1
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Zheng LW, Liu CC, Yu KD. Phase separations in oncogenesis, tumor progressions and metastasis: a glance from hallmarks of cancer. J Hematol Oncol 2023; 16:123. [PMID: 38110976 PMCID: PMC10726551 DOI: 10.1186/s13045-023-01522-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a novel principle for interpreting precise spatiotemporal coordination in living cells through biomolecular condensate (BMC) formation via dynamic aggregation. LLPS changes individual molecules into membrane-free, droplet-like BMCs with specific functions, which coordinate various cellular activities. The formation and regulation of LLPS are closely associated with oncogenesis, tumor progressions and metastasis, the specific roles and mechanisms of LLPS in tumors still need to be further investigated at present. In this review, we comprehensively summarize the conditions of LLPS and identify mechanisms involved in abnormal LLPS in cancer processes, including tumor growth, metastasis, and angiogenesis from the perspective of cancer hallmarks. We have also reviewed the clinical applications of LLPS in oncologic areas. This systematic summary of dysregulated LLPS from the different dimensions of cancer hallmarks will build a bridge for determining its specific functions to further guide basic research, finding strategies to intervene in LLPS, and developing relevant therapeutic approaches.
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Affiliation(s)
- Le-Wei Zheng
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cui-Cui Liu
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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2
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Xu W, Li X. Regulation of Pol II Pausing during Daily Gene Transcription in Mouse Liver. BIOLOGY 2023; 12:1107. [PMID: 37626993 PMCID: PMC10452108 DOI: 10.3390/biology12081107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Cell autonomous circadian oscillation is present in central and various peripheral tissues. The intrinsic tissue clock and various extrinsic cues drive gene expression rhythms. Transcription regulation is thought to be the main driving force for gene rhythms. However, how transcription rhythms arise remains to be fully characterized due to the fact that transcription is regulated at multiple steps. In particular, Pol II recruitment, pause release, and premature transcription termination are critical regulatory steps that determine the status of Pol II pausing and transcription output near the transcription start site (TSS) of the promoter. Recently, we showed that Pol II pausing exhibits genome-wide changes during daily transcription in mouse liver. In this article, we review historical as well as recent findings on the regulation of transcription rhythms by the circadian clock and other transcription factors, and the potential limitations of those results in explaining rhythmic transcription at the TSS. We then discuss our results on the genome-wide characteristics of daily changes in Pol II pausing, the possible regulatory mechanisms involved, and their relevance to future research on circadian transcription regulation.
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Affiliation(s)
| | - Xiaodong Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China;
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3
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Liu Z, Qin Z, Liu Y, Xia X, He L, Chen N, Hu X, Peng X. Liquid‒liquid phase separation: roles and implications in future cancer treatment. Int J Biol Sci 2023; 19:4139-4156. [PMID: 37705755 PMCID: PMC10496506 DOI: 10.7150/ijbs.81521] [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: 12/04/2022] [Accepted: 07/23/2023] [Indexed: 09/15/2023] Open
Abstract
Liquid‒liquid phase separation (LLPS) is a phenomenon driven by weak interactions between biomolecules, such as proteins and nucleic acids, that leads to the formation of distinct liquid-like condensates. Through LLPS, membraneless condensates are formed, selectively concentrating specific proteins while excluding other molecules to maintain normal cellular functions. Emerging evidence shows that cancer-related mutations cause aberrant condensate assembly, resulting in disrupted signal transduction, impaired DNA repair, and abnormal chromatin organization and eventually contributing to tumorigenesis. The objective of this review is to summarize recent advancements in understanding the potential implications of LLPS in the contexts of cancer progression and therapeutic interventions. By interfering with LLPS, it may be possible to restore normal cellular processes and inhibit tumor progression. The underlying mechanisms and potential drug targets associated with LLPS in cancer are discussed, shedding light on promising opportunities for novel therapeutic interventions.
