1
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Walker RL, Hornicek FJ, Duan Z. Transcriptional regulation and therapeutic potential of cyclin-dependent kinase 9 (CDK9) in sarcoma. Biochem Pharmacol 2024; 226:116342. [PMID: 38848777 DOI: 10.1016/j.bcp.2024.116342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Sarcomas include various subtypes comprising two significant groups - soft tissue and bone sarcomas. Although the survival rate for some sarcoma subtypes has improved over time, the current methods of treatment remain efficaciously limited, as recurrent, and metastatic diseases remain a major obstacle. There is a need for better options and therapeutic strategies in treating sarcoma. Cyclin dependent kinase 9 (CDK9) is a transcriptional kinase and has emerged as a promising target for treating various cancers. The aberrant expression and activation of CDK9 have been observed in several sarcoma subtypes, including rhabdomyosarcoma, synovial sarcoma, osteosarcoma, Ewing sarcoma, and chordoma. Enhanced CDK9 expression has also been correlated with poorer prognosis in sarcoma patients. As a master regulator of transcription, CDK9 promotes transcription elongation by phosphorylation and releasing RNA polymerase II (RNAPII) from its promoter proximal pause. Release of RNAPII from this pause induces transcription of critical genes in the tumor cell. Overexpression and activation of CDK9 have been observed to lead to the expression of oncogenes, including MYC and MCL-1, that aid sarcoma development and progression. Inhibition of CDK9 in sarcoma has been proven to reduce these oncogenes' expression and decrease proliferation and growth in different sarcoma cells. Currently, there are several CDK9 inhibitors in preclinical and clinical investigations. This review aims to highlight the recent discovery and results on the transcriptional role and therapeutic potential of CDK9 in sarcoma.
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Affiliation(s)
- Robert L Walker
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA
| | - Francis J Hornicek
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA
| | - Zhenfeng Duan
- Department of Orthopedic Surgery, Sarcoma Biology Laboratory, Sylvester Comprehensive Cancer Center, and the University of Miami Miller School of Medicine, Papanicolaou Cancer Research Building, 1550 N.W. 10(th) Avenue, Miami, FL 33136. USA.
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2
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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3
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Birkenheuer CH, Baines JD. Aberrant RNA polymerase initiation and processivity on the genome of a herpes simplex virus 1 mutant lacking ICP27. J Virol 2024; 98:e0071224. [PMID: 38780246 PMCID: PMC11237563 DOI: 10.1128/jvi.00712-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Within the first 15 minutes of infection, herpes simplex virus 1 immediate early proteins repurpose cellular RNA polymerase (Pol II) for viral transcription. An important role of the viral-infected cell protein 27 (ICP27) is to facilitate viral pre-mRNA processing and export viral mRNA to the cytoplasm. Here, we use precision nuclear run-on followed by deep sequencing (PRO-seq) to characterize transcription of a viral ICP27 null mutant. At 1.5 and 3 hours post infection (hpi), we observed increased total levels of Pol II on the mutant viral genome and accumulation of Pol II downstream of poly A sites indicating increased levels of initiation and processivity. By 6 hpi, Pol II accumulation on specific mutant viral genes was higher than that on wild-type virus either at or upstream of poly A signals, depending on the gene. The PRO-seq profile of the ICP27 mutant on late genes at 6 hpi was similar but not identical to that caused by treatment with flavopiridol, a known inhibitor of RNA processivity. This pattern was different from PRO-seq profiles of other α gene mutants and upon inhibition of viral DNA replication with PAA. Together, these results indicate that ICP27 contributes to the repression of aberrant viral transcription at 1.5 and 3 hpi by inhibiting initiation and decreasing RNA processivity. However, ICP27 is needed to enhance processivity on most late genes by 6 hpi in a mechanism distinguishable from its role in viral DNA replication.IMPORTANCEWe developed and validated the use of a processivity index for precision nuclear run-on followed by deep sequencing data. The processivity index calculations confirm infected cell protein 27 (ICP27) induces downstream of transcription termination on certain host genes. The processivity indices and whole gene probe data implicate ICP27 in transient immediate early gene-mediated repression, a process that also requires ICP4, ICP22, and ICP0. The data indicate that ICP27 directly or indirectly regulates RNA polymerase (Pol II) initiation and processivity on specific genes at specific times post infection. These observations support specific and varied roles for ICP27 in regulating Pol II activity on viral genes in addition to its known roles in post transcriptional mRNA processing and export.
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Affiliation(s)
- Claire H. Birkenheuer
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Joel D. Baines
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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4
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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5
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Calvo-Roitberg E, Carroll CL, Venev SV, Kim G, Mick ST, Dekker J, Fiszbein A, Pai AA. mRNA initiation and termination are spatially coordinated. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574404. [PMID: 38260419 PMCID: PMC10802295 DOI: 10.1101/2024.01.05.574404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The expression of a precise mRNA transcriptome is crucial for establishing cell identity and function, with dozens of alternative isoforms produced for a single gene sequence. The regulation of mRNA isoform usage occurs by the coordination of co-transcriptional mRNA processing mechanisms across a gene. Decisions involved in mRNA initiation and termination underlie the largest extent of mRNA isoform diversity, but little is known about any relationships between decisions at both ends of mRNA molecules. Here, we systematically profile the joint usage of mRNA transcription start sites (TSSs) and polyadenylation sites (PASs) across tissues and species. Using both short and long read RNA-seq data, we observe that mRNAs preferentially using upstream TSSs also tend to use upstream PASs, and congruently, the usage of downstream sites is similarly paired. This observation suggests that mRNA 5' end choice may directly influence mRNA 3' ends. Our results suggest a novel "Positional Initiation-Termination Axis" (PITA), in which the usage of alternative terminal sites are coupled based on the order in which they appear in the genome. PITA isoforms are more likely to encode alternative protein domains and use conserved sites. PITA is strongly associated with the length of genomic features, such that PITA is enriched in longer genes with more area devoted to regions that regulate alternative 5' or 3' ends. Strikingly, we found that PITA genes are more likely than non-PITA genes to have multiple, overlapping chromatin structural domains related to pairing of ordinally coupled start and end sites. In turn, PITA coupling is also associated with fast RNA Polymerase II (RNAPII) trafficking across these long gene regions. Our findings indicate that a combination of spatial and kinetic mechanisms couple transcription initiation and mRNA 3' end decisions based on ordinal position to define the expression mRNA isoforms.
