1
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Hussain MS, Eltaib L, Rana AJ, Maqbool M, Ashique S, Alanazi MN, Khan Y, Agrawal M. Exploiting E3 ligases for lung cancer therapy: The promise of DCAF-PROTACs. Pathol Res Pract 2025; 270:156001. [PMID: 40359818 DOI: 10.1016/j.prp.2025.156001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2025] [Revised: 05/06/2025] [Accepted: 05/06/2025] [Indexed: 05/15/2025]
Abstract
Lung cancer remains the leading cause of cancer-related mortality, underscoring the urgent need for novel therapeutic strategies. One emerging approach in drug development targets oncogenic proteins via the ubiquitin-proteasome system (UPS), specifically through proteolysis-targeting chimeras (PROTACs). Among the various E3 ligase complexes, the CRL4 complex-comprising DDB1 and CUL4-associated factors (DCAFs)-has garnered attention for its roles in cellular homeostasis, DNA repair, and oncogenesis. This review explores the therapeutic potential of DCAF-based PROTACs (DCAF-PROTACs) in lung cancer by focusing on the substrate receptors DCAF13, DCAF15, and DCAF16, which mediate CRL4-dependent ubiquitination. We first discuss the dysregulation of DCAF proteins in lung cancer and then elaborate on their mechanistic role in facilitating target-specific protein degradation via DCAF-E3 ligase complexes. Recent studies show that DCAF-PROTACs selectively degrade oncogenic proteins, addressing treatment resistance and tumor heterogeneity. Notably, DCAF13 promotes lung adenocarcinoma by destabilizing p53, while DCAF15-PROTACs target and degrade RBM39 effectively. Additionally, the development of electrophilic PROTACs targeting DCAF16 presents a promising avenue for degrading nuclear proteins. Despite these advancements, several challenges must be addressed prior to clinical translation, including issues related to drug bioavailability, stability, and emerging resistance mechanisms. This review also explores the potential of combination therapies, particularly with immunotherapy, to enhance tumor specificity and therapeutic efficacy. Ultimately, the deployment of DCAF-PROTACs marks a significant advancement in precision oncology, offering a novel and targeted approach to protein degradation-based cancer treatment.
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Affiliation(s)
- Md Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Prem Nagar, Dehradun, Uttarakhand 248007, India.
| | - Lina Eltaib
- Department of Pharmaceutics, College of Pharmacy, Northern Border University, Rafha, Saudi Arabia
| | - Amita Joshi Rana
- College of Pharmacy, Graphic Era Hill University, Bhimtal, Uttarakhand 263136, India
| | - Mudasir Maqbool
- Department of Pharmacology, Government Medical College Baramulla, Jammu and Kashmir 193103, India
| | - Sumel Ashique
- Department of Pharmaceutical Technology, Bharat Technology, Uluberia, West Bengal 711316, India
| | - Mashael N Alanazi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha, Saudi Arabia
| | - Yumna Khan
- Institute of Biotechnology and Genetic Engineering (Health Division), The University of Agriculture, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Mohit Agrawal
- Department of Pharmacology, School of Medical & Allied Sciences, K.R. Mangalam University, Gurugram 122103, India
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2
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Zhou L, Li K, Hunt AG. Natural variation in the plant polyadenylation complex. FRONTIERS IN PLANT SCIENCE 2024; 14:1303398. [PMID: 38317838 PMCID: PMC10839035 DOI: 10.3389/fpls.2023.1303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Messenger RNA polyadenylation, the process wherein the primary RNA polymerase II transcript is cleaved and a poly(A) tract added, is a key step in the expression of genes in plants. Moreover, it is a point at which gene expression may be regulated by determining the functionality of the mature mRNA. Polyadenylation is mediated by a complex (the polyadenylation complex, or PAC) that consists of between 15 and 20 subunits. While the general functioning of these subunits may be inferred by extending paradigms established in well-developed eukaryotic models, much remains to be learned about the roles of individual subunits in the regulation of polyadenylation in plants. To gain further insight into this, we conducted a survey of variability in the plant PAC. For this, we drew upon a database of naturally-occurring variation in numerous geographic isolates of Arabidopsis thaliana. For a subset of genes encoding PAC subunits, the patterns of variability included the occurrence of premature stop codons in some Arabidopsis accessions. These and other observations lead us to conclude that some genes purported to encode PAC subunits in Arabidopsis are actually pseudogenes, and that others may encode proteins with dispensable functions in the plant. Many subunits of the PAC showed patterns of variability that were consistent with their roles as essential proteins in the cell. Several other PAC subunits exhibit patterns of variability consistent with selection for new or altered function. We propose that these latter subunits participate in regulatory interactions important for differential usage of poly(A) sites.
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Affiliation(s)
| | | | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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3
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Wang M, Li W, Tomimatsu N, Yu CH, Ji JH, Alejo S, Witus SR, Alimbetov D, Fitzgerald O, Wu B, Wang Q, Huang Y, Gan Y, Dong F, Kwon Y, Sareddy GR, Curiel TJ, Habib AA, Hromas R, Dos Santos Passos C, Yao T, Ivanov DN, Brzovic PS, Burma S, Klevit RE, Zhao W. Crucial roles of the BRCA1-BARD1 E3 ubiquitin ligase activity in homology-directed DNA repair. Mol Cell 2023; 83:3679-3691.e8. [PMID: 37797621 PMCID: PMC10591799 DOI: 10.1016/j.molcel.2023.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/08/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
The tumor-suppressor breast cancer 1 (BRCA1) in complex with BRCA1-associated really interesting new gene (RING) domain 1 (BARD1) is a RING-type ubiquitin E3 ligase that modifies nucleosomal histone and other substrates. The importance of BRCA1-BARD1 E3 activity in tumor suppression remains highly controversial, mainly stemming from studying mutant ligase-deficient BRCA1-BARD1 species that we show here still retain significant ligase activity. Using full-length BRCA1-BARD1, we establish robust BRCA1-BARD1-mediated ubiquitylation with specificity, uncover multiple modes of activity modulation, and construct a truly ligase-null variant and a variant specifically impaired in targeting nucleosomal histones. Cells expressing either of these BRCA1-BARD1 separation-of-function alleles are hypersensitive to DNA-damaging agents. Furthermore, we demonstrate that BRCA1-BARD1 ligase is not only required for DNA resection during homology-directed repair (HDR) but also contributes to later stages for HDR completion. Altogether, our findings reveal crucial, previously unrecognized roles of BRCA1-BARD1 ligase activity in genome repair via HDR, settle prior controversies regarding BRCA1-BARD1 ligase functions, and catalyze new efforts to uncover substrates related to tumor suppression.
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Affiliation(s)
- Meiling Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenjing Li
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nozomi Tomimatsu
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Corey H Yu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jae-Hoon Ji
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Salvador Alejo
- Department of Obstetrics & Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Samuel R Witus
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Dauren Alimbetov
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - O'Taveon Fitzgerald
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Bo Wu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Qijing Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yuxin Huang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yaqi Gan
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Felix Dong
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Gangadhara R Sareddy
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Tyler J Curiel
- Geisel School of Medicine at Dartmouth and Department of Medicine, Dartmouth Health, Lebanon, NH 03765, USA
| | - Amyn A Habib
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert Hromas
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Carolina Dos Santos Passos
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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4
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Sfaxi R, Biswas B, Boldina G, Cadix M, Servant N, Chen H, Larson DR, Dutertre M, Robert C, Vagner S. Post-transcriptional polyadenylation site cleavage maintains 3'-end processing upon DNA damage. EMBO J 2023; 42:e112358. [PMID: 36762421 PMCID: PMC10068322 DOI: 10.15252/embj.2022112358] [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: 08/12/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
The recognition of polyadenylation signals (PAS) in eukaryotic pre-mRNAs is usually coupled to transcription termination, occurring while pre-mRNA is chromatin-bound. However, for some pre-mRNAs, this 3'-end processing occurs post-transcriptionally, i.e., through a co-transcriptional cleavage (CoTC) event downstream of the PAS, leading to chromatin release and subsequent PAS cleavage in the nucleoplasm. While DNA-damaging agents trigger the shutdown of co-transcriptional chromatin-associated 3'-end processing, specific compensatory mechanisms exist to ensure efficient 3'-end processing for certain pre-mRNAs, including those that encode proteins involved in the DNA damage response, such as the tumor suppressor p53. We show that cleavage at the p53 polyadenylation site occurs in part post-transcriptionally following a co-transcriptional cleavage event. Cells with an engineered deletion of the p53 CoTC site exhibit impaired p53 3'-end processing, decreased mRNA and protein levels of p53 and its transcriptional target p21, and altered cell cycle progression upon UV-induced DNA damage. Using a transcriptome-wide analysis of PAS cleavage, we identify additional pre-mRNAs whose PAS cleavage is maintained in response to UV irradiation and occurring post-transcriptionally. These findings indicate that CoTC-type cleavage of pre-mRNAs, followed by PAS cleavage in the nucleoplasm, allows certain pre-mRNAs to escape 3'-end processing inhibition in response to UV-induced DNA damage.
