is located in axons of developing motoneurons, and its depletion causes defects in axon growth. Here, we used individual nucleotide-resolution cross-linking and immunoprecipitation (iCLIP) to determine the RNA interactome of hnRNP R in motoneurons. We identified ∼3,500 RNA targets, predominantly with functions in synaptic transmission and axon guidance. Among the RNA targets identified by iCLIP, the noncoding RNA 7SK was the top interactor of hnRNP R. We detected 7SK in the nucleus and also in the cytosol of motoneurons. In axons, 7SK localized in close proximity to hnRNP R, and depletion of hnRNP R reduced axonal 7SK. Furthermore, suppression of 7SK led to defective axon growth that was accompanied by axonal transcriptome alterations similar to those caused by hnRNP R depletion. Using a series of 7SK-deletion mutants, we show that the function of 7SK in axon elongation depends on its interaction with hnRNP R but not with the PTEF-B complex involved in transcriptional regulation. These results propose a role for 7SK as an essential interactor of hnRNP R to regulate its function in axon maintenance.
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225
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Wang C, Jin H, Gao D, Wang L, Evers B, Xue Z, Jin G, Lieftink C, Beijersbergen RL, Qin W, Bernards R. A CRISPR screen identifies CDK7 as a therapeutic target in hepatocellular carcinoma. Cell Res 2018; 28:690-692. [PMID: 29507396 DOI: 10.1038/s41422-018-0020-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/17/2018] [Accepted: 02/06/2018] [Indexed: 02/04/2023] Open
Affiliation(s)
- Cun Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Haojie Jin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Dongmei Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Liqin Wang
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Bastiaan Evers
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Zheng Xue
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Guangzhi Jin
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China.
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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226
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Pourteimoor V, Paryan M, Mohammadi‐Yeganeh S. microRNA as a systemic intervention in the specific breast cancer subtypes with C‐MYC impacts; introducing subtype‐based appraisal tool. J Cell Physiol 2018; 233:5655-5669. [DOI: 10.1002/jcp.26399] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 12/18/2022]
Affiliation(s)
| | - Mahdi Paryan
- Department of Research and Development, Production and Research ComplexPasteur Institute of IranTehranIran
| | - Samira Mohammadi‐Yeganeh
- Cellular and Molecular Biology Research CenterShahid Beheshti University of Medical SciencesTehranIran
- Department of Biotechnology, School of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran
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227
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Abstract
Hexim1 acts as a tumor suppressor and is involved in the regulation of innate immunity. It was initially described as a non-coding RNA-dependent regulator of transcription. Here, we detail how 7SK RNA binds to Hexim1 and turns it into an inhibitor of the positive transcription elongation factor (P-TEFb). In addition to its action on P-TEFb, it plays a role in a variety of different mechanisms: it controls the stability of transcription factor components and assists binding of transcription factors to their targets.
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Affiliation(s)
- Annemieke A Michels
- a IBENS , Ecole Normale Supérieure UMR CNRS 8107, UA INSERM 1024 , 46 rue d'Ulm Paris Cedex France
| | - Olivier Bensaude
- a IBENS , Ecole Normale Supérieure UMR CNRS 8107, UA INSERM 1024 , 46 rue d'Ulm Paris Cedex France
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228
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Specific Recognition of Arginine Methylated Histone Tails by JMJD5 and JMJD7. Sci Rep 2018; 8:3275. [PMID: 29459673 PMCID: PMC5818494 DOI: 10.1038/s41598-018-21432-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
We have reported that JMJD5 and JMJD7 (JMJD5/7) are responsible for the clipping of arginine methylated histone tails to generate "tailless nucleosomes", which could release the pausing RNA polymerase II (Pol II) into productive transcription elongation. JMJD5/7 function as endopeptidases that cleave histone tails specifically adjacent to methylated arginine residues and continue to degrade N-terminal residues of histones via their aminopeptidase activity. Here, we report structural and biochemical studies on JMJD5/7 to understand the basis of substrate recognition and catalysis mechanism by this JmjC subfamily. Recognition between these enzymes and histone substrates is specific, which is reflected by the binding data between enzymes and substrates. High structural similarity between JMJD5 and JMJD7 is reflected by the shared common substrates and high binding affinity. However, JMJD5 does not bind to arginine methylated histone tails with additional lysine acetylation while JMJD7 does not bind to arginine methylated histone tails with additional lysine methylation. Furthermore, the complex structures of JMJD5 and arginine derivatives revealed a Tudor domain-like binding pocket to accommodate the methylated sidechain of arginine, but not lysine. There also exists a glutamine close to the catalytic center, which may suggest a unique imidic acid mediated catalytic mechanism for proteolysis by JMJD5/7.