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Affiliation(s)
| | | | - Sergey V. Venev
- Department of Systems Biology, University Massachusetts Chan Medical School, Worcester, MA
| | - GyeungYun Kim
- Department of Biology, Boston University, Boston, MA
| | | | - Job Dekker
- Department of Systems Biology, University Massachusetts Chan Medical School, Worcester, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Ana Fiszbein
- Department of Biology, Boston University, Boston, MA
- Center for Computing & Data Sciences, Boston University, Boston, MA
| | - Athma A. Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA
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6
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Hofstetter J, Ogunleye A, Kutschke A, Buchholz LM, Wolf E, Raabe T, Gallant P. Spt5 interacts genetically with Myc and is limiting for brain tumor growth in Drosophila. Life Sci Alliance 2024; 7:e202302130. [PMID: 37935464 PMCID: PMC10629571 DOI: 10.26508/lsa.202302130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/09/2023] Open
Abstract
The transcription factor SPT5 physically interacts with MYC oncoproteins and is essential for efficient transcriptional activation of MYC targets in cultured cells. Here, we use Drosophila to address the relevance of this interaction in a living organism. Spt5 displays moderate synergy with Myc in fast proliferating young imaginal disc cells. During later development, Spt5-knockdown has no detectable consequences on its own, but strongly enhances eye defects caused by Myc overexpression. Similarly, Spt5-knockdown in larval type 2 neuroblasts has only mild effects on brain development and survival of control flies, but dramatically shrinks the volumes of experimentally induced neuroblast tumors and significantly extends the lifespan of tumor-bearing animals. This beneficial effect is still observed when Spt5 is knocked down systemically and after tumor initiation, highlighting SPT5 as a potential drug target in human oncology.
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Affiliation(s)
- Julia Hofstetter
- https://ror.org/00fbnyb24 Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ayoola Ogunleye
- https://ror.org/00fbnyb24 Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - André Kutschke
- https://ror.org/00fbnyb24 Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Lisa Marie Buchholz
- https://ror.org/00fbnyb24 Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Elmar Wolf
- https://ror.org/00fbnyb24 Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thomas Raabe
- https://ror.org/00fbnyb24 Molecular Genetics, Biocenter, Am Hubland, University of Würzburg, Würzburg, Germany
| | - Peter Gallant
- https://ror.org/00fbnyb24 Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
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7
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Wu T, Yu B, Xu Y, Du Z, Zhang Z, Wang Y, Chen H, Zhang LA, Chen R, Ma F, Gong W, Yu S, Qiu Z, Wu H, Xu X, Wang J, Li Z, Bian J. Discovery of Selective and Potent Macrocyclic CDK9 Inhibitors for the Treatment of Osimertinib-Resistant Non-Small-Cell Lung Cancer. J Med Chem 2023; 66:15340-15361. [PMID: 37870244 DOI: 10.1021/acs.jmedchem.3c01400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Effectiveness of epidermal growth factor receptor (EGFR) inhibitors, including Osimertinib, for treating non-small-cell lung cancer (NSCLC) is limited due to the continuous emergence of drug resistance. Hence, it is urgent to develop new therapeutic approaches. CDK9, a key regulator of RNA transcription, has emerged as a promising target for the development of antitumor drugs due to its crucial role in modulating the levels of antiapoptotic protein Mcl-1. Herein, we present the synthesis, optimization, and evaluation of selective CDK9 inhibitors with a macrocyclic scaffold that effectively suppresses the growth of NSCLC cells. Notably, compound Z11, a potent CDK9 inhibitor (IC50 = 3.20 nM) with good kinase selectivity, significantly inhibits cell proliferation and colony formation and induces apoptosis in Osimertinib-resistant H1975 cells. Furthermore, Z11 demonstrates a significant suppression of tumor growth in six patient-derived organoids, including three organoids resistant to Osimertinib. Overall, Z11 served as a promising macrocycle-based CDK9 inhibitor for treating Osimertinib-resistant NSCLC.
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Affiliation(s)
- Tizhi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Bin Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yifan Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zekun Du
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhiming Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yuxiao Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Haoming Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Li Ao Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Rui Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Feihai Ma
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Weihong Gong
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Sixian Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhixia Qiu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Hongxi Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xi Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jubo Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R. China
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8
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Wang Z, Himanen SV, Haikala HM, Friedel CC, Vihervaara A, Barborič M. Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release. Nucleic Acids Res 2023; 51:10970-10991. [PMID: 37811895 PMCID: PMC10639066 DOI: 10.1093/nar/gkad792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
P-TEFb and CDK12 facilitate transcriptional elongation by RNA polymerase II. Given the prominence of both kinases in cancer, gaining a better understanding of their interplay could inform the design of novel anti-cancer strategies. While down-regulation of DNA repair genes in CDK12-targeted cancer cells is being explored therapeutically, little is known about mechanisms and significance of transcriptional induction upon inhibition of CDK12. We show that selective targeting of CDK12 in colon cancer-derived cells activates P-TEFb via its release from the inhibitory 7SK snRNP. In turn, P-TEFb stimulates Pol II pause release at thousands of genes, most of which become newly dependent on P-TEFb. Amongst the induced genes are those stimulated by hallmark pathways in cancer, including p53 and NF-κB. Consequently, CDK12-inhibited cancer cells exhibit hypersensitivity to inhibitors of P-TEFb. While blocking P-TEFb triggers their apoptosis in a p53-dependent manner, it impedes cell proliferation irrespective of p53 by preventing induction of genes downstream of the DNA damage-induced NF-κB signaling. In summary, stimulation of Pol II pause release at the signal-responsive genes underlies the functional dependence of CDK12-inhibited cancer cells on P-TEFb. Our study establishes the mechanistic underpinning for combinatorial targeting of CDK12 with either P-TEFb or the induced oncogenic pathways in cancer.
