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Mandal K, Tomar SK, Kumar Santra M. Decoding the ubiquitin language: Orchestrating transcription initiation and gene expression through chromatin remodelers and histones. Gene 2024; 904:148218. [PMID: 38307220 DOI: 10.1016/j.gene.2024.148218] [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: 10/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
Eukaryotic transcription is a finely orchestrated process and it is controlled by transcription factors as well as epigenetic regulators. Transcription factors and epigenetic regulators undergo different types of posttranslational modifications including ubiquitination to control transcription process. Ubiquitination, traditionally associated with protein degradation, has emerged as a crucial contributor to the regulation of chromatin structure through ubiquitination of histone and chromatin remodelers. Ubiquitination introduces new layers of intricacy to the regulation of transcription initiation through controlling the equilibrium between euchromatin and heterochromatin states. Nucleosome, the fundamental units of chromatin, spacing in euchromatin and heterochromatin states are regulated by histone modification and chromatin remodeling complexes. Chromatin remodeling complexes actively sculpt the chromatin architecture and thereby influence the transcriptional states of genes. Therefore, understanding the dynamic behavior of nucleosome spacing is critical as it impacts various cellular functions through controlling gene expression profiles. In this comprehensive review, we discussed the intricate interplay between ubiquitination and transcription initiation, and illuminated the underlying molecular mechanisms that occur in a variety of biological contexts. This exploration sheds light on the complex regulatory networks that govern eukaryotic transcription, providing important insights into the fine orchestration of gene expression and chromatin dynamics.
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Affiliation(s)
- Kartik Mandal
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Shiva Kumar Tomar
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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2
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Kinyamu HK, Bennett BD, Ward JM, Archer TK. Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:1082-1099. [PMID: 38625038 PMCID: PMC11019832 DOI: 10.1158/2767-9764.crc-23-0476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/26/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
The 26S proteasome is the major protein degradation machinery in cells. Cancer cells use the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibitors have emerged as effective cancer therapeutics, but how they work mechanistically remains unclear. Here, using integrative genomic analysis, we discovered unexpected reprogramming of the chromatin landscape and RNA polymerase II (RNAPII) transcription initiation in breast cancer cells treated with the proteasome inhibitor MG132. The cells acquired dynamic changes in chromatin accessibility at specific genomic loci termed differentially open chromatin regions (DOCR). DOCRs with decreased accessibility were promoter proximal and exhibited unique chromatin architecture associated with divergent RNAPII transcription. Conversely, DOCRs with increased accessibility were primarily distal to transcription start sites and enriched in oncogenic superenhancers predominantly accessible in non-basal breast tumor subtypes. These findings describe the mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology. SIGNIFICANCE Our study provides a strong basis for understanding the mechanisms by which proteasome inhibitors exert anticancer effects. We find open chromatin regions that change during proteasome inhibition, are typically accessible in non-basal breast cancers.
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Affiliation(s)
- H. Karimi Kinyamu
- Chromatin and Gene Expression Section, National Institute of Environmental Health Sciences, Durham, North Carolina
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
- National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Brian D. Bennett
- National Institute of Environmental Health Sciences, Durham, North Carolina
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Durham, North Carolina
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - James M. Ward
- National Institute of Environmental Health Sciences, Durham, North Carolina
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Durham, North Carolina
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina
| | - Trevor K. Archer
- Chromatin and Gene Expression Section, National Institute of Environmental Health Sciences, Durham, North Carolina
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Durham, North Carolina
- National Institute of Environmental Health Sciences, Durham, North Carolina
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3
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van Dijk AD, Hoff FW, Qiu Y, Hubner SE, Go RL, Ruvolo VR, Leonti AR, Gerbing RB, Gamis AS, Aplenc R, Kolb EA, Alonzo TA, Meshinchi S, de Bont ESJM, Horton TM, Kornblau SM. Chromatin Profiles Are Prognostic of Clinical Response to Bortezomib-Containing Chemotherapy in Pediatric Acute Myeloid Leukemia: Results from the COG AAML1031 Trial. Cancers (Basel) 2024; 16:1448. [PMID: 38672531 PMCID: PMC11048007 DOI: 10.3390/cancers16081448] [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: 02/22/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The addition of the proteasome inhibitor bortezomib to standard chemotherapy did not improve survival in pediatric acute myeloid leukemia (AML) when all patients were analyzed as a group in the Children's Oncology Group phase 3 trial AAML1031 (NCT01371981). Proteasome inhibition influences the chromatin landscape and proteostasis, and we hypothesized that baseline proteomic analysis of histone- and chromatin-modifying enzymes (HMEs) would identify AML subgroups that benefitted from bortezomib addition. A proteomic profile of 483 patients treated with AAML1031 chemotherapy was generated using a reverse-phase protein array. A relatively high expression of 16 HME was associated with lower EFS and higher 3-year relapse risk after AML standard treatment compared to low expressions (52% vs. 29%, p = 0.005). The high-HME profile correlated with more transposase-accessible chromatin, as demonstrated via ATAC-sequencing, and the bortezomib addition improved the 3-year overall survival compared with standard therapy (62% vs. 75%, p = 0.033). These data suggest that there are pediatric AML populations that respond well to bortezomib-containing chemotherapy.
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Affiliation(s)
- Anneke D. van Dijk
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.W.H.)
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Fieke W. Hoff
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.W.H.)
