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Mérida-Cerro JA, Maraver-Cárdenas P, Rondón AG, Aguilera A. Rat1 promotes premature transcription termination at R-loops. Nucleic Acids Res 2024; 52:3623-3635. [PMID: 38281203 DOI: 10.1093/nar/gkae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid structures formed by a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in yeast. Importantly, we demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such structures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, providing an entry site for Rat1. Thus, we have uncovered an unanticipated function of Rat1 as a transcription restoring factor opening up the possibility that it may also promote transcription through other genomic DNA structures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relieved by Rat1, it will cause genomic instability, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.
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Affiliation(s)
- José Antonio Mérida-Cerro
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Pablo Maraver-Cárdenas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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2
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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3
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Wang T, Li J, Yang L, Wu M, Ma Q. The Role of Long Non-coding RNAs in Human Imprinting Disorders: Prospective Therapeutic Targets. Front Cell Dev Biol 2021; 9:730014. [PMID: 34760887 PMCID: PMC8573313 DOI: 10.3389/fcell.2021.730014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
Genomic imprinting is a term used for an intergenerational epigenetic inheritance and involves a subset of genes expressed in a parent-of-origin-dependent way. Imprinted genes are expressed preferentially from either the paternally or maternally inherited allele. Long non-coding RNAs play essential roles in regulating this allele-specific expression. In several well-studied imprinting clusters, long non-coding RNAs have been found to be essential in regulating temporal- and spatial-specific establishment and maintenance of imprinting patterns. Furthermore, recent insights into the epigenetic pathological mechanisms underlying human genomic imprinting disorders suggest that allele-specific expressed imprinted long non-coding RNAs serve as an upstream regulator of the expression of other protein-coding or non-coding imprinted genes in the same cluster. Aberrantly expressed long non-coding RNAs result in bi-allelic expression or silencing of neighboring imprinted genes. Here, we review the emerging roles of long non-coding RNAs in regulating the expression of imprinted genes, especially in human imprinting disorders, and discuss three strategies targeting the central long non-coding RNA UBE3A-ATS for the purpose of developing therapies for the imprinting disorders Prader-Willi syndrome and Angelman syndrome. In summary, a better understanding of long non-coding RNA-related mechanisms is key to the development of potential therapeutic targets for human imprinting disorders.
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Affiliation(s)
- Tingxuan Wang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianjian Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liuyi Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Manyin Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qing Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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4
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Abstract
Double-stranded RNA (dsRNA) is produced both by virus and host. Its recognition by the melanoma differentiation-associated gene 5 (MDA5) initiates type I interferon responses. How can a host distinguish self-transcripts from nonself to ensure that responses are targeted correctly? Here, I discuss a role for MDA5 helicase in inducing Z-RNA formation by Alu inverted repeat (AIR) elements. These retroelements have highly conserved sequences that favor Z-formation, creating a site for the dsRNA-specific deaminase enzyme ADAR1 to dock. The subsequent editing destabilizes the dsRNA, ending further interaction with MDA5 and terminating innate immune responses directed against self. By enabling self-recognition, Alu retrotransposons, once invaders, now are genetic elements that keep immune responses in check. I also discuss the possible but less characterized roles of the other helicases in modulating innate immune responses, focusing on DExH-box helicase 9 (DHX9) and Mov10 RISC complex RNA helicase (MOV10). DHX9 and MOV10 function differently from MDA5, but still use nucleic acid structure, rather than nucleotide sequence, to define self. Those genetic elements encoding the alternative conformations involved, referred to as flipons, enable helicases to dynamically shape a cell's repertoire of responses. In the case of MDA5, Alu flipons switch off the dsRNA-dependent responses against self. I suggest a number of genetic systems in which to study interactions between flipons and helicases further.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, Charlestown, Massachusetts, United States of America
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5
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Abstract
Physiological and pathological roles for R-loop structures continue to be discovered, and studies suggest that R-loops could contribute to human disease. R-loops are nucleic acid structures characterized by a DNA:RNA hybrid and displaced single-stranded DNA that occur in connection with transcription. R-loops form naturally and have been shown to be important for a number of physiological processes such as mitochondrial replication initiation, class switch recombination, DNA repair, modulating DNA topology, and regulation of gene expression. However, subsets of R-loops or persistent R-loops lead to DNA breaks, chromosome rearrangement, and genome instability. In addition, R-loops have been linked to human diseases, specifically neurological disorders and cancer. Of the large amount of research produced recently on R-loops, this review covers evidence for R-loop involvement in normal cellular physiology and pathophysiology, as well as describing factors that contribute to R-loop regulation.