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Affiliation(s)
- Zhijia Wang
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Samu V Himanen
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Heidi M Haikala
- Translational Immunology Research Program (TRIMM), Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki FIN-00014, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki FIN-00014, Finland
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Anniina Vihervaara
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Matjaž Barborič
- Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
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9
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Dollinger R, Deng EB, Schultz J, Wu S, Deorio HR, Gilmour DS. Assessment of the roles of Spt5-nucleic acid contacts in promoter proximal pausing of RNA polymerase II. J Biol Chem 2023; 299:105106. [PMID: 37517697 PMCID: PMC10482750 DOI: 10.1016/j.jbc.2023.105106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
Promoter proximal pausing of RNA polymerase II (Pol II) is a critical transcriptional regulatory mechanism in metazoans that requires the transcription factor DRB sensitivity-inducing factor (DSIF) and the inhibitory negative elongation factor (NELF). DSIF, composed of Spt4 and Spt5, establishes the pause by recruiting NELF to the elongation complex. However, the role of DSIF in pausing beyond NELF recruitment remains unclear. We used a highly purified in vitro system and Drosophila nuclear extract to investigate the role of DSIF in promoter proximal pausing. We identified two domains of Spt5, the KOW4 and NGN domains, that facilitate Pol II pausing. The KOW4 domain promotes pausing through its interaction with the nascent RNA while the NGN domain does so through a short helical motif that is in close proximity to the non-transcribed DNA template strand. Removal of this sequence in Drosophila has a male-specific dominant negative effect. The alpha-helical motif is also needed to support fly viability. We also show that the interaction between the Spt5 KOW1 domain and the upstream DNA helix is required for DSIF association with the Pol II elongation complex. Disruption of the KOW1-DNA interaction is dominant lethal in vivo. Finally, we show that the KOW2-3 domain of Spt5 mediates the recruitment of NELF to the elongation complex. In summary, our results reveal additional roles for DSIF in transcription regulation and identify specific domains important for facilitating Pol II pausing.
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Affiliation(s)
- Roberta Dollinger
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Eilene B Deng
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Josie Schultz
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sharon Wu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Haley R Deorio
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.
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10
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Wang M, Chen Q, Wang S, Xie H, Liu J, Huang R, Xiang Y, Jiang Y, Tian D, Bian E. Super-enhancers complexes zoom in transcription in cancer. J Exp Clin Cancer Res 2023; 42:183. [PMID: 37501079 PMCID: PMC10375641 DOI: 10.1186/s13046-023-02763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Super-enhancers (SEs) consist of multiple typical enhancers enriched at high density with transcription factors, histone-modifying enzymes and cofactors. Oncogenic SEs promote tumorigenesis and malignancy by altering protein-coding gene expression and noncoding regulatory element function. Therefore, they play central roles in the treatment of cancer. Here, we review the structural characteristics, organization, identification, and functions of SEs and the underlying molecular mechanism by which SEs drive oncogenic transcription in tumor cells. We then summarize abnormal SE complexes, SE-driven coding genes, and noncoding RNAs involved in tumor development. In summary, we believe that SEs show great potential as biomarkers and therapeutic targets.
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Affiliation(s)
- MengTing Wang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - QingYang Chen
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - ShuJie Wang
- Department of Clinical MedicineThe Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - RuiXiang Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YuFei Xiang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - YanYi Jiang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
| | - DaSheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
| | - ErBao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, 230601, Anhui Province, China.
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
- School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
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11
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Li G, Kang Y, Feng X, Wang G, Yuan Y, Li Z, Du L, Xu B. Dynamic changes of enhancer and super enhancer landscape in degenerated nucleus pulposus cells. Life Sci Alliance 2023; 6:e202201854. [PMID: 37012048 PMCID: PMC10070812 DOI: 10.26508/lsa.202201854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Inflammatory cascade and extracellular matrix remodeling have been identified as pivotal pathological factors in the progression of intervertebral disc degeneration (IDD), but the mechanisms underlying the aberrant activation of transcription during nucleus pulposus (NP) cell degeneration remain elusive. Super-enhancers (SEs) are large clusters of adjacent lone enhancers, which control expression modes of cellular fate and pathogenic genes. Here, we showed that SEs underwent tremendous remodeling during NP cell degeneration and that SE-related transcripts were most abundant in inflammatory cascade and extracellular matrix remodeling processes. Inhibition of cyclin-dependent kinase 7, a transcriptional kinase-mediated transcriptional initiation in trans-acting SE complex, constricted the transcription of inflammatory cascades, and extracellular matrix remodeling-related genes such as IL1β and MMP3 in NP cells, meanwhile, also restrained the transcription of Mmp16, Tnfrsf21, and Il11ra1 to retard IDD in rats. In summary, our findings clarify SEs control the transcription of genes associated with inflammatory cascade and extracellular matrix remodeling during NP cell degeneration and identify inhibition of the cyclin-dependent kinase 7, required for SE-mediated transcriptional activation, as a therapeutic option for IDD.
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Affiliation(s)
- Guowang Li
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Yuxiang Kang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Guohua Wang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Yue Yuan
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Zhenhua Li
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
| | - Lilong Du
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
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12
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Su S, Xue Y, Lee SK, Zhang Y, Fan J, De S, Sharov A, Wang W. A dual-activity topoisomerase complex promotes both transcriptional activation and repression in response to starvation. Nucleic Acids Res 2023; 51:2415-2433. [PMID: 36794732 PMCID: PMC10018333 DOI: 10.1093/nar/gkad086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Topoisomerases are required to release topological stress generated by RNA polymerase II (RNAPII) during transcription. Here, we show that in response to starvation, the complex of topoisomerase 3b (TOP3B) and TDRD3 can enhance not only transcriptional activation, but also repression, which mimics other topoisomerases that can also alter transcription in both directions. The genes enhanced by TOP3B-TDRD3 are enriched with long and highly-expressed ones, which are also preferentially stimulated by other topoisomerases, suggesting that different topoisomerases may recognize their targets through a similar mechanism. Specifically, human HCT116 cells individually inactivated for TOP3B, TDRD3 or TOP3B topoisomerase activity, exhibit similarly disrupted transcription for both starvation-activated genes (SAGs) and starvation-repressed genes (SRGs). Responding to starvation, both TOP3B-TDRD3 and the elongating form of RNAPII exhibit concomitantly increased binding to TOP3B-dependent SAGs, at binding sites that overlap. Notably, TOP3B inactivation decreases the binding of elongating RNAPII to TOP3B-dependent SAGs while increased it to SRGs. Furthermore, TOP3B-ablated cells display reduced transcription of several autophagy-associated genes and autophagy per se. Our data suggest that TOP3B-TDRD3 can promote both transcriptional activation and repression by regulating RNAPII distribution. In addition, the findings that it can facilitate autophagy may account for the shortened lifespan of Top3b-KO mice.