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Yihua Qiu
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Stefan E. Hubner
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Robin L. Go
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Vivian R. Ruvolo
- Department of Molecular Therapy and Hematology, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Alan S. Gamis
- Department of Hematology-Oncology, Children’s Mercy Hospitals and Clinics, Kansas City, MO 64108, USA
| | - Richard Aplenc
- Division of Pediatric Oncology and Stem Cell Transplant, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Edward A. Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Todd A. Alonzo
- COG Statistics and Data Center, Monrovia, CA 91016, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eveline S. J. M. de Bont
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.W.H.)
| | - Terzah M. Horton
- Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven M. Kornblau
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
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4
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Breckel CA, Johnson ZM, Hickey CM, Hochstrasser M. Yeast 26S proteasome nuclear import is coupled to nucleus-specific degradation of the karyopherin adaptor protein Sts1. Sci Rep 2024; 14:2048. [PMID: 38267508 PMCID: PMC10808114 DOI: 10.1038/s41598-024-52352-5] [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: 08/17/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024] Open
Abstract
In eukaryotes, the ubiquitin-proteasome system is an essential pathway for protein degradation and cellular homeostasis. 26S proteasomes concentrate in the nucleus of budding yeast Saccharomyces cerevisiae due to the essential import adaptor protein Sts1 and the karyopherin-α protein Srp1. Here, we show that Sts1 facilitates proteasome nuclear import by recruiting proteasomes to the karyopherin-α/β heterodimer. Following nuclear transport, the karyopherin proteins are likely separated from Sts1 through interaction with RanGTP in the nucleus. RanGTP-induced release of Sts1 from the karyopherin proteins initiates Sts1 proteasomal degradation in vitro. Sts1 undergoes karyopherin-mediated nuclear import in the absence of proteasome interaction, but Sts1 degradation in vivo is only observed when proteasomes successfully localize to the nucleus. Sts1 appears to function as a proteasome import factor during exponential growth only, as it is not found in proteasome storage granules (PSGs) during prolonged glucose starvation, nor does it appear to contribute to the rapid nuclear reimport of proteasomes following glucose refeeding and PSG dissipation. We propose that Sts1 acts as a single-turnover proteasome nuclear import factor by recruiting karyopherins for transport and undergoing subsequent RanGTP-initiated ubiquitin-independent proteasomal degradation in the nucleus.
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Affiliation(s)
- Carolyn Allain Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Zane M Johnson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Arvinas, Inc., 5 Science Park, New Haven, CT, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
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5
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Zeng M, Tang Z, Ren L, Wang H, Wang X, Zhu W, Mao X, Li Z, Mo X, Chen J, Han J, Kong D, Ji J, Carr AM, Liu C. Hepatitis B virus infection disrupts homologous recombination in hepatocellular carcinoma by stabilizing resection inhibitor ADRM1. J Clin Invest 2023; 133:e171533. [PMID: 37815873 PMCID: PMC10688980 DOI: 10.1172/jci171533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Many cancers harbor homologous recombination defects (HRDs). A HRD is a therapeutic target that is being successfully utilized in treatment of breast/ovarian cancer via synthetic lethality. However, canonical HRD caused by BRCAness mutations do not prevail in liver cancer. Here we report a subtype of HRD caused by the perturbation of a proteasome variant (CDW19S) in hepatitis B virus-bearing (HBV-bearing) cells. This amalgamate protein complex contained the 19S proteasome decorated with CRL4WDR70 ubiquitin ligase, and assembled at broken chromatin in a PSMD4Rpn10- and ATM-MDC1-RNF8-dependent manner. CDW19S promoted DNA end processing via segregated modules that promote nuclease activities of MRE11 and EXO1. Contrarily, a proteasomal component, ADRM1Rpn13, inhibited resection and was removed by CRL4WDR70-catalyzed ubiquitination upon commitment of extensive resection. HBx interfered with ADRM1Rpn13 degradation, leading to the imposition of ADRM1Rpn13-dependent resection barrier and consequent viral HRD subtype distinguishable from that caused by BRCA1 defect. Finally, we demonstrated that viral HRD in HBV-associated hepatocellular carcinoma can be exploited to restrict tumor progression. Our work clarifies the underlying mechanism of a virus-induced HRD subtype.
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Affiliation(s)
- Ming Zeng
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, China
| | - Zizhi Tang
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, China
| | - Laifeng Ren
- Department of Immunology, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China
| | - Haibin Wang
- Department of Pediatric Surgery, Wuhan Children’s Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojun Wang
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wenyuan Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiaobing Mao
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Zeyang Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xianming Mo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Chen
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junhong Han
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Daochun Kong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Antony M. Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Cong Liu
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, China
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6
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Kinyamu HK, Bennett BD, Ward JM, Archer T. Proteasome inhibition reprograms chromatin landscape in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562284. [PMID: 37904968 PMCID: PMC10614768 DOI: 10.1101/2023.10.13.562284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The 26S proteasome is the major protein degradation machinery in cells. Cancer cells use the proteasome to modulate gene expression networks that promote tumor growth. Proteasome inhibitors have emerged as effective cancer therapeutics, but how they work mechanistically remains unclear. Here, using integrative genomic analysis, we discovered unexpected reprogramming of the chromatin landscape and RNAPII transcription initiation in breast cancer cells treated with the proteasome inhibitor MG132. The cells acquired dynamic changes in chromatin accessibility at specific genomic loci termed Differentially Open Chromatin Regions (DOCRs). DOCRs with decreased accessibility were promoter proximal and exhibited unique chromatin architecture associated with divergent RNAPII transcription. Conversely, DOCRs with increased accessibility were primarily distal to transcription start sites and enriched in oncogenic super enhancers predominantly accessible in non-basal breast tumor subtypes. These findings describe the mechanisms by which the proteasome modulates the expression of gene networks intrinsic to breast cancer biology. Highlights Proteasome inhibition uncovers de novo Differential Open Chromatin Regions (DOCRs) in breast cancer cells. Proteasome inhibitor sensitive promoters exhibit a distinctive chromatin architecture with discrete transcription initiation patterns.Proteasome inhibition reprograms accessibility of super enhancers.Proteasome inhibitor sensitive super enhancers distinguish basal from non-basal breast cancer subtypes.