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Affiliation(s)
- Ryan Patrick Mackay
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Qinqin Xu
- Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
| | - Paul M Weinberger
- Department of Molecular and Cellular Physiology and Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA.,Department of Otolaryngology - Head & Neck Surgery, Louisiana State University Health Sciences Center - Shreveport, Shreveport, Louisiana, USA
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6
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7
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Herbert A. Simple Repeats as Building Blocks for Genetic Computers. Trends Genet 2020; 36:739-750. [PMID: 32690316 DOI: 10.1016/j.tig.2020.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 11/15/2022]
Abstract
Processing of RNA involves heterogeneous nuclear ribonucleoproteins. The simple sequence repeats (SSRs) they bind can also adopt alternative DNA structures, like Z DNA, triplexes, G quadruplexes, and I motifs. Those SSRs capable of switching conformation under physiological conditions (called flipons) are genetic elements that can encode alternative RNA processing by their effects on RNA processivity, most likely as DNA:RNA hybrids. Flipons are elements of a binary, instructive genetic code directing how genomic sequences are compiled into transcripts. The combinatorial nature of this code provides a rich set of options for creating genetic computers able to reproduce themselves and use a heritable and evolvable code to optimize survival. The underlying computational logic potentiates a diverse set of genetic programs that modify cis-mediated heritability and disease risk.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA.
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8
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Chedin F, Benham CJ. Emerging roles for R-loop structures in the management of topological stress. J Biol Chem 2020; 295:4684-4695. [PMID: 32107311 DOI: 10.1074/jbc.rev119.006364] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
R-loop structures are a prevalent class of alternative non-B DNA structures that form during transcription upon invasion of the DNA template by the nascent RNA. R-loops form universally in the genomes of organisms ranging from bacteriophages, bacteria, and yeasts to plants and animals, including mammals. A growing body of work has linked these structures to both physiological and pathological processes, in particular to genome instability. The rising interest in R-loops is placing new emphasis on understanding the fundamental physicochemical forces driving their formation and stability. Pioneering work in Escherichia coli revealed that DNA topology, in particular negative DNA superhelicity, plays a key role in driving R-loops. A clear role for DNA sequence was later uncovered. Here, we review and synthesize available evidence on the roles of DNA sequence and DNA topology in controlling R-loop formation and stability. Factoring in recent developments in R-loop modeling and single-molecule profiling, we propose a coherent model accounting for the interplay between DNA sequence and DNA topology in driving R-loop structure formation. This model reveals R-loops in a new light as powerful and reversible topological stress relievers, an insight that significantly expands the repertoire of R-loops' potential biological roles under both normal and aberrant conditions.
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Affiliation(s)
- Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616 .,Genome Center, University of California, Davis, California 95616
| | - Craig J Benham
- Genome Center, University of California, Davis, California 95616 .,Departments of Mathematics and Biomedical Engineering, University of California, Davis, California 95616
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9
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Belotserkovskii BP, Tornaletti S, D'Souza AD, Hanawalt PC. R-loop generation during transcription: Formation, processing and cellular outcomes. DNA Repair (Amst) 2018; 71:69-81. [PMID: 30190235 PMCID: PMC6340742 DOI: 10.1016/j.dnarep.2018.08.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
R-loops are structures consisting of an RNA-DNA duplex and an unpaired DNA strand. They can form during transcription upon nascent RNA "threadback" invasion into the DNA duplex to displace the non-template strand. Although R-loops occur naturally in all kingdoms of life and serve regulatory roles, they are often deleterious and can cause genomic instability. Of particular importance are the disastrous consequences when replication forks or transcription complexes collide with R-loops. The appropriate processing of R-loops is essential to avoid a number of human neurodegenerative and other clinical disorders. We provide a perspective on mechanistic aspects of R-loop formation and their resolution learned from studies in model systems. This should contribute to improved understanding of R-loop biological functions and enable their practical applications. We propose the novel employment of artificially-generated stable R-loops to selectively inactivate tumor cells.