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229
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Cdk-related kinase 9 regulates RNA polymerase II mediated transcription in Toxoplasma gondii. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:572-585. [PMID: 29466697 DOI: 10.1016/j.bbagrm.2018.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 11/20/2022]
Abstract
Cyclin-dependent kinases are an essential part of eukaryotic transcriptional machinery. In Apicomplexan parasites, the role and relevance of the kinases in the multistep process of transcription seeks more attention given the absence of full repertoire of canonical Cdks and cognate cyclin partners. In this study, we functionally characterize T. gondii Cdk-related kinase 9 (TgCrk9) showing maximal homology to eukaryotic Cdk9. An uncanonical cyclin, TgCyclin L, colocalizes with TgCrk9 in the parasite nucleus and co-immunoprecipitate, could activate the kinase in-vitro. We identify two threonines in conserved T-loop domain of TgCrk9 that are important for its activity. The activated TgCrk9 phosphorylates C-terminal domain (CTD) of TgRpb1, the largest subunit of RNA polymerase II highlighting its role in transcription. Selective chemical inhibition of TgCrk9 affected serine 2 phosphorylation in the heptapeptide repeats of TgRpb1-CTD towards 3' end of genes consistent with a possible role in transcription elongation. Interestingly, TgCrk9 kinase activity is regulated by the upstream TgCrk7 based CAK complex. TgCrk9 was found to functionally complement the role of its yeast counterpart Bur1 establishing its role as an important transcriptional kinase. In this study, we provide robust evidence that TgCrk9 is an important part of transcription machinery regulating gene expression in T. gondii.
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230
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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231
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Zhao Y, Dunker W, Yu YT, Karijolich J. The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events. Front Bioeng Biotechnol 2018; 6:8. [PMID: 29473035 PMCID: PMC5809436 DOI: 10.3389/fbioe.2018.00008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022] Open
Abstract
Pseudouridine is the most abundant internal RNA modification in stable noncoding RNAs (ncRNAs). It can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Pseudouridylation impacts both the biochemical and biophysical properties of RNAs and thus influences RNA-mediated cellular processes. The investigation of nuclear-ncRNA pseudouridylation has demonstrated that it is critical for the proper control of multiple stages of gene expression regulation. Here, we review how nuclear-ncRNA pseudouridylation contributes to transcriptional regulation and pre-mRNA splicing.
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Affiliation(s)
- Yang Zhao
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - William Dunker
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, School of Medicine, Vanderbilt University, Nashville, TN, United States.,Vanderbilt-Ingram Cancer Center, Nashville, TN, United States
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232
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Hajmirza A, Emadali A, Gauthier A, Casasnovas O, Gressin R, Callanan MB. BET Family Protein BRD4: An Emerging Actor in NFκB Signaling in Inflammation and Cancer. Biomedicines 2018; 6:biomedicines6010016. [PMID: 29415456 PMCID: PMC5874673 DOI: 10.3390/biomedicines6010016] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 02/04/2023] Open
Abstract
NFκB (Nuclear Factor-κ-light-chain-enhancer of activated B cells) signaling elicits global transcriptional changes by activating cognate promoters and through genome-wide remodeling of cognate regulatory elements called “super enhancers”. BET (Bromodomain and Extra-Terminal domain) protein family inhibitor studies have implicated BET protein member BRD4 and possibly other BET proteins in NFκB-dependent promoter and super-enhancer modulation. Members of the BET protein family are known to bind acetylated chromatin to facilitate access by transcriptional regulators to chromatin, as well as to assist the activity of transcription elongation complexes via CDK9/pTEFb. BET family member BRD4 has been shown to bind non-histone proteins and modulate their activity. One such protein is RELA, the NFκB co-activator. Specifically, BRD4 binds acetylated RELA, which increases its transcriptional transactivation activity and stability in the nucleus. In aggregate, this establishes an intimate link between NFκB and BET signaling, at least via BRD4. The present review provides a brief overview of the structure and function of BET family proteins and then examines the connections between NFκB and BRD4 signaling, using the inflammatory response and cancer cell signaling as study models. We also discuss the potential of BET inhibitors for relief of aberrant NFκB signaling in cancer, focusing on non-histone, acetyl-lysine binding functions.