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7
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Aliyaskarova U, Baiken Y, Renaud F, Couve S, Kisselev AF, Saparbaev M, Groisman R. NEIL3-mediated proteasomal degradation facilitates the repair of cisplatin-induced DNA damage in human cells. Sci Rep 2023; 13:5174. [PMID: 36997601 PMCID: PMC10063580 DOI: 10.1038/s41598-023-32186-3] [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: 07/11/2022] [Accepted: 03/23/2023] [Indexed: 04/01/2023] Open
Abstract
Anti-neoplastic effect of DNA cross-linking agents such as cisplatin, mitomycin C, and psoralen is attributed to their ability to induce DNA interstrand cross-links (ICLs), which block replication, transcription, and linear repair pathways by preventing DNA strand separation and trigger apoptosis. It is generally agreed that the Fanconi anemia (FA) pathway orchestrates the removal of ICLs by the combined actions of various DNA repair pathways. Recently, attention has been focused on the ability of the NEIL3-initiated base excision repair pathway to resolve psoralen- and abasic site-induced ICLs in an FA-independent manner. Intriguingly, overexpression of NEIL3 is associated with chemo-resistance and poor prognosis in many solid tumors. Here, using loss- and gain-of-function approaches, we demonstrate that NEIL3 confers resistance to cisplatin and participates in the removal of cisplatin-DNA adducts. Proteomic studies reveal that the NEIL3 protein interacts with the 26S proteasome in a cisplatin-dependent manner. NEIL3 mediates proteasomal degradation of WRNIP1, a protein involved in the early step of ICL repair. We propose that NEIL3 participates in the repair of ICL-stalled replication fork by recruitment of the proteasome to ensure a timely transition from lesion recognition to repair via the degradation of early-step vanguard proteins.
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Affiliation(s)
- Umit Aliyaskarova
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France
| | - Yeldar Baiken
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- School of Engineering and Digital Sciences, Nazarbayev University, Astana, Kazakhstan
| | - Flore Renaud
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France
- EPHE, PSL University, Paris, France
| | - Sophie Couve
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France
- EPHE, PSL University, Paris, France
| | - Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, PRB, 720 S. Donahue Dr., Auburn, AL, 36849, USA.
| | - Murat Saparbaev
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France.
| | - Regina Groisman
- Team «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR 9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, 94805, Villejuif Cedex, France.
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8
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Weeks O, Miller BM, Pepe-Mooney BJ, Oderberg IM, Freeburg SH, Smith CJ, North TE, Goessling W. Embryonic alcohol exposure disrupts the ubiquitin-proteasome system. JCI Insight 2022; 7:156914. [PMID: 36477359 PMCID: PMC9746913 DOI: 10.1172/jci.insight.156914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Ethanol (EtOH) is a commonly encountered teratogen that can disrupt organ development and lead to fetal alcohol spectrum disorders (FASDs); many mechanisms of developmental toxicity are unknown. Here, we used transcriptomic analysis in an established zebrafish model of embryonic alcohol exposure (EAE) to identify the ubiquitin-proteasome system (UPS) as a critical target of EtOH during development. Surprisingly, EAE alters 20S, 19S, and 11S proteasome gene expression and increases ubiquitylated protein load. EtOH and its metabolite acetaldehyde decrease proteasomal peptidase activity in a cell type-specific manner. Proteasome 20S subunit β 1 (psmb1hi2939Tg) and proteasome 26S subunit, ATPase 6 (psmc6hi3593Tg), genetic KOs define the developmental impact of decreased proteasome function. Importantly, loss of psmb1 or psmc6 results in widespread developmental abnormalities resembling EAE phenotypes, including growth restriction, abnormal craniofacial structure, neurodevelopmental defects, and failed hepatopancreas maturation. Furthermore, pharmacologic inhibition of chymotrypsin-like proteasome activity potentiates the teratogenic effects of EAE on craniofacial structure, the nervous system, and the endoderm. Our studies identify the proteasome as a target of EtOH exposure and signify that UPS disruptions contribute to craniofacial, neurological, and endodermal phenotypes in FASDs.
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Affiliation(s)
- Olivia Weeks
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bess M. Miller
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian J. Pepe-Mooney
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac M. Oderberg
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott H. Freeburg
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Colton J. Smith
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Trista E. North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Wolfram Goessling
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
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9
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Oliviero G, Kovalchuk S, Rogowska-Wrzesinska A, Schwämmle V, Jensen ON. Distinct and diverse chromatin-proteomes of ageing mouse organs reveal protein signatures that correlate with physiological functions. eLife 2022; 11:73524. [PMID: 35259090 PMCID: PMC8933006 DOI: 10.7554/elife.73524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temporal molecular changes in ageing mammalian organs are of relevance to disease aetiology because many age-related diseases are linked to changes in the transcriptional and epigenetic machinery that regulate gene expression. We performed quantitative proteome analysis of chromatin-enriched protein extracts to investigate the dynamics of the chromatin proteomes of the mouse brain, heart, lung, kidney, liver, and spleen at 3, 5, 10, and 15 months of age. Each organ exhibited a distinct chromatin proteome and sets of unique proteins. The brain and spleen chromatin proteomes were the most extensive, diverse, and heterogenous among the six organs. The spleen chromatin proteome appeared static during the lifespan, presenting a young phenotype that reflects the permanent alertness state and important role of this organ in physiological defence and immunity. We identified a total of 5928 proteins, including 2472 nuclear or chromatin-associated proteins across the six mouse organs. Up to 3125 proteins were quantified in each organ, demonstrating distinct and organ-specific temporal protein expression timelines and regulation at the post-translational level. Bioinformatics meta-analysis of these chromatin proteomes revealed distinct physiological and ageing-related features for each organ. Our results demonstrate the efficiency of organelle-specific proteomics for in vivo studies of a model organism and consolidate the hypothesis that chromatin-associated proteins are involved in distinct and specific physiological functions in ageing organs.
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Affiliation(s)
- Giorgio Oliviero
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Sergey Kovalchuk
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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10
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Guo X. Localized Proteasomal Degradation: From the Nucleus to Cell Periphery. Biomolecules 2022; 12:biom12020229. [PMID: 35204730 PMCID: PMC8961600 DOI: 10.3390/biom12020229] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/31/2022] Open
Abstract
The proteasome is responsible for selective degradation of most cellular proteins. Abundantly present in the cell, proteasomes not only diffuse in the cytoplasm and the nucleus but also associate with the chromatin, cytoskeleton, various membranes and membraneless organelles/condensates. How and why the proteasome gets to these specific subcellular compartments remains poorly understood, although increasing evidence supports the hypothesis that intracellular localization may have profound impacts on the activity, substrate accessibility and stability/integrity of the proteasome. In this short review, I summarize recent advances on the functions, regulations and targeting mechanisms of proteasomes, especially those localized to the nuclear condensates and membrane structures of the cell, and I discuss the biological significance thereof in mediating compartmentalized protein degradation.