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Affiliation(s)
- Boris P Belotserkovskii
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Silvia Tornaletti
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Alicia D D'Souza
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States
| | - Philip C Hanawalt
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, United States.
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10
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Raghunathan N, Kapshikar RM, Leela JK, Mallikarjun J, Bouloc P, Gowrishankar J. Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli. Nucleic Acids Res 2018; 46:3400-3411. [PMID: 29474582 PMCID: PMC5909445 DOI: 10.1093/nar/gky118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.
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Affiliation(s)
- Nalini Raghunathan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Rajvardhan M Kapshikar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jakku K Leela
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
| | - Jillella Mallikarjun
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
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11
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D'Souza AD, Belotserkovskii BP, Hanawalt PC. A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:158-166. [PMID: 29357316 PMCID: PMC5820110 DOI: 10.1016/j.bbagrm.2017.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 01/01/2023]
Abstract
The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription.
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Affiliation(s)
- Alicia D D'Souza
- Department of Biology, Stanford University, Stanford, CA 94305-5020, United States
| | | | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, CA 94305-5020, United States.
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12
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Sarkar K, Han SS, Wen KK, Ochs HD, Dupré L, Seidman MM, Vyas YM. R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome. J Allergy Clin Immunol 2017; 142:219-234. [PMID: 29248492 DOI: 10.1016/j.jaci.2017.11.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/07/2017] [Accepted: 11/10/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. OBJECTIVE We sought to define how dysfunctional gene transcription is causally linked to the degree of TH cell deficiency and genomic instability in the XLT/WAS clinical spectrum. METHODS In human TH1- or TH2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. RESULTS WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in TH1 cells relative to TH2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (TH1 genes) in TH1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (TH2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. CONCLUSION Transcriptional R-loop imbalance is a novel molecular defect causative in TH1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum and could be targeted therapeutically.
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Affiliation(s)
- Koustav Sarkar
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md
| | - Seong-Su Han
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md
| | - Kuo-Kuang Wen
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md
| | - Hans D Ochs
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, University of Washington, Seattle, Md
| | - Loïc Dupré
- INSERM, UMR1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, Md; Université Toulouse III Paul-Sabatier, Toulouse, Md; CNRS, UMR5282, Toulouse, Md; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Md; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Md
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health (NIH), NIH Biomedical Research Center, Baltimore, Md
| | - Yatin M Vyas
- Division of Pediatric Hematology-Oncology, Carver College of Medicine and the University of Iowa Stead Family Children's Hospital, Iowa City, Md.
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13
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Belotserkovskii BP, Soo Shin JH, Hanawalt PC. Strong transcription blockage mediated by R-loop formation within a G-rich homopurine-homopyrimidine sequence localized in the vicinity of the promoter. Nucleic Acids Res 2017; 45:6589-6599. [PMID: 28498974 PMCID: PMC5499740 DOI: 10.1093/nar/gkx403] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/08/2017] [Indexed: 02/07/2023] Open
Abstract
Guanine-rich (G-rich) homopurine–homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence. This transcription blockage is much less pronounced for a C-rich sequence, and is not significant for an A-rich sequence. Remarkably, the blockage is not pronounced if transcription is performed in the presence of RNase H, which specifically digests the RNA strands within RNA–DNA hybrids. The blockage also becomes less pronounced upon reduced RNA polymerase concentration. Based upon these observations and those from control experiments, we conclude that the blockage is primarily due to the formation of stable RNA–DNA hybrids (R-loops), which inhibit successive rounds of transcription. Our results could be relevant to transcription dynamics in vivo (e.g. transcription ‘bursting’) and may also have practical implications for the design of expression vectors.
