1
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Hu J, Xing Z, Yang H, Zhou Y, Guo L, Zhang X, Xu L, Liu Q, Ye J, Zhong X, Wang J, Lin R, Long E, Jiang J, Chen L, Pan Y, He L, Chen JY. Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases. iScience 2024; 27:110584. [PMID: 39188986 PMCID: PMC11345597 DOI: 10.1016/j.isci.2024.110584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/17/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024] Open
Abstract
R-loops play diverse functional roles, but controversial genomic localization of R-loops have emerged from experimental approaches, posing significant challenges for R-loop research. The development and application of an accurate computational tool for studying human R-loops remains an unmet need. Here, we introduce DeepER, a deep learning-enhanced R-loop prediction tool. DeepER showcases outstanding performance compared to existing tools, facilitating accurate genome-wide annotation of R-loops and a deeper understanding of the position- and context-dependent effects of nucleotide composition on R-loop formation. DeepER also unveils a strong association between certain tandem repeats and R-loop formation, opening a new avenue for understanding the mechanisms underlying some repeat expansion diseases. To facilitate broader utilization, we have developed a user-friendly web server as an integral component of R-loopBase. We anticipate that DeepER will find extensive applications in the field of R-loop research.
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Affiliation(s)
- Jiyun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zetong Xing
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongbing Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yongli Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Liufei Guo
- School of Computer Science and Technology, Xi’an University of Posts and Telecommunications, Xi’an, Shaanxi 710121, China
| | - Xianhong Zhang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Longsheng Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Qiong Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jing Ye
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaoming Zhong
- Center of Excellence for Leukemia Studies, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jixin Wang
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Ruoyao Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Erping Long
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
| | - Jiewei Jiang
- School of Electronic Engineering, Xi’an University of Posts and Telecommunications, Xi’an, Shaanxi 710121, China
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yongcheng Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lang He
- School of Computer Science and Technology, Xi’an University of Posts and Telecommunications, Xi’an, Shaanxi 710121, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Neurology at Nanjing Drum Tower Hospital, Nanjing University, Nanjing, Jiangsu 210023, China
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, Jiangsu 210023, China
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2
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Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024; 26:1025-1036. [PMID: 38914786 DOI: 10.1038/s41556-024-01437-4] [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: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Barrett AK, Shingare MR, Rechtsteiner A, Rodriguez KM, Le QN, Wijeratne TU, Mitchell CE, Membreno MW, Rubin SM, Müller GA. HDAC activity is dispensable for repression of cell-cycle genes by DREAM and E2F:RB complexes. Nat Commun 2024; 15:4450. [PMID: 38789411 PMCID: PMC11126580 DOI: 10.1038/s41467-024-48724-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) play a crucial role in transcriptional regulation and are implicated in various diseases, including cancer. They are involved in histone tail deacetylation and canonically linked to transcriptional repression. Previous studies suggested that HDAC recruitment to cell-cycle gene promoters via the retinoblastoma (RB) protein or the DREAM complex through SIN3B is essential for G1/S and G2/M gene repression during cell-cycle arrest and exit. Here we investigate the interplay among DREAM, RB, SIN3 proteins, and HDACs in the context of cell-cycle gene repression. Knockout of SIN3B does not globally derepress cell-cycle genes in non-proliferating HCT116 and C2C12 cells. Loss of SIN3A/B moderately upregulates several cell-cycle genes in HCT116 cells but does so independently of DREAM/RB. HDAC inhibition does not induce general upregulation of RB/DREAM target genes in arrested transformed or non-transformed cells. Our findings suggest that E2F:RB and DREAM complexes can repress cell-cycle genes without relying on HDAC activity.
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Affiliation(s)
- Alison K Barrett
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Manisha R Shingare
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Kelsie M Rodriguez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Quynh N Le
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Tilini U Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Corbin E Mitchell
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Miles W Membreno
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.
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4
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Mukhopadhyay P, Miller H, Stoja A, Bishop AJR. Approaches for Mapping and Analysis of R-loops. Curr Protoc 2024; 4:e1037. [PMID: 38666626 DOI: 10.1002/cpz1.1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
R-loops are nucleic acid structures composed of a DNA:RNA hybrid with a displaced non-template single-stranded DNA. Current approaches to identify and map R-loop formation across the genome employ either an antibody targeted against R-loops (S9.6) or a catalytically inactivated form of RNase H1 (dRNH1), a nuclease that can bind and resolve DNA:RNA hybrids via RNA exonuclease activity. This overview article outlines several ways to map R-loops using either methodology, explaining the differences and similarities among the approaches. Bioinformatic analysis of R-loops involves several layers of quality control and processing before visualizing the data. This article provides resources and tools that can be used to accurately process R-loop mapping data and explains the advantages and disadvantages of the resources as compared to one another. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Pramiti Mukhopadhyay
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | | | - Aiola Stoja
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
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5
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Tsao N, Olabode J, Rodell R, Sun H, Brickner JR, Tsai MS, Pollina EA, Chen CK, Mosammaparast N. YTHDC1 cooperates with the THO complex to prevent RNA damage-induced DNA breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585107. [PMID: 38559256 PMCID: PMC10979943 DOI: 10.1101/2024.03.14.585107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Certain environmental toxins are nucleic acid damaging agents, as are many chemotherapeutics used for cancer therapy. These agents induce various adducts in DNA as well as RNA. Indeed, most of the nucleic acid adducts (>90%) formed due to these chemicals, such as alkylating agents, occur in RNA 1 . However, compared to the well-studied mechanisms for DNA alkylation repair, the biological consequences of RNA damage are largely unexplored. Here, we demonstrate that RNA damage can directly result in loss of genome integrity. Specifically, we show that a human YTH domain-containing protein, YTHDC1, regulates alkylation damage responses in association with the THO complex (THOC) 2 . In addition to its established binding to N 6-methyladenosine (m6A)-containing RNAs, YTHDC1 binds to N 1-methyladenosine (m1A)-containing RNAs upon alkylation. In the absence of YTHDC1, alkylation damage results in increased alkylation damage sensitivity and DNA breaks. Such phenotypes are fully attributable to RNA damage, since an RNA-specific dealkylase can rescue these phenotypes. These R NA d amage-induced DNA b reaks (RDIBs) depend on R-loop formation, which in turn are processed by factors involved in transcription-coupled nucleotide excision repair. Strikingly, in the absence of YTHDC1 or THOC, an RNA m1A methyltransferase targeted to the nucleus is sufficient to induce DNA breaks. Our results uncover a unique role for YTHDC1-THOC in base damage responses by preventing RDIBs, providing definitive evidence for how damaged RNAs can impact genomic integrity.