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Affiliation(s)
- Xing Guo
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
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11
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Alvarado ME, Chaparro-Gutiérrez JJ, Calvo EP, Prada LF, Wasserman M. Activity of the Giardia intestinalis proteasome during encystation and its connection with the expression of the cyst wall protein 1 (CWP1). Acta Trop 2022; 225:106183. [PMID: 34627761 DOI: 10.1016/j.actatropica.2021.106183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/01/2022]
Abstract
Giardia is a parasite whose life cycle is composed of two stages: replicative trophozoites, responsible for the symptoms of the disease, and infective cysts, resistant to adverse environments outside of hosts. Proteasomes are multicatalytic peptidase complexes responsible for the specific degradation of proteins in eukaryotic cells. This study assessed the proteasome activity in the trophozoite and during encystation. Strong activation of the proteasome was observed during the differentiation of trophozoites into cysts, reaching its maximum level 24 h after the stimulus. We also found that the Giardia proteasome presents unusual characteristics related to higher eukaryotic proteasomes, making it an eventual therapeutic target. Here we tested the effects on the synthesis of a cyst wall protein by chemical inactivation of the proteasome and by overexpression or partial inhibition of the deubiquitinating protein RPN11 in transfected cells. Moreover, an analysis of the intracellular localization of RPN11 (an integral part of the proteasome regulatory particle) revealed major changes associated with the differentiation of trophozoites into cysts. This evidence further supports the important role of the proteasome in Giardia encystation.
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12
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Van Houten B, Schnable B, Kumar N. Chaperones for dancing on chromatin: Role of post-translational modifications in dynamic damage detection hand-offs during nucleotide excision repair. Bioessays 2021; 43:e2100011. [PMID: 33620094 PMCID: PMC9756857 DOI: 10.1002/bies.202100011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
We highlight a recent study exploring the hand-off of UV damage to several key nucleotide excision repair (NER) proteins in the cascade: UV-DDB, XPC and TFIIH. The delicate dance of DNA repair proteins is choreographed by the dynamic hand-off of DNA damage from one recognition complex to another damage verification protein or set of proteins. These DNA transactions on chromatin are strictly chaperoned by post-translational modifications (PTM). This new study examines the role that ubiquitylation and subsequent DDB2 degradation has during this process. In total, this study suggests an intricate cellular timer mechanism that under normal conditions DDB2 helps recruit and ubiquitylate XPC, stabilizing XPC at damaged sites. If DDB2 persists at damaged sites too long, it is turned over by auto-ubiquitylation and removed from DNA by the action of VCP/p97 for degradation in the 26S proteosome.
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Affiliation(s)
- Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC-Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brittani Schnable
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UPMC-Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Namrata Kumar
- UPMC-Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
- Molecular Genetics and Developmental Biology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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13
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Fesquet D, Llères D, Grimaud C, Viganò C, Méchali F, Boulon S, Coux O, Bonne-Andrea C, Baldin V. The 20S proteasome activator PA28γ controls the compaction of chromatin. J Cell Sci 2021; 134:134/3/jcs257717. [PMID: 33526472 DOI: 10.1242/jcs.257717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022] Open
Abstract
PA28γ (also known as PSME3), a nuclear activator of the 20S proteasome, is involved in the degradation of several proteins regulating cell growth and proliferation and in the dynamics of various nuclear bodies, but its precise cellular functions remain unclear. Here, using a quantitative FLIM-FRET based microscopy assay monitoring close proximity between nucleosomes in living human cells, we show that PA28γ controls chromatin compaction. We find that its depletion induces a decompaction of pericentromeric heterochromatin, which is similar to what is observed upon the knockdown of HP1β (also known as CBX1), a key factor of the heterochromatin structure. We show that PA28γ is present at HP1β-containing repetitive DNA sequences abundant in heterochromatin and, importantly, that HP1β on its own is unable to drive chromatin compaction without the presence of PA28γ. At the molecular level, we show that this novel function of PA28γ is independent of its stable interaction with the 20S proteasome, and most likely depends on its ability to maintain appropriate levels of H3K9me3 and H4K20me3, histone modifications that are involved in heterochromatin formation. Overall, our results implicate PA28γ as a key factor involved in the regulation of the higher order structure of chromatin.
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Affiliation(s)
- Didier Fesquet
- Centre de Recherche de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293 Montpellier, France
| | - David Llères
- Institut de Génétique Moléculaire de Montpellier (IGMM), Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Charlotte Grimaud
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Institut Régional du Cancer (ICM), Université de Montpellier, CNRS Route de Mende, 34293 Montpellier, France
| | - Cristina Viganò
- Centre de Recherche de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Francisca Méchali
- Centre de Recherche de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Séverine Boulon
- Centre de Recherche de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Olivier Coux
- Centre de Recherche de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Catherine Bonne-Andrea
- Centre de Recherche de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Véronique Baldin
- Centre de Recherche de Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, 34293 Montpellier, France
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14
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Cell cycle-dependent localization of the proteasome to chromatin. Sci Rep 2020; 10:5801. [PMID: 32242037 PMCID: PMC7118148 DOI: 10.1038/s41598-020-62697-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/12/2020] [Indexed: 11/08/2022] Open
Abstract
An integrative understanding of nuclear events including transcription in normal and cancer cells requires comprehensive and quantitative measurement of protein dynamics that underlie such events. However, the low abundance of most nuclear proteins hampers their detailed functional characterization. We have now comprehensively quantified the abundance of nuclear proteins with the use of proteomics approaches in both normal and transformed human diploid fibroblasts. We found that subunits of the 26S proteasome complex were markedly down-regulated in the nuclear fraction of the transformed cells compared with that of the wild-type cells. The intranuclear proteasome abundance appeared to be inversely related to the rate of cell cycle progression, with restraint of the cell cycle being associated with an increase in the amount of proteasome subunits in the nucleus, suggesting that the nuclear proteasome content is dependent on the cell cycle. Furthermore, chromatin enrichment for proteomics (ChEP) analysis revealed enrichment of the proteasome in the chromatin fraction of quiescent cells and its apparent dissociation from chromatin in transformed cells. Our results thus suggest that translocation of the nuclear proteasome to chromatin may play an important role in control of the cell cycle and oncogenesis through regulation of chromatin-associated transcription factors.