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Affiliation(s)
- Rym Sfaxi
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Biswendu Biswas
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Paris, France.,INSERM U981, Gustave Roussy, Gustave Roussy, Villejuif, France.,Université Paris Sud, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Galina Boldina
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mandy Cadix
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Nicolas Servant
- INSERM U900, Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | - Huimin Chen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Martin Dutertre
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Caroline Robert
- INSERM U981, Gustave Roussy, Gustave Roussy, Villejuif, France.,Université Paris Sud, Université Paris-Saclay, Kremlin-Bicêtre, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, Orsay, France.,Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, INSERM U1278, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Paris, France
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5
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Hawsawi YM, Shams A, Theyab A, Abdali WA, Hussien NA, Alatwi HE, Alzahrani OR, Oyouni AAA, Babalghith AO, Alreshidi M. BARD1 mystery: tumor suppressors are cancer susceptibility genes. BMC Cancer 2022; 22:599. [PMID: 35650591 PMCID: PMC9161512 DOI: 10.1186/s12885-022-09567-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/14/2022] [Indexed: 12/24/2022] Open
Abstract
The full-length BRCA1-associated RING domain 1 (BARD1) gene encodes a 777-aa protein. BARD1 displays a dual role in cancer development and progression as it acts as a tumor suppressor and an oncogene. Structurally, BARD1 has homologous domains to BRCA1 that aid their heterodimer interaction to inhibit the progression of different cancers such as breast and ovarian cancers following the BRCA1-dependant pathway. In addition, BARD1 was shown to be involved in other pathways that are involved in tumor suppression (BRCA1-independent pathway) such as the TP53-dependent apoptotic signaling pathway. However, there are abundant BARD1 isoforms exist that are different from the full-length BARD1 due to nonsense and frameshift mutations, or deletions were found to be associated with susceptibility to various cancers including neuroblastoma, lung, breast, and cervical cancers. This article reviews the spectrum of BARD1 full-length genes and its different isoforms and their anticipated associated risk. Additionally, the study also highlights the role of BARD1 as an oncogene in breast cancer patients and its potential uses as a prognostic/diagnostic biomarker and as a therapeutic target for cancer susceptibility testing and treatment.
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Affiliation(s)
- Yousef M Hawsawi
- King Faisal Specialist Hospital and Research Center- Research Center, KFSH&RC, MBC-J04, P.O. Box 40047, Jeddah, 21499, Saudi Arabia. .,College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh, 11533, Saudi Arabia.
| | - Anwar Shams
- Department of Pharmacology, College of Medicine, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Abdulrahman Theyab
- College of Medicine, Al-Faisal University, P.O. Box 50927, Riyadh, 11533, Saudi Arabia.,Department of Pharmacology, College of Medicine, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia.,Department of Laboratory Medicine, Security Forces Hospital, Mecca, Kingdom of Saudi Arabia
| | - Wed A Abdali
- King Faisal Specialist Hospital and Research Center- Research Center, KFSH&RC, MBC-J04, P.O. Box 40047, Jeddah, 21499, Saudi Arabia
| | - Nahed A Hussien
- Department of Zoology, Faculty of Science, Cairo University, Giza, 12613, Egypt.,Department of Biology, College of Science, Taif University, P.O Box 11099, Taif, 21944, Saudi Arabia
| | - Hanan E Alatwi
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia.,Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Othman R Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia.,Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Atif Abdulwahab A Oyouni
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia.,Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Ahmad O Babalghith
- Medical genetics Department, College of Medicine, Umm Alqura University, Makkah, Saudi Arabia
| | - Mousa Alreshidi
- Departement of biology, College of Science, University of Hail, Hail, Saudi Arabia.,Molecular Diagnostic and Personalized Therapeutic Unit, University of Hail, Hail, Saudi Arabia
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6
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Spada S, Luke B, Danckwardt S. The Bidirectional Link Between RNA Cleavage and Polyadenylation and Genome Stability: Recent Insights From a Systematic Screen. Front Genet 2022; 13:854907. [PMID: 35571036 PMCID: PMC9095915 DOI: 10.3389/fgene.2022.854907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The integrity of the genome is governed by multiple processes to ensure optimal survival and to prevent the inheritance of deleterious traits. While significant progress has been made to characterize components involved in the DNA Damage Response (DDR), little is known about the interplay between RNA processing and the maintenance of genome stability. Here, we describe the emerging picture of an intricate bidirectional coupling between RNA processing and genome integrity in an integrative manner. By employing insights from a recent large-scale RNAi screening involving the depletion of more than 170 components that direct (alternative) polyadenylation, we provide evidence of bidirectional crosstalk between co-transcriptional RNA 3′end processing and the DDR in a manner that optimizes genomic integrity. We provide instructive examples illustrating the wiring between the two processes and show how perturbations at one end are either compensated by buffering mechanisms at the other end, or even propel the initial insult and thereby become disease-eliciting as evidenced by various disorders.
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Affiliation(s)
- Stefano Spada
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Mainz, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
- Centre for Healthy Aging (CHA) Mainz, Mainz, Germany
- *Correspondence: Sven Danckwardt,
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7
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Ma H, Cai L, Lin J, Zhou K, Li QQ. Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation. FRONTIERS IN PLANT SCIENCE 2022; 13:866054. [PMID: 35401636 PMCID: PMC8993227 DOI: 10.3389/fpls.2022.866054] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 05/15/2023]
Abstract
Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in Arabidopsis thaliana and its halophytic relative Eutrema salsugineum with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both Arabidopsis and Eutrema, Eutrema possesses fewer APA genes than Arabidopsis (47% vs. 54%). However, the proportion of APA genes was significantly increased in Arabidopsis under salt stress but not in Eutrema. This indicated that Arabidopsis is more sensitive to salt stress and that Eutrema exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3' untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In Arabidopsis, genes that use distal poly(A) sites were enriched in response to salt stress. However, in Eutrema, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in Arabidopsis showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in Eutrema, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in Arabidopsis and Eutrema experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as CIPK21 and LEA4-5. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in Arabidopsis to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.
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Affiliation(s)
- Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
| | - Lingling Cai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Kaiyue Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
- *Correspondence: Qingshun Q. Li,
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8
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Wang M, Rogers CM, Alimbetov D, Zhao W. In Vitro Reconstitution of BRCA1-BARD1/RAD51-Mediated Homologous DNA Pairing. Methods Mol Biol 2022; 2444:207-225. [PMID: 35290640 DOI: 10.1007/978-1-0716-2063-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RAD51-mediated homologous recombination (HR) is a conserved mechanism for the repair of DNA double-strand breaks and the maintenance of DNA replication forks. Several breast and ovarian tumor suppressors, including BRCA1 and BARD1, have been implicated in HR since their discovery in the 1990s. However, a holistic understanding of how they participate in HR has been hampered by the immense challenge of expressing and purifying these large and unstable protein complexes for mechanistic analysis. Recently, we have overcome such a challenge for the BRCA1-BARD1 complex, allowing us to demonstrate its pivotal role in HR via the promotion of RAD51-mediated DNA strand invasion. In this chapter, we describe detailed procedures for the expression and purification of the BRCA1-BARD1 complex and in vitro assays using this tumor suppressor complex to examine its ability to promote RAD51-mediated homologous DNA pairing. This includes two distinct biochemical assays, namely, D-loop formation and synaptic complex assembly. These methods are invaluable for studying the BRCA1-BARD1 complex and its functional interplay with other factors in the HR process.
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Affiliation(s)
- Meiling Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Cody M Rogers
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Dauren Alimbetov
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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9
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Zhu Q, Huang J, Huang H, Li H, Yi P, Kloeber JA, Yuan J, Chen Y, Deng M, Luo K, Gao M, Guo G, Tu X, Yin P, Zhang Y, Su J, Chen J, Lou Z. RNF19A-mediated ubiquitination of BARD1 prevents BRCA1/BARD1-dependent homologous recombination. Nat Commun 2021; 12:6653. [PMID: 34789768 PMCID: PMC8599684 DOI: 10.1038/s41467-021-27048-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
BRCA1-BARD1 heterodimers act in multiple steps during homologous recombination (HR) to ensure the prompt repair of DNA double strand breaks. Dysfunction of the BRCA1 pathway enhances the therapeutic efficiency of poly-(ADP-ribose) polymerase inhibitors (PARPi) in cancers, but the molecular mechanisms underlying this sensitization to PARPi are not fully understood. Here, we show that cancer cell sensitivity to PARPi is promoted by the ring between ring fingers (RBR) protein RNF19A. We demonstrate that RNF19A suppresses HR by ubiquitinating BARD1, which leads to dissociation of BRCA1-BARD1 complex and exposure of a nuclear export sequence in BARD1 that is otherwise masked by BRCA1, resulting in the export of BARD1 to the cytoplasm. We provide evidence that high RNF19A expression in breast cancer compromises HR and increases sensitivity to PARPi. We propose that RNF19A modulates the cancer cell response to PARPi by negatively regulating the BRCA1-BARD1 complex and inhibiting HR-mediated DNA repair.
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Affiliation(s)
- Qian Zhu
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hongyang Huang
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, 999077, China
| | - Huan Li
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Peiqiang Yi
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China
| | - Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yong Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jun Su
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jiayi Chen
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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10
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [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: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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11
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van Breda SG, Mathijs K, Pieters H, Sági‐Kiss V, Kuhnle GG, Georgiadis P, Saccani G, Parolari G, Virgili R, Sinha R, Hemke G, Hung Y, Verbeke W, Masclee AA, Vleugels‐Simon CB, van Bodegraven AA, de Kok TM, the PHYTOME consortium. Replacement of Nitrite in Meat Products by Natural Bioactive Compounds Results in Reduced Exposure to N-Nitroso Compounds: The PHYTOME Project. Mol Nutr Food Res 2021; 65:e2001214. [PMID: 34382747 PMCID: PMC8530897 DOI: 10.1002/mnfr.202001214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/16/2021] [Indexed: 11/07/2022]
Abstract
SCOPE It has been proposed that endogenously form N-nitroso compounds (NOCs) are partly responsible for the link between red meat consumption and colorectal cancer (CRC) risk. As nitrite has been indicated as critical factor in the formation of NOCs, the impact of replacing the additive sodium nitrite (E250) by botanical extracts in the PHYTOME project is evaluated. METHOD AND RESULTS A human dietary intervention study is conducted in which healthy subjects consume 300 g of meat for 2 weeks, in subsequent order: conventional processed red meat, white meat, and processed red meat with standard or reduced levels of nitrite and added phytochemicals. Consumption of red meat products enriched with phytochemicals leads to a significant reduction in the faecal excretion of NOCs, as compared to traditionally processed red meat products. Gene expression changes identify cell proliferation as main affects molecular mechanism. High nitrate levels in drinking water in combination with processed red meat intake further stimulates NOC formation, an effect that could be mitigated by replacement of E250 by natural plant extracts. CONCLUSION These findings suggest that addition of natural extracts to conventionally processed red meat products may help to reduce CRC risk, which is mechanistically support by gene expression analyses.