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Affiliation(s)
- Zheran Liu
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zijian Qin
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yingtong Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu 610041, Sichuan, China
| | - Xi Xia
- Shanghai ETERN Biopharma Co., Ltd., Shanghai, China
| | - Ling He
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Na Chen
- School of Pharmacy, Chengdu Medical College, Xindu Avenue No 783, Chengdu, 610500, Sichuan Province, China
| | - Xiaolin Hu
- West China School of Nursing, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xingchen Peng
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
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4
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Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
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Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
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5
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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6
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Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling. Nat Commun 2021; 12:6318. [PMID: 34732721 PMCID: PMC8566496 DOI: 10.1038/s41467-021-26604-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 10/17/2021] [Indexed: 11/20/2022] Open
Abstract
RNA Polymerase II (Pol II) transcriptional recycling is a mechanism for which the required factors and contributions to overall gene expression levels are poorly understood. We describe an in vitro methodology facilitating unbiased identification of putative RNA Pol II transcriptional recycling factors and quantitative measurement of transcriptional output from recycled transcriptional components. Proof-of-principle experiments identified PAF1 complex components among recycling factors and detected defective transcriptional output from Pol II recycling following PAF1 depletion. Dynamic ChIP-seq confirmed PAF1 silencing triggered defective Pol II recycling in human cells. Prostate tumors exhibited enhanced transcriptional recycling, which was attenuated by antibody-based PAF1 depletion. These findings identify Pol II recycling as a potential target in cancer and demonstrate the applicability of in vitro and cellular transcription assays to characterize Pol II recycling in other disease states. RNA Polymerase II (Pol II) recycling can influence transcription efficiency. Here the authors describe an approach aimed at facilitating the identification of factors involved in Pol II recycling and identify PAF1 complex components as mediators of recycling.
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7
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Chen X, Qi Y, Wu Z, Wang X, Li J, Zhao D, Hou H, Li Y, Yu Z, Liu W, Wang M, Ren Y, Li Z, Yang H, Xu Y. Structural insights into preinitiation complex assembly on core promoters. Science 2021; 372:science.aba8490. [PMID: 33795473 DOI: 10.1126/science.aba8490] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 02/01/2021] [Accepted: 03/25/2021] [Indexed: 12/24/2022]
Abstract
Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.
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Affiliation(s)
- Xizi 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 200032, China
| | - Yilun Qi
- 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 200032, China
| | - Zihan Wu
- 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 200032, China
| | - Xinxin Wang
- 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 200032, China
| | - Jiabei Li
- 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 200032, China
| | - Dan Zhao
- 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 200032, China
| | - Haifeng Hou
- 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 200032, China
| | - Yan Li
- 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 200032, China
| | - Zishuo Yu
- 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 200032, China
| | - Weida Liu
- 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 200032, China
| | - Mo Wang
- 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 200032, China
| | - Yulei Ren
- 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 200032, China
| | - Ze Li
- 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 200032, China
| | - Huirong Yang
- 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 200032, China
| | - Yanhui Xu
- 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 200032, China. .,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.,Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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8
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Boija A, Klein IA, Young RA. Biomolecular Condensates and Cancer. Cancer Cell 2021; 39:174-192. [PMID: 33417833 PMCID: PMC8721577 DOI: 10.1016/j.ccell.2020.12.003] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022]
Abstract
Malignant transformation is characterized by dysregulation of diverse cellular processes that have been the subject of detailed genetic, biochemical, and structural studies, but only recently has evidence emerged that many of these processes occur in the context of biomolecular condensates. Condensates are membrane-less bodies, often formed by liquid-liquid phase separation, that compartmentalize protein and RNA molecules with related functions. New insights from condensate studies portend a profound transformation in our understanding of cellular dysregulation in cancer. Here we summarize key features of biomolecular condensates, note where they have been implicated-or will likely be implicated-in oncogenesis, describe evidence that the pharmacodynamics of cancer therapeutics can be greatly influenced by condensates, and discuss some of the questions that must be addressed to further advance our understanding and treatment of cancer.
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Affiliation(s)
- Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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9
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Abstract
RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol II is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription and cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins and protein complexes interact with Pol II to regulate its activity. In this review, we detail the structure and mechanism of over a dozen factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.g., DSIF, NELF, PAF, and P-TEFb). The structural basis for Pol II transcription regulation has advanced rapidly in the past decade, largely due to technological innovations in cryoelectron microscopy. Here, we summarize a wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms; we also highlight mechanistic questions that remain unanswered or controversial.