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15
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Budenholzer L, Breckel C, Hickey CM, Hochstrasser M. The Sts1 nuclear import adapter uses a non-canonical bipartite nuclear localization signal and is directly degraded by the proteasome. J Cell Sci 2020; 133:jcs.236158. [PMID: 32041904 DOI: 10.1242/jcs.236158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023] Open
Abstract
The proteasome is an essential regulator of protein homeostasis. In yeast and many mammalian cells, proteasomes strongly concentrate in the nucleus. Sts1 from the yeast Saccharomyces cerevisiae is an essential protein linked to proteasome nuclear localization. Here, we show that Sts1 contains a non-canonical bipartite nuclear localization signal (NLS) important for both nuclear localization of Sts1 itself and the proteasome. Sts1 binds the karyopherin-α import receptor (Srp1) stoichiometrically, and this requires the NLS. The NLS is essential for viability, and over-expressed Sts1 with an inactive NLS interferes with 26S proteasome import. The Sts1-Srp1 complex binds preferentially to fully assembled 26S proteasomes in vitro Sts1 is itself a rapidly degraded 26S proteasome substrate; notably, this degradation is ubiquitin independent in cells and in vitro and is inhibited by Srp1 binding. Mutants of Sts1 are stabilized, suggesting that its degradation is tightly linked to its role in localizing proteasomes to the nucleus. We propose that Sts1 normally promotes nuclear import of fully assembled proteasomes and is directly degraded by proteasomes without prior ubiquitylation following karyopherin-α release in the nucleus.
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Affiliation(s)
- Lauren Budenholzer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Carolyn Breckel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Christopher M Hickey
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA .,Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA
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16
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17
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Kinyamu HK, Bennett BD, Bushel PR, Archer TK. Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity. J Biol Chem 2019; 295:1271-1287. [PMID: 31806706 DOI: 10.1074/jbc.ra119.011174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/02/2019] [Indexed: 11/06/2022] Open
Abstract
Proteasome activity is required for diverse cellular processes, including transcriptional and epigenetic regulation. However, inhibiting proteasome activity can lead to an increase in transcriptional output that is correlated with enriched levels of trimethyl H3K4 and phosphorylated forms of RNA polymerase (Pol) II at the promoter and gene body. Here, we perform gene expression analysis and ChIP followed by sequencing (ChIP-seq) in MCF-7 breast cancer cells treated with the proteasome inhibitor MG132, and we further explore genome-wide effects of proteasome inhibition on the chromatin state and RNA Pol II transcription. Analysis of gene expression programs and chromatin architecture reveals that chemically inhibiting proteasome activity creates a distinct chromatin state, defined by spreading of the H3K4me3 mark into the gene bodies of differentially-expressed genes. The distinct H3K4me3 chromatin profile and hyperacetylated nucleosomes at transcription start sites establish a chromatin landscape that facilitates recruitment of Ser-5- and Ser-2-phosphorylated RNA Pol II. Subsequent transcriptional events result in diverse gene expression changes. Alterations of H3K36me3 levels in the gene body reflect productive RNA Pol II elongation of transcripts of genes that are induced, underscoring the requirement for proteasome activity at multiple phases of the transcriptional cycle. Finally, by integrating genomics data and pathway analysis, we find that the differential effects of proteasome inhibition on the chromatin state modulate genes that are fundamental for cancer cell survival. Together, our results uncover underappreciated downstream effects of proteasome inhibitors that may underlie targeting of distinct chromatin states and key steps of RNA Pol II-mediated transcription in cancer cells.
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Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Brian D Bennett
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709.,Integrative Bioinformatics Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
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18
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Werner CT, Mitra S, Martin JA, Stewart AF, Lepack AE, Ramakrishnan A, Gobira PH, Wang ZJ, Neve RL, Gancarz AM, Shen L, Maze I, Dietz DM. Ubiquitin-proteasomal regulation of chromatin remodeler INO80 in the nucleus accumbens mediates persistent cocaine craving. SCIENCE ADVANCES 2019; 5:eaay0351. [PMID: 31633032 PMCID: PMC6785264 DOI: 10.1126/sciadv.aay0351] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/14/2019] [Indexed: 05/07/2023]
Abstract
Neuroadaptations in the nucleus accumbens (NAc) underlie cue-induced cocaine craving that intensifies ("incubates") during abstinence and is believed to contribute to persistent relapse vulnerability. Changes in gene expression often govern perpetual behavioral abnormalities, but epigenetic plasticity during prolonged abstinence from drug exposure is poorly understood. We examined how E3 ubiquitin ligase TRIM3 dysregulates chromatin remodeler INO80 to mediate cocaine craving during prolonged abstinence. We found that INO80 expression increased in the NAc on abstinence day 30 (AD30) but not on AD1 following cocaine self-administration. Furthermore, TRIM3, which mediates degradation of INO80, was reduced on AD30, along with TRIM3-INO80 interaction. Viral-mediated gene transfer of INO80 or TRIM3 governed cocaine craving during prolonged abstinence. Lastly, chromatin immunoprecipitation followed by massively parallel DNA sequencing identified INO80-mediated transcriptional regulation of predicted pathways associated with cocaine plasticity. Together, these results demonstrate a novel ubiquitin-proteasomal-epigenetic mechanism by which TRIM3-INO80 mediates cocaine craving during prolonged abstinence.
