1
|
Székvölgyi L. Chromosomal R-loops: who R they? Biol Futur 2024; 75:177-182. [PMID: 38457033 DOI: 10.1007/s42977-024-00213-7] [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: 11/19/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
R-loops, composed of DNA-RNA hybrids and displaced single-stranded DNA, are known to pose a severe threat to genome integrity. Therefore, extensive research has focused on identifying regulatory proteins involved in controlling R-loop levels. These proteins play critical roles in preventing R-loop accumulation and associated genome instability. Herein I summarize recent knowledge on R-loop regulators affecting R-loop homeostasis, involving a wide array of R-loop screening methods that have enabled their characterization, from forward genetic and siRNA-based screens to proximity labeling and machine learning. These approaches not only deepen our understanding on R-loop formation processes, but also hold promise to find new targets in R-loop dysregulation associated with human pathologies.
Collapse
Affiliation(s)
- Lóránt Székvölgyi
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Department of Molecular and Nanopharmaceutics, Faculty of Pharmacy, University of Debrecen, Debrecen, 4032, Hungary.
| |
Collapse
|
2
|
Disha B, Mathew RP, Dalal AB, Mahato AK, Satyamoorthy K, Singh KK, Thangaraj K, Govindaraj P. Mitochondria in biology and medicine - 2023. Mitochondrion 2024; 76:101853. [PMID: 38423268 DOI: 10.1016/j.mito.2024.101853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Mitochondria are an indispensable part of the cell that plays a crucial role in regulating various signaling pathways, energy metabolism, cell differentiation, proliferation, and cell death. Since mitochondria have their own genetic material, they differ from their nuclear counterparts, and dysregulation is responsible for a broad spectrum of diseases. Mitochondrial dysfunction is associated with several disorders, including neuro-muscular disorders, cancer, and premature aging, among others. The intricacy of the field is due to the cross-talk between nuclear and mitochondrial genes, which has also improved our knowledge of mitochondrial functions and their pathogenesis. Therefore, interdisciplinary research and communication are crucial for mitochondrial biology and medicine due to the challenges they pose for diagnosis and treatment. The ninth annual conference of the Society for Mitochondria Research and Medicine (SMRM)- India, titled "Mitochondria in Biology and Medicine" was organized at the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India, on June 21-23, 2023. The latest advancements in the field of mitochondrial biology and medicine were discussed at the conference. In this article, we summarize the entire event for the benefit of researchers working in the field of mitochondrial biology and medicine.
Collapse
Affiliation(s)
- B Disha
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India
| | - Rohan Peter Mathew
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India; Manipal Academy of Higher Education, Manipal 576104, India
| | - Ashwin B Dalal
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India
| | - Ajay K Mahato
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India
| | - Kapaettu Satyamoorthy
- Shri Dharmasthala Manjunatheshwara (SDM) University, SDM College of Medical Sciences and Hospital, Manjushree Nagar, Sattur, Dharwad 580009, India
| | - Keshav K Singh
- Department of Genetics, School of Medicine, The University of Alabama at Birmingham, Kaul Genetics Building, Rm. 620, 720 20th St. South, Birmingham, AL, 35294, USA
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Periyasamy Govindaraj
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500039, India; Department of Neuropathology, National Institute of Mental Health and Neurosciences, Hosur Road, Bengaluru 560029, India.