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Affiliation(s)
- Shuaikun Su
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yutong Xue
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Seung Kyu Lee
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Yongqing Zhang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jinshui Fan
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alexei Sharov
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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13
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Welsh SA, Gardini A. Genomic regulation of transcription and RNA processing by the multitasking Integrator complex. Nat Rev Mol Cell Biol 2023; 24:204-220. [PMID: 36180603 PMCID: PMC9974566 DOI: 10.1038/s41580-022-00534-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/09/2022]
Abstract
In higher eukaryotes, fine-tuned activation of protein-coding genes and many non-coding RNAs pivots around the regulated activity of RNA polymerase II (Pol II). The Integrator complex is the only Pol II-associated large multiprotein complex that is metazoan specific, and has therefore been understudied for years. Integrator comprises at least 14 subunits, which are grouped into distinct functional modules. The phosphodiesterase activity of the core catalytic module is co-transcriptionally directed against several RNA species, including long non-coding RNAs (lncRNAs), U small nuclear RNAs (U snRNAs), PIWI-interacting RNAs (piRNAs), enhancer RNAs and nascent pre-mRNAs. Processing of non-coding RNAs by Integrator is essential for their biogenesis, and at protein-coding genes, Integrator is a key modulator of Pol II promoter-proximal pausing and transcript elongation. Recent studies have identified an Integrator-specific serine/threonine-protein phosphatase 2A (PP2A) module, which targets Pol II and other components of the basal transcription machinery. In this Review, we discuss how the activity of Integrator regulates transcription, RNA processing, chromatin landscape and DNA repair. We also discuss the diverse roles of Integrator in development and tumorigenesis.
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14
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Xie J, Libri D, Porrua O. Mechanisms of eukaryotic transcription termination at a glance. J Cell Sci 2023; 136:286227. [PMID: 36594557 DOI: 10.1242/jcs.259873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Transcription termination is the final step of a transcription cycle, which induces the release of the transcript at the termination site and allows the recycling of the polymerase for the next round of transcription. Timely transcription termination is critical for avoiding interferences between neighbouring transcription units as well as conflicts between transcribing RNA polymerases (RNAPs) and other DNA-associated processes, such as replication or DNA repair. Understanding the mechanisms by which the very stable transcription elongation complex is dismantled is essential for appreciating how physiological gene expression is maintained and also how concurrent processes that occur synchronously on the DNA are coordinated. Although the strategies employed by the different classes of eukaryotic RNAPs are traditionally considered to be different, novel findings point to interesting commonalities. In this Cell Science at a Glance and the accompanying poster, we review the current understanding about the mechanisms of transcription termination by the three eukaryotic RNAPs.
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Affiliation(s)
- Juanjuan Xie
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Domenico Libri
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Odil Porrua
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
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15
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Clopper KC, Taatjes DJ. Chemical inhibitors of transcription-associated kinases. Curr Opin Chem Biol 2022; 70:102186. [PMID: 35926294 PMCID: PMC10676000 DOI: 10.1016/j.cbpa.2022.102186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022]
Abstract
Transcription by RNA polymerase II (pol II) is regulated by kinases. In recent years, many selective and potent inhibitors of pol II transcription-associated kinases have been developed, and these molecules have advanced understanding of kinase function in mammalian cells. Here, we focus on chemical inhibitors of the transcription-associated kinases CDK7, CDK8, CDK9, CDK12, CDK13, and CDK19. We provide a brief overview of the function of these kinases and common activation mechanisms. We then highlight the advantages of kinase inhibitors compared with other basic research methods, and describe the caveats associated with non-selective compounds (e.g. flavopiridol). We conclude with strategies and recommendations for implementation of chemical inhibitors for experimental analysis of transcription-associated kinases.
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Affiliation(s)
- Kevin C Clopper
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA.
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16
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Abstract
Transcription elongation by RNA polymerase II (Pol II) has emerged as a regulatory hub in gene expression. A key control point occurs during early transcription elongation when Pol II pauses in the promoter-proximal region at the majority of genes in mammalian cells and at a large set of genes in Drosophila. An increasing number of trans-acting factors have been linked to promoter-proximal pausing. Some factors help to establish the pause, whereas others are required for the release of Pol II into productive elongation. A dysfunction of this elongation control point leads to aberrant gene expression and can contribute to disease development. The BET bromodomain protein BRD4 has been implicated in elongation control. However, only recently direct BRD4-specific functions in Pol II transcription elongation have been uncovered. This mainly became possible with technological advances that allow selective and rapid ablation of BRD4 in cells along with the availability of approaches that capture the immediate consequences on nascent transcription. This review sheds light on the experimental breakthroughs that led to the emerging view of BRD4 as a general regulator of transcription elongation.
