51
|
Replication Fork Protection Factors Controlling R-Loop Bypass and Suppression. Genes (Basel) 2017; 8:genes8010033. [PMID: 28098815 PMCID: PMC5295027 DOI: 10.3390/genes8010033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/02/2017] [Accepted: 01/09/2017] [Indexed: 12/17/2022] Open
Abstract
Replication–transcription conflicts have been a well-studied source of genome instability for many years and have frequently been linked to defects in RNA processing. However, recent characterization of replication fork-associated proteins has revealed that defects in fork protection can directly or indirectly stabilize R-loop structures in the genome and promote transcription–replication conflicts that lead to genome instability. Defects in essential DNA replication-associated activities like topoisomerase, or the minichromosome maintenance (MCM) helicase complex, as well as fork-associated protection factors like the Fanconi anemia pathway, both appear to mitigate transcription–replication conflicts. Here, we will highlight recent advances that support the concept that normal and robust replisome function itself is a key component of mitigating R-loop coupled genome instability.
Collapse
|
52
|
Lingering Questions about Enhancer RNA and Enhancer Transcription-Coupled Genomic Instability. Trends Genet 2017; 33:143-154. [PMID: 28087167 DOI: 10.1016/j.tig.2016.12.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/22/2016] [Accepted: 12/08/2016] [Indexed: 12/12/2022]
Abstract
Intergenic and intragenic enhancers found inside topologically associated regulatory domains (TADs) express noncoding RNAs, known as enhancer RNAs (eRNAs). Recent studies have indicated these eRNAs play a role in gene regulatory networks by controlling promoter and enhancer interactions and topology of higher-order chromatin structure. Misregulation of enhancer and promoter associated noncoding RNAs (ncRNAs) could stabilize deleterious secondary DNA structures, noncoding RNA associated DNA/RNA hybrid formation, and promote collisions of transcription complexes with replisomes. It is revealing that many chromosomal aberrations, some associated with malignancies, are present inside enhancer and/or promoter sequences. Here, we expand on current concepts to discuss enhancer RNAs and enhancer transcription, and how enhancer transcription influences genomic organization and integrity.
Collapse
|
53
|
Barzilai A, Schumacher B, Shiloh Y. Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev 2017; 161:4-18. [DOI: 10.1016/j.mad.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 02/06/2023]
|
54
|
Wu B, Wang Y, Wang C, Wang GG, Wu J, Wan YY. BPTF Is Essential for T Cell Homeostasis and Function. THE JOURNAL OF IMMUNOLOGY 2016; 197:4325-4333. [PMID: 27799308 DOI: 10.4049/jimmunol.1600642] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/03/2016] [Indexed: 12/31/2022]
Abstract
Bromodomain PHD finger transcription factor (BPTF), a ubiquitously expressed ATP-dependent chromatin-remodeling factor, is critical for epigenetically regulating DNA accessibility and gene expression. Although BPTF is important for the development of thymocytes, its function in mature T cells remains largely unknown. By specifically deleting BPTF from late double-negative 3/double-negative 4 stage of developing T cells, we found that BPTF was critical for the homeostasis of T cells via a cell-intrinsic manner. In addition, BPTF was essential for the maintenance and function of regulatory T (Treg) cells. Treg cell-specific BPTF deletion led to reduced Foxp3 expression, increased lymphocyte infiltration in the nonlymphoid organs, and a systemic autoimmune syndrome. These findings therefore reveal a vital role for BPTF in T and Treg cell function and immune homeostasis.
Collapse
Affiliation(s)
- Bing Wu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Yunqi Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Chaojun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jie Wu
- State Key Laboratory of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China; and
| | - Yisong Y Wan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; .,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| |
Collapse
|
55
|
Nascent Connections: R-Loops and Chromatin Patterning. Trends Genet 2016; 32:828-838. [PMID: 27793359 DOI: 10.1016/j.tig.2016.10.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 11/22/2022]
Abstract
RNA molecules, such as long noncoding RNAs (lncRNAs), have critical roles in regulating gene expression, chromosome architecture, and the modification states of chromatin. Recent developments suggest that RNA also influences gene expression and chromatin patterns through the interaction of nascent transcripts with their DNA template via the formation of co-transcriptional R-loop structures. R-loop formation over specific, conserved, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynamic feature of mammalian chromatin. Here, focusing primarily on mammalian systems, I describe the accumulating connections and possible mechanisms linking R-loop formation and chromatin patterning. The possible contribution of aberrant R-loops to pathological conditions is also discussed.