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Huang X, Balmer S, Lyu C, Xiang Y, Malik V, Wang H, Zhang Y, Cai B, Xie W, Hadjantonakis AK, Zhou H, Wang J. ZFP281 controls transcriptional and epigenetic changes promoting mouse pluripotent state transitions via DNMT3 and TET1. Dev Cell 2024; 59:465-481.e6. [PMID: 38237590 PMCID: PMC10923053 DOI: 10.1016/j.devcel.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 11/04/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024]
Abstract
The progression from naive through formative to primed in vitro pluripotent stem cell states recapitulates epiblast development in vivo during the peri-implantation period of mouse embryo development. Activation of the de novo DNA methyltransferases and reorganization of transcriptional and epigenetic landscapes are key events that occur during these pluripotent state transitions. However, the upstream regulators that coordinate these events are relatively underexplored. Here, using Zfp281 knockout mouse and degron knockin cell models, we identify the direct transcriptional activation of Dnmt3a/3b by ZFP281 in pluripotent stem cells. Chromatin co-occupancy of ZFP281 and DNA hydroxylase TET1, which is dependent on the formation of R-loops in ZFP281-targeted gene promoters, undergoes a "high-low-high" bimodal pattern regulating dynamic DNA methylation and gene expression during the naive-formative-primed transitions. ZFP281 also safeguards DNA methylation in maintaining primed pluripotency. Our study demonstrates a previously unappreciated role for ZFP281 in coordinating DNMT3A/3B and TET1 functions to promote pluripotent state transitions.
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Affiliation(s)
- Xin Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Sophie Balmer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cong Lyu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunlong Xiang
- Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Vikas Malik
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hailin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu Zhang
- Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200082, China
| | - Bishuang Cai
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wei Xie
- Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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7
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Hou Y, Li Y, Xiang JF, Tilahun K, Jiang J, Corces VG, Yao B. TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk. Cell Rep 2024; 43:113662. [PMID: 38184854 PMCID: PMC10857847 DOI: 10.1016/j.celrep.2023.113662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
TDP-43 is an RNA/DNA-binding protein that forms aggregates in various brain disorders. TDP-43 engages in many aspects of RNA metabolism, but its molecular roles in regulating genes and transposable elements (TEs) have not been extensively explored. Chronic TDP-43 knockdown impairs cell proliferation and cellular responses to DNA damage. At the molecular level, TDP-43 chronic deficiency affects gene expression either locally or distally by concomitantly altering the crosstalk between R-loops and 5-hydroxymethylcytosine (5hmC) in gene bodies and long-range enhancer/promoter interactions. Furthermore, TDP-43 knockdown induces substantial disease-relevant TE activation by influencing their R-loop and 5hmC homeostasis in a locus-specific manner. Together, our findings highlight the genomic roles of TDP-43 in modulating R-loop-5hmC coordination in coding genes, distal regulatory elements, and TEs, presenting a general and broad molecular mechanism underlying the contributions of proteinopathies to the etiology of neurodegenerative disorders.
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Affiliation(s)
- Yingzi Hou
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jian-Feng Xiang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kedamawit Tilahun
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jie Jiang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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8
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Hwang J, Palmer B, Myong S. Single-molecule observation of G-quadruplex and R-loop formation induced by transcription. Methods Enzymol 2024; 695:71-88. [PMID: 38521591 DOI: 10.1016/bs.mie.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Potential G-quadruplex forming sequences (PQS) are enriched in cancer-related genes and immunoglobulin class-switch recombination. They are prevalent in the 5'UTR of transcriptionally active genes, thereby contributing to the regulation of gene expression. We and others previously demonstrated that the PQS located in the non-template strand leads to an R-loop formation followed by a G-quadruplex (G4) formation during transcription. These structural changes increase mRNA production. Here, we present how single-molecule technique was used to observe cotranscriptional G4 and R-loop formation and to examine the impact on transcription, particularly for the initiation and elongation stages.
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Affiliation(s)
- Jihee Hwang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Bradleigh Palmer
- Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Sua Myong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States; Program in Cellular Molecular Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, MD, United States.
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9
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Martin RM, de Almeida MR, Gameiro E, de Almeida SF. Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics. Nucleic Acids Res 2023; 51:11010-11023. [PMID: 37819055 PMCID: PMC10639055 DOI: 10.1093/nar/gkad812] [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: 01/21/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
We have developed RHINO, a genetically encoded sensor that selectively binds RNA:DNA hybrids enabling live-cell imaging of cellular R-loops. RHINO comprises a tandem array of three copies of the RNA:DNA hybrid binding domain of human RNase H1 connected by optimized linker segments and fused to a fluorescent protein. This tool allows the measurement of R-loop abundance and dynamics in live cells with high specificity and sensitivity. Using RHINO, we provide a kinetic framework for R-loops at nucleoli, telomeres and protein-coding genes. Our findings demonstrate that R-loop dynamics vary significantly across these regions, potentially reflecting the distinct roles R-loops play in different chromosomal contexts. RHINO is a powerful tool for investigating the role of R-loops in cellular processes and their contribution to disease development and progression.
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Affiliation(s)
- Robert M Martin
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Madalena R de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Eduardo Gameiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
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10
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Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
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Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
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11
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Barrett A, Shingare MR, Rechtsteiner A, Wijeratne TU, Rodriguez KM, Rubin SM, Müller GA. HDAC activity is dispensable for repression of cell-cycle genes by DREAM and E2F:RB complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564489. [PMID: 37961464 PMCID: PMC10634886 DOI: 10.1101/2023.10.28.564489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Histone deacetylases (HDACs) are pivotal in transcriptional regulation, and their dysregulation has been associated with various diseases including cancer. One of the critical roles of HDAC-containing complexes is the deacetylation of histone tails, which is canonically linked to transcriptional repression. Previous research has indicated that HDACs are recruited to cell-cycle gene promoters through the RB protein or the DREAM complex via SIN3B and that HDAC activity is essential for repressing G1/S and G2/M cell-cycle genes during cell-cycle arrest and exit. In this study, we sought to explore the interdependence of DREAM, RB, SIN3 proteins, and HDACs in the context of cell-cycle gene repression. We found that genetic knockout of SIN3B did not lead to derepression of cell-cycle genes in non-proliferating HCT116 and C2C12 cells. A combined loss of SIN3A and SIN3B resulted in a moderate upregulation in mRNA expression of several cell-cycle genes in arrested HCT116 cells, however, these effects appeared to be independent of DREAM or RB. Furthermore, HDAC inhibition did not induce a general upregulation of RB and DREAM target gene expression in arrested transformed or non-transformed cells. Our findings provide evidence that E2F:RB and DREAM complexes can repress cell-cycle genes without reliance on HDAC activity.
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Affiliation(s)
- Alison Barrett
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
- Current Affiliation: Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA
| | - Manisha R. Shingare
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Tilini U. Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
- Current Affiliation: Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA
| | - Kelsie M. Rodriguez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Seth M. Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Gerd A. Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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12
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Matos-Rodrigues G, Hisey JA, Nussenzweig A, Mirkin SM. Detection of alternative DNA structures and its implications for human disease. Mol Cell 2023; 83:3622-3641. [PMID: 37863029 DOI: 10.1016/j.molcel.2023.08.018] [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: 06/19/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 10/22/2023]
Abstract
Around 3% of the genome consists of simple DNA repeats that are prone to forming alternative (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine quadruplexes (G4-DNA), and others, as well as composite RNA:DNA structures (e.g., R-loops, G-loops, and H-loops). These DNA structures are dynamic and favored by the unwinding of duplex DNA. For many years, the association of alternative DNA structures with genome function was limited by the lack of methods to detect them in vivo. Here, we review the recent advancements in the field and present state-of-the-art technologies and methods to study alternative DNA structures. We discuss the limitations of these methods as well as how they are beginning to provide insights into causal relationships between alternative DNA structures, genome function and stability, and human disease.