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Affiliation(s)
- Allison C Schier
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
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10
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Fant CB, Levandowski CB, Gupta K, Maas ZL, Moir J, Rubin JD, Sawyer A, Esbin MN, Rimel JK, Luyties O, Marr MT, Berger I, Dowell RD, Taatjes DJ. TFIID Enables RNA Polymerase II Promoter-Proximal Pausing. Mol Cell 2020; 78:785-793.e8. [PMID: 32229306 DOI: 10.1016/j.molcel.2020.03.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/15/2019] [Accepted: 03/05/2020] [Indexed: 02/07/2023]
Abstract
RNA polymerase II (RNAPII) transcription is governed by the pre-initiation complex (PIC), which contains TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, RNAPII, and Mediator. After initiation, RNAPII enzymes pause after transcribing less than 100 bases; precisely how RNAPII pausing is enforced and regulated remains unclear. To address specific mechanistic questions, we reconstituted human RNAPII promoter-proximal pausing in vitro, entirely with purified factors (no extracts). As expected, NELF and DSIF increased pausing, and P-TEFb promoted pause release. Unexpectedly, the PIC alone was sufficient to reconstitute pausing, suggesting RNAPII pausing is an inherent PIC function. In agreement, pausing was lost upon replacement of the TFIID complex with TATA-binding protein (TBP), and PRO-seq experiments revealed widespread disruption of RNAPII pausing upon acute depletion (t = 60 min) of TFIID subunits in human or Drosophila cells. These results establish a TFIID requirement for RNAPII pausing and suggest pause regulatory factors may function directly or indirectly through TFIID.
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Affiliation(s)
- Charli B Fant
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | | | - Kapil Gupta
- School of Biochemistry, Bristol Research Centre for Synthetic Biology, University of Bristol, Bristol, UK
| | - Zachary L Maas
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - John Moir
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Jonathan D Rubin
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Andrew Sawyer
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Meagan N Esbin
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Jenna K Rimel
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Olivia Luyties
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Michael T Marr
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Imre Berger
- School of Biochemistry, Bristol Research Centre for Synthetic Biology, University of Bristol, Bristol, UK
| | - Robin D Dowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA; BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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11
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Abstract
Mutated or dysregulated transcription factors represent a unique class of drug targets that mediate aberrant gene expression, including blockade of differentiation and cell death gene expression programmes, hallmark properties of cancers. Transcription factor activity is altered in numerous cancer types via various direct mechanisms including chromosomal translocations, gene amplification or deletion, point mutations and alteration of expression, as well as indirectly through non-coding DNA mutations that affect transcription factor binding. Multiple approaches to target transcription factor activity have been demonstrated, preclinically and, in some cases, clinically, including inhibition of transcription factor-cofactor protein-protein interactions, inhibition of transcription factor-DNA binding and modulation of levels of transcription factor activity by altering levels of ubiquitylation and subsequent proteasome degradation or by inhibition of regulators of transcription factor expression. In addition, several new approaches to targeting transcription factors have recently emerged including modulation of auto-inhibition, proteolysis targeting chimaeras (PROTACs), use of cysteine reactive inhibitors, targeting intrinsically disordered regions of transcription factors and combinations of transcription factor inhibitors with kinase inhibitors to block the development of resistance. These innovations in drug development hold great promise to yield agents with unique properties that are likely to impact future cancer treatment.
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Affiliation(s)
- John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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13
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Shao W, Alcantara SGM, Zeitlinger J. Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing. eLife 2019; 8:41461. [PMID: 31021316 PMCID: PMC6483594 DOI: 10.7554/elife.41461] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/04/2019] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase II (Pol II) pausing is a general regulatory step in transcription, yet the stability of paused Pol II varies widely between genes. Although paused Pol II stability correlates with core promoter elements, the contribution of individual sequences remains unclear, in part because no rapid assay is available for measuring the changes in Pol II pausing as a result of altered promoter sequences. Here, we overcome this hurdle by showing that ChIP-nexus captures the endogenous Pol II pausing on transfected plasmids. Using this reporter-ChIP-nexus assay in Drosophila cells, we show that the pausing stability is influenced by downstream promoter sequences, but that the strongest contribution to Pol II pausing comes from the initiator sequence, in which a single nucleotide, a G at the +2 position, is critical for stable Pol II pausing. These results establish reporter-ChIP-nexus as a valuable tool to analyze Pol II pausing.