Collapse
|
56
|
Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability. Nat Genet 2016; 48:1385-1395. [DOI: 10.1038/ng.3672] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022]
|
57
|
Wigington CP, Morris KJ, Newman LE, Corbett AH. The Polyadenosine RNA-binding Protein, Zinc Finger Cys3His Protein 14 (ZC3H14), Regulates the Pre-mRNA Processing of a Key ATP Synthase Subunit mRNA. J Biol Chem 2016; 291:22442-22459. [PMID: 27563065 DOI: 10.1074/jbc.m116.754069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
Polyadenosine RNA-binding proteins (Pabs) regulate multiple steps in gene expression. This protein family includes the well studied Pabs, PABPN1 and PABPC1, as well as the newly characterized Pab, zinc finger CCCH-type containing protein 14 (ZC3H14). Mutations in ZC3H14 are linked to a form of intellectual disability. To probe the function of ZC3H14, we performed a transcriptome-wide analysis of cells depleted of either ZC3H14 or the control Pab, PABPN1. Depletion of PABPN1 affected ∼17% of expressed transcripts, whereas ZC3H14 affected only ∼1% of expressed transcripts. To assess the function of ZC3H14 in modulating target mRNAs, we selected the gene encoding the ATP synthase F0 subunit C (ATP5G1) transcript. Knockdown of ZC3H14 significantly reduced ATP5G1 steady-state mRNA levels. Consistent with results suggesting that ATP5G1 turnover increases upon depletion of ZC3H14, double knockdown of ZC3H14 and the nonsense-mediated decay factor, UPF1, rescues ATP5G1 transcript levels. Furthermore, fractionation reveals an increase in the amount of ATP5G1 pre-mRNA that reaches the cytoplasm when ZC3H14 is depleted and that ZC3H14 binds to ATP5G1 pre-mRNA in the nucleus. These data support a role for ZC3H14 in ensuring proper nuclear processing and retention of ATP5G1 pre-mRNA. Consistent with the observation that ATP5G1 is a rate-limiting component for ATP synthase activity, knockdown of ZC3H14 decreases cellular ATP levels and causes mitochondrial fragmentation. These data suggest that ZC3H14 modulates pre-mRNA processing of select mRNA transcripts and plays a critical role in regulating cellular energy levels, observations that have broad implications for proper neuronal function.
Collapse
Affiliation(s)
- Callie P Wigington
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Kevin J Morris
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Laura E Newman
- From the Department of Biochemistry and.,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Anita H Corbett
- From the Department of Biochemistry and .,the Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| |
Collapse
|
58
|
Canonical DNA Repair Pathways Influence R-Loop-Driven Genome Instability. J Mol Biol 2016; 429:3132-3138. [PMID: 27452366 DOI: 10.1016/j.jmb.2016.07.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/05/2016] [Accepted: 07/12/2016] [Indexed: 12/22/2022]
Abstract
DNA repair defects create cancer predisposition in humans by fostering a higher rate of mutations. While DNA repair is quite well characterized, recent studies have identified previously unrecognized relationships between DNA repair and R-loop-mediated genome instability. R-loops are three-stranded nucleic acid structures in which RNA binds to genomic DNA to displace a loop of single-stranded DNA. Mutations in homologous recombination, nucleotide excision repair, crosslink repair, and DNA damage checkpoints have all now been linked to formation and function of transcription-coupled R-loops. This perspective will summarize recent literature linking DNA repair to R-loop-mediated genomic instability and discuss how R-loops may contribute to mutagenesis in DNA-repair-deficient cancers.
Collapse
|
59
|
Correa BR, de Araujo PR, Qiao M, Burns SC, Chen C, Schlegel R, Agarwal S, Galante PAF, Penalva LOF. Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma. Genome Biol 2016; 17:125. [PMID: 27287018 PMCID: PMC4901439 DOI: 10.1186/s13059-016-0990-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/24/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and transcriptomic analyses have become important tools to identify new avenues for therapies. RNA-binding proteins (RBPs) are master regulators of co- and post-transcriptional events; however, their role in GBM remains poorly understood. To further our knowledge of novel regulatory pathways that could contribute to gliomagenesis, we have conducted a systematic study of RBPs in GBM. RESULTS By measuring expression levels of 1542 human RBPs in GBM samples and glioma stem cell samples, we identified 58 consistently upregulated RBPs. Survival analysis revealed that increased expression of 21 RBPs was also associated with a poor prognosis. To assess the functional impact of those RBPs, we modulated their expression in GBM cell lines and performed viability, proliferation, and apoptosis assays. Combined results revealed a prominent oncogenic candidate, SNRPB, which encodes core spliceosome machinery components. To reveal the impact of SNRPB on splicing and gene expression, we performed its knockdown in a GBM cell line followed by RNA sequencing. We found that the affected genes were involved in RNA processing, DNA repair, and chromatin remodeling. Additionally, genes and pathways already associated with gliomagenesis, as well as a set of general cancer genes, also presented with splicing and expression alterations. CONCLUSIONS Our study provides new insights into how RBPs, and specifically SNRPB, regulate gene expression and directly impact GBM development.