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Affiliation(s)
- Simone G. van Breda
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - Karen Mathijs
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - Harm‐Jan Pieters
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - Virág Sági‐Kiss
- Department of Food & Nutritional SciencesUniversity of ReadingReadingUK
| | - Gunter G. Kuhnle
- Department of Food & Nutritional SciencesUniversity of ReadingReadingUK
| | - Panagiotis Georgiadis
- National Hellenic Research FoundationInstitute of BiologyMedicinal Chemistry and BiotechnologyAthensGreece
| | - Giovanna Saccani
- SSICA‐Experimental Station for the Food Preserving IndustryParmaItaly
| | - Giovanni Parolari
- SSICA‐Experimental Station for the Food Preserving IndustryParmaItaly
| | - Roberta Virgili
- SSICA‐Experimental Station for the Food Preserving IndustryParmaItaly
| | - Rashmi Sinha
- Division of Cancer Epidemiology & GeneticsNational Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Gert Hemke
- Hemke NutriconsultPrins Clauslaan 70, 5684 GB BestThe Netherlands
| | - Yung Hung
- Department of Agricultural EconomicsGhent UniversityCoupure links 653Gent9000Belgium
| | - Wim Verbeke
- Department of Agricultural EconomicsGhent UniversityCoupure links 653Gent9000Belgium
| | - Ad A. Masclee
- Division of Gastroenterology‐HepatologyDepartment of Internal MedicineMaastricht University Medical CenterMaastrichtThe Netherlands
| | | | | | - Theo M. de Kok
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
| | - the PHYTOME consortium
- Department of ToxicogenomicsGROW‐school for Oncology and Developmental BiologyMaastricht University Medical CenterP.O. Box 616, 6200 MD Maastrichtthe Netherlands
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12
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BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. Nature 2021; 591:665-670. [PMID: 33536619 PMCID: PMC8245199 DOI: 10.1038/s41586-020-03150-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Strong connections exist between R-loops (three-stranded structures harbouring an RNA:DNA hybrid and a displaced single-strand DNA), genome instability and human disease1-5. Indeed, R-loops are favoured in relevant genomic regions as regulators of certain physiological processes through which homeostasis is typically maintained. For example, transcription termination pause sites regulated by R-loops can induce the synthesis of antisense transcripts that enable the formation of local, RNA interference (RNAi)-driven heterochromation6. Pause sites are also protected against endogenous single-stranded DNA breaks by BRCA17. Hypotheses about how DNA repair is enacted at pause sites include a role for RNA, which is emerging as a normal, albeit unexplained, regulator of genome integrity8. Here we report that a species of single-stranded, DNA-damage-associated small RNA (sdRNA) is generated by a BRCA1-RNAi protein complex. sdRNAs promote DNA repair driven by the PALB2-RAD52 complex at transcriptional termination pause sites that form R-loops and are rich in single-stranded DNA breaks. sdRNA repair operates in both quiescent (G0) and proliferating cells. Thus, sdRNA repair can occur in intact tissue and/or stem cells, and may contribute to tumour suppression mediated by BRCA1.
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13
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Minten EV, Kapoor-Vazirani P, Li C, Zhang H, Balakrishnan K, Yu DS. SIRT2 promotes BRCA1-BARD1 heterodimerization through deacetylation. Cell Rep 2021; 34:108921. [PMID: 33789098 PMCID: PMC8108010 DOI: 10.1016/j.celrep.2021.108921] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 01/04/2023] Open
Abstract
The breast cancer type I susceptibility protein (BRCA1) and BRCA1-associated RING domain protein I (BARD1) heterodimer promote genome integrity through pleiotropic functions, including DNA double-strand break (DSB) repair by homologous recombination (HR). BRCA1-BARD1 heterodimerization is required for their mutual stability, HR function, and role in tumor suppression; however, the upstream signaling events governing BRCA1-BARD1 heterodimerization are unclear. Here, we show that SIRT2, a sirtuin deacetylase and breast tumor suppressor, promotes BRCA1-BARD1 heterodimerization through deacetylation. SIRT2 complexes with BRCA1-BARD1 and deacetylates conserved lysines in the BARD1 RING domain, interfacing BRCA1, which promotes BRCA1-BARD1 heterodimerization and consequently BRCA1-BARD1 stability, nuclear retention, and localization to DNA damage sites, thus contributing to efficient HR. Our findings define a mechanism for regulation of BRCA1-BARD1 heterodimerization through SIRT2 deacetylation, elucidating a critical upstream signaling event directing BRCA1-BARD1 heterodimerization, which facilitates HR and tumor suppression, and delineating a role for SIRT2 in directing DSB repair by HR. Minten et al. show that SIRT2, a sirtuin deacetylase and tumor suppressor protein, promotes BRCA1-BARD1 heterodimerization through deacetylation of BARD1 at conserved lysines within its RING domain. These findings elucidate a critical upstream signaling event directing BRCA1-BARD1 heterodimerization, which facilitates HR and tumor suppression.
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Affiliation(s)
- Elizabeth V Minten
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Priya Kapoor-Vazirani
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chunyang Li
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hui Zhang
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kamakshi Balakrishnan
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David S Yu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.
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14
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McDougall LI, Powell RM, Ratajska M, Lynch-Sutherland CF, Hossain SM, Wiggins GAR, Harazin-Lechowska A, Cybulska-Stopa B, Motwani J, Macaulay EC, Reid G, Walker LC, Ryś J, Eccles MR. Differential Expression of BARD1 Isoforms in Melanoma. Genes (Basel) 2021; 12:320. [PMID: 33672422 PMCID: PMC7927127 DOI: 10.3390/genes12020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 12/11/2022] Open
Abstract
Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified BARD1 splice variants in melanoma are warranted.
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Affiliation(s)
- Lorissa I. McDougall
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Ryan M. Powell
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Magdalena Ratajska
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
- Department of Biology and Medical Genetics, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Chi F. Lynch-Sutherland
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Sultana Mehbuba Hossain
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - George A. R. Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand; (G.A.R.W.); (L.C.W.)
| | - Agnieszka Harazin-Lechowska
- Department of Tumour Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland; (A.H.-L.); (J.R.)
| | - Bożena Cybulska-Stopa
- Department of Clinical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland;
| | - Jyoti Motwani
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Erin C. Macaulay
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Glen Reid
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
| | - Logan C. Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand; (G.A.R.W.); (L.C.W.)
| | - Janusz Ryś
- Department of Tumour Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland; (A.H.-L.); (J.R.)
| | - Michael R. Eccles
- Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand; (L.I.M.); (R.M.P.); (M.R.); (C.F.L.-S.); (S.M.H.); (J.M.); (E.C.M.); (G.R.)
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand
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15
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Śniadecki M, Brzeziński M, Darecka K, Klasa-Mazurkiewicz D, Poniewierza P, Krzeszowiec M, Kmieć N, Wydra D. BARD1 and Breast Cancer: The Possibility of Creating Screening Tests and New Preventive and Therapeutic Pathways for Predisposed Women. Genes (Basel) 2020; 11:genes11111251. [PMID: 33114377 PMCID: PMC7693009 DOI: 10.3390/genes11111251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 10/10/2020] [Indexed: 02/07/2023] Open
Abstract
Current oncological developments are based on improved understanding of genetics, and especially the discovery of genes whose alterations affect cell functions with consequences for the whole body. Our work is focused on the one of these genes, BRCA1-associated RING domain protein 1 (BARD1), and its oncogenic role in breast cancer. Most importantly, the study points to new avenues in the treatment and prevention of the most frequent female cancer based on BARD1 research. The BARD1 and BRCA1 (BReast CAncer type 1) proteins have similar structures and functions, and they combine to form the new molecule BARD1-BRCA1 heterodimer. The BARD1-BRCA1 complex is involved in genetic stabilization at the cellular level. It allows to mark abnormal DNA fragments by attaching ubiquitin to them. In addition, it blocks (by ubiquitination of RNA polymerase II) the transcription of damaged DNA. Ubiquitination, as well as stabilizing chromatin, or regulating the number of centrosomes, confirms the protective cooperation of BARD1 and BRCA1 in the stabilization of the genome. The overexpression of the oncogenic isoforms BARD1β and BARD1δ permit cancer development. The introduction of routine tests, for instance, to identify the presence of the BARD1β isoform, would make it possible to detect patients at high risk of developing cancer. On the other hand, introducing BARD1δ isoform blocking therapy, which would reduce estrogen sensitivity, may be a new line of cancer therapy with potential to modulate responses to existing treatments. It is possible that the BARD 1 gene offers new hope for improving breast cancer therapy.
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Affiliation(s)
- Marcin Śniadecki
- Department of Gynecology, Gynecologic Endocrinology and Gynecologic Oncology, Medical University of Gdańsk, Prof. Marian Smoluchowski Str. No. 17, 80-214 Gdańsk, Poland; (M.B.); (D.K.-M.); (M.K.); (D.W.)