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Affiliation(s)
| | - Julia A Hisey
- Department of Biology, Tufts University, Medford, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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13
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He X, Yuan J, Gao Z, Wang Y. Promoter R-Loops Recruit U2AF1 to Modulate Its Phase Separation and RNA Splicing. J Am Chem Soc 2023; 145:21646-21660. [PMID: 37733759 PMCID: PMC10557143 DOI: 10.1021/jacs.3c08204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 09/23/2023]
Abstract
R-loops and guanine quadruplexes (G4s) are secondary structures of nucleic acids that are ubiquitously present in cells and are enriched in promoter regions of genes. By employing a bioinformatic approach based on overlap analysis of transcription factor chromatin immunoprecipitation sequencing (ChIP-seq) data sets, we found that many splicing factors, including U2AF1 whose recognition of the 3' splicing site is crucial for pre-mRNA splicing, exhibit pronounced enrichment at endogenous R-loop- and DNA G4-structure loci in promoter regions of human genes. We also revealed that U2AF1 binds directly to R-loops and DNA G4 structures at a low-nM binding affinity. Additionally, we showed the ability of U2AF1 to undergo phase separation, which could be stimulated by binding with R-loops, but not duplex DNA, RNA/DNA hybrid, DNA G4, or single-stranded RNA. We also demonstrated that U2AF1 binds to promoter R-loops in human cells, and this binding competes with U2AF1's interaction with 3' splicing site and leads to augmented distribution of RNA polymerase II (RNAPII) to promoters over gene bodies, thereby modulating cotranscriptional pre-mRNA splicing. Together, we uncovered a group of candidate proteins that can bind to both R-loops and DNA G4s, revealed the direct and strong interactions of U2AF1 with these nucleic acid structures, and established a biochemical rationale for U2AF1's occupancy in gene promoters. We also unveiled that interaction with R-loops promotes U2AF1's phase separation, and our work suggests that U2AF1 modulates pre-mRNA splicing by regulating RNAPII's partition in transcription initiation versus elongation.
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Affiliation(s)
- Xiaomei He
- Department
of Chemistry, University of California Riverside, Riverside, California 92521-0403, United
States
| | - Jun Yuan
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California 92521-0403, United States
| | - Zi Gao
- Department
of Chemistry, University of California Riverside, Riverside, California 92521-0403, United
States
| | - Yinsheng Wang
- Department
of Chemistry, University of California Riverside, Riverside, California 92521-0403, United
States
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California 92521-0403, United States
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14
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Hall H. R-loops in neuronal aging. Aging (Albany NY) 2023; 15:8535-8536. [PMID: 37708290 PMCID: PMC10522376 DOI: 10.18632/aging.205070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/27/2023] [Indexed: 09/16/2023]
Affiliation(s)
- Hana Hall
- Biochemistry Department, Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47906, USA
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15
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Lyu R, Wu T, Park G, He YY, Chen M, He C. KAS-Analyzer: a novel computational framework for exploring KAS-seq data. BIOINFORMATICS ADVANCES 2023; 3:vbad121. [PMID: 37745002 PMCID: PMC10516523 DOI: 10.1093/bioadv/vbad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/09/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023]
Abstract
Motivation Kethoxal-assisted ssDNA sequencing (KAS-seq) is rapidly gaining popularity as a robust and effective approach to study the nascent dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source computational tools tailored for KAS-seq data are still lacking. Results Here, we introduce KAS-Analyzer, the first comprehensive computational framework aimed at streamlining and enhancing the analysis and interpretation of KAS-seq and spKAS-seq data. In addition to standard analyses, KAS-Analyzer offers many novel tools specifically designed for KAS-seq data, including, but not limited to: calculation of transcription-related metrics, identification of single-stranded transcribing (SST) enhancers, high-resolution mapping of R-loops, and differential RNA polymerase activity analysis. We provided a detailed overview of KAS-seq data and its diverse applications through the implementation of KAS-Analyzer. Using the example time-course KAS-seq datasets, we further showcase the robust capabilities of KAS-Analyzer for investigating dynamic transcriptional regulatory programs in response to UVB radiation. Availability and implementation KAS-Analyzer is available at https://github.com/Ruitulyu/KAS-Analyzer.
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Affiliation(s)
- Ruitu Lyu
- Department of Chemistry, The University of Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, IL 60637, United States
| | - Tong Wu
- Department of Chemistry, The University of Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, IL 60637, United States
| | - Gayoung Park
- Department of Medicine, The University of Chicago, Chicago, IL 60637, United States
| | - Yu-Ying He
- Department of Medicine, The University of Chicago, Chicago, IL 60637, United States
| | - Mengjie Chen
- Department of Medicine, The University of Chicago, Chicago, IL 60637, United States
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, IL 60637, United States
- Howard Hughes Medical Institute, The University of Chicago, IL 60637, United States
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, IL 60637, United States
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16
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Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K. G-quadruplexes associated with R-loops promote CTCF binding. Mol Cell 2023; 83:3064-3079.e5. [PMID: 37552993 PMCID: PMC10529333 DOI: 10.1016/j.molcel.2023.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/24/2023] [Accepted: 07/07/2023] [Indexed: 08/10/2023]
Abstract
CTCF is a critical regulator of genome architecture and gene expression that binds thousands of sites on chromatin. CTCF genomic localization is controlled by the recognition of a DNA sequence motif and regulated by DNA modifications. However, CTCF does not bind to all its potential sites in all cell types, raising the question of whether the underlying chromatin structure can regulate CTCF occupancy. Here, we report that R-loops facilitate CTCF binding through the formation of associated G-quadruplex (G4) structures. R-loops and G4s co-localize with CTCF at many genomic regions in mouse embryonic stem cells and promote CTCF binding to its cognate DNA motif in vitro. R-loop attenuation reduces CTCF binding in vivo. Deletion of a specific G4-forming motif in a gene reduces CTCF binding and alters gene expression. Conversely, chemical stabilization of G4s results in CTCF gains and accompanying alterations in chromatin organization, suggesting a pivotal role for G4 structures in reinforcing long-range genome interactions through CTCF.
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Affiliation(s)
- Phillip Wulfridge
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qingqing Yan
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel Rell
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Doherty
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Skye Jacobson
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Offley
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra Deliard
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kelly Feng
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer E Phillips-Cremins
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kavitha Sarma
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Huang X, Balmer S, Lyu C, Xiang Y, Malik V, Wang H, Zhang Y, Xie W, Hadjantonakis AK, Zhou H, Wang J. ZFP281 coordinates DNMT3 and TET1 for transcriptional and epigenetic control in pluripotent state transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534143. [PMID: 36993548 PMCID: PMC10055359 DOI: 10.1101/2023.03.24.534143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The progression from naive through formative to primed in vitro pluripotent stem cell states recapitulates the development of the epiblast in vivo during the peri-implantation period of mammalian development. Activation of the de novo DNA methyltransferases and reorganization of transcriptional and epigenetic landscapes are key events occurring during these pluripotent state transitions. However, the upstream regulators that coordinate these events are relatively underexplored. Here, using Zfp281 knockout mouse and degron knock-in cell models, we uncover the direct transcriptional activation of Dnmt3a/3b by ZFP281 in pluripotent stem cells. Chromatin co-occupancy of ZFP281 and DNA hydroxylase TET1, dependent on the formation of R loops in ZFP281-targeted gene promoters, undergoes a "high-low-high" bimodal pattern regulating dynamic DNA methylation and gene expression during the naïive-formative-primed transitions. ZFP281 also safeguards DNA methylation in maintaining primed pluripotency. Our study demonstrates a previously unappreciated role for ZFP281 in coordinating DNMT3A/3B and TET1 functions to promote pluripotent state transitions.