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Affiliation(s)
| | - Jane Hae Soo Shin
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
| | - Philip C Hanawalt
- Department of Biology, Stanford University, Stanford, CA 94305-5020, USA
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14
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Sanz LA, Hartono SR, Lim YW, Steyaert S, Rajpurkar A, Ginno PA, Xu X, Chédin F. Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals. Mol Cell 2016; 63:167-78. [PMID: 27373332 DOI: 10.1016/j.molcel.2016.05.032] [Citation(s) in RCA: 365] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 01/11/2016] [Accepted: 05/23/2016] [Indexed: 11/28/2022]
Abstract
R-loops are three-stranded nucleic acid structures formed upon annealing of an RNA strand to one strand of duplex DNA. We profiled R-loops using a high-resolution, strand-specific methodology in human and mouse cell types. R-loops are prevalent, collectively occupying up to 5% of mammalian genomes. R-loop formation occurs over conserved genic hotspots such as promoter and terminator regions of poly(A)-dependent genes. In most cases, R-loops occur co-transcriptionally and undergo dynamic turnover. Detailed epigenomic profiling revealed that R-loops associate with specific chromatin signatures. At promoters, R-loops associate with a hyper-accessible state characteristic of unmethylated CpG island promoters. By contrast, terminal R-loops associate with an enhancer- and insulator-like state and define a broad class of transcription terminators. Together, this suggests that the retention of nascent RNA transcripts at their site of expression represents an abundant, dynamic, and programmed component of the mammalian chromatin that affects chromatin patterning and the control of gene expression.
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Affiliation(s)
- Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Yoong Wearn Lim
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Sandra Steyaert
- Department of Mathematical Modeling, Statistics, and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Aparna Rajpurkar
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Paul A Ginno
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Xiaoqin Xu
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA 95616, USA.
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15
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Belotserkovskii BP. Torque-winding interdependence for a flexible polymer chain wound around a cylinder in the presence of obstacles. Phys Rev E 2016; 93:032509. [PMID: 27078407 DOI: 10.1103/physreve.93.032509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Indexed: 11/07/2022]
Abstract
Polymer chains winding around each other or around other objects occur in many natural systems; the physical consequences of this winding are therefore of significant interest. A polymer chain could be surrounded by various bulky objects (referred as obstacles), such as other macromolecules or macromolecular aggregates. Here we show that for a long flexible polymer chain wound around a cylinder, the presence of obstacles could modify the winding-torque interdependence, in some cases leading to phase-transition-like behavior in which the winding occurs only when the torque exceeds some critical value. Possible implications of this effect are discussed in relation to the biophysics of nucleic acids.
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Affiliation(s)
- Boris P Belotserkovskii
- Herrin Laboratories, Department of Biology, Stanford University, Stanford, California 94305-5020, USA
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16
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Laleman M, Baiesi M, Belotserkovskii BP, Sakaue T, Walter JC, Carlon E. Torque-Induced Rotational Dynamics in Polymers: Torsional Blobs and Thinning. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michiel Laleman
- Institute
for Theoretical Physics, KU Leuven, Celestijnenlaan 200D, Leuven, Belgium
| | - Marco Baiesi
- Department
of Physics and Astronomy, University of Padova, Via Marzolo 8, Padova, Italy
- INFN - Sezione di
Padova, Via Marzolo 8, Padova, Italy
| | - Boris P. Belotserkovskii
- Department
of Biology, Stanford University, 371 Serra Mall, Herrin Laboratories, Stanford, California 94305-5020, United States
| | - Takahiro Sakaue
- Department
of Physics, Kyushu University 33, Fukuoka 819-0395, Japan
| | - Jean-Charles Walter
- Laboratoire Charles Coulomb UMR 5221, Université de Montpellier & CNRS, F-34095, Montpellier, France
- Laboratoire de Microbiologie et Génétique Moléculaires UMR 5100, CNRS & Université Paul Sabatier, F-31000 Toulouse, France
| | - Enrico Carlon
- Institute
for Theoretical Physics, KU Leuven, Celestijnenlaan 200D, Leuven, Belgium
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17
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Abstract
The demonstration of DNA damage excision and repair replication by Setlow, Howard-Flanders, Hanawalt and their colleagues in the early 1960s, constituted the discovery of the ubiquitous pathway of nucleotide excision repair (NER). The serial steps in NER are similar in organisms from unicellular bacteria to complex mammals and plants, and involve recognition of lesions, adducts or structures that disrupt the DNA double helix, removal of a short oligonucleotide containing the offending lesion, synthesis of a repair patch copying the opposite undamaged strand, and ligation, to restore the DNA to its original form. The transcription-coupled repair (TCR) subpathway of NER, discovered nearly two decades later, is dedicated to the removal of lesions from the template DNA strands of actively transcribed genes. In this review I will outline the essential factors and complexes involved in NER in humans, and will comment on additional factors and metabolic processes that affect the efficiency of this important process.