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Affiliation(s)
- C. T. Werner
- Department of Pharmacology and Toxicology, Program in Neuroscience, Jacobs School of Medicine and Biomedical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - S. Mitra
- Department of Pharmacology and Toxicology, Program in Neuroscience, Jacobs School of Medicine and Biomedical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - J. A. Martin
- Department of Pharmacology and Toxicology, Program in Neuroscience, Jacobs School of Medicine and Biomedical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - A. F. Stewart
- Department of Pharmacology and Toxicology, Program in Neuroscience, Jacobs School of Medicine and Biomedical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - A. E. Lepack
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A. Ramakrishnan
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P. H. Gobira
- Department of Pharmacology and Toxicology, Program in Neuroscience, Jacobs School of Medicine and Biomedical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Z.-J. Wang
- Department of Pharmacology and Toxicology, Program in Neuroscience, Jacobs School of Medicine and Biomedical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - R. L. Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, MA, USA
| | - A. M. Gancarz
- Department of Psychology, California State University, Bakersfield, Bakersfield, CA, USA
| | - L. Shen
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - I. Maze
- Fishberg Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - D. M. Dietz
- Department of Pharmacology and Toxicology, Program in Neuroscience, Jacobs School of Medicine and Biomedical Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
- Department of Psychology, The State University of New York at Buffalo, Buffalo, NY, USA
- Corresponding author.
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19
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Aranda S, Alcaine-Colet A, Blanco E, Borràs E, Caillot C, Sabidó E, Di Croce L. Chromatin capture links the metabolic enzyme AHCY to stem cell proliferation. SCIENCE ADVANCES 2019; 5:eaav2448. [PMID: 30854431 PMCID: PMC6402848 DOI: 10.1126/sciadv.aav2448] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/28/2019] [Indexed: 05/19/2023]
Abstract
Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have designed an experimental strategy to survey the chromatome of proliferating cells by using the DNA-mediated chromatin pull-down (Dm-ChP) technology. Our approach provides a global view of cellular chromatome under normal physiological conditions and enables the identification of chromatin-bound proteins de novo. Integrating Dm-ChP with genomic and functional data, we have discovered an unexpected chromatin function for adenosylhomocysteinase, a major one-carbon pathway metabolic enzyme, in gene activation. Our study reveals a new regulatory axis between the metabolic state of pluripotent cells, ribosomal protein production, and cell division during the early phase of embryo development, in which the metabolic flux of methylation reactions is favored in a local milieu.
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Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Corresponding author. (S.A.); (L.D.C.)
| | - Anna Alcaine-Colet
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Claire Caillot
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author. (S.A.); (L.D.C.)
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20
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Zukowski A, Phillips J, Park S, Wu R, Gygi SP, Johnson AM. Proteomic profiling of yeast heterochromatin connects direct physical and genetic interactions. Curr Genet 2018; 65:495-505. [PMID: 30310994 DOI: 10.1007/s00294-018-0889-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/10/2018] [Accepted: 10/03/2018] [Indexed: 11/27/2022]
Abstract
Heterochromatin domains are stably repressed chromatin structures composed of a core assembly of silencing proteins that condense adjacent nucleosomes. The minimal heterochromatin structure can serve as a platform for recruitment of complementary regulatory factors. We find that a reconstituted budding yeast heterochromatin domain can act as a platform to recruit multiple factors that play a role in regulating heterochromatin function. We uncover the direct interaction between the SIR heterochromatin complex and a chromosomal boundary protein that restricts the spread of heterochromatin. We find that the SIR complex relieves a mechanism of auto-inhibition within the boundary protein Yta7, allowing the Yta7 bromodomain to engage chromatin. Our results suggest that budding yeast shares with other eukaryotes the ability to establish complex heterochromatin domains that coordinate multiple mechanisms of silencing regulation through physical interactions.
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Affiliation(s)
- Alexis Zukowski
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO, 80045, USA
- Molecular Biology Program, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Juliana Phillips
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO, 80045, USA
- Molecular Biology Program, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Soyeon Park
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO, 80309, USA
| | - Ronghu Wu
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Aaron M Johnson
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO, 80045, USA.
- Molecular Biology Program, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA.
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21
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Horzmann KA, Reidenbach LS, Thanki DH, Winchester AE, Qualizza BA, Ryan GA, Egan KE, Hedrick VE, Sobreira TJP, Peterson SM, Weber GJ, Wirbisky-Hershberger SE, Sepúlveda MS, Freeman JL. Embryonic atrazine exposure elicits proteomic, behavioral, and brain abnormalities with developmental time specific gene expression signatures. J Proteomics 2018; 186:71-82. [PMID: 30012420 PMCID: PMC6193558 DOI: 10.1016/j.jprot.2018.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 02/06/2023]
Abstract
Atrazine (ATZ), the second most commonly used herbicide in the United States, is an endocrine disrupting chemical linked to cancer and a common drinking water contaminant. This study further investigates ATZ-related developmental toxicity by testing the following hypotheses in zebrafish: the effects of embryonic ATZ exposure are dependent on timing of exposure; embryonic ATZ exposure alters brain development and function; and embryonic ATZ exposure changes protein abundance in carcinogenesis-related pathways. After exposing embryos to 0, 0.3, 3, or 30 parts per billion (ppb) ATZ, we monitored the expression of cytochrome P450 family 17 subfamily A member 1 (cyp17a1), glyoxalase I (glo1), ring finger protein 14 (rnf14), salt inducible kinase 2 (sik2), tetratricopeptide domain 3 (ttc3), and tumor protein D52 like 1 (tpd52l1) at multiple embryonic time points to determine normal expression and if ATZ exposure altered expression. Only cyp17a1 had normal dynamic expression, but ttc3 and tpd52l1 had ATZ-related expression changes before 72 h. Larvae exposed to 0.3 ppb ATZ had increased brain length, while larvae exposed to 30 ppb ATZ were hypoactive. Proteomic analysis identified altered protein abundance in pathways related to cellular function, neurodevelopment, and genital-tract cancer. The results indicate embryonic ATZ toxicity involves interactions of multiple pathways. SIGNIFICANCE This is the first report of proteomic alterations following embryonic exposure to atrazine, an environmentally persistent pesticide and common water contaminant. Although the transcriptomic alterations in larval zebrafish with embryonic atrazine exposure have been reported, neither the time at which gene expression changes occur nor the resulting proteomic changes have been investigated. This study seeks to address these knowledge gaps by evaluating atrazine's effect on gene expression through multiple time points during embryogenesis, and correlating changes in gene expression to pathological alterations in brain length and functional changes in behavior. Finally, pathway analysis of the proteomic alterations identifies connections between the molecular changes and functional outcomes associated with embryonic atrazine exposure.