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Affiliation(s)
- Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sophie Balmer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cong Lyu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yunlong Xiang
- Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Vikas Malik
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hailin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu Zhang
- Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200082, China
| | - Wei Xie
- Tsinghua Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Lead contact
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18
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Wu T, Lyu R, He C. spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity. SCIENCE ADVANCES 2022; 8:eabq2166. [PMID: 36449625 PMCID: PMC9710868 DOI: 10.1126/sciadv.abq2166] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/13/2022] [Indexed: 05/26/2023]
Abstract
R-loops affect transcription and genome stability. Dysregulation of R-loops is related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive ribonuclease H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq) to map R-loops by taking advantage of the presence of a ssDNA in the triplex structure. We show that spKAS-seq detects R-loops and their dynamics at coding sequences, enhancers, and other intergenic regions with as few as 50,000 cells. A joint analysis of R-loops and chromatin-bound RNA binding proteins (RBPs) suggested that R-loops can be RBP binding hotspots on the chromatin.
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Affiliation(s)
- Tong Wu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Ruitu Lyu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
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19
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Zhou J, Zhang W, Sun Q. R-loop: The new genome regulatory element in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2275-2289. [PMID: 36223078 DOI: 10.1111/jipb.13383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
An R-loop is a three-stranded chromatin structure that consists of a displaced single strand of DNA and an RNA:DNA hybrid duplex, which was thought to be a rare by-product of transcription. However, recent genome-wide data have shown that R-loops are widespread and pervasive in a variety of genomes, and a growing body of experimental evidence indicates that R-loops have both beneficial and harmful effects on an organism. To maximize benefit and avoid harm, organisms have evolved several means by which they tightly regulate R-loop levels. Here, we summarize our current understanding of the biogenesis and effects of R-loops, the mechanisms that regulate them, and methods of R-loop profiling, reviewing recent research advances on R-loops in plants. Furthermore, we provide perspectives on future research directions for R-loop biology in plants, which might lead to a more comprehensive understanding of R-loop functions in plant genome regulation and contribute to future agricultural improvements.
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Affiliation(s)
- Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
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20
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Khan ES, Danckwardt S. Pathophysiological Role and Diagnostic Potential of R-Loops in Cancer and Beyond. Genes (Basel) 2022; 13:genes13122181. [PMID: 36553448 PMCID: PMC9777984 DOI: 10.3390/genes13122181] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
R-loops are DNA-RNA hybrids that play multifunctional roles in gene regulation, including replication, transcription, transcription-replication collision, epigenetics, and preserving the integrity of the genome. The aberrant formation and accumulation of unscheduled R-loops can disrupt gene expression and damage DNA, thereby causing genome instability. Recent links between unscheduled R-loop accumulation and the abundance of proteins that modulate R-loop biogenesis have been associated with numerous human diseases, including various cancers. Although R-loops are not necessarily causative for all disease entities described to date, they can perpetuate and even exacerbate the initially disease-eliciting pathophysiology, making them structures of interest for molecular diagnostics. In this review, we discuss the (patho) physiological role of R-loops in health and disease, their surprising diagnostic potential, and state-of-the-art techniques for their detection.
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Affiliation(s)
- Essak S. Khan
- Posttranscriptional Gene Regulation, Cancer Research and Experimental Hemostasis, University Medical Center Mainz, 55131 Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- German Consortium for Translational Cancer Research (DKTK), DKFZ Frankfurt-Mainz, 60590 Frankfurt am Main, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, Cancer Research and Experimental Hemostasis, University Medical Center Mainz, 55131 Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, 55131 Mainz, Germany
- Correspondence:
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21
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Shi X, Teng H, Sun Z. An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops. Brief Bioinform 2022; 23:bbac441. [PMID: 36208174 PMCID: PMC9677470 DOI: 10.1093/bib/bbac441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022] Open
Abstract
Multiple types of non-canonical nucleic acid structures play essential roles in DNA recombination and replication, transcription, and genomic instability and have been associated with several human diseases. Thus, an increasing number of experimental and bioinformatics methods have been developed to identify these structures. To date, most reviews have focused on the features of non-canonical DNA/RNA structure formation, experimental approaches to mapping these structures, and the association of these structures with diseases. In addition, two reviews of computational algorithms for the prediction of non-canonical nucleic acid structures have been published. One of these reviews focused only on computational approaches for G4 detection until 2020. The other mainly summarized the computational tools for predicting cruciform, H-DNA and Z-DNA, in which the algorithms discussed were published before 2012. Since then, several experimental and computational methods have been developed. However, a systematic review including the conformation, sequencing mapping methods and computational prediction strategies for these structures has not yet been published. The purpose of this review is to provide an updated overview of conformation, current sequencing technologies and computational identification methods for non-canonical nucleic acid structures, as well as their strengths and weaknesses. We expect that this review will aid in understanding how these structures are characterised and how they contribute to related biological processes and diseases.
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Affiliation(s)
- Xiaohui Shi
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The first Affiliated Hospital of WMU; Beijing Institutes of Life Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Ouhai District, Wenzhou 325000, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Ouhai District, Wenzhou 325000, China
| | - Zhongsheng Sun
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The first Affiliated Hospital of WMU; Beijing Institutes of Life Science, Chinese Academy of Sciences; CAS Center for Excellence in Biotic Interactions and State Key Laboratory of Integrated Management of Pest Insects and Rodents, University of Chinese Academy of Sciences; Institute of Genomic Medicine, Wenzhou Medical University; IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital); Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Ouhai District, Wenzhou 325000, China
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22
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Henikoff S, Ahmad K. In situ tools for chromatin structural epigenomics. Protein Sci 2022; 31:e4458. [PMID: 36170035 PMCID: PMC9601787 DOI: 10.1002/pro.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Technological progress over the past 15 years has fueled an explosion in genome-wide chromatin profiling tools that take advantage of low-cost short-read sequencing technologies to map particular chromatin features. Here, we survey the recent development of epigenomic tools that provide precise positions of chromatin proteins genome-wide in intact cells or nuclei. Some profiling tools are based on tethering Micrococcal Nuclease to chromatin proteins of interest in situ, whereas others similarly tether Tn5 transposase to integrate DNA sequencing adapters (tagmentation) and so eliminate the need for library preparation. These in situ cleavage and tagmentation tools have gained in popularity over the past few years, with many protocol enhancements and adaptations for single-cell and spatial chromatin profiling. The application of experimental and computational tools to address problems in gene regulation, eukaryotic development, and human disease are helping to define the emerging field of chromatin structural epigenomics.
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Affiliation(s)
- Steven Henikoff
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Kami Ahmad
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
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23
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Fernández-Justel JM, Santa-María C, Martín-Vírgala S, Ramesh S, Ferrera-Lagoa A, Salinas-Pena M, Isoler-Alcaraz J, Maslon MM, Jordan A, Cáceres JF, Gómez M. Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner. Cell Rep 2022; 40:111329. [PMID: 36103831 PMCID: PMC7613722 DOI: 10.1016/j.celrep.2022.111329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/04/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022] Open
Abstract
Linker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we identify a function of histone H1 in chromatin structure and transcription using a range of genomic approaches. In the absence of histone H1, there is an increase in the transcription of non-coding RNAs, together with reduced levels of m6A modification leading to their accumulation on chromatin and causing replication-transcription conflicts. This strongly suggests that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism, and DNA replication to maintain genome performance.