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Affiliation(s)
- Wanqing Shao
- Stowers Institute for Medical Research, Kansas City, United States
| | | | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, United States
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14
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Choi UB, Sanabria H, Smirnova T, Bowen ME, Weninger KR. Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins. Biomolecules 2019; 9:biom9030114. [PMID: 30909517 PMCID: PMC6468417 DOI: 10.3390/biom9030114] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 01/08/2023] Open
Abstract
The common conception of intrinsically disordered proteins (IDPs) is that they stochastically sample all possible configurations driven by thermal fluctuations. This is certainly true for many IDPs, which behave as swollen random coils that can be described using polymer models developed for homopolymers. However, the variability in interaction energy between different amino acid sequences provides the possibility that some configurations may be strongly preferred while others are forbidden. In compact globular IDPs, core hydration and packing density can vary between segments of the polypeptide chain leading to complex conformational dynamics. Here, we describe a growing number of proteins that appear intrinsically disordered by biochemical and bioinformatic characterization but switch between restricted regions of conformational space. In some cases, spontaneous switching between conformational ensembles was directly observed, but few methods can identify when an IDP is acting as a restricted chain. Such switching between disparate corners of conformational space could bias ligand binding and regulate the volume of IDPs acting as structural or entropic elements. Thus, mapping the accessible energy landscape and capturing dynamics across a wide range of timescales are essential to recognize when an IDP is acting as such a switch.
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Affiliation(s)
- Ucheor B Choi
- Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, SC, 29634, USA.
| | - Tatyana Smirnova
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, 27695, USA.
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15
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Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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16
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Chong B, Li M, Li T, Yu M, Zhang Y, Liu Z. Conservation of Potentially Druggable Cavities in Intrinsically Disordered Proteins. ACS OMEGA 2018; 3:15643-15652. [PMID: 31458221 PMCID: PMC6643371 DOI: 10.1021/acsomega.8b02092] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/05/2018] [Indexed: 05/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) exist in highly dynamic conformational ensembles, which pose a major obstacle for drug development targeting IDPs because traditional rational drug design relies on unique three-dimensional structures. Here, we analyzed the conservation (especially structural conservation) of potentially druggable cavities in 22 ensembles of IDPs. It was found that there is considerable conservation for potentially druggable cavities within each ensemble. The average common atom percentage of potentially druggable cavities is as high as 54%. The average root-mean-squared deviation of common atoms ranges between 1 and 8 Å for multichain IDPs, and a common pocket is kept after direct alignment of cavities. In addition, the conservation of potentially druggable cavities varies among different proteins. In the comparison of multi- and single-chain IDPs, some multichain IDPs have an extremely high conservation, whereas another multichain IDPs' conservation appears worse, and the single-chain IDPs have relatively moderate conservations. This study is a new attempt to generally assess the potentially druggable cavities in IDPs for taking IDPs as druggable targets, and this work also lends support to the opinion of IDPs tending to bind to "multiconformational affinity" compounds.
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Affiliation(s)
- Bin Chong
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Maodong Li
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Tong Li
- Department
of Computer Science and Technology, Tsinghua
University, Beijing 100084, China
| | - Miao Yu
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Yugang Zhang
- Department
of Chemistry and Chemical Biology, Cornell
University, New York 14850, United States
| | - Zhirong Liu
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
- E-mail: (Z.L.)
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17
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LeBlanc SJ, Kulkarni P, Weninger KR. Single Molecule FRET: A Powerful Tool to Study Intrinsically Disordered Proteins. Biomolecules 2018; 8:biom8040140. [PMID: 30413085 PMCID: PMC6315554 DOI: 10.3390/biom8040140] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.