| |
Collapse
|
3
|
McNutt SW, Roychowdhury T, Pasala C, Nguyen HT, Thornton DT, Sharma S, Botticelli L, Digwal CS, Joshi S, Yang N, Panchal P, Chakrabarty S, Bay S, Markov V, Kwong C, Lisanti J, Chung SY, Ginsberg SD, Yan P, DeStanchina E, Corben A, Modi S, Alpaugh M, Colombo G, Erdjument-Bromage H, Neubert TA, Chalkley RJ, Baker PR, Burlingame AL, Rodina A, Chiosis G, Chu F. Phosphorylation-Driven Epichaperome Assembly: A Critical Regulator of Cellular Adaptability and Proliferation. RESEARCH SQUARE 2024:rs.3.rs-4114038. [PMID: 38645031 PMCID: PMC11030525 DOI: 10.21203/rs.3.rs-4114038/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The intricate protein-chaperone network is vital for cellular function. Recent discoveries have unveiled the existence of specialized chaperone complexes called epichaperomes, protein assemblies orchestrating the reconfiguration of protein-protein interaction networks, enhancing cellular adaptability and proliferation. This study delves into the structural and regulatory aspects of epichaperomes, with a particular emphasis on the significance of post-translational modifications in shaping their formation and function. A central finding of this investigation is the identification of specific PTMs on HSP90, particularly at residues Ser226 and Ser255 situated within an intrinsically disordered region, as critical determinants in epichaperome assembly. Our data demonstrate that the phosphorylation of these serine residues enhances HSP90's interaction with other chaperones and co-chaperones, creating a microenvironment conducive to epichaperome formation. Furthermore, this study establishes a direct link between epichaperome function and cellular physiology, especially in contexts where robust proliferation and adaptive behavior are essential, such as cancer and stem cell maintenance. These findings not only provide mechanistic insights but also hold promise for the development of novel therapeutic strategies targeting chaperone complexes in diseases characterized by epichaperome dysregulation, bridging the gap between fundamental research and precision medicine.
Collapse
Affiliation(s)
- Seth W McNutt
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
- co-first author, equally contributed to the work
| | - Tanaya Roychowdhury
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- co-first author, equally contributed to the work
| | - Chiranjeevi Pasala
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hieu T Nguyen
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Daniel T Thornton
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luke Botticelli
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nan Yang
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Souparna Chakrabarty
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sadik Bay
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vladimir Markov
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charlene Kwong
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jeanine Lisanti
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sun Young Chung
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephen D Ginsberg
- Departments of Psychiatry, Neuroscience & Physiology & the NYU Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, 10962, USA
| | - Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisa DeStanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Adriana Corben
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shanu Modi
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mary Alpaugh
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Hediye Erdjument-Bromage
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Thomas A Neubert
- Department of Neuroscience and Physiology and Neuroscience Institute, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Robert J Chalkley
- Mass Spectrometry Facility, University of California, San Francisco, California 94143, USA
| | - Peter R Baker
- Mass Spectrometry Facility, University of California, San Francisco, California 94143, USA
| | - Alma L Burlingame
- Mass Spectrometry Facility, University of California, San Francisco, California 94143, USA
| | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Division of Solid Tumors, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- These authors jointly supervised this work: Feixia Chu, Gabriela Chiosis
| | - Feixia Chu
- Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
- These authors jointly supervised this work: Feixia Chu, Gabriela Chiosis
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Kumar C, Remus D. Looping out of control: R-loops in transcription-replication conflict. Chromosoma 2024; 133:37-56. [PMID: 37419963 PMCID: PMC10771546 DOI: 10.1007/s00412-023-00804-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Transcription-replication conflict is a major cause of replication stress that arises when replication forks collide with the transcription machinery. Replication fork stalling at sites of transcription compromises chromosome replication fidelity and can induce DNA damage with potentially deleterious consequences for genome stability and organismal health. The block to DNA replication by the transcription machinery is complex and can involve stalled or elongating RNA polymerases, promoter-bound transcription factor complexes, or DNA topology constraints. In addition, studies over the past two decades have identified co-transcriptional R-loops as a major source for impairment of DNA replication forks at active genes. However, how R-loops impede DNA replication at the molecular level is incompletely understood. Current evidence suggests that RNA:DNA hybrids, DNA secondary structures, stalled RNA polymerases, and condensed chromatin states associated with R-loops contribute to the of fork progression. Moreover, since both R-loops and replication forks are intrinsically asymmetric structures, the outcome of R-loop-replisome collisions is influenced by collision orientation. Collectively, the data suggest that the impact of R-loops on DNA replication is highly dependent on their specific structural composition. Here, we will summarize our current understanding of the molecular basis for R-loop-induced replication fork progression defects.