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Affiliation(s)
- José Miguel Fernández-Justel
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Cristina Santa-María
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Sara Martín-Vírgala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Shreya Ramesh
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Alberto Ferrera-Lagoa
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Mónica Salinas-Pena
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Javier Isoler-Alcaraz
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe South Road, Edinburgh EH4 2XU, UK
| | - Albert Jordan
- Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe South Road, Edinburgh EH4 2XU, UK
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain.
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24
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R-Loop Formation in Meiosis: Roles in Meiotic Transcription-Associated DNA Damage. EPIGENOMES 2022; 6:epigenomes6030026. [PMID: 36135313 PMCID: PMC9498298 DOI: 10.3390/epigenomes6030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/24/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is specialized cell division during gametogenesis that produces genetically unique gametes via homologous recombination. Meiotic homologous recombination entails repairing programmed 200–300 DNA double-strand breaks generated during the early prophase. To avoid interference between meiotic gene transcription and homologous recombination, mammalian meiosis is thought to employ a strategy of exclusively transcribing meiotic or post-meiotic genes before their use. Recent studies have shown that R-loops, three-stranded DNA/RNA hybrid nucleotide structures formed during transcription, play a crucial role in transcription and genome integrity. Although our knowledge about the function of R-loops during meiosis is limited, recent findings in mouse models have suggested that they play crucial roles in meiosis. Given that defective formation of an R-loop can cause abnormal transcription and transcription-coupled DNA damage, the precise regulatory network of R-loops may be essential in vivo for the faithful progression of mammalian meiosis and gametogenesis.
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25
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Abstract
Enhancers confer precise spatiotemporal patterns of gene expression in response to developmental and environmental stimuli. Over the last decade, the transcription of enhancer RNAs (eRNAs) – nascent RNAs transcribed from active enhancers – has emerged as a key factor regulating enhancer activity. eRNAs are relatively short-lived RNA species that are transcribed at very high rates but also quickly degraded. Nevertheless, eRNAs are deeply intertwined within enhancer regulatory networks and are implicated in a number of transcriptional control mechanisms. Enhancers show changes in function and sequence over evolutionary time, raising questions about the relationship between enhancer sequences and eRNA function. Moreover, the vast majority of single nucleotide polymorphisms associated with human complex diseases map to the non-coding genome, with causal disease variants enriched within enhancers. In this Primer, we survey the diverse roles played by eRNAs in enhancer-dependent gene expression, evaluating different models for eRNA function. We also explore questions surrounding the genetic conservation of enhancers and how this relates to eRNA function and dysfunction. Summary: This Primer evaluates the ideas that underpin developing models for eRNA function, exploring cases in which perturbed eRNA function contributes to disease.
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Affiliation(s)
- Laura J. Harrison
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
| | - Daniel Bose
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
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26
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Miller HE, Montemayor D, Abdul J, Vines A, Levy SA, Hartono SR, Sharma K, Frost B, Chédin F, Bishop AJR. Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions. Nucleic Acids Res 2022; 50:7260-7286. [PMID: 35758606 PMCID: PMC9303298 DOI: 10.1093/nar/gkac537] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/16/2022] [Indexed: 12/13/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics, but their findings are challenging to generalize. This is due to the narrow biological scope of individual studies, the limitations of each mapping modality, and, in some cases, poor data quality. In this study, we reprocessed 810 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. From this data resource, we developed an accurate R-loop data quality control method, and we reveal the extent of poor-quality data within previously published studies. We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called 'R-loop regions' (RL regions). In the process, we identified a stark divergence between RL regions detected by S9.6 and dRNH-based mapping methods, particularly with respect to R-loop size, location, and colocalization with RNA binding factors. Taken together, this work provides a much-needed method to assess R-loop data quality and offers novel context regarding the differences between dRNH- and S9.6-based R-loop mapping approaches.
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Affiliation(s)
- Henry E Miller
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.,Bioinformatics Research Network, Atlanta, GA, USA
| | - Daniel Montemayor
- Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.,Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Jebriel Abdul
- Bioinformatics Research Network, Atlanta, GA, USA.,Department of Biology, University of Ottawa, Ottawa, Canada
| | - Anna Vines
- Bioinformatics Research Network, Atlanta, GA, USA.,Faculty of Arts, University of Bristol, Bristol, U.K
| | - Simon A Levy
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Bioinformatics Research Network, Atlanta, GA, USA.,Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.,Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA
| | - Kumar Sharma
- Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.,Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Bess Frost
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.,Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.,May's Cancer Center, UT Health San Antonio, San Antonio, TX, USA
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27
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High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome Biol 2022; 23:159. [PMID: 35851062 PMCID: PMC9290270 DOI: 10.1186/s13059-022-02727-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary structures. The roles of DNA and RNA secondary structures in transcriptional regulation remain incompletely understood. However, advances in high-throughput assays have enabled genome wide characterization of some secondary structures. Here, we describe their regulatory functions in promoters and 3’UTRs, providing insights into key mechanisms through which they regulate gene expression. We discuss their implication in human disease, and how advances in molecular technologies and emerging high-throughput experimental methods could provide additional insights.
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28
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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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29
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Pan X, Huang LF. Multi-omics to characterize the functional relationships of R-loops with epigenetic modifications, RNAPII transcription and gene expression. Brief Bioinform 2022; 23:6618633. [DOI: 10.1093/bib/bbac238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
Abnormal accumulation of R-loops results in replication stress, genome instability, chromatin alterations and gene silencing. Little research has been done to characterize functional relationships among R-loops, histone marks, RNA polymerase II (RNAPII) transcription and gene regulation. We built extremely randomized trees (ETs) models to predict the genome-wide R-loops using RNAPII and multiple histone modifications chromatin immunoprecipitation (ChIP)-seq, DNase-seq, Global Run-On sequencing (GRO-seq) and R-loop profiling data. We compared the performance of ET models to multiple machine learning approaches, and the proposed ET models achieved the best and extremely robust performances. Epigenetic profiles are highly predictive of R-loops genome-widely and they are strongly associated with R-loop formation. In addition, the presence of R-loops is significantly correlated with RNAPII transcription activity, H3K4me3 and open chromatin around the transcription start site, and H3K9me1 and H3K9me3 around the transcription termination site. RNAPII pausing defects were correlated with 5′R-loops accumulation, and transcriptional termination defects and read-throughs were correlated with 3′R-loops accumulation. Furthermore, we found driver genes with 5′R-loops and RNAPII pausing defects express significantly higher and genes with 3′R-loops and read-through transcription express significantly lower than genes without R-loops. These driver genes are enriched with chromosomal instability, Hippo–Merlin signaling Dysregulation, DNA damage response and TGF-β pathways, indicating R-loops accumulating at the 5′ end of genes play oncogenic roles, whereas at the 3′ end of genes play tumor-suppressive roles in tumorigenesis.