Collapse
Affiliation(s)
- Bruna R Correa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | | | - Mei Qiao
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | - Suzanne C Burns
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | - Chen Chen
- Georgetown University Medical Center, Washington, DC, USA
| | | | - Seema Agarwal
- Georgetown University Medical Center, Washington, DC, USA
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.
| | - Luiz O F Penalva
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA.
- Department of Cellular and Structural Biology, UTHSCSA, San Antonio, TX, USA.
| |
Collapse
|
60
|
Hale CJ, Potok ME, Lopez J, Do T, Liu A, Gallego-Bartolome J, Michaels SD, Jacobsen SE. Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana. PLoS Genet 2016; 12:e1006092. [PMID: 27253878 PMCID: PMC4890748 DOI: 10.1371/journal.pgen.1006092] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/10/2016] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes are regulated by epigenetic marks that act to modulate transcriptional control as well as to regulate DNA replication and repair. In Arabidopsis thaliana, mutation of the ATXR5 and ATXR6 histone methyltransferases causes reduction in histone H3 lysine 27 monomethylation, transcriptional upregulation of transposons, and a genome instability defect in which there is an accumulation of excess DNA corresponding to pericentromeric heterochromatin. We designed a forward genetic screen to identify suppressors of the atxr5/6 phenotype that uncovered loss-of-function mutations in two components of the TREX-2 complex (AtTHP1, AtSAC3B), a SUMO-interacting E3 ubiquitin ligase (AtSTUbL2) and a methyl-binding domain protein (AtMBD9). Additionally, using a reverse genetic approach, we show that a mutation in a plant homolog of the tumor suppressor gene BRCA1 enhances the atxr5/6 phenotype. Through characterization of these mutations, our results suggest models for the production atxr5 atxr6-induced extra DNA involving conflicts between the replicative and transcriptional processes in the cell, and suggest that the atxr5 atxr6 transcriptional defects may be the cause of the genome instability defects in the mutants. These findings highlight the critical intersection of transcriptional silencing and DNA replication in the maintenance of genome stability of heterochromatin. In eukaryotic genomes cellular processes such as transcription and replication need to be tightly controlled in order to promote genomic stability and prevent deleterious mutations. In Arabidopsis thaliana, two redundant histone methyltransferases, ATXR5 and ATXR6, are responsible for the deposition of a silencing epigenetic mark, histone H3 lysine 27 monomethylation. Loss of ATXR5/6 results in transcriptional activation of transposable elements (TEs), upregulation of DNA damage response genes and a genomic instability defect characterized as an excess of DNA corresponding to heterochromatin regions. Using a genetic screen, we sought to find suppressors of the atxr5/6 phenotype, and interestingly, we identified multiple genes implicated in general transcriptional activity. Through genomic characterization of the mutants our data suggest a model where transcriptional silencing of heterochromatin during S-phase is required for proper replication and maintenance of genome stability. These findings emphasize the important relationship between chromatin, transcriptional control and replication in the maintenance of genome stability in a eukaryotic system and identify new players involved in these processes.
Collapse
Affiliation(s)
- Christopher J. Hale
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Center for Precision Diagnostics, University of Washington, Seattle, Washington, United States of America
| | - Magdalena E. Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Jennifer Lopez
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Truman Do
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Ao Liu
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Scott D. Michaels
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
61
|
Boeing S, Williamson L, Encheva V, Gori I, Saunders RE, Instrell R, Aygün O, Rodriguez-Martinez M, Weems JC, Kelly GP, Conaway JW, Conaway RC, Stewart A, Howell M, Snijders AP, Svejstrup JQ. Multiomic Analysis of the UV-Induced DNA Damage Response. Cell Rep 2016; 15:1597-1610. [PMID: 27184836 PMCID: PMC4893159 DOI: 10.1016/j.celrep.2016.04.047] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/25/2016] [Accepted: 04/10/2016] [Indexed: 12/21/2022] Open
Abstract
In order to facilitate the identification of factors and pathways in the cellular response to UV-induced DNA damage, several descriptive proteomic screens and a functional genomics screen were performed in parallel. Numerous factors could be identified with high confidence when the screen results were superimposed and interpreted together, incorporating biological knowledge. A searchable database, bioLOGIC, which provides access to relevant information about a protein or process of interest, was established to host the results and facilitate data mining. Besides uncovering roles in the DNA damage response for numerous proteins and complexes, including Integrator, Cohesin, PHF3, ASC-1, SCAF4, SCAF8, and SCAF11, we uncovered a role for the poorly studied, melanoma-associated serine/threonine kinase 19 (STK19). Besides effectively uncovering relevant factors, the multiomic approach also provides a systems-wide overview of the diverse cellular processes connected to the transcription-related DNA damage response.
