1
|
Zhao YM, Jiang Y, Wang JZ, Cao S, Zhu H, Wang WK, Yu J, Liu J, Hui J. GPATCH4 functions as a regulator of nucleolar R-loops in hepatocellular carcinoma cells. Nucleic Acids Res 2025; 53:gkaf438. [PMID: 40401559 PMCID: PMC12096074 DOI: 10.1093/nar/gkaf438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 04/03/2025] [Accepted: 05/15/2025] [Indexed: 05/23/2025] Open
Abstract
Emerging evidence suggests that dysregulated RNA-binding proteins (RBPs) are associated with a wide variety of cancers. However, the exact roles and pathways of RBPs in the tumorigenesis of hepatocellular carcinoma (HCC), the most common subtype of liver cancer, remain largely unknown. Here, we systematically searched for altered RBP candidates in HCC through multi-omics data integrative analyses and identified that GPATCH4 gene is amplified in >70% HCC patients and its high expression predicts poor prognosis. We mapped the in vivo RNA binding sites of GPATCH4 by iCLIP-seq and characterized that GPATCH4 primarily bound ribosomal RNA (rRNAs). GPATCH4 promoted HCC cell proliferation and transformation both in vitro and in vivo through increasing rRNA transcription and global protein synthesis. GPATCH4 is mainly localized in the nucleolus and helps to unwind RNA loops formed at the rDNA through interacting with DDX21 via its C-terminal intrinsically disordered region. Removal of accumulated R-loops induced by GPATCH4 depletion rescued decreased rRNA transcription and cell proliferation. Taken together, we characterized the understudied GPATCH4 as an RBP with oncogenic function in HCC and revealed a new mechanism by which GPATCH4 functions as a regulator of nucleolar R-loops to control rRNA transcription through interacting with DDX21.
Collapse
Affiliation(s)
- Yi-Ming Zhao
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Jiang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jin-Zhu Wang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shang Cao
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Zhu
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei-Kang Wang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian Yu
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaquan Liu
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jingyi Hui
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
2
|
Lago S, Poli V, Fol L, Botteon M, Busi F, Turdo A, Gaggianesi M, Ciani Y, D'Amato G, Fagnocchi L, Fasciani A, Demichelis F, Todaro M, Zippo A. ANP32E drives vulnerability to ATR inhibitors by inducing R-loops-dependent transcription replication conflicts in triple negative breast cancer. Nat Commun 2025; 16:4602. [PMID: 40382323 PMCID: PMC12085574 DOI: 10.1038/s41467-025-59804-0] [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: 01/29/2024] [Accepted: 05/02/2025] [Indexed: 05/20/2025] Open
Abstract
Oncogene-induced replicative stress (RS) drives tumor progression by disrupting genome stability, primarily through transcription-replication conflicts (TRCs), which promote R-loop accumulation and trigger the DNA damage response (DDR). In this study, we investigate the role of chromatin regulators in exacerbating TRCs and R-loop accumulation in cancer. We find that in breast cancer patients, the simultaneous upregulation of MYC and the H2A.Z-specific chaperone ANP32E correlates with increased genomic instability. Genome-wide analyses reveal that ANP32E-driven H2A.Z turnover alters RNA polymerase II processivity, leading to the accumulation of long R-loops at TRC sites. Furthermore, we show that ANP32E overexpression enhances TRC formation and activates an ATR-dependent DDR, predisposing cancer cells to R-loop-mediated genomic fragility. By exploiting the vulnerability of ANP32E-expressing cancer cells to ATR inhibitors, we find that tumors relied on this DDR pathway, whose inhibition halts their pro-metastatic capacity. These findings identify ANP32E as a key driver of TRC-induced genomic instability, indicating ATR inhibition as a potential therapeutic strategy for ANP32E-overexpressing tumors.
Collapse
Affiliation(s)
- Sara Lago
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Vittoria Poli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Lisa Fol
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Mattia Botteon
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Federica Busi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alice Turdo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Miriam Gaggianesi
- Department of Precision Medicine in Medical, Surgical and Critical Care, University of Palermo, 90127, Palermo, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Giacomo D'Amato
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Luca Fagnocchi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alessandra Fasciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Matilde Todaro
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Alessio Zippo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
| |
Collapse
|
3
|
Snyder RJ, Shankar U, Delker D, Soerianto W, Burdick JT, Cheung VG, Watts JA. Guanine quadruplexes mediate mitochondrial RNA polymerase pausing. BMC Biol 2025; 23:129. [PMID: 40361112 PMCID: PMC12076976 DOI: 10.1186/s12915-025-02229-4] [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: 12/03/2024] [Accepted: 04/30/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND The information content within nucleic acids extends beyond the primary sequence to include secondary structures with functional roles in transcription regulation. Guanine-rich sequences form structures called guanine quadruplexes that result from non-canonical base pairing between guanine residues. These stable guanine quadruplex structures are prevalent in gene promoters in nuclear DNA and are known to be associated with promoter proximal pausing of some genes. However, the transcriptional impact of guanine quadruplexes that form in nascent RNA is poorly understood. RESULTS We examined mitochondrial RNA polymerase (POLRMT) pausing patterns in primary human skin fibroblast cells using the precision nuclear run-on assay and uncovered over 400 pause sites on the mitochondrial genome. We identified that these pauses frequently occur following guanine-rich sequences where quadruplexes form. Using an in vitro primer extension assay, we show that quadruplexes formed in nascent RNA act as mediators of POLRMT pausing, and in cell-based assays their stabilization disrupts POLRMT transcription. Cells exposed to a guanine-quadruplex stabilizing agent (RHPS4) had diminished mitochondrial gene expression and significantly lowered cellular respiration within 24 h. The resulting ATP stress was sufficient to reduce active transport in renal epithelia. CONCLUSIONS Our findings connect RNA guanine quadruplex-mediated pausing with the regulation of POLRMT transcription and mitochondrial function. We demonstrate that tuning of quadruplex dynamics in nascent RNA, rather than template DNA upstream of the polymerase, is sufficient to regulate mitochondrial gene expression.