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Affiliation(s)
- Xingxin Pan
- Division of Experimental Hematology and Cancer Biology , Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 , USA
| | - L Frank Huang
- Division of Experimental Hematology and Cancer Biology , Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 , USA
- Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH 45229 , USA
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30
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Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Guillermo E. Parada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Martin Hemberg
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
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31
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Spada S, Luke B, Danckwardt S. The Bidirectional Link Between RNA Cleavage and Polyadenylation and Genome Stability: Recent Insights From a Systematic Screen. Front Genet 2022; 13:854907. [PMID: 35571036 PMCID: PMC9095915 DOI: 10.3389/fgene.2022.854907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The integrity of the genome is governed by multiple processes to ensure optimal survival and to prevent the inheritance of deleterious traits. While significant progress has been made to characterize components involved in the DNA Damage Response (DDR), little is known about the interplay between RNA processing and the maintenance of genome stability. Here, we describe the emerging picture of an intricate bidirectional coupling between RNA processing and genome integrity in an integrative manner. By employing insights from a recent large-scale RNAi screening involving the depletion of more than 170 components that direct (alternative) polyadenylation, we provide evidence of bidirectional crosstalk between co-transcriptional RNA 3′end processing and the DDR in a manner that optimizes genomic integrity. We provide instructive examples illustrating the wiring between the two processes and show how perturbations at one end are either compensated by buffering mechanisms at the other end, or even propel the initial insult and thereby become disease-eliciting as evidenced by various disorders.
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Affiliation(s)
- Stefano Spada
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg University, Mainz, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
- German Centre for Cardiovascular Research (DZHK), Berlin, Germany
- Centre for Healthy Aging (CHA) Mainz, Mainz, Germany
- *Correspondence: Sven Danckwardt,
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32
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Proximity labeling identifies a repertoire of site-specific R-loop modulators. Nat Commun 2022; 13:53. [PMID: 35013239 PMCID: PMC8748879 DOI: 10.1038/s41467-021-27722-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/06/2021] [Indexed: 11/11/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures that accumulate on chromatin in neurological diseases and cancers and contribute to genome instability. Using a proximity-dependent labeling system, we identified distinct classes of proteins that regulate R-loops in vivo through different mechanisms. We show that ATRX suppresses R-loops by interacting with RNAs and preventing R-loop formation. Our proteomics screen also discovered an unexpected enrichment for proteins containing zinc fingers and homeodomains. One of the most consistently enriched proteins was activity-dependent neuroprotective protein (ADNP), which is frequently mutated in ASD and causal in ADNP syndrome. We find that ADNP resolves R-loops in vitro and that it is necessary to suppress R-loops in vivo at its genomic targets. Furthermore, deletion of the ADNP homeodomain severely diminishes R-loop resolution activity in vitro, results in R-loop accumulation at ADNP targets, and compromises neuronal differentiation. Notably, patient-derived human induced pluripotent stem cells that contain an ADNP syndrome-causing mutation exhibit R-loop and CTCF accumulation at ADNP targets. Our findings point to a specific role for ADNP-mediated R-loop resolution in physiological and pathological neuronal function and, more broadly, to a role for zinc finger and homeodomain proteins in R-loop regulation, with important implications for developmental disorders and cancers. R-loops are three-stranded nucleic acid structures that contribute to genome instability and accumulate in neurological diseases. Here the authors identify R-loop proximal factors, which are enriched for zinc finger and homeodomain proteins, including activity-dependent neuroprotective protein (ADNP). ADNP plays a role in R-loop resolution and loss-of-function leads to R-loop accumulation.
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33
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Abstract
RNase H1 has become an essential tool to uncover the physiological and pathological roles of R-loops, three-stranded structures consisting of and RNA-DNA hybrid opposite to a single DNA strand (ssDNA). RNase H1 degrades the RNA portion of the R-loops returning the two DNA strands to double-stranded form (dsDNA). Overexpression of RNase H1 in different systems has helped to address the questions of where R-loops are located, their abundance, and mechanisms of formation, stability, and degradation. In this chapter we review multiple studies that used RNase H1 as an instrument to investigate R-loops multiple functions and their relevance in health and diseases.
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Affiliation(s)
- Susana M Cerritelli
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kiran Sakhuja
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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34
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Wulfridge P, Yan Q, Sarma K. Targeted Nuclease Approaches for Mapping Native R-Loops. Methods Mol Biol 2022; 2528:373-380. [PMID: 35704205 DOI: 10.1007/978-1-0716-2477-7_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
R-loops are three-stranded, DNA:RNA hybrid-containing structures that form naturally throughout the genome as a consequence of transcription. Accurately determining the genomic locations and strand of origin of R-loops is critical to understanding their roles in gene regulation and disease. Here, we describe a nuclease-based protocol for genome-wide and strand-specific R-loop detection, which we term MapR. This method targets native R-loops for cleavage and release using a modified RNase H enzyme, followed by deep sequencing. An extension of the protocol, BisMapR, can additionally introduce strand specificity via non-denaturing bisulfite conversion of the R-loop's single-stranded DNA component. MapR and BisMapR identify R-loops with high resolution and low background, can be performed with low cell input, and require short experimental time.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Qingqing Yan
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
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35
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Wang H, Li C, Liang K. Genome-Wide Native R-Loop Profiling by R-Loop Cleavage Under Targets and Tagmentation (R-Loop CUT&Tag). Methods Mol Biol 2022; 2528:345-357. [PMID: 35704203 DOI: 10.1007/978-1-0716-2477-7_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
R-loops are three-stranded nucleic acid structures that consist of a DNA-RNA hybrid and a displaced single-stranded DNA. R-loops occur during transcription and participate in multiple physiological processes such as DNA repair, modulating DNA topology, and regulation of gene transcription. Dysfunctional R-loops associate with several human diseases such as neurological disorders and cancer. Therefore, accurately and comprehensively profiling native R-loops is crucial to understand their functions under both physiological and pathological conditions. Here, we describe a convenient native R-loop profiling method, R-loop CUT&Tag, which combines a DNA-RNA hybrid sensor (GST-His6-2 × HBD or S9.6 antibody) with a pA-Tn5-based cleavage under targets and tagmentation approach. R-loop CUT&Tag starts with 0.5 million cells and can sensitively detect native and specific R-loops at the promoter, gene body, and enhancer regions.
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Affiliation(s)
- Honghong Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.
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36
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García-Rubio M, Soler-Oliva ME, Aguilera A. Genome-Wide Analysis of DNA-RNA Hybrids in Yeast by DRIPc-Seq and DRIP-Seq. Methods Mol Biol 2022; 2528:429-443. [PMID: 35704208 DOI: 10.1007/978-1-0716-2477-7_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA-RNA hybrids are required for several natural processes in the cell, such as replication and transcription. However, the misregulation of its metabolism is an important source of genetic instability, a hallmark of diseases including cancer. For this reason, genome-wide detection of DNA-RNA hybrids is becoming essential to identify new factors that play a role in its formation or resolution and to understand the global changes in its dynamics because of genetic alterations or chemical treatments. Here, we describe two different immunoprecipitation-based procedures for the genome-wide profiling of DNA-RNA hybrids in the yeast Saccharomyces cerevisiae: DRIP-seq and DRIPc-seq.
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Affiliation(s)
- María García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - María E Soler-Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain.