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Affiliation(s)
- Katharine A Horzmann
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Leeah S Reidenbach
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Devang H Thanki
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Anna E Winchester
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Brad A Qualizza
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Geoffrey A Ryan
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Kaitlyn E Egan
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Victoria E Hedrick
- Bindley Bioscience Center, Discovery Park, Purdue University, West Lafayette, IN 47907, United States
| | - Tiago J P Sobreira
- Bindley Bioscience Center, Discovery Park, Purdue University, West Lafayette, IN 47907, United States
| | - Samuel M Peterson
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Gregory J Weber
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States
| | | | - Maria S Sepúlveda
- Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, United States
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States; Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States.
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22
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Abstract
The molecular basis responsible for tolerance following inflammatory response to lipopolysaccharide (LPS) is not well understood. We hypothesized that inflammation/tolerance in monocytes/ macrophages is dependent on the proteases of proteasome. To test our hypothesis, first, we examined the expression of different proteasome subunits in different human and mouse monocytes/macrophages. Secondly, we investigated the effect of proteasome subunits/ proteases on LPS-induced expression of tumor necrosis factor-α (TNF-α) and nitric oxide (NO) during inflammation and tolerance using mouse RAW 264.7 macrophages, THP1 cells, and cluster of differentiation 14 positive (CD14) human monocytes. We found that RAW 264.7 cells (XYZ), mouse peritoneal resident, thioglycollate-elicited macrophages, primed RAW 264.7 (XYZ, LMP), and human monocytes (LMP) expressed different types of proteasome subunits/activities. Cells containing predominantly either LMP subunits (such as THP-1 and human monocytes), or only X, Y, Z subunits (RAW 264.7 cells not primed) could only induce TNF-α, but not NO, while cells containing all five to six subunits (XYZ, LMP) of the proteasome could induce both mediators in response to LPS. Distinct states of inflammation/tolerance in LPS treated cells, strongly correlated with an upregulation or downregulation of proteasome's subunits (proteases), respectively. Moreover, interferon-γ treatment of tolerant cells caused robust induction of proteasome's subunit expression in mouse macrophages and human monocytes, and cells regained their ability to respond to LPS. These studies are vital for understanding function of proteasome's subunits during inflammation/tolerance in mouse and human cells, and for design of therapeutic strategies for all diseases based on inflammation.
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23
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Abstract
This study compares the native structures of cytosolic and nuclear proteasomes, visualized directly within cells. The assembly states and functional states of proteasomes in each compartment were similar, indicating comparable levels of proteolytic activity per proteasome. Nuclear proteasomes were tethered to two different sites at the nuclear pore complex (NPC): the inner nuclear membrane and the NPC basket. Structural analysis revealed mechanistic details of the two tethering interactions. These results present direct evidence that proteasomes bind at NPCs, establishing a cellular hub for protein degradation at the gateway between the nucleus and cytoplasm. This work demonstrates how cryo-electron tomography can reveal biological mechanisms by directly observing the interactions between molecular complexes within the native cellular environment. The partitioning of cellular components between the nucleus and cytoplasm is the defining feature of eukaryotic life. The nuclear pore complex (NPC) selectively gates the transport of macromolecules between these compartments, but it is unknown whether surveillance mechanisms exist to reinforce this function. By leveraging in situ cryo-electron tomography to image the native cellular environment of Chlamydomonas reinhardtii, we observed that nuclear 26S proteasomes crowd around NPCs. Through a combination of subtomogram averaging and nanometer-precision localization, we identified two classes of proteasomes tethered via their Rpn9 subunits to two specific NPC locations: binding sites on the NPC basket that reflect its eightfold symmetry and more abundant binding sites at the inner nuclear membrane that encircle the NPC. These basket-tethered and membrane-tethered proteasomes, which have similar substrate-processing state frequencies as proteasomes elsewhere in the cell, are ideally positioned to regulate transcription and perform quality control of both soluble and membrane proteins transiting the NPC.
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24
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Seo HD, Kwon CS, Lee D. The 19S proteasome regulates subtelomere silencing and facultative heterochromatin formation in fission yeast. Curr Genet 2017; 64:741-752. [PMID: 29214404 DOI: 10.1007/s00294-017-0792-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/14/2017] [Accepted: 11/27/2017] [Indexed: 12/27/2022]
Abstract
Accumulating evidence shows that non-proteolytic functions of the proteasome are as crucial as its well-known proteolytic function in regulating cellular activities. In our recent work, we showed that the 19S proteasome mediates the heterochromatin spreading of centromeric heterochromatin in non-proteolytic manner. However, the involvement of the proteasome in other heterochromatin regions remained largely unknown. In the present study, we investigated the non-proteolytic role of the 19S proteasome in subtelomere and facultative heterochromatin regions. Using the non-proteolytic mutant, rpt4-1, we show that the 19S proteasome is involved in regulating subtelomere silencing and facultative heterochromatin formation in fission yeast. In addition to this proteasome-related regulation, we also observed a distinct pathway that regulates subtelomere silencing and facultative heterochromatin formation through the Paf1 complex subunit, Leo1. Our comparison of the two pathways revealed a new group of heterochromatin domains that are regulated exclusively by the proteasome pathway. Taken together, our findings reveal that the proteasome is involved in the global regulation of facultative and constitutive heterochromatin.
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Affiliation(s)
- Hogyu David Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Chang Seob Kwon
- Department of Chemistry and Biology, Korea Science Academy of KAIST, Busan, 47162, South Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea.