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Affiliation(s)
- Elisabeth Altendorfer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yelizaveta Mochalova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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17
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Tellier M, Zaborowska J, Neve J, Nojima T, Hester S, Fournier M, Furger A, Murphy S. CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation. EMBO Rep 2022; 23:e54520. [PMID: 35980303 PMCID: PMC9535751 DOI: 10.15252/embr.202154520] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/13/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
CDK9 is a kinase critical for the productive transcription of protein-coding genes by RNA polymerase II (pol II). As part of P-TEFb, CDK9 phosphorylates the carboxyl-terminal domain (CTD) of pol II and elongation factors, which allows pol II to elongate past the early elongation checkpoint (EEC) encountered soon after initiation. We show that, in addition to halting pol II at the EEC, loss of CDK9 activity causes premature termination of transcription across the last exon, loss of polyadenylation factors from chromatin, and loss of polyadenylation of nascent transcripts. Inhibition of the phosphatase PP2A abrogates the premature termination and loss of polyadenylation caused by CDK9 inhibition, indicating that this kinase/phosphatase pair regulates transcription elongation and RNA processing at the end of protein-coding genes. We also confirm the splicing factor SF3B1 as a target of CDK9 and show that SF3B1 in complex with polyadenylation factors is lost from chromatin after CDK9 inhibition. These results emphasize the important roles that CDK9 plays in coupling transcription elongation and termination to RNA maturation downstream of the EEC.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | | | - Jonathan Neve
- Department of BiochemistryUniversity of OxfordOxfordUK
| | - Takayuki Nojima
- Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Svenja Hester
- Department of BiochemistryUniversity of OxfordOxfordUK
| | | | - Andre Furger
- Department of BiochemistryUniversity of OxfordOxfordUK
| | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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18
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Santana JF, Collins GS, Parida M, Luse DS, Price D. Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB and XPB. Nucleic Acids Res 2022; 50:9127-9148. [PMID: 35947745 PMCID: PMC9458433 DOI: 10.1093/nar/gkac678] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
The effects of rapid acute depletion of components of RNA polymerase II (Pol II) general transcription factors (GTFs) that are thought to be critical for formation of preinitiation complexes (PICs) and initiation in vitro were quantified in HAP1 cells using precision nuclear run-on sequencing (PRO-Seq). The average dependencies for each factor across >70 000 promoters varied widely even though levels of depletions were similar. Some of the effects could be attributed to the presence or absence of core promoter elements such as the upstream TBP-specificity motif or downstream G-rich sequences, but some dependencies anti-correlated with such sequences. While depletion of TBP had a large effect on most Pol III promoters only a small fraction of Pol II promoters were similarly affected. TFIIB depletion had the largest general effect on Pol II and also correlated with apparent termination defects downstream of genes. Our results demonstrate that promoter activity is combinatorially influenced by recruitment of TFIID and sequence-specific transcription factors. They also suggest that interaction of the preinitiation complex (PIC) with nucleosomes can affect activity and that recruitment of TFIID containing TBP only plays a positive role at a subset of promoters.
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Affiliation(s)
- Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Geoffrey S Collins
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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19
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Song A, Chen FX. The pleiotropic roles of SPT5 in transcription. Transcription 2022; 13:53-69. [PMID: 35876486 PMCID: PMC9467590 DOI: 10.1080/21541264.2022.2103366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Initially discovered by genetic screens in budding yeast, SPT5 and its partner SPT4 form a stable complex known as DSIF in metazoa, which plays pleiotropic roles in multiple steps of transcription. SPT5 is the most conserved transcription elongation factor, being found in all three domains of life; however, its structure has evolved to include new domains and associated posttranslational modifications. These gained features have expanded transcriptional functions of SPT5, likely to meet the demand for increasingly complex regulation of transcription in higher organisms. This review discusses the pleiotropic roles of SPT5 in transcription, including RNA polymerase II (Pol II) stabilization, enhancer activation, Pol II pausing and its release, elongation, and termination, with a focus on the most recent progress of SPT5 functions in regulating metazoan transcription.
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Affiliation(s)
- Aixia Song
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
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20
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Mohamed AA, Vazquez Nunez R, Vos SM. Structural advances in transcription elongation. Curr Opin Struct Biol 2022; 75:102422. [PMID: 35816930 DOI: 10.1016/j.sbi.2022.102422] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/22/2022] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
Transcription is the first step of gene expression and involves RNA polymerases. After transcription initiation, RNA polymerase enters elongation followed by transcription termination at the end of the gene. Only recently, structures of transcription elongation complexes bound to key transcription elongation factors have been determined in bacterial and eukaryotic systems. These structures have revealed numerous insights including the basis for transcriptional pausing, RNA polymerase interaction with large complexes such as the ribosome and the spliceosome, and the transition into productive elongation. Here, we review these structures and describe areas for future research.
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Affiliation(s)
- Abdallah A Mohamed
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA. https://twitter.com/AMohamed_98
| | - Roberto Vazquez Nunez
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA. https://twitter.com/rjareth
| | - Seychelle M Vos
- Massachusetts Institute of Technology, Department of Biology, 31 Ames St., Cambridge, MA 02142, USA.
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21
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Targeting cyclin-dependent kinase 9 in cancer therapy. Acta Pharmacol Sin 2022; 43:1633-1645. [PMID: 34811514 PMCID: PMC9253122 DOI: 10.1038/s41401-021-00796-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinase (CDK) 9 associates mainly with cyclin T1 and forms the positive transcription elongation factor b (p-TEFb) complex responsible for transcriptional regulation. It has been shown that CDK9 modulates the expression and activity of oncogenes, such as MYC and murine double minute 4 (MDM4), and it also plays an important role in development and/or maintenance of the malignant cell phenotype. Malfunction of CDK9 is frequently observed in numerous cancers. Recent studies have highlighted the function of CDK9 through a variety of mechanisms in cancers, including the formation of new complexes and epigenetic alterations. Due to the importance of CDK9 activation in cancer cells, CDK9 inhibitors have emerged as promising candidates for cancer therapy. Natural product-derived and chemically synthesized CDK9 inhibitors are being examined in preclinical and clinical research. In this review, we summarize the current knowledge on the role of CDK9 in transcriptional regulation, epigenetic regulation, and different cellular factor interactions, focusing on new advances. We show the importance of CDK9 in mediating tumorigenesis and tumor progression. Then, we provide an overview of some CDK9 inhibitors supported by multiple oncologic preclinical and clinical investigations. Finally, we discuss the perspective and challenge of CDK9 modulation in cancer.
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22
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Liu Z, Wu A, Wu Z, Wang T, Pan Y, Li B, Zhang X, Yu M. TOX4 facilitates promoter-proximal pausing and C-terminal domain dephosphorylation of RNA polymerase II in human cells. Commun Biol 2022; 5:300. [PMID: 35365735 PMCID: PMC8975821 DOI: 10.1038/s42003-022-03214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
TOX4 is one of the regulatory factors of PP1 phosphatases with poorly understood functions. Here we show that chromatin occupancy pattern of TOX4 resembles that of RNA polymerase II (Pol II), and its loss increases cellular level of C-terminal domain (CTD) phosphorylated Pol II but mainly decreases Pol II occupancy on promoters. In addition, elongation rate analyses by 4sUDRB-seq suggest that TOX4 restricts pause release and early elongation but promotes late elongation. Moreover, TT-seq analyses indicate that TOX4 loss mainly decreases transcriptional output. Mechanistically, TOX4 may restrict pause release through facilitating CTD serine 2 and DSIF dephosphorylation, and promote Pol II recycling and reinitiation through facilitating CTD serines 2 and 5 dephosphorylation. Furthermore, among the PP1 phosphatases, TOX4 preferentially binds PP1α and is capable of facilitating Pol II CTD dephosphorylation in vitro. These results lay the foundation for a better understanding of the role of TOX4 in transcriptional regulation. As a role of TOX4, one of the regulatory proteins of PP1 phosphatases, in transcriptional regulation, authors here show that TOX4 restricts pause release and early productive elongation, and promotes Pol II recycling and transcriptional reinitiation.