Collapse
Affiliation(s)
- Stefan Boeing
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK; Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Laura Williamson
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Ilaria Gori
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Rebecca E Saunders
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Rachael Instrell
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ozan Aygün
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Marta Rodriguez-Martinez
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Juston C Weems
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gavin P Kelly
- Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Aengus Stewart
- Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Michael Howell
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK.
| |
Collapse
|
62
|
Bacolla A, Tainer JA, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res 2016; 44:5673-88. [PMID: 27084947 PMCID: PMC4937311 DOI: 10.1093/nar/gkw261] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes and often create oncogenic fusion genes. An obligate step in the generation of such gross rearrangements is the formation of DNA double-strand breaks (DSBs). Since the genomic distribution of rearrangement breakpoints is non-random, intrinsic cellular factors may predispose certain genomic regions to breakage. Notably, certain DNA sequences with the potential to fold into secondary structures [potential non-B DNA structures (PONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structures with implications in DNA replication and transcription] can stimulate the formation of DNA DSBs. Here, we tested the postulate that these DNA sequences might be found at, or in close proximity to, rearrangement breakpoints. By analyzing the distribution of PONDS-forming sequences within ±500 bases of 19 947 translocation and 46 365 sequence-characterized deletion breakpoints in cancer genomes, we find significant association between PONDS-forming repeats and cancer breakpoints. Specifically, (AT)n, (GAA)n and (GAAA)n constitute the most frequent repeats at translocation breakpoints, whereas A-tracts occur preferentially at deletion breakpoints. Translocation breakpoints near PONDS-forming repeats also recur in different individuals and patient tumor samples. Hence, PONDS-forming sequences represent an intrinsic risk factor for genomic rearrangements in cancer genomes.
Collapse
Affiliation(s)
- Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| |
Collapse
|
63
|
Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC. The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast. Nucleic Acids Res 2015; 44:1703-17. [PMID: 26682798 PMCID: PMC4770224 DOI: 10.1093/nar/gkv1473] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 12/03/2015] [Indexed: 01/07/2023] Open
Abstract
The formation of RNA–DNA hybrids, referred to as R-loops, can promote genome instability and cancer development. Yet the mechanisms by which R-loops compromise genome instability are poorly understood. Here, we establish roles for the evolutionarily conserved Nrl1 protein in pre-mRNA splicing regulation, R-loop suppression and in maintaining genome stability. nrl1Δ mutants exhibit endogenous DNA damage, are sensitive to exogenous DNA damage, and have defects in homologous recombination (HR) repair. Concomitantly, nrl1Δ cells display significant changes in gene expression, similar to those induced by DNA damage in wild-type cells. Further, we find that nrl1Δ cells accumulate high levels of R-loops, which co-localize with HR repair factors and require Rad51 and Rad52 for their formation. Together, our findings support a model in which R-loop accumulation and subsequent DNA damage sequesters HR factors, thereby compromising HR repair at endogenously or exogenously induced DNA damage sites, leading to genome instability.