- Correspondence: ; Tel.: +48-501-337-941
| | - Michał Brzeziński
- Department of Gynecology, Gynecologic Endocrinology and Gynecologic Oncology, Medical University of Gdańsk, Prof. Marian Smoluchowski Str. No. 17, 80-214 Gdańsk, Poland; (M.B.); (D.K.-M.); (M.K.); (D.W.)
| | - Katarzyna Darecka
- St. Adalbert’s Hospital, Department of Gynecology and Obstetrics, St. Jean Paul 2nd No. 50 Avenue, 80-462 Gdańsk, Poland;
| | - Dagmara Klasa-Mazurkiewicz
- Department of Gynecology, Gynecologic Endocrinology and Gynecologic Oncology, Medical University of Gdańsk, Prof. Marian Smoluchowski Str. No. 17, 80-214 Gdańsk, Poland; (M.B.); (D.K.-M.); (M.K.); (D.W.)
| | - Patryk Poniewierza
- Warsaw College of Engineering and Health, The Battle of Warsaw 1920. Str. No. 18, 02-366 Warsaw, Poland;
| | - Marta Krzeszowiec
- Department of Gynecology, Gynecologic Endocrinology and Gynecologic Oncology, Medical University of Gdańsk, Prof. Marian Smoluchowski Str. No. 17, 80-214 Gdańsk, Poland; (M.B.); (D.K.-M.); (M.K.); (D.W.)
| | - Natalia Kmieć
- Department of Oncology and Radiotherapy, University Clinical Center in Gdańsk, Prof. Marian Smoluchowski Str. No. 17, 80-214 Gdańsk, Poland;
| | - Dariusz Wydra
- Department of Gynecology, Gynecologic Endocrinology and Gynecologic Oncology, Medical University of Gdańsk, Prof. Marian Smoluchowski Str. No. 17, 80-214 Gdańsk, Poland; (M.B.); (D.K.-M.); (M.K.); (D.W.)
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16
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The Effects of Genetic and Epigenetic Alterations of BARD1 on the Development of Non-Breast and Non-Gynecological Cancers. Genes (Basel) 2020; 11:genes11070829. [PMID: 32708251 PMCID: PMC7396976 DOI: 10.3390/genes11070829] [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: 06/28/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023] Open
Abstract
Breast Cancer 1 (BRCA1) gene is a well-characterized tumor suppressor gene, mutations of which are primarily found in women with breast and ovarian cancers. BRCA1-associated RING domain 1 (BARD1) gene has also been identified as an important tumor suppressor gene in breast, ovarian, and uterine cancers. Underscoring the functional significance of the BRCA1 and BARD1 interactions, prevalent mutations in the BRCA1 gene are found in its RING domain, through which it binds the RING domain of BARD1. BARD1-BRCA1 heterodimer plays a crucial role in a variety of DNA damage response (DDR) pathways, including DNA damage checkpoint and homologous recombination (HR). However, many mutations in both BARD1 and BRCA1 also exist in other domains that significantly affect their biological functions. Intriguingly, recent genome-wide studies have identified various single nucleotide polymorphisms (SNPs), genetic alterations, and epigenetic modifications in or near the BARD1 gene that manifested profound effects on tumorigenesis in a variety of non-breast and non-gynecological cancers. In this review, we will briefly discuss the molecular functions of BARD1, including its BRCA1-dependent as well as BRCA1-independent functions. We will then focus on evaluating the common BARD1 related SNPs as well as genetic and epigenetic changes that occur in the non-BRCA1-dominant cancers, including neuroblastoma, lung, and gastrointestinal cancers. Furthermore, the pro- and anti-tumorigenic functions of different SNPs and BARD1 variants will also be discussed.
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17
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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18
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Yang W, Hsu PL, Yang F, Song JE, Varani G. Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals. Nucleic Acids Res 2019; 46:493-503. [PMID: 29186539 PMCID: PMC5778602 DOI: 10.1093/nar/gkx1177] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/13/2017] [Indexed: 01/18/2023] Open
Abstract
Cleavage stimulation factor (CstF) is a highly conserved protein complex composed of three subunits that recognizes G/U-rich sequences downstream of the polyadenylation signal of eukaryotic mRNAs. While CstF has been identified over 25 years ago, the architecture and contribution of each subunit to RNA recognition have not been fully understood. In this study, we provide a structural basis for the recruitment of CstF-50 to CstF via interaction with CstF-77 and establish that the hexameric assembly of CstF creates a high affinity platform to target various G/U-rich sequences. We further demonstrate that CstF-77 boosts the affinity of the CstF-64 RRM to the RNA targets and CstF-50 fine tunes the ability of the complex to recognize G/U sequences of certain lengths and content.
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Affiliation(s)
- Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Peter L Hsu
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Jae-Eun Song
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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19
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Fernandes VC, Golubeva VA, Di Pietro G, Shields C, Amankwah K, Nepomuceno TC, de Gregoriis G, Abreu RBV, Harro C, Gomes TT, Silva RF, Suarez-Kurtz G, Couch FJ, Iversen ES, Monteiro ANA, Carvalho MA. Impact of amino acid substitutions at secondary structures in the BRCT domains of the tumor suppressor BRCA1: Implications for clinical annotation. J Biol Chem 2019; 294:5980-5992. [PMID: 30765603 DOI: 10.1074/jbc.ra118.005274] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/06/2019] [Indexed: 01/07/2023] Open
Abstract
Genetic testing for BRCA1, a DNA repair protein, can identify carriers of pathogenic variants associated with a substantially increased risk for breast and ovarian cancers. However, an association with increased risk is unclear for a large fraction of BRCA1 variants present in the human population. Most of these variants of uncertain clinical significance lead to amino acid changes in the BRCA1 protein. Functional assays are valuable tools to assess the potential pathogenicity of these variants. Here, we systematically probed the effects of substitutions in the C terminus of BRCA1: the N- and C-terminal borders of its tandem BRCT domain, the BRCT-[N-C] linker region, and the α1 and α'1 helices in BRCT-[N] and -[C]. Using a validated transcriptional assay based on a fusion of the GAL4 DNA-binding domain to the BRCA1 C terminus (amino acids 1396-1863), we assessed the functional impact of 99 missense variants of BRCA1. We include the data obtained for these 99 missense variants in a joint analysis to generate the likelihood of pathogenicity for 347 missense variants in BRCA1 using VarCall, a Bayesian integrative statistical model. The results from this analysis increase our understanding of BRCA1 regions less tolerant to changes, identify functional borders of structural domains, and predict the likelihood of pathogenicity for 98% of all BRCA1 missense variants in this region recorded in the population. This knowledge will be critical for improving risk assessment and clinical treatment of carriers of BRCA1 variants.
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Affiliation(s)
- Vanessa C Fernandes
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Volha A Golubeva
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliano Di Pietro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Universidade Federal de Sergipe, Campus São Cristóvão, Brazil 49100-000
| | - Cara Shields
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Kwabena Amankwah
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Thales C Nepomuceno
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050; the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliana de Gregoriis
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Renata B V Abreu
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Carly Harro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Department of Cell Biology, Microbiology, College of Arts and Sciences, University of South Florida Cancer Biology Ph.D. Program, Tampa, Florida 33612
| | - Thiago T Gomes
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Ricceli F Silva
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Guilherme Suarez-Kurtz
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Fergus J Couch
- the Department of Laboratory Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Edwin S Iversen
- the Department of Statistics, Duke University, Durham, North Carolina 27710
| | - Alvaro N A Monteiro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612.
| | - Marcelo A Carvalho
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050.
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20
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Pilyugin M, André PA, Ratajska M, Kuzniacka A, Limon J, Tournier BB, Colas J, Laurent G, Irminger-Finger I. Antagonizing functions of BARD1 and its alternatively spliced variant BARD1δ in telomere stability. Oncotarget 2018; 8:9339-9353. [PMID: 28030839 PMCID: PMC5354735 DOI: 10.18632/oncotarget.14068] [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] [Received: 10/20/2016] [Accepted: 12/15/2016] [Indexed: 11/25/2022] Open
Abstract
Previous reports have shown that expression of BARD1δ, a deletion-bearing isoform of BARD1, correlates with tumor aggressiveness and progression. We show that expression of BARD1δ induces cell cycle arrest in vitro and in vivo in non-malignant cells. We investigated the mechanism that leads to proliferation arrest and found that BARD1δ overexpression induced mitotic arrest with chromosome and telomere aberrations in cell cultures, in transgenic mice, and in cells from human breast and ovarian cancer patients with BARD1 mutations. BARD1δ binds more efficiently than BARD1 to telomere binding proteins and causes their depletion from telomeres, leading to telomere and chromosomal instability. While this induces cell cycle arrest, cancer cells lacking G2/M checkpoint controls might continue to proliferate despite the BARD1δ-induced chromosomal instability. These features of BARD1δ may make it a genome permutator and a driver of continuous uncontrolled proliferation of cancer cells.