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Affiliation(s)
- Sharonda J LeBlanc
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA.
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA.
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18
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Joo YJ, Ficarro SB, Soares LM, Chun Y, Marto JA, Buratowski S. Downstream promoter interactions of TFIID TAFs facilitate transcription reinitiation. Genes Dev 2017; 31:2162-2174. [PMID: 29203645 PMCID: PMC5749164 DOI: 10.1101/gad.306324.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/09/2017] [Indexed: 11/24/2022]
Abstract
TFIID binds promoter DNA to recruit RNA polymerase II and other basal factors for transcription. Although the TATA-binding protein (TBP) subunit of TFIID is necessary and sufficient for in vitro transcription, the TBP-associated factor (TAF) subunits recognize downstream promoter elements, act as coactivators, and interact with nucleosomes. In yeast nuclear extracts, transcription induces stable TAF binding to downstream promoter DNA, promoting subsequent activator-independent transcription reinitiation. In vivo, promoter responses to TAF mutations correlate with the level of downstream, rather than overall, Taf1 cross-linking. We propose a new model in which TAFs function as reinitiation factors, accounting for the differential responses of promoters to various transcription factor mutations.
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Affiliation(s)
- Yoo Jin Joo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Blais Proteomics Center, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Luis M Soares
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Blais Proteomics Center, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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19
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Zhang Z, Tjian R. Measuring dynamics of eukaryotic transcription initiation: Challenges, insights and opportunities. Transcription 2017; 9:159-165. [PMID: 28920762 PMCID: PMC5927711 DOI: 10.1080/21541264.2017.1363017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transcription of protein-encoding genes in eukaryotic cells is a dynamically coordinated process. Many of the key transcription regulators contain functionally essential intrinsically disordered regions (IDRs), the dynamic nature of which creates extra challenges to traditional biochemical analyses. Recent advances in single-molecule fluorescence imaging technology have enabled direct visualization of these rapid, complex and dynamic molecular interactions in real time.
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Affiliation(s)
| | - Robert Tjian
- b Howard Hughes Medical Institute, Li Ka Shing Center for Biomedical and Health Sciences and Department of Molecular and Cell Biology, University of California , Berkeley , CA , USA
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20
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An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations. Biophys J 2017; 113:550-557. [PMID: 28793210 DOI: 10.1016/j.bpj.2017.06.042] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/31/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Intrinsically disordered proteins play important roles throughout biology, yet our understanding of the relationship between their sequences, structural properties, and functions remains incomplete. The dynamic nature of these proteins, however, makes them difficult to characterize structurally. Many disordered proteins can attain both compact and expanded conformations, and the level of expansion may be regulated and important for function. Experimentally, the level of compaction and shape is often determined either by small-angle x-ray scattering experiments or pulsed-field-gradient NMR diffusion measurements, which provide ensemble-averaged estimates of the radius of gyration and hydrodynamic radius, respectively. Often, these experiments are interpreted using molecular simulations or are used to validate them. We here provide, to our knowledge, a new and efficient method to calculate the hydrodynamic radius of a disordered protein chain from a model of its structural ensemble. In particular, starting from basic concepts in polymer physics, we derive a relationship between the radius of gyration of a structure and its hydrodynamic ratio, which in turn can be used, for example, to compare a simulated ensemble of conformations to NMR diffusion measurements. The relationship may also be valuable when using NMR diffusion measurements to restrain molecular simulations.