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Affiliation(s)
- Graciela Spivak
- Department of Biology, Stanford University, Stanford, CA 94305-5020,USA.
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18
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Belotserkovskii BP. Relationships between the winding angle, the characteristic radius, and the torque for a long polymer chain wound around a cylinder: implications for RNA winding around DNA during transcription. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022709. [PMID: 25353511 DOI: 10.1103/physreve.89.022709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 06/04/2023]
Abstract
Long polymer chains are ubiquitous in biological systems and their mechanical properties have significant impact upon biological processes. Of particular interest is the situation in which polymer chains are wound around each other or around other objects. We have analyzed the parameters of a long Gaussian polymer chain wound around a cylinder as a function of the torque applied to the ends of the chain. We have shown that for sufficiently long polymer chains, an average winding angle and a characteristic radius of the chain can be determined from a modified Bessel function of purely imaginary order, in which the value of the order is equivalent to the applied torque, normalized to the product of the absolute temperature and the Boltzmann constant. The obtained results are consistent with a simplified interpretation in terms of "torsional blobs," and this could be extended to nonideal chains with excluded volumes. We have also extended our results to the case of a polymer chain rotating in viscous medium. Our results could be used to estimate the mechanical strains that appear in DNA and RNA during transcription, as these might initiate formation of unusual DNA structures, invasion of RNA into the DNA duplex (R-loop formation), and modulation of the interactions of DNA and RNA with proteins.
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Affiliation(s)
- Boris P Belotserkovskii
- Department of Biology, Stanford University, 371 Serra Mall, Herrin Labs, Stanford, California 94305-5020, USA
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19
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Deaconescu AM. RNA polymerase between lesion bypass and DNA repair. Cell Mol Life Sci 2013; 70:4495-509. [PMID: 23807206 PMCID: PMC11113250 DOI: 10.1007/s00018-013-1384-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 05/13/2013] [Accepted: 05/23/2013] [Indexed: 11/29/2022]
Abstract
DNA damage leads to heritable changes in the genome via DNA replication. However, as the DNA helix is the site of numerous other transactions, notably transcription, DNA damage can have diverse repercussions on cellular physiology. In particular, DNA lesions have distinct effects on the passage of transcribing RNA polymerases, from easy bypass to almost complete block of transcription elongation. The fate of the RNA polymerase positioned at a lesion is largely determined by whether the lesion is structurally subtle and can be accommodated and eventually bypassed, or bulky, structurally distorting and requiring remodeling/complete dissociation of the transcription elongation complex, excision, and repair. Here we review cellular responses to DNA damage that involve RNA polymerases with a focus on bacterial transcription-coupled nucleotide excision repair and lesion bypass via transcriptional mutagenesis. Emphasis is placed on the explosion of new structural information on RNA polymerases and relevant DNA repair factors and the mechanistic models derived from it.
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Affiliation(s)
- Alexandra M Deaconescu
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, 415 South St., MS029, Waltham, MA, 02454, USA,
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20
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Belotserkovskii BP, Mirkin SM, Hanawalt PC. DNA sequences that interfere with transcription: implications for genome function and stability. Chem Rev 2013; 113:8620-37. [PMID: 23972098 DOI: 10.1021/cr400078y] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation. Proc Natl Acad Sci U S A 2013; 110:13938-43. [PMID: 23918391 DOI: 10.1073/pnas.1305426110] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are oppositely imprinted autism-spectrum disorders with known genetic bases, but complex epigenetic mechanisms underlie their pathogenesis. The PWS/AS locus on 15q11-q13 is regulated by an imprinting control region that is maternally methylated and silenced. The PWS imprinting control region is the promoter for a one megabase paternal transcript encoding the ubiquitous protein-coding Snrpn gene and multiple neuron-specific noncoding RNAs, including the PWS-related Snord116 repetitive locus of small nucleolar RNAs and host genes, and the antisense transcript to AS-causing ubiquitin ligase encoding Ube3a (Ube3a-ATS). Neuron-specific transcriptional progression through Ube3a-ATS correlates with paternal Ube3a silencing and chromatin decondensation. Interestingly, topoisomerase inhibitors, including topotecan, were recently identified in an unbiased drug screen for compounds that could reverse the silent paternal allele of Ube3a in neurons, but the mechanism of topotecan action on the PWS/AS locus is unknown. Here, we demonstrate that topotecan treatment stabilizes the formation of RNA:DNA hybrids (R loops) at G-skewed repeat elements within paternal Snord116, corresponding to increased chromatin decondensation and inhibition of Ube3a-ATS expression. Neural precursor cells from paternal Snord116 deletion mice exhibit increased Ube3a-ATS levels in differentiated neurons and show a reduced effect of topotecan compared with wild-type neurons. These results demonstrate that the AS candidate drug topotecan acts predominantly through stabilizing R loops and chromatin decondensation at the paternally expressed PWS Snord116 locus. Our study holds promise for targeted therapies to the Snord116 locus for both AS and PWS.