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Affiliation(s)
- Maxim Pilyugin
- Department of Gynecology and Obstetrics Geneva University Hospitals, Geneva, Switzerland
| | - Pierre-Alain André
- Department of Gynecology and Obstetrics Geneva University Hospitals, Geneva, Switzerland
| | - Magdalena Ratajska
- Department of Biology and Genetics, Medical University of Gdansk, Poland.,Centre for Cell Therapy and Regenerative Medicine, University of Western Australia and Institute of Respiratory Health, Nedlands, Australia
| | - Alina Kuzniacka
- Department of Biology and Genetics, Medical University of Gdansk, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, Poland
| | - Benjamin B Tournier
- Department of Neuropsychiatry, Vulnerability Biomarkers Unit, University Hospital of Geneva, Geneva, Switzerland
| | - Julien Colas
- Department of Gynecology and Obstetrics Geneva University Hospitals, Geneva, Switzerland
| | - Geoff Laurent
- Centre for Cell Therapy and Regenerative Medicine, University of Western Australia and Institute of Respiratory Health, Nedlands, Australia
| | - Irmgard Irminger-Finger
- Department of Gynecology and Obstetrics Geneva University Hospitals, Geneva, Switzerland.,Centre for Cell Therapy and Regenerative Medicine, University of Western Australia and Institute of Respiratory Health, Nedlands, Australia.,Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
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21
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mRNA Processing Factor CstF-50 and Ubiquitin Escort Factor p97 Are BRCA1/BARD1 Cofactors Involved in Chromatin Remodeling during the DNA Damage Response. Mol Cell Biol 2018; 38:MCB.00364-17. [PMID: 29180510 PMCID: PMC5789026 DOI: 10.1128/mcb.00364-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/14/2017] [Indexed: 02/08/2023] Open
Abstract
The cellular response to DNA damage is an intricate mechanism that involves the interplay among several pathways. In this study, we provide evidence of the roles of the polyadenylation factor cleavage stimulation factor 50 (CstF-50) and the ubiquitin (Ub) escort factor p97 as cofactors of BRCA1/BARD1 E3 Ub ligase, facilitating chromatin remodeling during the DNA damage response (DDR). CstF-50 and p97 formed complexes with BRCA1/BARD1, Ub, and some BRCA1/BARD1 substrates, such as RNA polymerase (RNAP) II and histones. Furthermore, CstF-50 and p97 had an additive effect on the activation of the ubiquitination of these BRCA1/BARD1 substrates during DDR. Importantly, as a result of these functional interactions, BRCA1/BARD1/CstF-50/p97 had a specific effect on the chromatin structure of genes that were differentially expressed. This study provides new insights into the roles of RNA processing, BRCA1/BARD1, the Ub pathway, and chromatin structure during DDR.
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22
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Zhao W, Steinfeld JB, Liang F, Chen X, Maranon DG, Ma CJ, Kwon Y, Rao T, Wang W, Chen S, Song X, Deng Y, Jimenez-Sainz J, Lu L, Jensen RB, Xiong Y, Kupfer GM, Wiese C, Greene EC, Sung P. BRCA1-BARD1 promotes RAD51-mediated homologous DNA pairing. Nature 2017; 550:360-365. [PMID: 28976962 PMCID: PMC5800781 DOI: 10.1038/nature24060] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/08/2017] [Indexed: 12/18/2022]
Abstract
The tumour suppressor complex BRCA1-BARD1 functions in the repair of DNA double-stranded breaks by homologous recombination. During this process, BRCA1-BARD1 facilitates the nucleolytic resection of DNA ends to generate a single-stranded template for the recruitment of another tumour suppressor complex, BRCA2-PALB2, and the recombinase RAD51. Here, by examining purified wild-type and mutant BRCA1-BARD1, we show that both BRCA1 and BARD1 bind DNA and interact with RAD51, and that BRCA1-BARD1 enhances the recombinase activity of RAD51. Mechanistically, BRCA1-BARD1 promotes the assembly of the synaptic complex, an essential intermediate in RAD51-mediated DNA joint formation. We provide evidence that BRCA1 and BARD1 are indispensable for RAD51 stimulation. Notably, BRCA1-BARD1 mutants with weakened RAD51 interactions show compromised DNA joint formation and impaired mediation of homologous recombination and DNA repair in cells. Our results identify a late role of BRCA1-BARD1 in homologous recombination, an attribute of the tumour suppressor complex that could be targeted in cancer therapy.
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Affiliation(s)
- Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Justin B. Steinfeld
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Fengshan Liang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
- Section of Hematology-Oncology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaoyong Chen
- Section of Hematology-Oncology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - David G. Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Chu Jian Ma
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Timsi Rao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sheng Chen
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xuemei Song
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Yanhong Deng
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Judit Jimenez-Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lucy Lu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Gary M. Kupfer
- Section of Hematology-Oncology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Eric C. Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
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23
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Choudhary RK, Siddiqui MQ, Thapa PS, Gadewal N, Nachimuthu SK, Varma AK. Structural basis to stabilize the domain motion of BARD1-ARD BRCT by CstF50. Sci Rep 2017. [PMID: 28634376 PMCID: PMC5478621 DOI: 10.1038/s41598-017-03816-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BRCA1 associated ring domain protein 1(BARD1) is a tumor suppressor protein having a wide role in cellular processes like cell-cycle checkpoint, DNA damage repair and maintenance of genomic integrity. Germ-line mutation Gln 564 His discovered in linker region of BARD1 leads to loss of binding to Cleavage stimulating factor (CstF50), which in turn instigates the premature mRNA transcript formation and apoptosis. We have studied the dynamics of ARD domain present in the BARD1 wild-type and mutant protein in association with CstF50 using biophysical, biochemical and molecular dynamics simulations. It has been observed that the ARD domain is relatively more flexible than the BRCT domain of BARD1. Further relative orientations of both the ARD and BRCT domains varies due to the highly flexible nature of the connecting linker region present between the domains. It has been observed that mutant ARD domain is more dynamic in nature compared to wild-type protein. Molecular docking studies between BARD1 Gln 564 His mutant and CstF50 shows the loss of interactions. Furthermore, domain motion of ARD present in BARD1 was stabilized when complexed with CstF50.
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Affiliation(s)
- Rajan Kumar Choudhary
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410 210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India
| | - Mohd Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410 210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India
| | - Pankaj S Thapa
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410 210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410 210, India.,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India
| | - Senthil Kumar Nachimuthu
- Department of Biotechnology, Mizoram University (A Central University) Aizawl, 796 004, Mizoram, India
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410 210, India. .,Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400 094, India.
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24
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Newman M, Sfaxi R, Saha A, Monchaud D, Teulade-Fichou MP, Vagner S. The G-Quadruplex-Specific RNA Helicase DHX36 Regulates p53 Pre-mRNA 3'-End Processing Following UV-Induced DNA Damage. J Mol Biol 2016; 429:3121-3131. [PMID: 27940037 DOI: 10.1016/j.jmb.2016.11.033] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/26/2016] [Accepted: 11/30/2016] [Indexed: 12/17/2022]
Abstract
Pre-mRNA 3'-end processing, the process through which almost all eukaryotic mRNAs acquire a poly(A) tail is generally inhibited during the cellular DNA damage response leading to a profound impact on the level of protein expression since unprocessed transcripts at the 3'-end will be degraded or unable to be transported to the cytoplasm. However, a compensatory mechanism involving the binding of the hnRNP H/F family of RNA binding proteins to an RNA G-quadruplex (G4) structure located in the vicinity of a polyadenylation site has previously been described to allow the transcript encoding the p53 tumour suppressor protein to be properly processed during DNA damage and to provide the cells with a way to react to DNA damage. Here we report that the DEAH (Asp-Glu-Ala-His) box RNA helicase DHX36/RHAU/G4R1, which specifically binds to and resolves parallel-stranded G4, is necessary to maintain p53 pre-mRNA 3'-end processing following UV-induced DNA damage. DHX36 binds to the p53 RNA G4, while mutation of the G4 impairs the ability of DHX36 to maintain pre-mRNA 3'-end processing. Stabilization of the p53 RNA G4 with two different G4 ligands (PNADOTASQ and PhenDC3), which is expected from previous studies to prevent DHX36 from binding and unwinding G4s, also impairs p53 pre-mRNA 3'-end processing following UV. Our work identifies DHX36 as a new actor in the compensatory mechanisms that are in place to ensure that the mRNAs encoding p53 are still processed following UV.
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Affiliation(s)
- Michelle Newman
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France
| | - Rym Sfaxi
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France
| | - Abhijit Saha
- Institut Curie, PSL Research University, CNRS UMR9187-INSERM U1196, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, UMR9187-INSERM U1196, F-91405 Orsay, France
| | - David Monchaud
- Institute of Molecular Chemistry, University of Dijon, ICMUB CNRS UMR6302, F-21078 Dijon, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, CNRS UMR9187-INSERM U1196, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, UMR9187-INSERM U1196, F-91405 Orsay, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR3348, F-91405 Orsay, France; Université Paris Sud, Université Paris-Saclay, CNRS UMR3348, F-91405 Orsay, France; Equipe Labellisée Ligue Contre le Cancer, F-91405 Orsay, France.
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25
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Fontana GA, Rigamonti A, Lenzken SC, Filosa G, Alvarez R, Calogero R, Bianchi ME, Barabino SML. Oxidative stress controls the choice of alternative last exons via a Brahma-BRCA1-CstF pathway. Nucleic Acids Res 2016; 45:902-914. [PMID: 27591253 PMCID: PMC5314785 DOI: 10.1093/nar/gkw780] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 01/08/2023] Open
Abstract
Alternative splicing of terminal exons increases transcript and protein diversity. How physiological and pathological stimuli regulate the choice between alternative terminal exons is, however, largely unknown. Here, we show that Brahma (BRM), the ATPase subunit of the hSWI/SNF chromatin-remodeling complex interacts with BRCA1/BARD1, which ubiquitinates the 50 kDa subunit of the 3′ end processing factor CstF. This results in the inhibition of transcript cleavage at the proximal poly(A) site and a shift towards inclusion of the distal terminal exon. Upon oxidative stress, BRM is depleted, cleavage inhibition is released, and inclusion of the proximal last exon is favoored. Our findings elucidate a novel regulatory mechanism, distinct from the modulation of transcription elongation by BRM that controls alternative splicing of internal exons.