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Seo HD, Choi Y, Kim M, Kang K, Urano T, Lee D. The 19S proteasome is directly involved in the regulation of heterochromatin spreading in fission yeast. J Biol Chem 2017; 292:17144-17155. [PMID: 28784663 DOI: 10.1074/jbc.m117.790824] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/17/2017] [Indexed: 01/12/2023] Open
Abstract
Cumulative evidence suggests that non-proteolytic functions of the proteasome are involved in transcriptional regulation, mRNA export, and ubiquitin-dependent histone modification and thereby modulate the intracellular levels of regulatory proteins implicated in controlling key cellular functions. To date, the non-proteolytic roles of the proteasome have been mainly investigated in euchromatin; their effects on heterochromatin are largely unknown. Here, using fission yeast as a model, we randomly mutagenized the subunits of the 19S proteasome subcomplex and sought to uncover a direct role of the proteasome in heterochromatin regulation. We identified a mutant allele, rpt4-1, that disrupts a non-proteolytic function of the proteasome, also known as a non-proteolytic allele. Experiments performed using rpt4-1 cells revealed that the proteasome is involved in the regulation of heterochromatin spreading to prevent its uncontrolled invasion into neighboring euchromatin regions. Intriguingly, the phenotype of the non-proteolytic rpt4-1 mutant resembled that of epe1Δ cells, which lack the Epe1 protein that counteracts heterochromatin spreading. Both mutants exhibited variegated gene-silencing phenotypes across yeast colonies, spreading of heterochromatin, bypassing of the requirement for RNAi in heterochromatin formation at the outer repeat region (otr), and up-regulation of RNA polymerase II. Further analysis revealed Mst2, another factor that antagonizes heterochromatin spreading, may function redundantly with Rpt4. These observations suggest that the 19S proteasome may be involved in modulating the activities of Epe1 and Mst2. In conclusion, our findings indicate that the proteasome appears to have a heterochromatin-regulating function that is independent of its canonical function in proteolysis.
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Affiliation(s)
- Hogyu David Seo
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Yoonjung Choi
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Minhoo Kim
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, Chungnam 31116, South Korea, and
| | - Takeshi Urano
- Department of Biochemistry, Faculty of Medicine, Shimane University, Shimane 690-8504, Izumo, Japan
| | - Daeyoup Lee
- From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea,
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Malod-Dognin N, Pržulj N. Omics Data Complementarity Underlines Functional Cross-Communication in Yeast. J Integr Bioinform 2017; 14:/j/jib.ahead-of-print/jib-2017-0018/jib-2017-0018.xml. [PMID: 28600905 PMCID: PMC6042824 DOI: 10.1515/jib-2017-0018] [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: 03/22/2017] [Accepted: 04/18/2017] [Indexed: 11/26/2022] Open
Abstract
Mapping the complete functional layout of a cell and understanding the cross-talk between different processes are fundamental challenges. They elude us because of the incompleteness and noisiness of molecular data and because of the computational intractability of finding the exact answer. We perform a simple integration of three types of baker’s yeast omics data to elucidate the functional organization and lines of cross-functional communication. We examine protein–protein interaction (PPI), co-expression (COEX) and genetic interaction (GI) data, and explore their relationship with the gold standard of functional organization, the Gene Ontology (GO). We utilize a simple framework that identifies functional cross-communication lines in each of the three data types, in GO, and collectively in the integrated model of the three omics data types; we present each of them in our new Functional Organization Map (FOM) model. We compare the FOMs of the three omics datasets with the FOM of GO and find that GI is in best agreement with GO, followed COEX and PPI. We integrate the three FOMs into a unified FOM and find that it is in better agreement with the FOM of GO than those of any omics dataset alone, demonstrating functional complementarity of different omics data.
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Ahuja JS, Sandhu R, Mainpal R, Lawson C, Henley H, Hunt PA, Yanowitz JL, Börner GV. Control of meiotic pairing and recombination by chromosomally tethered 26S proteasome. Science 2017; 355:408-411. [PMID: 28059715 DOI: 10.1126/science.aaf4778] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 09/12/2016] [Accepted: 12/05/2016] [Indexed: 12/11/2022]
Abstract
During meiosis, paired homologous chromosomes (homologs) become linked via the synaptonemal complex (SC) and crossovers. Crossovers mediate homolog segregation and arise from self-inflicted double-strand breaks (DSBs). Here, we identified a role for the proteasome, the multisubunit protease that degrades proteins in the nucleus and cytoplasm, in homolog juxtaposition and crossing over. Without proteasome function, homologs failed to pair and instead remained associated with nonhomologous chromosomes. Although dispensable for noncrossover formation, a functional proteasome was required for a coordinated transition that entails SC assembly between longitudinally organized chromosome axes and stable strand exchange of crossover-designated DSBs. Notably, proteolytic core and regulatory proteasome particles were recruited to chromosomes by Zip3, the ortholog of mammalian E3 ligase RNF212, and SC protein Zip1 . We conclude that proteasome functions along meiotic chromosomes are evolutionarily conserved.
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Affiliation(s)
- Jasvinder S Ahuja
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University (CSU), Cleveland, OH, USA
| | - Rima Sandhu
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University (CSU), Cleveland, OH, USA
| | - Rana Mainpal
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Crystal Lawson
- School of Molecular Biosciences, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Hanna Henley
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University (CSU), Cleveland, OH, USA
| | - Patricia A Hunt
- School of Molecular Biosciences, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Judith L Yanowitz
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - G Valentin Börner
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University (CSU), Cleveland, OH, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.,Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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28
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Maneix L, Catic A. Touch and go: nuclear proteolysis in the regulation of metabolic genes and cancer. FEBS Lett 2016; 590:908-23. [PMID: 26832397 PMCID: PMC4833644 DOI: 10.1002/1873-3468.12087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/15/2016] [Accepted: 01/26/2016] [Indexed: 01/07/2023]
Abstract
The recruitment of transcription factors to promoters and enhancers is a critical step in gene regulation. Many of these proteins are quickly removed from DNA after they completed their function. Metabolic genes in particular are dynamically regulated and continuously adjusted to cellular requirements. Transcription factors controlling metabolism are therefore under constant surveillance by the ubiquitin–proteasome system, which can degrade DNA‐bound proteins in a site‐specific manner. Several of these metabolic transcription factors are critical to cancer cells, as they promote uncontrolled growth and proliferation. This review highlights recent findings in the emerging field of nuclear proteolysis and outlines novel paradigms for cancer treatment, with an emphasis on multiple myeloma.
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Affiliation(s)
- Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - André Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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Sengupta S, Henry RW. Regulation of the retinoblastoma–E2F pathway by the ubiquitin–proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1289-97. [DOI: 10.1016/j.bbagrm.2015.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 12/16/2022]
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