Collapse
Affiliation(s)
- Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.
| |
Collapse
|
6
|
Girasol MJ, Briggs EM, Marques CA, Batista JM, Beraldi D, Burchmore R, Lemgruber L, McCulloch R. Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation. Nucleic Acids Res 2023; 51:11123-11141. [PMID: 37843098 PMCID: PMC10639054 DOI: 10.1093/nar/gkad836] [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: 05/26/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of genomes that provide a diverse and growing range of activities. Understanding of these functions has been informed by characterising the proteins that interact with the hybrids, but all such analyses have so far focused on mammals, meaning it is unclear if a similar spectrum of RNA-DNA hybrid interactors is found in other eukaryotes. The African trypanosome is a single-cell eukaryotic parasite of the Discoba grouping and displays substantial divergence in several aspects of core biology from its mammalian host. Here, we show that DNA-RNA hybrid immunoprecipitation coupled with mass spectrometry recovers 602 putative interactors in T. brucei mammal- and insect-infective cells, some providing activities also found in mammals and some lineage-specific. We demonstrate that loss of three factors, two putative helicases and a RAD51 paralogue, alters T. brucei nuclear RNA-DNA hybrid and DNA damage levels. Moreover, loss of each factor affects the operation of the parasite immune survival mechanism of antigenic variation. Thus, our work reveals the broad range of activities contributed by RNA-DNA hybrids to T. brucei biology, including new functions in host immune evasion as well as activities likely fundamental to eukaryotic genome function.
Collapse
Affiliation(s)
- Mark J Girasol
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of the Philippines Manila, College of Medicine, Manila, Philippines
| | - Emma M Briggs
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of Edinburgh, Institute for Immunology and Infection Research, School of Biological Sciences, Edinburgh, UK
| | - Catarina A Marques
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - José M Batista
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Dario Beraldi
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard Burchmore
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Leandro Lemgruber
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard McCulloch
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| |
Collapse
|
7
|
Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
Collapse
Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| |
Collapse
|
8
|
Fleck K, McNutt S, Chu F, Jeffers V. An apicomplexan bromodomain protein, TgBDP1, associates with diverse epigenetic factors to regulate essential transcriptional processes in Toxoplasma gondii. mBio 2023; 14:e0357322. [PMID: 37350586 PMCID: PMC10470533 DOI: 10.1128/mbio.03573-22] [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: 12/24/2022] [Accepted: 04/18/2023] [Indexed: 06/24/2023] Open
Abstract
The protozoan pathogen Toxoplasma gondii relies on tight regulation of gene expression to invade and establish infection in its host. The divergent gene regulatory mechanisms of Toxoplasma and related apicomplexan pathogens rely heavily on regulators of chromatin structure and histone modifications. The important contribution of histone acetylation for Toxoplasma in both acute and chronic infection has been demonstrated, where histone acetylation increases at active gene loci. However, the direct consequences of specific histone acetylation marks and the chromatin pathway that influences transcriptional regulation in response to the modification are unclear. As a reader of lysine acetylation, the bromodomain serves as a mediator between the acetylated histone and transcriptional regulators. Here we show that the bromodomain protein, TgBDP1, which is conserved among Apicomplexa and within the Alveolata superphylum, is essential for Toxoplasma asexual proliferation. Using cleavage under targets and tagmentation, we demonstrate that TgBDP1 is recruited to transcriptional start sites of a large proportion of parasite genes. Transcriptional profiling during TgBDP1 knockdown revealed that loss of TgBDP1 leads to major dysregulation of gene expression, implying multiple roles for TgBDP1 in both gene activation and repression. This is supported by interactome analysis of TgBDP1 demonstrating that TgBDP1 forms a core complex with two other bromodomain proteins and an ApiAP2 factor. This core complex appears to interact with other epigenetic factors such as nucleosome remodeling complexes. We conclude that TgBDP1 interacts with diverse epigenetic regulators to exert opposing influences on gene expression in the Toxoplasma tachyzoite. IMPORTANCE Histone acetylation is critical for proper regulation of gene expression in the single-celled eukaryotic pathogen Toxoplasma gondii. Bromodomain proteins are "readers" of histone acetylation and may link the modified chromatin to transcription factors. Here, we show that the bromodomain protein TgBDP1 is essential for parasite survival and that loss of TgBDP1 results in global dysregulation of gene expression. TgBDP1 is recruited to the promoter region of a large proportion of parasite genes, forms a core complex with two other bromodomain proteins, and interacts with different transcriptional regulatory complexes. We conclude that TgBDP1 is a key factor for sensing specific histone modifications to influence multiple facets of transcriptional regulation in Toxoplasma gondii.