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Affiliation(s)
- Azadeh Hajmirza
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université de Grenoble-Alpes, F-38042 Grenoble, France.
| | - Anouk Emadali
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université de Grenoble-Alpes, F-38042 Grenoble, France.
- Pôle Recherche, Grenoble-Alpes University Hospital, F-38043 Grenoble, France.
| | - Arnaud Gauthier
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université de Grenoble-Alpes, F-38042 Grenoble, France.
| | - Olivier Casasnovas
- Département d'Hématologie Clinique, Dijon University Hospital, F-21000 Dijon, France.
| | - Rémy Gressin
- Département d'Hématologie Clinique, Grenoble-Alpes University Hospital, F-38043 Grenoble, France.
| | - Mary B Callanan
- INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université de Grenoble-Alpes, F-38042 Grenoble, France.
- Centre for Innovation in Cancer Genetics and Epigenetics, Dijon University Hospital, F-21000 Dijon, France.
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233
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Li Y, Liu M, Chen LF, Chen R. P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II. Transcription 2018; 9:88-94. [PMID: 28102758 PMCID: PMC5834220 DOI: 10.1080/21541264.2017.1281864] [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: 12/05/2016] [Revised: 01/09/2017] [Accepted: 01/09/2017] [Indexed: 12/26/2022] Open
Abstract
The release of a paused Pol II depends on the recruitment of P-TEFb. Recent studies showed that both active P-TEFb and inactive P-TEFb (7SK snRNP) can be recruited to the promoter regions of global genes by different mechanisms. Here, we summarize the recent advances on these distinct recruitment mechanisms.
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Affiliation(s)
- You Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Min Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Lin-Feng Chen
- Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ruichuan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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234
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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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235
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Erwin GS, Grieshop MP, Ali A, Qi J, Lawlor M, Kumar D, Ahmad I, McNally A, Teider N, Worringer K, Sivasankaran R, Syed DN, Eguchi A, Ashraf M, Jeffery J, Xu M, Park PMC, Mukhtar H, Srivastava AK, Faruq M, Bradner JE, Ansari AZ. Synthetic transcription elongation factors license transcription across repressive chromatin. Science 2017; 358:1617-1622. [PMID: 29192133 PMCID: PMC6037176 DOI: 10.1126/science.aan6414] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022]
Abstract
The release of paused RNA polymerase II into productive elongation is highly regulated, especially at genes that affect human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators. Here we present Syn-TEF1, a molecule that actively enables transcription across repressive GAA repeats that silence frataxin expression in Friedreich's ataxia, a terminal neurodegenerative disease with no effective therapy. The modular design of Syn-TEF1 defines a general framework for developing a class of molecules that license transcription elongation at targeted genomic loci.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew P Grieshop
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asfa Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepak Kumar
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Istaq Ahmad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Anna McNally
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Natalia Teider
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Katie Worringer
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Rajeev Sivasankaran
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Deeba N Syed
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Md Ashraf
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Justin Jeffery
- Small Animal Imaging Facility, University of Wisconsin Carbone Cancer Center, Madison, WI 53792, USA
| | - Mousheng Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hasan Mukhtar
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Achal K Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA 02139, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
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236
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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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237
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Bromodomain-containing Protein 4 Activates Voltage-gated Sodium Channel 1.7 Transcription in Dorsal Root Ganglia Neurons to Mediate Thermal Hyperalgesia in Rats. Anesthesiology 2017; 127:862-877. [DOI: 10.1097/aln.0000000000001809] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Background
Bromodomain-containing protein 4 binds acetylated promoter histones and promotes transcription; however, the role of bromodomain-containing protein 4 in inflammatory hyperalgesia remains unclear.
Methods
Male Sprague–Dawley rats received hind paw injections of complete Freund’s adjuvant to induce hyperalgesia. The dorsal root ganglia were examined to detect changes in bromodomain-containing protein 4 expression and the activation of genes involved in the expression of voltage-gated sodium channel 1.7, which is a key pain-related ion channel.