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Affiliation(s)
- Gabriele A Fontana
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Aurora Rigamonti
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Silvia C Lenzken
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Giuseppe Filosa
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Reinaldo Alvarez
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Raffaele Calogero
- Department of Biotechnology and Health Sciences, University of Torino, Via Nizza 52, I-10126 Torino, Italy
| | - Marco E Bianchi
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute and University, Via Olgettina 60, 20132 Milan, Italy
| | - Silvia M L Barabino
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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26
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Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov 2016; 2:16013. [PMID: 27462460 PMCID: PMC4906801 DOI: 10.1038/celldisc.2016.13] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage response and cancer. Moreover, intronic alternative cleavage and polyadenylation site activation during DNA damage response correlates with a decrease in U1 snRNA levels, and is reversible by U1 snRNA overexpression. Importantly, U1 snRNA overexpression mitigates ultraviolet-induced apoptosis. Together, these data reveal a significant gene regulatory scheme in DNA damage response where U1 snRNA impacts gene expression via the U1-alternative cleavage and polyadenylation axis.
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27
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Ogorodnikov A, Kargapolova Y, Danckwardt S. Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end. Pflugers Arch 2016; 468:993-1012. [PMID: 27220521 PMCID: PMC4893057 DOI: 10.1007/s00424-016-1828-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023]
Abstract
The human transcriptome is highly dynamic, with each cell type, tissue, and organ system expressing an ensemble of transcript isoforms that give rise to considerable diversity. Apart from alternative splicing affecting the "body" of the transcripts, extensive transcriptome diversification occurs at the 3' end. Transcripts differing at the 3' end can have profound physiological effects by encoding proteins with distinct functions or regulatory properties or by affecting the mRNA fate via the inclusion or exclusion of regulatory elements (such as miRNA or protein binding sites). Importantly, the dynamic regulation at the 3' end is associated with various (patho)physiological processes, including the immune regulation but also tumorigenesis. Here, we recapitulate the mechanisms of constitutive mRNA 3' end processing and review the current understanding of the dynamically regulated diversity at the transcriptome 3' end. We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.
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Affiliation(s)
- Anton Ogorodnikov
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Yulia Kargapolova
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Langenbeckstr 1, 55131, Mainz, Germany.
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28
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Vohhodina J, Harkin DP, Savage KI. Dual roles of DNA repair enzymes in RNA biology/post-transcriptional control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:604-19. [PMID: 27126972 DOI: 10.1002/wrna.1353] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022]
Abstract
Despite consistent research into the molecular principles of the DNA damage repair pathway for almost two decades, it has only recently been found that RNA metabolism is very tightly related to this pathway, and the two ancient biochemical mechanisms act in alliance to maintain cellular genomic integrity. The close links between these pathways are well exemplified by examining the base excision repair pathway, which is now well known for dual roles of many of its members in DNA repair and RNA surveillance, including APE1, SMUG1, and PARP1. With additional links between these pathways steadily emerging, this review aims to provide a summary of the emerging roles for DNA repair proteins in the post-transcriptional regulation of RNAs. WIREs RNA 2016, 7:604-619. doi: 10.1002/wrna.1353 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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29
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New concepts on BARD1: Regulator of BRCA pathways and beyond. Int J Biochem Cell Biol 2016; 72:1-17. [DOI: 10.1016/j.biocel.2015.12.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/09/2023]
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30
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Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G, Proudfoot NJ, Livingston DM. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol Cell 2015; 57:636-647. [PMID: 25699710 PMCID: PMC4351672 DOI: 10.1016/j.molcel.2015.01.011] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/21/2014] [Accepted: 01/05/2015] [Indexed: 11/07/2022]
Abstract
The mechanisms contributing to transcription-associated genomic instability are both complex and incompletely understood. Although R-loops are normal transcriptional intermediates, they are also associated with genomic instability. Here, we show that BRCA1 is recruited to R-loops that form normally over a subset of transcription termination regions. There it mediates the recruitment of a specific, physiological binding partner, senataxin (SETX). Disruption of this complex led to R-loop-driven DNA damage at those loci as reflected by adjacent γ-H2AX accumulation and ssDNA breaks within the untranscribed strand of relevant R-loop structures. Genome-wide analysis revealed widespread BRCA1 binding enrichment at R-loop-rich termination regions (TRs) of actively transcribed genes. Strikingly, within some of these genes in BRCA1 null breast tumors, there are specific insertion/deletion mutations located close to R-loop-mediated BRCA1 binding sites within TRs. Thus, BRCA1/SETX complexes support a DNA repair mechanism that addresses R-loop-based DNA damage at transcriptional pause sites. Endogenous BRCA1 and senataxin (SETX) interact in a BRCA1-driven process BRCA1/SETX complexes are recruited to R-loop-associated termination regions (TRs) BRCA1/SETX complexes suppress transcriptional DNA damage arising at nearby R-loops BRCA1 breast cancers reveal indel mutations near BRCA1 TR binding regions
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Affiliation(s)
- Elodie Hatchi
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| | | | - Steffen Ventz
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Angela Yen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT, Cambridge, MA 02139, USA
| | | | - Stoil Dimitrov
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Shailja Pathania
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Kristine M McKinney
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Matthew L Eaton
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT, Cambridge, MA 02139, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT, Cambridge, MA 02139, USA
| | - Sarah J Hill
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Giovanni Parmigiani
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | | | - David M Livingston
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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31
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Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev 2014; 28:1957-75. [PMID: 25184681 PMCID: PMC4197947 DOI: 10.1101/gad.241620.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BRCA1 is a breast and ovarian tumor suppressor. Given its numerous incompletely understood functions and the possibility that more exist, we performed complementary systematic screens in search of new BRCA1 protein-interacting partners. New BRCA1 functions and/or a better understanding of existing ones were sought. Among the new interacting proteins identified, genetic interactions were detected between BRCA1 and four of the interactors: TONSL, SETX, TCEANC, and TCEA2. Genetic interactions were also detected between BRCA1 and certain interactors of TONSL, including both members of the FACT complex. From these results, a new BRCA1 function in the response to transcription-associated DNA damage was detected. Specifically, new roles for BRCA1 in the restart of transcription after UV damage and in preventing or repairing damage caused by stabilized R loops were identified. These roles are likely carried out together with some of the newly identified interactors. This new function may be important in BRCA1 tumor suppression, since the expression of several interactors, including some of the above-noted transcription proteins, is repeatedly aberrant in both breast and ovarian cancers.
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Affiliation(s)
- Sarah J Hill
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas Rolland
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Guillaume Adelmant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Xianfang Xia
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Matthew S Owen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Amélie Dricot
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Travis I Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; The Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Nidhi Sahni
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Yves Jacob
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, F-75015 Paris, France; UMR3569, Centre National de la Recherche Scientifique, F-75015 Paris, France; Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, F-75015 Paris, France
| | - Tong Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Kristine M McKinney
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Allison P Clark
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shengdar Q Tsai
- Molecular Pathology Unit, Center for Computational and Integrative Biology, Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; The Broad Institute, Cambridge, Massachusetts 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Marc Vidal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Suzanne Gaudet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David E Hill
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David M Livingston
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
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Di Giammartino DC, Manley JL. New links between mRNA polyadenylation and diverse nuclear pathways. Mol Cells 2014; 37:644-9. [PMID: 25081038 PMCID: PMC4179132 DOI: 10.14348/molcells.2014.0177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 06/28/2014] [Indexed: 11/27/2022] Open
Abstract
The 3' ends of most eukaryotic messenger RNAs must undergo a maturation step that includes an endonuc-leolytic cleavage followed by addition of a polyadenylate tail. While this reaction is catalyzed by the action of only two enzymes it is supported by an unexpectedly large number of proteins. This complexity reflects the necessity of coordinating this process with other nuclear events, and growing evidence indicates that even more factors than previously thought are necessary to connect 3' processing to additional cellular pathways. In this review we summarize the current understanding of the molecular machinery involved in this step of mRNA maturation, focusing on new core and auxiliary proteins that connect polyadenylation to splicing, DNA damage, transcription and cancer.
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Affiliation(s)
| | - James L Manley
- Columbia University, Department of Biological Sciences, New York NY, 10027, USA
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Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery. Mol Cell Biol 2014; 34:1894-910. [PMID: 24591651 DOI: 10.1128/mcb.00084-14] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Processing of mRNA precursors (pre-mRNAs) by polyadenylation is an essential step in gene expression. Polyadenylation consists of two steps, cleavage and poly(A) synthesis, and requires multiple cis elements in the pre-mRNA and a megadalton protein complex bearing the two essential enzymatic activities. While genetic and biochemical studies remain the major approaches in characterizing these factors, structural biology has emerged during the past decade to help understand the molecular assembly and mechanistic details of the process. With structural information about more proteins and higher-order complexes becoming available, we are coming closer to obtaining a structural blueprint of the polyadenylation machinery that explains both how this complex functions and how it is regulated and connected to other cellular processes.
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34
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A recently evolved class of alternative 3'-terminal exons involved in cell cycle regulation by topoisomerase inhibitors. Nat Commun 2014; 5:3395. [PMID: 24577238 DOI: 10.1038/ncomms4395] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 02/06/2014] [Indexed: 12/13/2022] Open
Abstract
Alternative 3'-terminal exons, which use intronic polyadenylation sites, are generally less conserved and expressed at lower levels than the last exon of genes. Here we discover a class of human genes, in which the last exon appeared recently during evolution, and the major gene product uses an alternative 3'-terminal exon corresponding to the ancestral last exon of the gene. This novel class of alternative 3'-terminal exons are downregulated on a large scale by doxorubicin, a cytostatic drug targeting topoisomerase II, and play a role in cell cycle regulation, including centromere-kinetochore assembly. The RNA-binding protein HuR/ELAVL1 is a major regulator of this specific set of alternative 3'-terminal exons. HuR binding to the alternative 3'-terminal exon in the pre-messenger RNA promotes its splicing, and is reduced by topoisomerase inhibitors. These findings provide new insights into the evolution, function and molecular regulation of alternative 3'-terminal exons.