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Affiliation(s)
- Ziling Liu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Aiwei Wu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Zhen Wu
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Talang Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Yixuan Pan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Xumin Zhang
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ming Yu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China. .,Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China.
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23
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Düster R, Ji Y, Pan KT, Urlaub H, Geyer M. Functional characterization of the human Cdk10/Cyclin Q complex. Open Biol 2022; 12:210381. [PMID: 35291876 PMCID: PMC8924752 DOI: 10.1098/rsob.210381] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) are key players in cell cycle regulation and transcription. The CDK-family member Cdk10 is important for neural development and can act as a tumour suppressor, but the underlying molecular mechanisms are largely unknown. Here, we provide an in-depth analysis of Cdk10 substrate specificity and function. Using recombinant Cdk10/CycQ protein complexes, we characterize RNA pol II CTD, c-MYC and RB1 as in vitro protein substrates. Using an analogue-sensitive mutant kinase, we identify 89 different Cdk10 phosphosites in HEK cells originating from 66 different proteins. Among these, proteins involved in cell cycle, translation, stress response, growth signalling, as well as rRNA, and mRNA transcriptional regulation, are found. Of a set of pan-selective CDK- and Cdk9-specific inhibitors tested, all inhibited Cdk10/CycQ at least five times weaker than their proposed target kinases. We also identify Cdk10 as an in vitro substrate of Cdk1 and Cdk5 at multiple sites, allowing for a potential cross-talk between these CDKs. With this functional characterization, Cdk10 adopts a hybrid position in both cell cycle and transcriptional regulation.
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Affiliation(s)
- Robert Düster
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Yanlong Ji
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, 37077 Göttingen, Germany,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany,Frankfurt Cancer Institute, Goethe University, 60596 Frankfurt am Main, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, 37077 Göttingen, Germany,Institute of Clinical Chemistry, Bioanalytics Group, University Medical Center Göttingen, Göttingen, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
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24
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Control of non-productive RNA polymerase II transcription via its early termination in metazoans. Biochem Soc Trans 2022; 50:283-295. [PMID: 35166324 DOI: 10.1042/bst20201140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Transcription establishes the universal first step of gene expression where RNA is produced by a DNA-dependent RNA polymerase. The most versatile of eukaryotic RNA polymerases, RNA polymerase II (Pol II), transcribes a broad range of DNA including protein-coding and a variety of non-coding transcription units. Although Pol II can be configured as a durable enzyme capable of transcribing hundreds of kilobases, there is reliable evidence of widespread abortive Pol II transcription termination shortly after initiation, which is often followed by rapid degradation of the associated RNA. The molecular details underlying this phenomenon are still vague but likely reflect the action of quality control mechanisms on the early Pol II complex. Here, we summarize current knowledge of how and when such promoter-proximal quality control is asserted on metazoan Pol II.
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25
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Vervoort SJ, Devlin JR, Kwiatkowski N, Teng M, Gray NS, Johnstone RW. Targeting transcription cycles in cancer. Nat Rev Cancer 2022; 22:5-24. [PMID: 34675395 DOI: 10.1038/s41568-021-00411-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Accurate control of gene expression is essential for normal development and dysregulation of transcription underpins cancer onset and progression. Similar to cell cycle regulation, RNA polymerase II-driven transcription can be considered as a unidirectional multistep cycle, with thousands of unique transcription cycles occurring in concert within each cell. Each transcription cycle comprises recruitment, initiation, pausing, elongation, termination and recycling stages that are tightly controlled by the coordinated action of transcriptional cyclin-dependent kinases and their cognate cyclins as well as the opposing activity of transcriptional phosphatases. Oncogenic dysregulation of transcription can entail defective control of gene expression, either at select loci or more globally, impacting a large proportion of the genome. The resultant dependency on the core-transcriptional machinery is believed to render 'transcriptionally addicted' cancers sensitive to perturbation of transcription. Based on these findings, small molecules targeting transcriptional cyclin-dependent kinases and associated proteins hold promise for the treatment of cancer. Here, we utilize the transcription cycles concept to explain how dysregulation of these finely tuned gene expression processes may drive tumorigenesis and how therapeutically beneficial responses may arise from global or selective transcriptional perturbation. This conceptual framework helps to explain tumour-selective transcriptional dependencies and facilitates the rational design of combination therapies.
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Affiliation(s)
- Stephin J Vervoort
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jennifer R Devlin
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas Kwiatkowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mingxing Teng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA.
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
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Hu S, Peng L, Xu C, Wang Z, Song A, Chen FX. SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape. Mol Cell 2021; 81:4425-4439.e6. [PMID: 34534457 DOI: 10.1016/j.molcel.2021.08.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/19/2021] [Accepted: 08/23/2021] [Indexed: 12/24/2022]
Abstract
Transcription progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Here we utilize a rapid degradation system and reveal crucial functions of SPT5 in maintaining cellular and chromatin RNA polymerase II (Pol II) levels. Rapid SPT5 depletion causes a pronounced reduction of paused Pol II at promoters and enhancers, distinct from negative elongation factor (NELF) degradation resulting in short-distance paused Pol II redistribution. Most genes exhibit downregulation, but not upregulation, accompanied by greatly impaired transcription activation, altered chromatin landscape at enhancers, and severe Pol II processivity defects at gene bodies. Phosphorylation of an SPT5 linker at serine 666 potentiates pause release and is antagonized by Integrator-PP2A (INTAC) targeting SPT5 and Pol II, while phosphorylation of the SPT5 C-terminal region links to 3' end termination. Our findings position SPT5 as an essential positive regulator of global transcription.
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Affiliation(s)
- Shibin Hu
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Linna Peng
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Congling Xu
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhenning Wang
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Aixia Song
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, China; Shanghai Key Laboratory of Radiation Oncology, Shanghai, China.