Results
The intraplantar complete Freund’s adjuvant injections resulted in thermal hyperalgesia (4.0 ± 1.5 s; n = 7). The immunohistochemistry and immunoblotting results demonstrated an increase in the bromodomain-containing protein 4–expressing dorsal root ganglia neurons (3.78 ± 0.38 fold; n = 7) and bromodomain-containing protein 4 protein levels (2.62 ± 0.39 fold; n = 6). After the complete Freund’s adjuvant injection, histone H3 protein acetylation was enhanced in the voltage-gated sodium channel 1.7 promoter, and cyclin-dependent kinase 9 and phosphorylation of RNA polymerase II were recruited to this area. Furthermore, the voltage-gated sodium channel 1.7–mediated currents were enhanced in neurons of the complete Freund’s adjuvant rats (55 ± 11 vs. 19 ± 9 pA/pF; n = 4 to 6 neurons). Using bromodomain-containing protein 4–targeted antisense small interfering RNA to the complete Freund’s adjuvant–treated rats, the authors demonstrated a reduction in the expression of bromodomain-containing protein 4 (0.68 ± 0.16 fold; n = 7), a reduction in thermal hyperalgesia (7.5 ± 1.5 s; n = 7), and a reduction in the increased voltage-gated sodium channel 1.7 currents (21 ± 4 pA/pF; n = 4 to 6 neurons).
Conclusions
Complete Freund’s adjuvant triggers enhanced bromodomain-containing protein 4 expression, ultimately leading to the enhanced excitability of nociceptive neurons and thermal hyperalgesia. This effect is likely mediated by the enhanced expression of voltage-gated sodium channel 1.7.
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238
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Hong H, Zeng Y, Jian W, Li L, Lin L, Mo Y, Liu M, Fang S, Xia Y. CDK7 inhibition suppresses rheumatoid arthritis inflammation via blockage of NF-κB activation and IL-1β/IL-6 secretion. J Cell Mol Med 2017; 22:1292-1301. [PMID: 29083085 PMCID: PMC5783872 DOI: 10.1111/jcmm.13414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/04/2017] [Indexed: 12/23/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by joint swelling, joint tenderness and destruction of synovial joints, leading to severe disability. Anti‐inflammatory drugs and disease‐modifying anti‐rheumatic drugs (DMARDs) may improve RA process. However, in most patients the treatment effect is still not satisfactory. Cyclin‐dependent kinase 7 (CDK7) plays a well‐established role in the regulation of the eukaryotic cell division cycle, and recent studies indicated that it exerted anti‐inflammatory effect. In our previous research, we found that inhibition of CDK7 by highly selective inhibitor BS‐181 significantly impeded the development of collagen‐induced arthritis (CIA) mice. However, the underlying mechanism of CDK7 in RA remains to be explored. We elucidated the molecular mechanism of CDK7 inhibition in RA inflammation by administration of CDK7 highly selective inhibitor BS‐181 and siRNA‐CDK7. We found that both IL‐1β, IL‐6, IL‐8 and RANKL transcript levels and IL‐1β/IL‐6 secretion were effectively suppressed by BS‐181 treatment as well as CDK7 knockdown. Furthermore, CDK7 inhibition prevented NF‐κB signalling pathway activation and restrained p65 nuclear translocation. Moreover, CDK7 selective inhibitor BS‐181 also blocked phosphorylation of p65 in MH7A cells. These results strongly indicate that CDK7 inhibition by BS‐181 and siRNA‐CDK7 significantly suppresses rheumatoid arthritis inflammation, which may be via blockage of NF‐κB signalling pathway and IL‐1β/IL‐6 secretion.
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Affiliation(s)
- Honghai Hong
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yingmin Zeng
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenxuan Jian
- DME center, Clinical Pharmacology Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lei Li
- Department of Reproductive Medicine Center, Key Laboratory for Reproductive Medicine of Guangdong Province, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liying Lin
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yousheng Mo
- DME center, Clinical Pharmacology Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meiling Liu
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuhuan Fang
- DME center, Clinical Pharmacology Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yong Xia
- Department of Clinical Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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239
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Abstract
In this issue of Molecular Cell, Morchikh et al. (2017) describe a new ribonuclear complex built around HEXIM1 and the long non-coding RNA NEAT1. This complex regulates the innate immune response to DNA viruses and is distinct from the HEXIM1-7SK RNA complex that regulates transcription elongation.