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Abstract
SIGNIFICANCE Production of proteins requires the synthesis, maturation, and export of mRNAs before their translation in the cytoplasm. Endogenous and exogenous sources of DNA damage pose a challenge to the co-ordinated regulation of gene expression, because the integrity of the DNA template can be compromised by DNA lesions. Cells recognize and respond to this DNA damage through a variety of DNA damage responses (DDRs). Failure to deal with DNA damage appropriately can lead to genomic instability and cancer. RECENT ADVANCES The p53 tumor suppressor plays a dominant role in DDR-dependent changes in gene expression, but this transcription factor is not solely responsible for all changes. Recent evidence indicates that RNA metabolism is integral to DDRs as well. In particular, post-transcriptional processes are emerging as important contributors to these complex responses. CRITICAL ISSUES Transcriptional, post-transcriptional, and translational regulation of gene expression is subject to changes in response to DNA damage. How these processes are intertwined in the unfolding of DDR is not fully understood. FUTURE DIRECTIONS Many complex regulatory responses combine to determine cell fate after DNA damage. Understanding how transcriptional, post-transcriptional, and translational processes interdigitate to create a web of regulatory interactions will be one of the key challenges to fully understand DDRs.
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Affiliation(s)
- Bruce C McKay
- Department of Biology, Institute of Biochemistry, Carleton University , Ottawa, Canada
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36
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Rulten SL, Rotheray A, Green RL, Grundy GJ, Moore DAQ, Gómez-Herreros F, Hafezparast M, Caldecott KW. PARP-1 dependent recruitment of the amyotrophic lateral sclerosis-associated protein FUS/TLS to sites of oxidative DNA damage. Nucleic Acids Res 2013; 42:307-14. [PMID: 24049082 PMCID: PMC3874156 DOI: 10.1093/nar/gkt835] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is associated with progressive degeneration of motor neurons. Several of the genes associated with this disease encode proteins involved in RNA processing, including fused-in-sarcoma/translocated-in-sarcoma (FUS/TLS). FUS is a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of proteins that bind thousands of pre-mRNAs and can regulate their splicing. Here, we have examined the possibility that FUS is also a component of the cellular response to DNA damage. We show that both GFP-tagged and endogenous FUS re-localize to sites of oxidative DNA damage induced by UVA laser, and that FUS recruitment is greatly reduced or ablated by an inhibitor of poly (ADP-ribose) polymerase activity. Consistent with this, we show that recombinant FUS binds directly to poly (ADP-ribose) in vitro, and that both GFP-tagged and endogenous FUS fail to accumulate at sites of UVA laser induced damage in cells lacking poly (ADP-ribose) polymerase-1. Finally, we show that GFP-FUSR521G, harbouring a mutation that is associated with ALS, exhibits reduced ability to accumulate at sites of UVA laser-induced DNA damage. Together, these data suggest that FUS is a component of the cellular response to DNA damage, and that defects in this response may contribute to ALS.
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Affiliation(s)
- Stuart L Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK and School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG
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Abstract
Mutations of the breast and ovarian cancer susceptibility gene 1 (BRCA1) account for about 40-45% of hereditary breast cancer cases. Moreover, a significant fraction of sporadic (non-hereditary) breast and ovarian cancers exhibit reduced or absent expression of the BRCA1 protein, suggesting an additional role for BRCA1 in sporadic cancers. BRCA1 follows the classic pattern of a highly penetrant Knudsen-type tumor suppressor gene in which one allele is inactivated through a germ-line mutation and the other is mutated or deleted within the tumor. BRCA1 is a multi-functional protein but it is not fully understood which function(s) is (are) most important for tumor suppression, nor is it clear why BRCA1-mutations confer a high risk for breast and ovarian cancers and not a broad spectrum of tumor types. Here, we will review BRCA1 functions in the DNA damage response (DDR), which are likely to contribute to tumor suppression. In the process, we will highlight some of the controversies and unresolved issues in the field. We will also describe a recently identified and under-investigated role for BRCA1 in the regulation of telomeres and the implications of this role in the DDR and cancer suppression.
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Affiliation(s)
- Eliot M Rosen
- Department of Oncology, Georgetown University School of Medicine Washington, DC, USA ; Department of Biochemistry, Molecular and Cellular Biology, Georgetown University School of Medicine Washington, DC, USA ; Department of Radiation Medicine, Georgetown University School of Medicine Washington, DC, USA
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38
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Abstract
Systemic response to DNA damage and other stresses is a complex process that includes changes in the regulation and activity of nearly all stages of gene expression. One gene regulatory mechanism used by eukaryotes is selection among alternative transcript isoforms that differ in polyadenylation [poly(A)] sites, resulting in changes either to the coding sequence or to portions of the 3' UTR that govern translation, stability, and localization. To determine the extent to which this means of regulation is used in response to DNA damage, we conducted a global analysis of poly(A) site usage in Saccharomyces cerevisiae after exposure to the UV mimetic, 4-nitroquinoline 1-oxide (4NQO). Two thousand thirty-one genes were found to have significant variation in poly(A) site distributions following 4NQO treatment, with a strong bias toward loss of short transcripts, including many with poly(A) sites located within the protein coding sequence (CDS). We further explored one possible mechanism that could contribute to the widespread differences in mRNA isoforms. The change in poly(A) site profile was associated with an inhibition of cleavage and polyadenylation in cell extract and a decrease in the levels of several key subunits in the mRNA 3'-end processing complex. Sequence analysis identified differences in the cis-acting elements that flank putatively suppressed and enhanced poly(A) sites, suggesting a mechanism that could discriminate between variable and constitutive poly(A) sites. Our analysis indicates that variation in mRNA length is an important part of the regulatory response to DNA damage.
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Virtanen A, Henriksson N, Nilsson P, Nissbeck M. Poly(A)-specific ribonuclease (PARN): an allosterically regulated, processive and mRNA cap-interacting deadenylase. Crit Rev Biochem Mol Biol 2013; 48:192-209. [PMID: 23496118 DOI: 10.3109/10409238.2013.771132] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Deadenylation of eukaryotic mRNA is a mechanism critical for mRNA function by influencing mRNA turnover and efficiency of protein synthesis. Here, we review poly(A)-specific ribonuclease (PARN), which is one of the biochemically best characterized deadenylases. PARN is unique among the currently known eukaryotic poly(A) degrading nucleases, being the only deadenylase that has the capacity to directly interact during poly(A) hydrolysis with both the m(7)G-cap structure and the poly(A) tail of the mRNA. In short, PARN is a divalent metal-ion dependent poly(A)-specific, processive and cap-interacting 3'-5' exoribonuclease that efficiently degrades poly(A) tails of eukaryotic mRNAs. We discuss in detail the mechanisms of its substrate recognition, catalysis, allostery and processive mode of action. On the basis of biochemical and structural evidence, we present and discuss a working model for PARN action. Models of regulation of PARN activity by trans-acting factors are discussed as well as the physiological relevance of PARN.
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Affiliation(s)
- Anders Virtanen
- Department of Cell and Molecular Biology, Program of Chemical Biology, Uppsala University, Uppsala, Sweden.
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Millevoi S, Moine H, Vagner S. G-quadruplexes in RNA biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:495-507. [PMID: 22488917 DOI: 10.1002/wrna.1113] [Citation(s) in RCA: 220] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
G-quadruplexes are noncanonical structures formed by G-rich DNA and RNA sequences that fold into a four-stranded conformation. Experimental studies and computational predictions show that RNA G-quadruplexes are present in transcripts associated with telomeres, in noncoding sequences of primary transcripts and within mature transcripts. RNA G-quadruplexes at these specific locations play important roles in key cellular functions, including telomere homeostasis and gene expression. Indeed, RNA G-quadruplexes appear as important regulators of pre-mRNA processing (splicing and polyadenylation), RNA turnover, mRNA targeting and translation. The regulatory mechanisms controlled by RNA G-quadruplexes involve the binding of protein factors that modulate G-quadruplex conformation and/or serve as a bridge to recruit additional protein regulators. In this review, we summarize the current knowledge on the role of G-quadruplexes in RNA biology with particular emphasis on the molecular mechanisms underlying their specific function in RNA metabolism occurring in physiological or pathological conditions.
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Affiliation(s)
- Stefania Millevoi
- Inserm UMR 1037, University of Toulouse III, Cancer Research Center of Toulouse, Toulouse 31432, Cedex 4, France.