Collapse
Affiliation(s)
- Lucia Aronica
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria Department of Oncology, Stanford University, Stanford 94305, USA
| | - Torben Kasparek
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | - David Ruchman
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria
| | - Yamile Marquez
- Department of Medical Biochemistry, Max F. Perutz Laboratories,Medical University of Vienna, Vienna A-1030, Austria
| | - Lubos Cipak
- Cancer Research Institute, Slovak Academy of Sciences, Bratislava 81438, Slovakia
| | - Ingrid Cipakova
- Cancer Research Institute, Slovak Academy of Sciences, Bratislava 81438, Slovakia
| | - Dorothea Anrather
- Max F. Perutz Laboratories, Mass Spectrometry Facility, Vienna A-1030, Austria
| | - Barbora Mikolaskova
- Cancer Research Institute, Slovak Academy of Sciences, Bratislava 81438, Slovakia
| | - Maximilian Radtke
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria
| | - Sovan Sarkar
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | - Chen-Chun Pai
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | | | - Carol Walker
- CRUK/MRC Oxford Institute for Radiation Oncology, Oxford OX37DQ , UK
| | - Kuo-Fang Shen
- University of Southern California, Los Angeles 90089-0911, USA
| | - Renee Schroeder
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, Vienna A-1030, Austria
| | - Andrea Barta
- Department of Medical Biochemistry, Max F. Perutz Laboratories,Medical University of Vienna, Vienna A-1030, Austria
| | | | | |
Collapse
|
64
|
Munroe SH, Morales CH, Duyck TH, Waters PD. Evolution of the Antisense Overlap between Genes for Thyroid Hormone Receptor and Rev-erbα and Characterization of an Exonic G-Rich Element That Regulates Splicing of TRα2 mRNA. PLoS One 2015; 10:e0137893. [PMID: 26368571 PMCID: PMC4569393 DOI: 10.1371/journal.pone.0137893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/24/2015] [Indexed: 11/18/2022] Open
Abstract
The α-thyroid hormone receptor gene (TRα) codes for two functionally distinct proteins: TRα1, the α-thyroid hormone receptor; and TRα2, a non-hormone-binding variant. The final exon of TRα2 mRNA overlaps the 3' end of Rev-erbα mRNA, which encodes another nuclear receptor on the opposite strand of DNA. To understand the evolution of this antisense overlap, we sequenced these genes and mRNAs in the platypus Orthorhynchus anatinus. Despite its strong homology with other mammals, the platypus TRα/Rev-erbα locus lacks elements essential for expression of TRα2. Comparative analysis suggests that alternative splicing of TRα2 mRNA expression evolved in a stepwise fashion before the divergence of eutherian and marsupial mammals. A short G-rich element (G30) located downstream of the alternative 3'splice site of TRα2 mRNA and antisense to the 3'UTR of Rev-erbα plays an important role in regulating TRα2 splicing. G30 is tightly conserved in eutherian mammals, but is absent in marsupials and monotremes. Systematic deletions and substitutions within G30 have dramatically different effects on TRα2 splicing, leading to either its inhibition or its enhancement. Mutations that disrupt one or more clusters of G residues enhance splicing two- to three-fold. These results suggest the G30 sequence can adopt a highly structured conformation, possibly a G-quadruplex, and that it is part of a complex splicing regulatory element which exerts both positive and negative effects on TRα2 expression. Since mutations that strongly enhance splicing in vivo have no effect on splicing in vitro, it is likely that the regulatory role of G30 is mediated through linkage of transcription and splicing.
Collapse
Affiliation(s)
- Stephen H. Munroe
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
- * E-mail:
| | - Christopher H. Morales
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Tessa H. Duyck
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Australia, Sydney, Australia
| |
Collapse
|
65
|
hPso4/hPrp19: a critical component of DNA repair and DNA damage checkpoint complexes. Oncogene 2015; 35:2279-86. [PMID: 26364595 DOI: 10.1038/onc.2015.321] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/15/2022]
Abstract
Genome integrity is vital to cellular homeostasis and its forfeiture is linked to deleterious consequences-cancer, immunodeficiency, genetic disorders and premature aging. The human ubiquitin ligase Pso4/Prp19 has emerged as a critical component of multiple DNA damage response (DDR) signaling networks. It not only senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, but also regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Accordingly, by virtue of its regulatory and structural interactions with key proteins critical for genome integrity-DNA double-strand break (DSB) repair, DNA interstrand crosslink repair, repair of stalled replication forks and DNA end joining-it fills a unique niche in restoring genomic integrity after multiple types of DNA damage and thus has a vital role in maintaining chromatin integrity and cellular functions. These properties may underlie its ability to thwart replicative senescence and, not surprisingly, have been linked to the self-renewal and colony-forming ability of murine hematopoietic stem cells. This review highlights recent advances in hPso4 research that provides a fascinating glimpse into the pleiotropic activities of a ubiquitously expressed multifunctional E3 ubiquitin ligase.
Collapse
|
66
|
Simmons MP, Bachy C, Sudek S, van Baren MJ, Sudek L, Ares M, Worden AZ. Intron Invasions Trace Algal Speciation and Reveal Nearly Identical Arctic and Antarctic Micromonas Populations. Mol Biol Evol 2015; 32:2219-35. [PMID: 25998521 PMCID: PMC4540971 DOI: 10.1093/molbev/msv122] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.