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27
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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28
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A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination. Mol Cell 2021; 81:3589-3603.e13. [PMID: 34324863 DOI: 10.1016/j.molcel.2021.06.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/14/2021] [Accepted: 06/22/2021] [Indexed: 12/15/2022]
Abstract
Transcription elongation has emerged as a regulatory hub in gene expression of metazoans. A major control point occurs during early elongation before RNA polymerase II (Pol II) is released into productive elongation. Prior research has linked BRD4 with transcription elongation. Here, we use rapid BET protein and BRD4-selective degradation along with quantitative genome-wide approaches to investigate direct functions of BRD4 in Pol II transcription regulation. Notably, as an immediate consequence of acute BRD4 loss, promoter-proximal pause release is impaired, and transcriptionally engaged Pol II past this checkpoint undergoes readthrough transcription. An integrated proteome-wide analysis uncovers elongation and 3'-RNA processing factors as core BRD4 interactors. BRD4 ablation disrupts the recruitment of general 3'-RNA processing factors at the 5'-control region, which correlates with RNA cleavage and termination defects. These studies, performed in human cells, reveal a BRD4-mediated checkpoint and begin to establish a molecular link between 5'-elongation control and 3'-RNA processing.
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29
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Pan C, Lei Z, Wang S, Wang X, Wei D, Cai X, Luoreng Z, Wang L, Ma Y. Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle. BMC Genomics 2021; 22:532. [PMID: 34253191 PMCID: PMC8276410 DOI: 10.1186/s12864-021-07653-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/27/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. RESULTS We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. CONCLUSION In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.
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Affiliation(s)
- Cuili Pan
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Zhaoxiong Lei
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Shuzhe Wang
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Xiaoyan Cai
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China
| | - Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan, 750021, China.
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, 750021, China.
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.
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30
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Narain A, Bhandare P, Adhikari B, Backes S, Eilers M, Dölken L, Schlosser A, Erhard F, Baluapuri A, Wolf E. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Mol Cell 2021; 81:3110-3127.e14. [PMID: 34233157 PMCID: PMC8354102 DOI: 10.1016/j.molcel.2021.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/24/2021] [Accepted: 06/11/2021] [Indexed: 01/22/2023]
Abstract
SPT6 is a histone chaperone that tightly binds RNA polymerase II (RNAPII) during transcription elongation. However, its primary role in transcription is uncertain. We used targeted protein degradation to rapidly deplete SPT6 in human cells and analyzed defects in RNAPII behavior by a multi-omics approach and mathematical modeling. Our data indicate that SPT6 is a crucial factor for RNAPII processivity and is therefore required for the productive transcription of protein-coding genes. Unexpectedly, SPT6 also has a vital role in RNAPII termination, as acute depletion induced readthrough transcription for thousands of genes. Long-term depletion of SPT6 induced cryptic intragenic transcription, as observed earlier in yeast. However, this phenotype was not observed upon acute SPT6 depletion and therefore can be attributed to accumulated epigenetic perturbations in the prolonged absence of SPT6. In conclusion, targeted degradation of SPT6 allowed the temporal discrimination of its function as an epigenetic safeguard and RNAPII elongation factor. Auxin-inducible degradation discriminates direct roles of human SPT6 in transcription Acute loss of SPT6 globally impairs RNAPII processivity and speed SPT6 is required for efficient transcription termination on protein-coding genes Long-term loss of SPT6 ultimately results in cryptic intragenic transcription
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Affiliation(s)
- Ashwin Narain
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Bikash Adhikari
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Simone Backes
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Florian Erhard
- Computational Systems Virology and Bioinformatics, Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University of Würzburg, Beethovenstraße 1A, 97080 Würzburg, Germany.
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31
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CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci 2021; 78:5543-5567. [PMID: 34146121 PMCID: PMC8257543 DOI: 10.1007/s00018-021-03878-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), the kinase component of positive transcription elongation factor b (P-TEFb), is essential for transcription of most protein-coding genes by RNA polymerase II (RNAPII). By releasing promoter-proximally paused RNAPII into gene bodies, CDK9 controls the entry of RNAPII into productive elongation and is, therefore, critical for efficient synthesis of full-length messenger (m)RNAs. In recent years, new players involved in P-TEFb-dependent processes have been identified and an important function of CDK9 in coordinating elongation with transcription initiation and termination has been unveiled. As the regulatory functions of CDK9 in gene expression continue to expand, a number of human pathologies, including cancers, have been associated with aberrant CDK9 activity, underscoring the need to properly regulate CDK9. Here, I provide an overview of CDK9 function and regulation, with an emphasis on CDK9 dysregulation in human diseases.
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32
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Vervoort SJ, Welsh SA, Devlin JR, Barbieri E, Knight DA, Offley S, Bjelosevic S, Costacurta M, Todorovski I, Kearney CJ, Sandow JJ, Fan Z, Blyth B, McLeod V, Vissers JHA, Pavic K, Martin BP, Gregory G, Demosthenous E, Zethoven M, Kong IY, Hawkins ED, Hogg SJ, Kelly MJ, Newbold A, Simpson KJ, Kauko O, Harvey KF, Ohlmeyer M, Westermarck J, Gray N, Gardini A, Johnstone RW. The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer. Cell 2021; 184:3143-3162.e32. [PMID: 34004147 PMCID: PMC8567840 DOI: 10.1016/j.cell.2021.04.022] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/27/2020] [Accepted: 04/14/2021] [Indexed: 12/18/2022]
Abstract
Gene expression by RNA polymerase II (RNAPII) is tightly controlled by cyclin-dependent kinases (CDKs) at discrete checkpoints during the transcription cycle. The pausing checkpoint following transcription initiation is primarily controlled by CDK9. We discovered that CDK9-mediated, RNAPII-driven transcription is functionally opposed by a protein phosphatase 2A (PP2A) complex that is recruited to transcription sites by the Integrator complex subunit INTS6. PP2A dynamically antagonizes phosphorylation of key CDK9 substrates including DSIF and RNAPII-CTD. Loss of INTS6 results in resistance to tumor cell death mediated by CDK9 inhibition, decreased turnover of CDK9 phospho-substrates, and amplification of acute oncogenic transcriptional responses. Pharmacological PP2A activation synergizes with CDK9 inhibition to kill both leukemic and solid tumor cells, providing therapeutic benefit in vivo. These data demonstrate that fine control of gene expression relies on the balance between kinase and phosphatase activity throughout the transcription cycle, a process dysregulated in cancer that can be exploited therapeutically.