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41
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BRACking news on triple-negative/basal-like breast cancers: how BRCA1 deficiency may result in the development of a selective tumor subtype. Cancer Metastasis Rev 2011; 31:131-42. [DOI: 10.1007/s10555-011-9336-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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42
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Yang Q, Doublié S. Structural biology of poly(A) site definition. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:732-47. [PMID: 21823232 DOI: 10.1002/wrna.88] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
3' processing is an essential step in the maturation of all messenger RNAs (mRNAs) and is a tightly coupled two-step reaction: endonucleolytic cleavage at the poly(A) site is followed by the addition of a poly(A) tail, except for metazoan histone mRNAs, which are cleaved but not polyadenylated. The recognition of a poly(A) site is coordinated by the sequence elements in the mRNA 3' UTR and associated protein factors. In mammalian cells, three well-studied sequence elements, UGUA, AAUAAA, and GU-rich, are recognized by three multisubunit factors: cleavage factor I(m) (CFI(m) ), cleavage and polyadenylation specificity factor (CPSF), and cleavage stimulation factor (CstF), respectively. In the yeast Saccharomyces cerevisiae, UA repeats and A-rich sequence elements are recognized by Hrp1p and cleavage factor IA. Structural studies of protein-RNA complexes have helped decipher the mechanisms underlying sequence recognition and shed light on the role of protein factors in poly(A) site selection and 3' processing machinery assembly. In this review we focus on the interactions between the mRNA cis-elements and the protein factors (CFI(m) , CPSF, CstF, and homologous factors from yeast and other eukaryotes) that define the poly(A) site. WIREs RNA 2011 2 732-747 DOI: 10.1002/wrna.88 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Qin Yang
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, USA
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43
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Decorsière A, Cayrel A, Vagner S, Millevoi S. Essential role for the interaction between hnRNP H/F and a G quadruplex in maintaining p53 pre-mRNA 3'-end processing and function during DNA damage. Genes Dev 2011; 25:220-5. [PMID: 21289067 DOI: 10.1101/gad.607011] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Following DNA damage, mRNA 3'-end formation is inhibited, contributing to repression of mRNA synthesis. Here we investigated how DNA-damaged cells accomplish p53 mRNA 3'-end formation when normal mechanisms of pre-mRNA 3'-end processing regulation are inhibited. The underlying mechanism involves the interaction between a G-quadruplex structure located downstream from the p53 cleavage site and hnRNP H/F. Importantly, this interaction is critical for p53 expression and contributes to p53-mediated apoptosis. Our results uncover the existence of a specific rescue mechanism of 3'-end processing regulation allowing stress-induced p53 accumulation and function in apoptosis.
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44
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p53 inhibits mRNA 3′ processing through its interaction with the CstF/BARD1 complex. Oncogene 2011; 30:3073-83. [DOI: 10.1038/onc.2011.29] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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45
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Moreno-Morcillo M, Minvielle-Sébastia L, Mackereth C, Fribourg S. Hexameric architecture of CstF supported by CstF-50 homodimerization domain structure. RNA (NEW YORK, N.Y.) 2011; 17:412-418. [PMID: 21233223 PMCID: PMC3039141 DOI: 10.1261/rna.2481011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 12/08/2010] [Indexed: 05/30/2023]
Abstract
The Cleavage stimulation Factor (CstF) complex is composed of three subunits and is essential for pre-mRNA 3'-end processing. CstF recognizes U and G/U-rich cis-acting RNA sequence elements and helps stabilize the Cleavage and Polyadenylation Specificity Factor (CPSF) at the polyadenylation site as required for productive RNA cleavage. Here, we describe the crystal structure of the N-terminal domain of Drosophila CstF-50 subunit. It forms a compact homodimer that exposes two geometrically opposite, identical, and conserved surfaces that may serve as binding platform. Together with previous data on the structure of CstF-77, homodimerization of CstF-50 N-terminal domain supports the model in which the functional state of CstF is a heterohexamer.
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Affiliation(s)
- María Moreno-Morcillo
- Institut Européen de Chimie et Biologie, Institut National de la Santé et de la Recherche Médicale (INSERM) U869, Pessac, France
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Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Literature curation of protein interactions: measuring agreement across major public databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2010; 2010:baq026. [PMID: 21183497 PMCID: PMC3011985 DOI: 10.1093/database/baq026] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Literature curation of protein interaction data faces a number of challenges. Although curators increasingly adhere to standard data representations, the data that various databases actually record from the same published information may differ significantly. Some of the reasons underlying these differences are well known, but their global impact on the interactions collectively curated by major public databases has not been evaluated. Here we quantify the agreement between curated interactions from 15 471 publications shared across nine major public databases. Results show that on average, two databases fully agree on 42% of the interactions and 62% of the proteins curated from the same publication. Furthermore, a sizable fraction of the measured differences can be attributed to divergent assignments of organism or splice isoforms, different organism focus and alternative representations of multi-protein complexes. Our findings highlight the impact of divergent curation policies across databases, and should be relevant to both curators and data consumers interested in analyzing protein-interaction data generated by the scientific community. Database URL:http://wodaklab.org/iRefWeb
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Affiliation(s)
- Andrei L Turinsky
- Molecular Structure and Function Program, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada
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Dr. Jekyll and Mr. Hyde: The Two Faces of the FUS/EWS/TAF15 Protein Family. Sarcoma 2010; 2011:837474. [PMID: 21197473 PMCID: PMC3005952 DOI: 10.1155/2011/837474] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 10/20/2010] [Accepted: 11/01/2010] [Indexed: 12/13/2022] Open
Abstract
FUS, EWS, and TAF15 form the FET family of RNA-binding proteins whose genes are found rearranged with various transcription factor genes predominantly in sarcomas and in rare hematopoietic and epithelial cancers. The resulting fusion gene products have attracted considerable interest as diagnostic and promising therapeutic targets. So far, oncogenic FET fusion proteins have been regarded as strong transcription factors that aberrantly activate or repress target genes of their DNA-binding fusion partners. However, the role of the transactivating domain in the context of the normal FET proteins is poorly defined, and, therefore, our knowledge on how FET aberrations impact on tumor biology is incomplete. Since we believe that a full understanding of aberrant FET protein function can only arise from looking at both sides of the coin, the good and the evil, this paper summarizes evidence for the central function of FET proteins in bridging RNA transcription, processing, transport, and DNA repair.
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48
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Nuclear deadenylation/polyadenylation factors regulate 3' processing in response to DNA damage. EMBO J 2010; 29:1674-87. [PMID: 20379136 DOI: 10.1038/emboj.2010.59] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 03/05/2010] [Indexed: 12/23/2022] Open
Abstract
We previously showed that mRNA 3' end cleavage reaction in cell extracts is strongly but transiently inhibited under DNA-damaging conditions. The cleavage stimulation factor-50 (CstF-50) has a role in this response, providing a link between transcription-coupled RNA processing and DNA repair. In this study, we show that CstF-50 interacts with nuclear poly(A)-specific ribonuclease (PARN) using in vitro and in extracts of UV-exposed cells. The CstF-50/PARN complex formation has a role in the inhibition of 3' cleavage and activation of deadenylation upon DNA damage. Extending these results, we found that the tumour suppressor BARD1, which is involved in the UV-induced inhibition of 3' cleavage, strongly activates deadenylation by PARN in the presence of CstF-50, and that CstF-50/BARD1 can revert the cap-binding protein-80 (CBP80)-mediated inhibition of PARN activity. We also provide evidence that PARN along with the CstF/BARD1 complex participates in the regulation of endogenous transcripts under DNA-damaging conditions. We speculate that the interplay between polyadenylation, deadenylation and tumour-suppressor factors might prevent the expression of prematurely terminated messengers, contributing to control of gene expression under different cellular conditions.
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Singh P, Alley TL, Wright SM, Kamdar S, Schott W, Wilpan RY, Mills KD, Graber JH. Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes. Cancer Res 2010; 69:9422-30. [PMID: 19934316 DOI: 10.1158/0008-5472.can-09-2236] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular cancer diagnostics are an important clinical advance in cancer management, but new methods are still needed. In this context, gene expression signatures obtained by microarray represent a useful molecular diagnostic. Here, we describe novel probe-level microarray analyses that reveal connections between mRNA processing and neoplasia in multiple tumor types, with diagnostic potential. We now show that characteristic differences in mRNA processing, primarily in the 3'-untranslated region, define molecular signatures that can distinguish similar tumor subtypes with different survival characteristics, with at least 74% accuracy. Using a mouse model of B-cell leukemia/lymphoma, we find that differences in transcript isoform abundance are likely due to both alternative polyadenylation (APA) and differential degradation. While truncation of the 3'-UTR is the most common observed pattern, genes with elongated transcripts were also observed, and distinct groups of affected genes are found in related but distinct tumor types. Genes with elongated transcripts are overrepresented in ontology categories related to cell-cell adhesion and morphology. Analysis of microarray data from human primary tumor samples revealed similar phenomena. Western blot analysis of selected proteins confirms that changes in the 3'-UTR can correlate with changes in protein expression. Our work suggests that alternative mRNA processing, particularly APA, can be a powerful molecular biomarker with prognostic potential. Finally, these findings provide insights into the molecular mechanisms of gene deregulation in tumorigenesis.
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Affiliation(s)
- Priyam Singh
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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Millevoi S, Vagner S. Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation. Nucleic Acids Res 2009; 38:2757-74. [PMID: 20044349 PMCID: PMC2874999 DOI: 10.1093/nar/gkp1176] [Citation(s) in RCA: 304] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Messenger RNA (mRNA) 3′ end formation is a nuclear process through which all eukaryotic primary transcripts are endonucleolytically cleaved and most of them acquire a poly(A) tail. This process, which consists in the recognition of defined poly(A) signals of the pre-mRNAs by a large cleavage/polyadenylation machinery, plays a critical role in gene expression. Indeed, the poly(A) tail of a mature mRNA is essential for its functions, including stability, translocation to the cytoplasm and translation. In addition, this process serves as a bridge in the network connecting the different transcription, capping, splicing and export machineries. It also participates in the quantitative and qualitative regulation of gene expression in a variety of biological processes through the selection of single or alternative poly(A) signals in transcription units. A large number of protein factors associates with this machinery to regulate the efficiency and specificity of this process and to mediate its interaction with other nuclear events. Here, we review the eukaryotic 3′ end processing machineries as well as the comprehensive set of regulatory factors and discuss the different molecular mechanisms of 3′ end processing regulation by proposing several overlapping models of regulation.
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Affiliation(s)
- Stefania Millevoi
- Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France.
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