Collapse
Affiliation(s)
- Melinda P Simmons
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA Department of Ocean Sciences, University of California Santa Cruz
| | - Charles Bachy
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | | | - Lisa Sudek
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA
| | - Manuel Ares
- Department of Molecular, Cell & Developmental Biology, University of California Santa Cruz
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA Department of Ocean Sciences, University of California Santa Cruz Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
| |
Collapse
|
67
|
Abstract
The immunoglobulin diversification processes of somatic hypermutation and class switch recombination critically rely on transcription-coupled targeting of activation-induced cytidine deaminase (AID) to Ig loci in activated B lymphocytes. AID catalyzes deamination of cytidine deoxynucleotides on exposed single-stranded DNA. In addition to driving immunoglobulin diversity, promiscuous targeting of AID mutagenic activity poses a deleterious threat to genomic stability. Recent genome-wide studies have uncovered pervasive AID activity throughout the B cell genome. It is increasingly apparent that AID activity is frequently targeted to genomic loci undergoing early transcription termination where RNA exosome promotes the resolution of stalled transcription complexes via cotranscriptional RNA degradation mechanisms. Here, we review aspects and consequences of eukaryotic transcription that lead to early termination, RNA exosome recruitment, and ultimately targeting of AID mutagenic activity.
Collapse
Affiliation(s)
- Evangelos Pefanis
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
| | - Uttiya Basu
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
| |
Collapse
|
68
|
Shirai CL, Ley JN, White BS, Kim S, Tibbitts J, Shao J, Ndonwi M, Wadugu B, Duncavage EJ, Okeyo-Owuor T, Liu T, Griffith M, McGrath S, Magrini V, Fulton RS, Fronick C, O'Laughlin M, Graubert TA, Walter MJ. Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo. Cancer Cell 2015; 27:631-43. [PMID: 25965570 PMCID: PMC4430854 DOI: 10.1016/j.ccell.2015.04.008] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/16/2015] [Accepted: 04/13/2015] [Indexed: 01/12/2023]
Abstract
Heterozygous somatic mutations in the spliceosome gene U2AF1 occur in ∼ 11% of patients with myelodysplastic syndromes (MDS), the most common adult myeloid malignancy. It is unclear how these mutations contribute to disease. We examined in vivo hematopoietic consequences of the most common U2AF1 mutation using a doxycycline-inducible transgenic mouse model. Mice expressing mutant U2AF1(S34F) display altered hematopoiesis and changes in pre-mRNA splicing in hematopoietic progenitor cells by whole transcriptome analysis (RNA-seq). Integration with human RNA-seq datasets determined that common mutant U2AF1-induced splicing alterations are enriched in RNA processing genes, ribosomal genes, and recurrently mutated MDS and acute myeloid leukemia-associated genes. These findings support the hypothesis that mutant U2AF1 alters downstream gene isoform expression, thereby contributing to abnormal hematopoiesis in patients with MDS.
Collapse
Affiliation(s)
- Cara Lunn Shirai
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - James N Ley
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Brian S White
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Sanghyun Kim
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Justin Tibbitts
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Jin Shao
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Matthew Ndonwi
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Brian Wadugu
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Theresa Okeyo-Owuor
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tuoen Liu
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Malachi Griffith
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Sean McGrath
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Vincent Magrini
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Robert S Fulton
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Catrina Fronick
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | | | - Timothy A Graubert
- Massachusetts General Hospital/Harvard Medical School, Boston, MA 02114, USA
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA.
| |
Collapse
|
69
|
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: 331] [Impact Index Per Article: 36.8] [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
Collapse
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.
| |
Collapse
|
70
|
Naro C, Bielli P, Pagliarini V, Sette C. The interplay between DNA damage response and RNA processing: the unexpected role of splicing factors as gatekeepers of genome stability. Front Genet 2015; 6:142. [PMID: 25926848 PMCID: PMC4397863 DOI: 10.3389/fgene.2015.00142] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/25/2015] [Indexed: 12/22/2022] Open
Abstract
Genome integrity is constantly threatened by endogenous and exogenous factors. However, its preservation is ensured by a network of pathways that prevent and/or repair the lesion, which constitute the DNA damage response (DDR). Expression of the key proteins involved in the DDR is controlled by numerous post-transcriptional mechanisms, among which pre-mRNA splicing stands out. Intriguingly, several splicing factors (SFs) have been recently shown to play direct functions in DNA damage prevention and repair, which go beyond their expected splicing activity. At the same time, evidence is emerging that DNA repair proteins (DRPs) can actively sustain the DDR by acting as post-transcriptional regulator of gene expression, in addition to their well-known role in the mechanisms of signaling and repair of the lesion. Herein, we will review these non-canonical functions of both SFs and DRPs, which suggest the existence of a tight interplay between splicing regulation and canonical DNA safeguard mechanisms ensuring genome stability.