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21
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Currie SL, Lau DKW, Doane JJ, Whitby FG, Okon M, McIntosh LP, Graves BJ. Structured and disordered regions cooperatively mediate DNA-binding autoinhibition of ETS factors ETV1, ETV4 and ETV5. Nucleic Acids Res 2017; 45:2223-2241. [PMID: 28161714 PMCID: PMC5389675 DOI: 10.1093/nar/gkx068] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/29/2017] [Indexed: 12/21/2022] Open
Abstract
Autoinhibition enables spatial and temporal regulation of cellular processes by coupling protein activity to surrounding conditions, often via protein partnerships or signaling pathways. We report the molecular basis of DNA-binding autoinhibition of ETS transcription factors ETV1, ETV4 and ETV5, which are often overexpressed in prostate cancer. Inhibitory elements that cooperate to repress DNA binding were identified in regions N- and C-terminal of the ETS domain. Crystal structures of these three factors revealed an α-helix in the C-terminal inhibitory domain that packs against the ETS domain and perturbs the conformation of its DNA-recognition helix. Nuclear magnetic resonance spectroscopy demonstrated that the N-terminal inhibitory domain (NID) is intrinsically disordered, yet utilizes transient intramolecular interactions with the DNA-recognition helix of the ETS domain to mediate autoinhibition. Acetylation of selected lysines within the NID activates DNA binding. This investigation revealed a distinctive mechanism for DNA-binding autoinhibition in the ETV1/4/5 subfamily involving a network of intramolecular interactions not present in other ETS factors. These distinguishing inhibitory elements provide a platform through which cellular triggers, such as protein–protein interactions or post-translational modifications, may specifically regulate the function of these oncogenic proteins.
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Affiliation(s)
- Simon L Currie
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Desmond K W Lau
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Jedediah J Doane
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
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22
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p53 Dynamically Directs TFIID Assembly on Target Gene Promoters. Mol Cell Biol 2017; 37:MCB.00085-17. [PMID: 28416636 DOI: 10.1128/mcb.00085-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/11/2017] [Indexed: 12/24/2022] Open
Abstract
p53 is a central regulator that turns on vast gene networks to maintain cellular integrity in the presence of various stimuli. p53 activates transcription initiation in part by aiding recruitment of TFIID to the promoter. However, the precise means by which p53 dynamically interacts with TFIID to facilitate assembly on target gene promoters remains elusive. To address this key issue, we have undertaken an integrated approach involving single-molecule fluorescence microscopy, single-particle cryo-electron microscopy, and biochemistry. Our real-time single-molecule imaging data demonstrate that TFIID alone binds poorly to native p53 target promoters. p53 unlocks TFIID's ability to bind DNA by stabilizing TFIID contacts with both the core promoter and a region within p53's response element. Analysis of single-molecule dissociation kinetics reveals that TFIID interacts with promoters via transient and prolonged DNA binding modes that are each regulated by p53. Importantly, our structural work reveals that TFIID's conversion to a rearranged DNA binding conformation is enhanced in the presence of DNA and p53. Notably, TFIID's interaction with DNA induces p53 to rapidly dissociate, which likely leads to additional rounds of p53-mediated recruitment of other basal factors. Collectively, these findings indicate that p53 dynamically escorts and loads TFIID onto its target promoters.
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23
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Zhang Z, English BP, Grimm JB, Kazane SA, Hu W, Tsai A, Inouye C, You C, Piehler J, Schultz PG, Lavis LD, Revyakin A, Tjian R. Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis. Genes Dev 2017; 30:2106-2118. [PMID: 27798851 PMCID: PMC5066616 DOI: 10.1101/gad.285395.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/01/2016] [Indexed: 11/25/2022]
Abstract
In this study, Zhang et al present a single-molecule imaging-based dynamic analysis of human RNA polymerase II preinitiation complex (PIC) assembly. They established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented by live-cell imaging and performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II). A “step-wise” preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, we established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Here we performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB–promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II–TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions.