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Affiliation(s)
- Olivier Bensaude
- IBENS-CNRS UMR 8197-INSERM U1024-Ecole Normale Supérieure 46, Rue d'Ulm, Cedex 05, 75230 Paris, France.
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240
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CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II. Mol Cell 2017; 68:491-503.e5. [PMID: 29056321 DOI: 10.1016/j.molcel.2017.09.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 07/13/2017] [Accepted: 09/21/2017] [Indexed: 11/21/2022]
Abstract
Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
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241
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Sweta K, Dabas P, Jain K, Sharma N. The amino-terminal domain of ELL transcription elongation factor is essential for ELL function in Schizosaccharomyces pombe. MICROBIOLOGY-SGM 2017; 163:1641-1653. [PMID: 29043956 DOI: 10.1099/mic.0.000554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transcriptional elongation is a critical step for regulating expression of protein-coding genes. Multiple transcription elongation factors have been identified in vitro, but the physiological roles of many of them are still not clearly understood. The ELL (Eleven nineteen Lysine rich Leukemia) family of transcription elongation factors are conserved from fission yeast to humans. Schizosaccharomyces pombe contains a single ELL homolog (SpELL) that is not essential for its survival. Therefore to gain insights into the in vivo cellular functions of SpELL, we identified phenotypes associated with deletion of ell1 in S. pombe. Our results demonstrate that SpELL is required for normal growth of S. pombe cells. Furthermore, cells lacking ell1+ exhibit a decrease in survival when exposed to DNA-damaging conditions, but their growth is not affected under environmental stress conditions. ELL orthologs in different organisms contain three conserved domains, an amino-terminal domain, a middle domain and a carboxyl-terminal domain. We also carried out an in vivo functional mapping of these conserved domains within S. pombe ELL and uncovered a critical role for its amino-terminus in regulating all its cellular functions, including growth under different conditions, transcriptional elongation potential and interaction with S. pombe EAF. Taken together our results suggest that the domain organization of ELL proteins is conserved across species, but the in vivo functions as well as the relationship between the various domains and roles of ELL show species-specific differences.
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Affiliation(s)
- Kumari Sweta
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi-110078, India
| | - Preeti Dabas
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi-110078, India
| | - Kamal Jain
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi-110078, India
| | - Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi-110078, India
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242
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The bromodomain and extraterminal domain inhibitor bromosporine synergistically reactivates latent HIV-1 in latently infected cells. Oncotarget 2017; 8:94104-94116. [PMID: 29212213 PMCID: PMC5706859 DOI: 10.18632/oncotarget.21585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/21/2017] [Indexed: 11/25/2022] Open
Abstract
The long-lived latent HIV-1 reservoir is the major barrier for complete cure of Acquired Immune Deficiency Syndrome (AIDS). Here we report that a novel bromodomain and extraterminal domain (BET) inhibitor bromosporine which can broadly target BETs, is able to potently reactivate HIV-1 replication in different latency models alone and more powerful when combined with prostratin or TNF-α. Furthermore, the treatment with bromosporine induced HIV-1 full-length transcripts in resting CD4+ T cells from infected individuals with suppressive antiretroviral therapy (ART) ex vivo, with no obvious cytotoxicity or global activation of T cell. Finally, our data suggest that Tat plays a critical role in the bromosporine-mediated reactivation of latent HIV-1, which involved the increase of CDK9 T-loop phosphorylation. In summary, we found that the BET inhibitor bromosporine, alone or with other activators, might be a candidate for future HIV-1 eradication strategies.
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243
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Egloff S, Studniarek C, Kiss T. 7SK small nuclear RNA, a multifunctional transcriptional regulatory RNA with gene-specific features. Transcription 2017; 9:95-101. [PMID: 28820318 DOI: 10.1080/21541264.2017.1344346] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The 7SK small nuclear RNA is a multifunctional transcriptional regulatory RNA that controls the nuclear activity of the positive transcription elongation factor b (P-TEFb), specifically targets P-TEFb to the promoter regions of selected protein-coding genes and promotes transcription of RNA polymerase II-specific spliceosomal small nuclear RNA genes.