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37
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TET deficiency perturbs mature B cell homeostasis and promotes oncogenesis associated with accumulation of G-quadruplex and R-loop structures. Nat Immunol 2021; 23:99-108. [PMID: 34937926 PMCID: PMC8772520 DOI: 10.1038/s41590-021-01087-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 11/02/2021] [Indexed: 01/02/2023]
Abstract
Enzymes of the TET family are methylcytosine dioxygenases that undergo frequent mutational or functional inactivation in human cancers. Recurrent loss-of-function mutations in TET proteins are frequent in human diffuse large B cell lymphoma (DLBCL). Here, we investigate the role of TET proteins in B cell homeostasis and development of B cell lymphomas with features of DLBCL. We show that deletion of Tet2 and Tet3 genes in mature B cells in mice perturbs B cell homeostasis and results in spontaneous development of germinal center (GC)-derived B cell lymphomas with increased G-quadruplexes and R-loops. At a genome-wide level, G-quadruplexes and R-loops were associated with increased DNA double-strand breaks (DSBs) at immunoglobulin switch regions. Deletion of the DNA methyltransferase DNMT1 in TET-deficient B cells prevented expansion of GC B cells, diminished the accumulation of G-quadruplexes and R-loops and delayed B lymphoma development, consistent with the opposing functions of DNMT and TET enzymes in DNA methylation and demethylation. Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated depletion of nucleases and helicases that regulate G-quadruplexes and R-loops decreased the viability of TET-deficient B cells. Our studies suggest a molecular mechanism by which TET loss of function might predispose to the development of B cell malignancies.
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38
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R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun 2021; 12:7314. [PMID: 34916496 PMCID: PMC8677849 DOI: 10.1038/s41467-021-27530-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription poses a threat to genomic stability through the formation of R-loops that can obstruct progression of replication forks. R-loops are three-stranded nucleic acid structures formed by an RNA-DNA hybrid with a displaced non-template DNA strand. We developed RNA-DNA Proximity Proteomics to map the R-loop proximal proteome of human cells using quantitative mass spectrometry. We implicate different cellular proteins in R-loop regulation and identify a role of the tumor suppressor DDX41 in opposing R-loop and double strand DNA break accumulation in promoters. DDX41 is enriched in promoter regions in vivo, and can unwind RNA-DNA hybrids in vitro. R-loop accumulation upon loss of DDX41 is accompanied with replication stress, an increase in the formation of double strand DNA breaks and transcriptome changes associated with the inflammatory response. Germline loss-of-function mutations in DDX41 lead to predisposition to acute myeloid leukemia in adulthood. We propose that R-loop accumulation and genomic instability-associated inflammatory response may contribute to the development of familial AML with mutated DDX41.
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39
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Lin R, Zhong X, Zhou Y, Geng H, Hu Q, Huang Z, Hu J, Fu XD, Chen L, Chen JY. R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. Nucleic Acids Res 2021; 50:D303-D315. [PMID: 34792163 PMCID: PMC8728142 DOI: 10.1093/nar/gkab1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/28/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.
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Affiliation(s)
- Ruoyao Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Yongli Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huichao Geng
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qingxi Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhihao Huang
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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40
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Kim A, Wang GG. R-loop and its functions at the regulatory interfaces between transcription and (epi)genome. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194750. [PMID: 34461314 PMCID: PMC8627470 DOI: 10.1016/j.bbagrm.2021.194750] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 01/08/2023]
Abstract
R-loop represents a prevalent and specialized chromatin structure critically involved in a wide range of biological processes. In particular, co-transcriptional R-loops, produced often due to RNA polymerase pausing or RNA biogenesis malfunction, can initiate molecular events to context-dependently regulate local gene transcription and crosstalk with chromatin modifications. Cellular "readers" of R-loops are identified, exerting crucial impacts on R-loop homeostasis and gene regulation. Mounting evidence also supports R-loop deregulation as a frequent, sometimes initiating, event during the development of human pathologies, notably cancer and neurological disorder. The purpose of this review is to cover recent advances in understanding the fundamentals of R-loop biology, which have started to unveil complex interplays of R-loops with factors involved in various biological processes such as transcription, RNA processing and epitranscriptomic modification (such as N6-methyladenosine), DNA damage sensing and repair, and epigenetic regulation.
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Affiliation(s)
- Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
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41
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Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
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Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
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42
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Castillo-Guzman D, Chédin F. Defining R-loop classes and their contributions to genome instability. DNA Repair (Amst) 2021; 106:103182. [PMID: 34303066 PMCID: PMC8691176 DOI: 10.1016/j.dnarep.2021.103182] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/20/2023]
Abstract
R-loops are non-B DNA structures that form during transcription when the nascent RNA anneals to the template DNA strand forming a RNA:DNA hybrid. Understanding the genomic distribution and function of R-loops is an important goal, since R-loops have been implicated in a number of adaptive and maladaptive processes under physiological and pathological conditions. Based on R-loop mapping datasets, we propose the existence of two main classes of R-loops, each associated with unique characteristics. Promoter-paused R-loops (Class I) are short R-loops that form at high frequency during promoter-proximal pausing by RNA polymerase II. Elongation-associated R-loops (Class II) are long structures that occur throughout gene bodies at modest frequencies. We further discuss the relationships between each R-loop class with instances of genome instability and suggest that increased class I R-loops, resulting from enhanced promoter-proximal pausing, represent the main culprits for R-loop mediated genome instability under pathological conditions.
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Affiliation(s)
- Daisy Castillo-Guzman
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA, 95616, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA, 95616, United States.
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43
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Gao J, Zhang P, Li X, Wu W, Wei H, Zhang W. Toward an understanding of the detection and function of R-loops in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6110-6122. [PMID: 34115858 DOI: 10.1093/jxb/erab280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/10/2021] [Indexed: 06/12/2023]
Abstract
Although lagging behind studies in humans and other mammals, studies of R-loops in plants have recently entered an exciting stage in which the roles of R-loops in gene expression, genome stability, epigenomic signatures, and plant development and stress responses are being elucidated. Here, we review the strengths and weaknesses of existing methodologies, which were largely developed for R-loop studies in mammals, and then discuss the potential challenges of applying these methodologies to R-loop studies in plants. We then focus on recent advances in the functional characterization of R-loops in Arabidopsis thaliana and rice. Recent studies in plants indicate that there are coordinated relationships between R-loops and gene expression, and between R-loops and epigenomic signatures that depend, in part, on the types of R-loops involved. Finally, we discuss the emerging roles of R-loops in plants and directions for future research.
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Affiliation(s)
- Jingjing Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Xinxu Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
| | - Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China
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44
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Wu T, Nance J, Chu F, Fazzio TG. Characterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression. Mol Cell Proteomics 2021; 20:100142. [PMID: 34478875 PMCID: PMC8461376 DOI: 10.1016/j.mcpro.2021.100142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/21/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part because of the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs that form R-loops-RNA-DNA hybrid structures that include a displaced strand of ssDNA. R-loops generally form cotranscriptionally and have important roles in regulation of gene expression, immunoglobulin class switching, and other processes. However, unresolved R-loops can lead to DNA damage and chromosome instability. To identify factors that may bind and regulate R-loop accumulation or mediate R-loop-dependent functions, we used a comparative immunoprecipitation/MS approach, with and without RNA-protein crosslinking, to identify a stringent set of R-loop-binding proteins in mouse embryonic stem cells. We identified 364 R-loop-interacting proteins, which were highly enriched for proteins with predicted RNA-binding functions. We characterized several R-loop-interacting proteins of the DEAD-box family of RNA helicases and found that these proteins localize to the nucleolus and, to a lesser degree, the nucleus. Consistent with their localization patterns, we found that these helicases are required for rRNA processing and regulation of gene expression. Surprisingly, depletion of these helicases resulted in misregulation of highly overlapping sets of protein-coding genes, including many genes that function in differentiation and development. We conclude that R-loop-interacting DEAD-box helicases have nonredundant roles that are critical for maintaining the normal embryonic stem cell transcriptome.