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Affiliation(s)
- Zhengjian Zhang
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Brian P English
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Jonathan B Grimm
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Stephanie A Kazane
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 USA
| | - Wenxin Hu
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Albert Tsai
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Carla Inouye
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.,Li Ka Shing Center for Biomedical and Health Sciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Changjiang You
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 USA
| | - Luke D Lavis
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Andrey Revyakin
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Robert Tjian
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA.,Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.,Li Ka Shing Center for Biomedical and Health Sciences, University of California at Berkeley, Berkeley, California 94720, USA
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24
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Fox SJ, Kannan S. Probing the dynamics of disorder. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:57-62. [PMID: 28554553 DOI: 10.1016/j.pbiomolbio.2017.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/25/2016] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
Abstract
Intrinsically disordered proteins (IDPs) play an important role in many diseases. IDPs are a large and important class of proteins; estimated to represent a significant fraction of many genomes. In contrast to protein-protein interactions between well-folded proteins, IDPs typically bind to targets using short consecutive stretches of amino acids. Structures of IDPs complexed with a target have shown great diversity in binding modes. However, how this binding diversity is achieved at the molecular level is not well understood. Unfortunately, the prediction and detailed characterization of IDPs experimentally is still a very challenging task; however molecular mechanics based molecular dynamics simulation are well suited for studying the dynamic behavior of IDPs. We look into the current state for force fields for simulating IDPs and an example of how these methods have been applied to the p53 protein. p53 is one of the most extensively studied IDPs, with multiple intrinsically disordered regulatory domains that mediate its interactions with many other proteins engaged in multiple biological pathways. We show how molecular dynamics simulations can be used to elucidate on the mechanisms involved in selection of the different binding partners.
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Affiliation(s)
- Stephen John Fox
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore.
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25
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Abstract
Eukaryotic gene transcription requires the assembly at the promoter of a large preinitiation complex (PIC) that includes RNA polymerase II (Pol II) and the general transcription factors TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH. The size and complexity of Pol II, TFIID, and TFIIH have precluded their reconstitution from heterologous systems, and purification relies on scarce endogenous sources. Together with their conformational flexibility and the transient nature of their interactions, these limitations had precluded structural characterization of the PIC. In the last few years, however, progress in cryo-electron microscopy (cryo-EM) has made possible the visualization, at increasingly better resolution, of large PIC assemblies in different functional states. These structures can now be interpreted in near-atomic detail and provide an exciting structural framework for past and future functional studies, giving us unique mechanistic insight into the complex process of transcription initiation.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department and QB3 Institute, University of California, Berkeley, California 94720-3220
- Howard Hughes Medical Institute, Berkeley, California 94720-3220
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Lab, California 94720-3220;
| | - Robert K Louder
- Biophysics Graduate Group, University of California, Berkeley, California 94720-3220
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500
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26
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Shammas SL. Mechanistic roles of protein disorder within transcription. Curr Opin Struct Biol 2017; 42:155-161. [PMID: 28262589 DOI: 10.1016/j.sbi.2017.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 12/28/2022]
Abstract
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.
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Affiliation(s)
- Sarah L Shammas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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27
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Abstract
TFIID is a large protein complex required for the recognition and binding of eukaryotic gene core promoter sequences and for the recruitment of the rest of the general transcription factors involved in initiation of eukaryotic protein gene transcription. Cryo-electron microscopy studies have demonstrated the conformational complexity of human TFIID, where one-third of the mass of the complex can shift its position by well over 100 Å. This conformational plasticity appears to be linked to the capacity of TFIID to bind DNA, and suggests how it would allow both the recognition of different core promoter elements and the tuning of its binding affinity by regulatory factors.