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Affiliation(s)
- Sylvain Egloff
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Centre de Biologie Intégrative, Université Paul Sabatier , Toulouse , France
| | - Cécilia Studniarek
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Centre de Biologie Intégrative, Université Paul Sabatier , Toulouse , France
| | - Tamás Kiss
- a Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Centre de Biologie Intégrative, Université Paul Sabatier , Toulouse , France.,b Biological Research Centre , Hungarian Academy of Sciences , Szeged , Hungary
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244
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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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245
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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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246
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Appling FD, Lucius AL, Schneider DA. Quantifying the influence of 5'-RNA modifications on RNA polymerase I activity. Biophys Chem 2017; 230:84-88. [PMID: 28893424 DOI: 10.1016/j.bpc.2017.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022]
Abstract
For ensemble and single-molecule analyses of transcription, the use of synthetic transcription elongation complexes has been a versatile and powerful tool. However, structural analyses demonstrate that short RNA substrates, often employed in these assays, would occupy space within the RNA polymerase. Most commercial RNA oligonucleotides do not carry a 5'-triphosphate as would be present on a natural, de novo synthesized RNA. To examine the effects of 5'-moities on transcription kinetics, we measured nucleotide addition and 3'-dinucleotide cleavage by eukaryotic RNA polymerase I using 5'-hydroxyl and 5'-triphosphate RNA substrates. We found that 5' modifications had no discernable effect on the kinetics of nucleotide addition; however, we observed clear, but modest, effects on the rate of backtracking and/or dinucleotide cleavage. These data suggest that the 5'-end may influence RNA polymerase translocation, consistent with previous prokaryotic studies, and these findings may have implications on kinetic barriers that confront RNA polymerases during the transition from initiation to elongation.
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Affiliation(s)
- Francis D Appling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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247
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Wang P, Lu P, Qu X, Shen Y, Zeng H, Zhu X, Zhu Y, Li X, Wu H, Xu J, Lu H, Ma Z, Zhu H. Reactivation of HIV-1 from Latency by an Ingenol Derivative from Euphorbia Kansui. Sci Rep 2017; 7:9451. [PMID: 28842560 PMCID: PMC5573388 DOI: 10.1038/s41598-017-07157-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/23/2017] [Indexed: 02/07/2023] Open
Abstract
Cells harboring latent HIV-1 pose a major obstacle to eradication of the virus. The ‘shock and kill’ strategy has been broadly explored to purge the latent reservoir; however, none of the current latency-reversing agents (LRAs) can safely and effectively activate the latent virus in patients. In this study, we report an ingenol derivative called EK-16A, isolated from the traditional Chinese medicinal herb Euphorbia kansui, which displays great potential in reactivating latent HIV-1. A comparison of the doses used to measure the potency indicated EK-16A to be 200-fold more potent than prostratin in reactivating HIV-1 from latently infected cell lines. EK-16A also outperformed prostratin in ex vivo studies on cells from HIV-1-infected individuals, while maintaining minimal cytotoxicity effects on cell viability and T cell activation. Furthermore, EK-16A exhibited synergy with other LRAs in reactivating latent HIV-1. Mechanistic studies indicated EK-16A to be a PKCγ activator, which promoted both HIV-1 transcription initiation by NF-κB and elongation by P-TEFb signal pathways. Further investigations aimed to add this compound to the therapeutic arsenal for HIV-1 eradication are in the pipeline.
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Affiliation(s)
- Pengfei Wang
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Panpan Lu
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiying Qu
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yinzhong Shen
- Department of Infectious Diseases, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200433, China
| | - Hanxian Zeng
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaoli Zhu
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xian Li
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hao Wu
- Center for Infectious Diseases, Beijing You'an Hospital, Capital Medical University, Beijing, 100069, China
| | - Jianqing Xu
- Department of Infectious Diseases, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200433, China
| | - Hongzhou Lu
- Department of Infectious Diseases, and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200433, China
| | - Zhongjun Ma
- Institute of Marine Biology, Ocean College, Zhejiang University, Hangzhou, 310058, China.