Collapse
Affiliation(s)
- Chiara Naro
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Vittoria Pagliarini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| | - Claudio Sette
- Department of Biomedicine and Prevention, University of Rome Tor Vergata , Rome, Italy ; Laboratory of Neuroembryology, Fondazione Santa Lucia , Rome, Italy
| |
Collapse
|
71
|
Koo CX, Kobiyama K, Shen YJ, LeBert N, Ahmad S, Khatoo M, Aoshi T, Gasser S, Ishii KJ. RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression. J Biol Chem 2015; 290:7463-73. [PMID: 25623070 PMCID: PMC4367256 DOI: 10.1074/jbc.m115.636365] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RNA:DNA hybrids form in the nuclei and mitochondria of cells as transcription-induced R-loops or G-quadruplexes, but exist only in the cytosol of virus-infected cells. Little is known about the existence of RNA:DNA hybrids in the cytosol of virus-free cells, in particular cancer or transformed cells. Here, we show that cytosolic RNA:DNA hybrids are present in various human cell lines, including transformed cells. Inhibition of RNA polymerase III (Pol III), but not DNA polymerase, abrogated cytosolic RNA:DNA hybrids. Cytosolic RNA:DNA hybrids bind to several components of the microRNA (miRNA) machinery-related proteins, including AGO2 and DDX17. Furthermore, we identified miRNAs that are specifically regulated by Pol III, providing a potential link between RNA:DNA hybrids and the miRNA machinery. One of the target genes, exportin-1, is shown to regulate cytosolic RNA:DNA hybrids. Taken together, we reveal previously unknown mechanism by which Pol III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells.
Collapse
Affiliation(s)
- Christine Xing'er Koo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, the Laboratory of Adjuvant Innovation and
| | - Kouji Kobiyama
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yu J Shen
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Nina LeBert
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Shandar Ahmad
- the Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), Ibaraki, Osaka 567-0085, Japan, and
| | - Muznah Khatoo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Taiki Aoshi
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Stephan Gasser
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456,
| | - Ken J Ishii
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
72
|
End of the beginning: elongation and termination features of alternative modes of chromosomal replication initiation in bacteria. PLoS Genet 2015; 11:e1004909. [PMID: 25569209 PMCID: PMC4287441 DOI: 10.1371/journal.pgen.1004909] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In bacterial cells, bidirectional replication of the circular chromosome is initiated from a single origin (oriC) and terminates in an antipodal terminus region such that movement of the pair of replication forks is largely codirectional with transcription. The terminus region is flanked by discrete Ter sequences that act as polar, or direction-dependent, arrest sites for fork progression. Alternative oriC-independent modes of replication initiation are possible, one of which is constitutive stable DNA replication (cSDR) from transcription-associated RNA–DNA hybrids or R-loops. Here, I discuss the distinctive attributes of fork progression and termination associated with different modes of bacterial replication initiation. Two hypothetical models are proposed: that head-on collisions between pairs of replication forks, which are a feature of replication termination in all kingdoms of life, provoke bilateral fork reversal reactions; and that cSDR is characterized by existence of distinct subpopulations in bacterial cultures and a widespread distribution of origins in the genome, each with a small firing potential. Since R-loops are known to exist in eukaryotic cells and to inflict genome damage in G1 phase, it is possible that cSDR-like events promote aberrant replication initiation even in eukaryotes.
Collapse
|
73
|
Wigington CP, Jung J, Rye EA, Belauret SL, Philpot AM, Feng Y, Santangelo PJ, Corbett AH. Post-transcriptional regulation of programmed cell death 4 (PDCD4) mRNA by the RNA-binding proteins human antigen R (HuR) and T-cell intracellular antigen 1 (TIA1). J Biol Chem 2014; 290:3468-87. [PMID: 25519906 DOI: 10.1074/jbc.m114.631937] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Post-transcriptional processing of mRNA transcripts plays a critical role in establishing the gene expression profile of a cell. Such processing events are mediated by a host of factors, including RNA-binding proteins and microRNAs. A number of critical cellular pathways are subject to regulation at multiple levels that allow fine-tuning of key biological responses. Programmed cell death 4 (PDCD4) is a tumor suppressor and an important modulator of mRNA translation that is regulated by a number of mechanisms, most notably as a target of the oncomiR, miR-21. Here, we provide evidence for post-transcriptional regulation of PDCD4 by the RNA-binding proteins, HuR and TIA1. Complementary approaches reveal binding of both HuR and TIA1 to the PDCD4 transcript. Consistent with a model where RNA-binding proteins modulate the PDCD4 transcript, knockdown of HuR and/or TIA1 results in a significant decrease in steady-state PDCD4 mRNA and protein levels. However, fractionation experiments suggest that the mode of regulation of the PDCD4 transcript likely differs in the cytoplasm and the nucleus as the pool of PDCD4 mRNA present in the cytoplasm is more stable than the nuclear pool of PDCD4 transcript. We observe a competitive mode of binding between HuR and TIA1 on the PDCD4 transcript in the cytoplasm, suggesting that these two factors dynamically interact with one another as well as the PDCD4 transcript to maintain tight control of PDCD4 levels. Overall, this study reveals an additional set of regulatory interactions that modulate the expression of PDCD4, a key pro-apoptotic factor, and also reveals new insights into how HuR and TIA1 functions are integrated to achieve such regulation.