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22
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Belotserkovskii BP, Neil AJ, Saleh SS, Shin JHS, Mirkin SM, Hanawalt PC. Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks. Nucleic Acids Res 2012; 41:1817-28. [PMID: 23275544 PMCID: PMC3561996 DOI: 10.1093/nar/gks1333] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation.
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23
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Liu CR, Chang CR, Chern Y, Wang TH, Hsieh WC, Shen WC, Chang CY, Chu IC, Deng N, Cohen S, Cheng TH. Spt4 Is Selectively Required for Transcription of Extended Trinucleotide Repeats. Cell 2012; 148:690-701. [DOI: 10.1016/j.cell.2011.12.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 10/03/2011] [Accepted: 12/13/2011] [Indexed: 10/28/2022]
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24
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Geisler S, Lojek L, Khalil AM, Baker KE, Coller J. Decapping of long noncoding RNAs regulates inducible genes. Mol Cell 2012; 45:279-91. [PMID: 22226051 DOI: 10.1016/j.molcel.2011.11.025] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 10/21/2011] [Accepted: 11/23/2011] [Indexed: 12/16/2022]
Abstract
Decapping represents a critical control point in regulating expression of protein coding genes. Here, we demonstrate that decapping also modulates expression of long noncoding RNAs (lncRNAs). Specifically, levels of >100 lncRNAs in yeast are controlled by decapping and are degraded by a pathway that occurs independent of decapping regulators. We find many lncRNAs degraded by DCP2 are expressed proximal to inducible genes. Of these, we show several genes required for galactose utilization are associated with lncRNAs that have expression patterns inversely correlated with their mRNA counterpart. Moreover, decapping of these lncRNAs is critical for rapid and robust induction of GAL gene expression. Failure to destabilize a lncRNA known to exert repressive histone modifications results in perpetuation of a repressive chromatin state that contributes to reduced plasticity of gene activation. We propose that decapping and lncRNA degradation serve a vital role in transcriptional regulation specifically at inducible genes.
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Affiliation(s)
- Sarah Geisler
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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25
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Gómez-González B, García-Rubio M, Bermejo R, Gaillard H, Shirahige K, Marín A, Foiani M, Aguilera A. Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles. EMBO J 2011; 30:3106-19. [PMID: 21701562 DOI: 10.1038/emboj.2011.206] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 05/25/2011] [Indexed: 11/09/2022] Open
Abstract
THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis and prevents transcription-associated recombination. Whether or not it has a ubiquitous role in the genome is unknown. Chromatin immunoprecipitation (ChIP)-chip studies reveal that the Hpr1 component of THO and the Sub2 RNA-dependent ATPase have genome-wide distributions at active ORFs in yeast. In contrast to RNA polymerase II, evenly distributed from promoter to termination regions, THO and Sub2 are absent at promoters and distributed in a gradual 5' → 3' gradient. This is accompanied by a genome-wide impact of THO-Sub2 deletions on expression of highly expressed, long and high G+C-content genes. Importantly, ChIP-chips reveal an over-recruitment of Rrm3 in active genes in THO mutants that is reduced by RNaseH1 overexpression. Our work establishes a genome-wide function for THO-Sub2 in transcription elongation and mRNP biogenesis that function to prevent the accumulation of transcription-mediated replication obstacles, including R-loops.
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Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Sevilla, Spain
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