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Affiliation(s)
- Tong Wu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jennifer Nance
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Feixia Chu
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
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45
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DNA-RNA Hybrid (R-Loop): From a Unified Picture of the Mammalian Telomere to the Genome-Wide Profile. Cells 2021; 10:cells10061556. [PMID: 34205454 PMCID: PMC8233970 DOI: 10.3390/cells10061556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 01/16/2023] Open
Abstract
Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular extract without antibody that allows their physical isolation and determination of their RNA nucleotide sequence. We then define in the normal mouse and human sperm genomes the notion of stable DNA associated RNA terminal R-loop complexes, including TERRA molecules synthesized from local promoters of every chromosome. Furthermore, the first strong evidence of all telomeric structures, applied additionally to the whole murine sperm genome compared to the testes, showed reproducible R-loop complexes of the whole genome and suggesting a defined profile in the sperm genome for the next generation.
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46
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Addo FG, Zhang S, Manirakiza B, Ohore OE, Shudong Y. The impacts of straw substrate on biofloc formation, bacterial community and nutrient removal in shrimp ponds. BIORESOURCE TECHNOLOGY 2021; 326:124727. [PMID: 33548819 DOI: 10.1016/j.biortech.2021.124727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
This study explored biofloc technology for shrimp culture based on straw substrates with a size of 40 mu, 80 mu, and 120 mu. Straw substrates utilization stimulated shrimp growth compared to control. Treatment with 40 mu had the best ammonium (71.60%) and nitrite nitrogen (77.78%) removal rates generally. In all biofloc treatments, Proteobacteria (4.10-56.1%) was the most dominant phylum, followed by Bacteroidetes (2.44-38.21%), Planctomycetes (0.45-21.41%), and Verrucomicrobia (1.2-10.30%). Redundancy analysis showed that salinity was a significant factor closely related to the microbial community in biofloc. The environmental parameters (DO > pH > TN > NH4+-N > COD > Salinity > EC), nitrification, and denitrification genes (amoA > napA > nirK) were significant factors that interrelated with the bacterial genus in the network analysis. This study highlighted a novel technology of reusing agricultural waste that transformed inorganic nitrogen using nutrient recycling to control water quality in the culture system and produced microbial proteins that served as a natural nutritional supplement to enhance shrimp growth.
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Affiliation(s)
- Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Benjamin Manirakiza
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
| | - Okugbe Ebiotubo Ohore
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yuan Shudong
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Anhui Transport Consulting & Design Institute Co., Ltd, Hefei, PR China
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47
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Wulfridge P, Sarma K. A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide. eLife 2021; 10:65146. [PMID: 33620319 PMCID: PMC7901872 DOI: 10.7554/elife.65146] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/16/2021] [Indexed: 01/28/2023] Open
Abstract
R-loops are three-stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation is associated with genome instability and is observed in neurodevelopmental diseases and cancers. Genome-wide profiling of R-loops in normal and diseased cells can help identify locations of pathogenic R-loops and advance efforts to attenuate them. We present an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce genome-wide profiles that retain strand information. BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. In mouse embryonic stem cells, we apply BisMapR to find that gene promoters form R-loops in both directions and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation program, The Wistar Institute, Philadelphia, United States.,Epigenetics Institute, University of Pennsylvania, Philadelphia, United States
| | - Kavitha Sarma
- Gene Expression and Regulation program, The Wistar Institute, Philadelphia, United States.,Epigenetics Institute, University of Pennsylvania, Philadelphia, United States
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48
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Chédin F, Hartono SR, Sanz LA, Vanoosthuyse V. Best practices for the visualization, mapping, and manipulation of R-loops. EMBO J 2021; 40:e106394. [PMID: 33411340 PMCID: PMC7883053 DOI: 10.15252/embj.2020106394] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 11/10/2020] [Indexed: 01/12/2023] Open
Abstract
R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution has significant impacts on genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here, we review the main existing methodologies for R-loop mapping and assess their limitations as well as the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we propose a possible resolution for the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.
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Affiliation(s)
- Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Vincent Vanoosthuyse
- Laboratoire de Biologie et Modélisation de la CelluleCNRSUMR 5239Univ LyonÉcole Normale Supérieure de LyonLyonFrance
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49
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Abstract
R-loops are abundant, RNA-containing chromatin structures that form in the genomes of both eukaryotes and prokaryotes. Devising methods to identify the precise genomic locations of R-loops is critical to understand how these structures regulate numerous cellular processes, including replication, termination, and chromosome segregation, and how their unscheduled formation results in disease. Here, we describe a new, highly sensitive, and antibody-independent method, MapR, to profile native R-loops genome wide. MapR takes advantage of the natural specificity of the RNase H enzyme to recognize DNA:RNA hybrids, a defining feature of R-loops, and combines it with a CUT&RUN approach to target, cleave, and release R-loops that can then be sequenced. MapR has low background, is faster than current R-loop detection technologies, and can be performed in any cell type without the need to generate stable cell lines. © 2020 by John Wiley & Sons, Inc.
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Affiliation(s)
- Qingqing Yan
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania.,Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania.,Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania
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50
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Wang K, Wang H, Li C, Yin Z, Xiao R, Li Q, Xiang Y, Wang W, Huang J, Chen L, Fang P, Liang K. Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor. SCIENCE ADVANCES 2021; 7:7/8/eabe3516. [PMID: 33597247 PMCID: PMC7888926 DOI: 10.1126/sciadv.abe3516] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/30/2020] [Indexed: 05/08/2023]
Abstract
An R loop is a unique triple-stranded structure that participates in multiple key biological processes and is relevant to human diseases. Accurate and comprehensive R loop profiling is a prerequisite for R loops studies. However, current R loop mapping methods generate large discrepancies, therefore an independent method is in urgent need. Here, we establish an independent R loop CUT&Tag (Tn5-based cleavage under targets and tagmentation) method by combining CUT&Tag and GST-His6-2×HBD (glutathione S-transferase-hexahistidine-2× hybrid-binding domain), an artificial DNA-RNA hybrid sensor that specifically recognizes the DNA-RNA hybrids. We demonstrate that the R loop CUT&Tag is sensitive, reproducible, and convenient for native R loop mapping with high resolution, and find that the capture strategies, instead of the specificity of sensors, largely contribute to the disparities among different methods. Together, we provide an independent strategy for genomic profiling of native R loops and help resolve discrepancies among multiple R loop mapping methods.
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Affiliation(s)
- Kang Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Honghong Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhinang Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Ruijing Xiao
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Qiuzi Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, P.R. China
| | - Ying Xiang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wen Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jian Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, P.R. China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, P.R. China
| | - Pingping Fang
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Research Center for Medicine and Structural Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
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