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering and Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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248
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Jiang YY, Lin DC, Mayakonda A, Hazawa M, Ding LW, Chien WW, Xu L, Chen Y, Xiao JF, Senapedis W, Baloglu E, Kanojia D, Shang L, Xu X, Yang H, Tyner JW, Wang MR, Koeffler HP. Targeting super-enhancer-associated oncogenes in oesophageal squamous cell carcinoma. Gut 2017; 66:1358-1368. [PMID: 27196599 PMCID: PMC5912916 DOI: 10.1136/gutjnl-2016-311818] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/11/2016] [Accepted: 04/20/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Oesophageal squamous cell carcinoma (OSCC) is an aggressive malignancy and the major histological subtype of oesophageal cancer. Although recent large-scale genomic analysis has improved the description of the genetic abnormalities of OSCC, few targetable genomic lesions have been identified, and no molecular therapy is available. This study aims to identify druggable candidates in this tumour. DESIGN High-throughput small-molecule inhibitor screening was performed to identify potent anti-OSCC compounds. Whole-transcriptome sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) were conducted to decipher the mechanisms of action of CDK7 inhibition in OSCC. A variety of in vitro and in vivo cellular assays were performed to determine the effects of candidate genes on OSCC malignant phenotypes. RESULTS The unbiased high-throughput small-molecule inhibitor screening led us to discover a highly potent anti-OSCC compound, THZ1, a specific CDK7 inhibitor. RNA-Seq revealed that low-dose THZ1 treatment caused selective inhibition of a number of oncogenic transcripts. Notably, further characterisation of the genomic features of these THZ1-sensitive transcripts demonstrated that they were frequently associated with super-enhancer (SE). Moreover, SE analysis alone uncovered many OSCC lineage-specific master regulators. Finally, integrative analysis of both THZ1-sensitive and SE-associated transcripts identified a number of novel OSCC oncogenes, including PAK4, RUNX1, DNAJB1, SREBF2 and YAP1, with PAK4 being a potential druggable kinase. CONCLUSIONS Our integrative approaches led to a catalogue of SE-associated master regulators and oncogenic transcripts, which may significantly promote both the understanding of OSCC biology and the development of more innovative therapies.
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Affiliation(s)
- Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Masaharu Hazawa
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wen-Wen Chien
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ye Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - William Senapedis
- Department of Drug Discovery, Karyopharm Therapeutics Inc., Newton, Massachusetts, USA
| | - Erkan Baloglu
- Department of Drug Discovery, Karyopharm Therapeutics Inc., Newton, Massachusetts, USA
| | - Deepika Kanojia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Li Shang
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Xu
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jeffrey W Tyner
- Department of Cell, Developmental & Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, Los Angeles School of Medicine, Los Angeles, California, USA
- National University Cancer Institute, National University Health System and National University of Singapore, Singapore, Singapore
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249
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Dynamic Change of Transcription Pausing through Modulating NELF Protein Stability Regulates Granulocytic Differentiation. Blood Adv 2017; 1:1358-1367. [PMID: 28868519 DOI: 10.1182/bloodadvances.2017008383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The NELF complex is a metazoan-specific factor essential for establishing transcription pausing. Although NELF has been implicated in cell fate regulation, the cellular regulation of NELF and its intrinsic role in specific lineage differentiation remains largely unknown. Using mammalian hematopoietic differentiation as a model system, here we identified a dynamic change of NELF-mediated transcription pausing as a novel mechanism regulating hematopoietic differentiation. We found a sharp decrease of NELF protein abundance upon granulocytic differentiation and a subsequent genome-wide reduction of transcription pausing. This loss of pausing coincides with activation of granulocyte-affiliated genes and diminished expression of progenitor markers. Functional studies revealed that sustained expression of NELF inhibits granulocytic differentiation, whereas NELF depletion in progenitor cells leads to premature differentiation towards the granulocytic lineage. Our results thus uncover a previously unrecognized regulation of transcription pausing by modulating NELF protein abundance to control cellular differentiation.
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250
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Lu X, Batugedara G, Lee M, Prudhomme J, Bunnik EM, Le Roch K. Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2017; 45:7825-7840. [PMID: 28531310 PMCID: PMC5737683 DOI: 10.1093/nar/gkx464] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022] Open
Abstract
Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular players that regulate stage-specific gene expression and Pol II pausing will contribute to our continuous search for novel antimalarial drug targets.
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MESH Headings
- Animals
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Genes, Protozoan
- Humans
- Malaria, Falciparum/blood
- Malaria, Falciparum/parasitology
- Plasmodium falciparum/genetics
- Plasmodium falciparum/growth & development
- Plasmodium falciparum/pathogenicity
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- Sequence Analysis, RNA
- Transcription, Genetic
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Affiliation(s)
- Xueqing Maggie Lu
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Gayani Batugedara
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Michael Lee
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
| | - Evelien M. Bunnik
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
- Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Karine G. Le Roch
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
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