Collapse
Affiliation(s)
- Krista Fleck
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Seth McNutt
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Feixia Chu
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Victoria Jeffers
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| |
Collapse
|
9
|
|
10
|
Boleslavska B, Oravetzova A, Shukla K, Nascakova Z, Ibini O, Hasanova Z, Andrs M, Kanagaraj R, Dobrovolna J, Janscak P. DDX17 helicase promotes resolution of R-loop-mediated transcription-replication conflicts in human cells. Nucleic Acids Res 2022; 50:12274-12290. [PMID: 36453994 PMCID: PMC9757067 DOI: 10.1093/nar/gkac1116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures composed of an RNA:DNA hybrid and displaced DNA strand. These structures can halt DNA replication when formed co-transcriptionally in the opposite orientation to replication fork progression. A recent study has shown that replication forks stalled by co-transcriptional R-loops can be restarted by a mechanism involving fork cleavage by MUS81 endonuclease, followed by ELL-dependent reactivation of transcription, and fork religation by the DNA ligase IV (LIG4)/XRCC4 complex. However, how R-loops are eliminated to allow the sequential restart of transcription and replication in this pathway remains elusive. Here, we identified the human DDX17 helicase as a factor that associates with R-loops and counteracts R-loop-mediated replication stress to preserve genome stability. We show that DDX17 unwinds R-loops in vitro and promotes MUS81-dependent restart of R-loop-stalled forks in human cells in a manner dependent on its helicase activity. Loss of DDX17 helicase induces accumulation of R-loops and the formation of R-loop-dependent anaphase bridges and micronuclei. These findings establish DDX17 as a component of the MUS81-LIG4-ELL pathway for resolution of R-loop-mediated transcription-replication conflicts, which may be involved in R-loop unwinding.
Collapse
Affiliation(s)
- Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic,Faculty of Science, Charles University in Prague, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Anna Oravetzova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic,Faculty of Science, Charles University in Prague, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Kaustubh Shukla
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | | | - Zdenka Hasanova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Radhakrishnan Kanagaraj
- School of Life Sciences, University of Bedfordshire, Park Square, Luton LU1 3JU, UK,School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK,Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - Jana Dobrovolna
- Correspondence may also be addressed to Jana Dobrovolna. Tel: +420 241063127;
| | - Pavel Janscak
- To whom correspondence should be addressed. Tel: +41 44 6353470;
| |
Collapse
|
11
|
Bruno T, Corleone G, Catena V, Cortile C, De Nicola F, Fabretti F, Gumenyuk S, Pisani F, Mengarelli A, Passananti C, Fanciulli M. AATF/Che-1 localizes to paraspeckles and suppresses R-loops accumulation and interferon activation in Multiple Myeloma. EMBO J 2022; 41:e109711. [PMID: 35929179 PMCID: PMC9670196 DOI: 10.15252/embj.2021109711] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 01/13/2023] Open
Abstract
Several kinds of stress promote the formation of three-stranded RNA:DNA hybrids called R-loops. Insufficient clearance of these structures promotes genomic instability and DNA damage, which ultimately contribute to the establishment of cancer phenotypes. Paraspeckle assemblies participate in R-loop resolution and preserve genome stability, however, the main determinants of this mechanism are still unknown. This study finds that in Multiple Myeloma (MM), AATF/Che-1 (Che-1), an RNA-binding protein fundamental to transcription regulation, interacts with paraspeckles via the lncRNA NEAT1_2 (NEAT1) and directly localizes on R-loops. We systematically show that depletion of Che-1 produces a marked accumulation of RNA:DNA hybrids. We provide evidence that such failure to resolve R-loops causes sustained activation of a systemic inflammatory response characterized by an interferon (IFN) gene expression signature. Furthermore, elevated levels of R-loops and of mRNA for paraspeckle genes in patient cells are linearly correlated with Multiple Myeloma progression. Moreover, increased interferon gene expression signature in patients is associated with markedly poor prognosis. Taken together, our study indicates that Che-1/NEAT1 cooperation prevents excessive inflammatory signaling in Multiple Myeloma by facilitating the clearance of R-loops. Further studies on different cancer types are needed to test if this mechanism is ubiquitously conserved and fundamental for cell homeostasis.