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Affiliation(s)
- Stephin J Vervoort
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia.
| | - Sarah A Welsh
- The Wistar Institute, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer R Devlin
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | | | - Deborah A Knight
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Sarah Offley
- The Wistar Institute, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefan Bjelosevic
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Matteo Costacurta
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Izabela Todorovski
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Conor J Kearney
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute, Parkville 3010, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Zheng Fan
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Benjamin Blyth
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia
| | - Victoria McLeod
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia
| | - Joseph H A Vissers
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Karolina Pavic
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku FI-20014, Finland; Institute of Biomedicine, University of Turku, Turku FI-20014, Finland
| | - Ben P Martin
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Gareth Gregory
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton 3168, VIC, Australia
| | | | - Magnus Zethoven
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute, Parkville 3010, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Edwin D Hawkins
- The Walter and Eliza Hall Institute, Parkville 3010, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Simon J Hogg
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Madison J Kelly
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | - Andrea Newbold
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia
| | | | - Otto Kauko
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku FI-20014, Finland; Institute of Biomedicine, University of Turku, Turku FI-20014, Finland
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia; Department of Anatomy and Developmental Biology, and Biomedicine Discovery Institute, Monash University, Clayton 3168, VIC, Australia
| | - Michael Ohlmeyer
- Mount Sinai School of Medicine, New York, NY 10029, USA; Atux Iskay LLC, Plainsboro, NJ 08536, USA
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku FI-20014, Finland; Institute of Biomedicine, University of Turku, Turku FI-20014, Finland
| | | | | | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne 3000, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville 3010, VIC, Australia.
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33
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Cossa G, Parua PK, Eilers M, Fisher RP. Protein phosphatases in the RNAPII transcription cycle: erasers, sculptors, gatekeepers, and potential drug targets. Genes Dev 2021; 35:658-676. [PMID: 33888562 PMCID: PMC8091971 DOI: 10.1101/gad.348315.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, Cossa et al. discuss the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle. The transcription cycle of RNA polymerase II (RNAPII) is governed at multiple points by opposing actions of cyclin-dependent kinases (CDKs) and protein phosphatases, in a process with similarities to the cell division cycle. While important roles of the kinases have been established, phosphatases have emerged more slowly as key players in transcription, and large gaps remain in understanding of their precise functions and targets. Much of the earlier work focused on the roles and regulation of sui generis and often atypical phosphatases—FCP1, Rtr1/RPAP2, and SSU72—with seemingly dedicated functions in RNAPII transcription. Decisive roles in the transcription cycle have now been uncovered for members of the major phosphoprotein phosphatase (PPP) family, including PP1, PP2A, and PP4—abundant enzymes with pleiotropic roles in cellular signaling pathways. These phosphatases appear to act principally at the transitions between transcription cycle phases, ensuring fine control of elongation and termination. Much is still unknown, however, about the division of labor among the PPP family members, and their possible regulation by or of the transcriptional kinases. CDKs active in transcription have recently drawn attention as potential therapeutic targets in cancer and other diseases, raising the prospect that the phosphatases might also present opportunities for new drug development. Here we review the current knowledge and outstanding questions about phosphatases in the context of the RNAPII transcription cycle.
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Affiliation(s)
- Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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34
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Jaeger MG, Winter GE. Fast-acting chemical tools to delineate causality in transcriptional control. Mol Cell 2021; 81:1617-1630. [PMID: 33689749 DOI: 10.1016/j.molcel.2021.02.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/20/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
Multi-dimensional omics profiling continues to illuminate the complexity of cellular processes. Because of difficult mechanistic interpretation of phenotypes induced by slow perturbation, fast experimental setups are increasingly used to dissect causal interactions directly in cells. Here we review a growing body of studies that leverage rapid pharmacological perturbation to delineate causality in gene control. When coupled with kinetically matched readouts, fast chemical genetic tools allow recording of primary phenotypes before confounding secondary effects manifest. The toolbox encompasses directly acting probes, such as active-site inhibitors and proteolysis-targeting chimeras, as well as strategies using genetic engineering to render target proteins chemically tractable, such as analog-sensitive and degron systems. We anticipate that extrapolation of these concepts to single-cell setups will further transform our mechanistic understanding of transcriptional control in the future. Importantly, the concept of leveraging speed to derive causality should be broadly applicable to many aspects of biological regulation.
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Affiliation(s)
- Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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Understanding transcription across scales: From base pairs to chromosomes. Mol Cell 2021; 81:1601-1616. [PMID: 33770487 DOI: 10.1016/j.molcel.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The influence of genome organization on transcription is central to our understanding of cell type specification. Higher-order genome organization is established through short- and long-range DNA interactions. Coordination of these interactions, from single atoms to entire chromosomes, plays a fundamental role in transcriptional control of gene expression. Loss of this coupling can result in disease. Analysis of transcriptional regulation typically involves disparate experimental approaches, from structural studies that define angstrom-level interactions to cell-biological and genomic approaches that assess mesoscale relationships. Thus, to fully understand the mechanisms that regulate gene expression, it is critical to integrate the findings gained across these distinct size scales. In this review, I illustrate fundamental ways in which cells regulate transcription in the context of genome organization.
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Dollinger R, Gilmour DS. Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans. J Mol Biol 2021; 433:166897. [PMID: 33640324 DOI: 10.1016/j.jmb.2021.166897] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Regulation of transcription is a tightly choreographed process. The establishment of RNA polymerase II promoter proximal pausing soon after transcription initiation and the release of Pol II into productive elongation are key regulatory processes that occur in early elongation. We describe the techniques and tools that have become available for the study of promoter proximal pausing and their utility for future experiments. We then provide an overview of the factors and interactions that govern a multipartite pausing process and address emerging questions surrounding the mechanism of RNA polymerase II's subsequent advancement into the gene body. Finally, we address remaining controversies and future areas of study.
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Affiliation(s)
- Roberta Dollinger
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 462 North Frear, University Park, PA 16802, USA.
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 465A North Frear, University Park, PA 16802, USA.
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