Collapse
Affiliation(s)
- Callie P Wigington
- From the Department of Biochemistry and Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Jeenah Jung
- the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, and Emory University, Atlanta, Georgia 30332
| | - Emily A Rye
- From the Department of Biochemistry and Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, Georgia 30322
| | - Sara L Belauret
- the School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30322
| | - Akahne M Philpot
- From the Department of Biochemistry and the Summer Scholars Research Program, Winship Cancer Institute, Atlanta, Georgia 30332, and
| | - Yue Feng
- the Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Philip J Santangelo
- the Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, and Emory University, Atlanta, Georgia 30332
| | | |
Collapse
|
74
|
Arora R, Lee Y, Wischnewski H, Brun CM, Schwarz T, Azzalin CM. RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells. Nat Commun 2014; 5:5220. [PMID: 25330849 PMCID: PMC4218956 DOI: 10.1038/ncomms6220] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/10/2014] [Indexed: 12/21/2022] Open
Abstract
A fraction of cancer cells maintain telomeres through the telomerase-independent, ‘Alternative Lengthening of Telomeres’ (ALT) pathway. ALT relies on homologous recombination (HR) between telomeric sequences; yet, what makes ALT telomeres recombinogenic remains unclear. Here we show that the RNA endonuclease RNaseH1 regulates the levels of RNA–DNA hybrids between telomeric DNA and the long noncoding RNA TERRA, and is a key mediator of telomere maintenance in ALT cells. RNaseH1 associated to telomeres specifically in ALT cells and its depletion led to telomeric hybrid accumulation, exposure of single-stranded telomeric DNA, activation of replication protein A at telomeres and abrupt telomere excision. Conversely, overexpression of RNaseH1 weakened the recombinogenic nature of ALT telomeres and led to telomere shortening. Altering cellular RNaseH1 levels did not perturb telomere homoeostasis in telomerase-positive cells. RNaseH1 maintains regulated levels of telomeric RNA–DNA hybrids at ALT telomeres to trigger HR without compromising telomere integrity too severely. A subset of cancers maintains telomere length independently of telomerase by activating alternative lengthening of telomeres (ALT) pathways. Here the authors show that RNaseH1 modulates telomeric homologous recombination frequencies in ALT cells by regulating the levels of RNA–DNA hybrids between TERRA and telomeric DNA.
Collapse
Affiliation(s)
- Rajika Arora
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Yongwoo Lee
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Harry Wischnewski
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Catherine M Brun
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Tobias Schwarz
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| |
Collapse
|
75
|
Britton S, Dernoncourt E, Delteil C, Froment C, Schiltz O, Salles B, Frit P, Calsou P. DNA damage triggers SAF-A and RNA biogenesis factors exclusion from chromatin coupled to R-loops removal. Nucleic Acids Res 2014; 42:9047-62. [PMID: 25030905 PMCID: PMC4132723 DOI: 10.1093/nar/gku601] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We previously identified the heterogeneous ribonucleoprotein SAF-A/hnRNP U as a substrate for DNA-PK, a protein kinase involved in DNA damage response (DDR). Using laser micro-irradiation in human cells, we report here that SAF-A exhibits a two-phase dynamics at sites of DNA damage, with a rapid and transient recruitment followed by a prolonged exclusion. SAF-A recruitment corresponds to its binding to Poly(ADP-ribose) while its exclusion is dependent on the activity of ATM, ATR and DNA-PK and reflects the dissociation from chromatin of SAF-A associated with ongoing transcription. Having established that SAF-A RNA-binding domain recapitulates SAF-A dynamics, we show that this domain is part of a complex comprising several mRNA biogenesis proteins of which at least two, FUS/TLS and TAFII68/TAF15, exhibit similar biphasic dynamics at sites of damage. Using an original reporter for live imaging of DNA:RNA hybrids (R-loops), we show a transient transcription-dependent accumulation of R-loops at sites of DNA damage that is prolonged upon inhibition of RNA biogenesis factors exclusion. We propose that a new component of the DDR is an active anti-R-loop mechanism operating at damaged transcribed sites which includes the exclusion of mRNA biogenesis factors such as SAF-A, FUS and TAF15.
Collapse
Affiliation(s)
- Sébastien Britton
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Emma Dernoncourt
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Christine Delteil
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Carine Froment
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Odile Schiltz
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Bernard Salles
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex 4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe Labellisée Ligue Nationale Contre le Cancer
| |
Collapse
|