Collapse
Affiliation(s)
- Tiziana Bruno
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Giacomo Corleone
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Valeria Catena
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Clelia Cortile
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of CologneUniversity of CologneCologneGermany,Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Svitlana Gumenyuk
- Hematology UnitIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Francesco Pisani
- Hematology UnitIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Andrea Mengarelli
- Hematology UnitIRCCS Regina Elena National Cancer InstituteRomeItaly
| | - Claudio Passananti
- Department of Molecular Medicine, CNR‐Institute of Molecular Biology and PathologySapienza University of RomeRomeItaly
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research AreaIRCCS Regina Elena National Cancer InstituteRomeItaly
| |
Collapse
|
12
|
Kumar A, Fournier LA, Stirling PC. Integrative analysis and prediction of human R-loop binding proteins. G3 (BETHESDA, MD.) 2022; 12:jkac142. [PMID: 35666183 PMCID: PMC9339281 DOI: 10.1093/g3journal/jkac142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
In the past decade, there has been a growing appreciation for R-loop structures as important regulators of the epigenome, telomere maintenance, DNA repair, and replication. Given these numerous functions, dozens, or potentially hundreds, of proteins could serve as direct or indirect regulators of R-loop writing, reading, and erasing. In order to understand common properties shared amongst potential R-loop binding proteins, we mined published proteomic studies and distilled 10 features that were enriched in R-loop binding proteins compared with the rest of the proteome. Applying an easy-ensemble machine learning approach, we used these R-loop binding protein-specific features along with their amino acid composition to create random forest classifiers that predict the likelihood of a protein to bind to R-loops. Known R-loop regulating pathways such as splicing, DNA damage repair and chromatin remodeling are highly enriched in our datasets, and we validate 2 new R-loop binding proteins LIG1 and FXR1 in human cells. Together these datasets provide a reference to pursue analyses of novel R-loop regulatory proteins.
Collapse
Affiliation(s)
| | | | - Peter C Stirling
- Corresponding author: Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z1L3, Canada.
| |
Collapse
|
13
|
Alecki C, Vera M. Role of Nuclear Non-Canonical Nucleic Acid Structures in Organismal Development and Adaptation to Stress Conditions. Front Genet 2022; 13:823241. [PMID: 35281835 PMCID: PMC8906566 DOI: 10.3389/fgene.2022.823241] [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: 11/26/2021] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
Over the last decades, numerous examples have involved nuclear non-coding RNAs (ncRNAs) in the regulation of gene expression. ncRNAs can interact with the genome by forming non-canonical nucleic acid structures such as R-loops or DNA:RNA triplexes. They bind chromatin and DNA modifiers and transcription factors and favor or prevent their targeting to specific DNA sequences and regulate gene expression of diverse genes. We review the function of these non-canonical nucleic acid structures in regulating gene expression of multicellular organisms during development and in response to different stress conditions and DNA damage using examples described in several organisms, from plants to humans. We also overview recent techniques developed to study where R-loops or DNA:RNA triplexes are formed in the genome and their interaction with proteins.
Collapse
Affiliation(s)
- Célia Alecki
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| |
Collapse
|