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Affiliation(s)
- Eva Nogales
- a Molecular and Cell Biology Department and QB3 Institute , UC Berkeley , CA , USA.,b Howard Hughes Medical Institute , UC Berkeley , CA , USA.,c Molecular Biophysics and Integrative Bio-Imaging Division , Lawrence Berkeley National Lab , CA , USA
| | - Jie Fang
- b Howard Hughes Medical Institute , UC Berkeley , CA , USA
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28
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Feigerle JT, Weil PA. The C Terminus of the RNA Polymerase II Transcription Factor IID (TFIID) Subunit Taf2 Mediates Stable Association of Subunit Taf14 into the Yeast TFIID Complex. J Biol Chem 2016; 291:22721-22740. [PMID: 27587401 DOI: 10.1074/jbc.m116.751107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/31/2016] [Indexed: 12/22/2022] Open
Abstract
The evolutionarily conserved RNA polymerase II transcription factor D (TFIID) complex is composed of TATA box-binding protein (TBP) and 13 TBP-associated factors (Tafs). The mechanisms by which many Taf subunits contribute to the essential function of TFIID are only poorly understood. To address this gap in knowledge, we present the results of a molecular genetic dissection of the TFIID subunit Taf2. Through systematic site-directed mutagenesis, we have discovered 12 taf2 temperature-sensitive (ts) alleles. Two of these alleles display growth defects that can be strongly suppressed by overexpression of the yeast-specific TFIID subunit TAF14 but not by overexpression of any other TFIID subunit. In Saccharomyces cerevisiae, Taf14 is also a constituent of six other transcription-related complexes, making interpretation of its role in each of these complexes difficult. Although Taf14 is not conserved as a TFIID subunit in metazoans, it is conserved through its chromatin-binding YEATS domain. Based on the Taf2-Taf14 genetic interaction, we demonstrate that Taf2 and Taf14 directly interact and mapped the Taf2-Taf14 interaction domains. We used this information to identify a Taf2 separation-of-function variant (Taf2-ΔC). Although Taf2-ΔC no longer interacts with Taf14 in vivo or in vitro, it stably incorporates into the TFIID complex. In addition, purified Taf2-ΔC mutant TFIID is devoid of Taf14, making this variant a powerful reagent for determining the role of Taf14 in TFIID function. Furthermore, we characterized the mechanism through which Taf14 suppresses taf2ts alleles, shedding light on how Taf2-Taf14 interaction contributes to TFIID complex organization and identifying a potential role for Taf14 in mediating TFIID-chromatin interactions.
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Affiliation(s)
- Jordan T Feigerle
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615
| | - P Anthony Weil
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615
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29
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Abstract
The transcription cycle can be roughly divided into three stages: initiation, elongation, and termination. Understanding the molecular events that regulate all these stages requires a dynamic view of the underlying processes. The development of techniques to visualize and quantify transcription in single living cells has been essential in revealing the transcription kinetics. They have revealed that (a) transcription is heterogeneous between cells and (b) transcription can be discontinuous within a cell. In this review, we discuss the progress in our quantitative understanding of transcription dynamics in living cells, focusing on all parts of the transcription cycle. We present the techniques allowing for single-cell transcription measurements, review evidence from different organisms, and discuss how these experiments have broadened our mechanistic understanding of transcription regulation.
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Affiliation(s)
- Tineke L Lenstra
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Joseph Rodriguez
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Huimin Chen
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
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30
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Kannan S, Lane DP, Verma CS. Long range recognition and selection in IDPs: the interactions of the C-terminus of p53. Sci Rep 2016; 6:23750. [PMID: 27030593 PMCID: PMC4814905 DOI: 10.1038/srep23750] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 11/09/2022] Open
Abstract
The C-terminal domain of p53 is an extensively studied IDP, interacting with different partners through multiple distinct conformations. To explore the interplay between preformed structural elements and intrinsic fluctuations in its folding and binding we combine extensive atomistic equilibrium and non-equilibrium simulations. We find that the free peptide segment rapidly interconverts between ordered and disordered states with significant populations of the conformations that are seen in the complexed states. The underlying global folding-binding landscape points to a synergistic mechanism in which recognition is dictated via long range electrostatic recognition which results in the formation of reactive structures as far away as 10 Å, and binding proceeds with the steering of selected conformations followed by induced folding at the target surface or within a close range.
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Affiliation(s)
| | - David P Lane
- p53 Laboratory (A*STAR), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Chandra S Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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31
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Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature 2016; 531:604-9. [PMID: 27007846 PMCID: PMC4856295 DOI: 10.1038/nature17394] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 02/03/2016] [Indexed: 12/11/2022]
Abstract
The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation.
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32
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Csizmok V, Follis AV, Kriwacki RW, Forman-Kay JD. Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling. Chem Rev 2016; 116:6424-62. [PMID: 26922996 DOI: 10.1021/acs.chemrev.5b00548] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent ∼30% of the proteome and enable unique regulatory mechanisms. In this review, we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of conformational ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultrasensitivity" and "regulated folding and unfolding". We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information.
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Affiliation(s)
- Veronika Csizmok
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center , Memphis, Tennessee 38163, United States
| | - Julie D Forman-Kay
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto , Toronto, ON M5S 1A8, Canada
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