Collapse
Affiliation(s)
- Ryan J Snyder
- Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Uma Shankar
- Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Don Delker
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Winny Soerianto
- Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Joshua T Burdick
- Department of Pediatrics, Division of Neurology, University of Michigan, Ann Arbor, MI, USA
| | - Vivian G Cheung
- Department of Pediatrics, Division of Neurology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Jason A Watts
- Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
- Department of Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
4
|
Zhao Y, Metzler AD, Li Y, Urlich P, Wang Y, Gilbert DM, Yao B, Tang H. Interferon-dependent R-loop induction by Zika virus contributes to growth attenuation. PNAS NEXUS 2025; 4:pgaf147. [PMID: 40386679 PMCID: PMC12082298 DOI: 10.1093/pnasnexus/pgaf147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 03/31/2025] [Indexed: 05/20/2025]
Abstract
Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here, we link the ZIKV-induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R loops at specific loci strongly enriched in the interferon (IFN)-stimulated genes (ISGs). Bromouridine sequencing results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of IFN receptor eliminated the R loops on ISGs and partially rescued S-phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN-dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.
Collapse
Affiliation(s)
- Yijing Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Anna D Metzler
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paola Urlich
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Yilin Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA 92121, USA
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| |
Collapse
|
5
|
Li Y, Sheng Y, Di C, Yao H. Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops. Mol Cell 2025; 85:1686-1702.e5. [PMID: 40112807 DOI: 10.1016/j.molcel.2025.02.019] [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: 07/30/2024] [Revised: 01/30/2025] [Accepted: 02/21/2025] [Indexed: 03/22/2025]
Abstract
R-loops are pervasive triplex nucleic acid structures across diverse organisms, yet their biological functions remain incompletely understood. Here, we develop R-loop identification assisted by nucleases and sequencing (RIAN-seq), a nuclease-assisted, antibody-free sequencing technology, to map R-loops at base-pair resolution. By digesting single-stranded RNA (ssRNA), single-stranded DNA (ssDNA), and double-stranded DNA (dsDNA) with nuclease P1, T5 exonuclease, and lambda exonuclease while preserving RNA:DNA hybrids, RIAN-seq achieves unprecedented precision in identifying the position and size of R-loops, detecting an order of magnitude more R-loops than existing methods. Approximately 50% of RNA:DNA hybrids span between 60 and 130 bp, with many forming previously undetectable clusters. Clustered R-loops at promoters recruit zinc-finger proteins VEZF1 and SP5, enhancing transcription in a number-dependent manner and resisting transcriptional perturbation. Conversely, R-loops featuring the Y(C/T)M(A/C)CAG motif at both ends contribute to DNA damage, a phenomenon conserved from yeast to mammalian cells. Our findings reveal a dual role for R-loops: clustered R-loops promote gene expression, while YMCAG-associated R-loops compromise genome stability.
Collapse
Affiliation(s)
- Yaoyi Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yingliang Sheng
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chao Di
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| |
Collapse
|
6
|
Stanek TJ, Kneebone A, Lawlor MA, Cao W, Ellison CE. Complex determinants of R-loop formation at transposable elements and major DNA satellites. Genetics 2025; 229:iyaf035. [PMID: 40036798 PMCID: PMC12005256 DOI: 10.1093/genetics/iyaf035] [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: 12/30/2024] [Revised: 02/19/2025] [Accepted: 02/22/2025] [Indexed: 03/06/2025] Open
Abstract
Aberrant activation of transposable elements (TEs) has been a well-documented source of genomic instability and disease, stemming from their insertion into genes and their imposition of epigenetic effects on nearby loci. However, the extent to which their disruptive effects involve concomitant or subsequent formation of DNA:RNA hybrids (R-loops) remains unknown. Here, we used DNA:RNA immunoprecipitation followed by high-throughput sequencing (DRIP-seq) to map the R-loop profiles of TEs and satellites in Drosophila melanogaster ovaries in control and rhino knockout flies, where dozens of TE families are derepressed. We observe that R-loops form primarily in LTR retrotransposons that carry A/T-rich sequence motifs, which are known to favor R-loop formation at genes in Drosophila and other species. We also report evidence of R-loop formation at 11 of 14 highly abundant D. melanogaster DNA satellites. R-loop formation is positively correlated with expression level for both TEs and satellites; however, neither sequence content nor expression fully explain which repeat families form R-loops, suggesting other factors are at play. Finally, by analyzing population frequencies of R-loop-forming TEs, we present evidence that TE copies with high R-loop signal may be under stronger negative selection, which suggests that R-loop formation by TEs may be deleterious to their host. Collectively, these results provide insight into the determinants of R-loop formation at repetitive elements.
Collapse
Affiliation(s)
- Timothy J Stanek
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Pathology, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Adam Kneebone
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Matthew A Lawlor
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christopher E Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| |
Collapse
|
7
|
Palmer B, Lee CY, Yang L, Paul T, Myong S. High-frequency transcription leads to rapid R-loop formation. J Biol Chem 2025; 301:108514. [PMID: 40250562 DOI: 10.1016/j.jbc.2025.108514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 03/31/2025] [Accepted: 04/09/2025] [Indexed: 04/20/2025] Open
Abstract
R-loops are transcriptionally generated three-stranded nucleic acid structures where the mRNA hybridizes with template DNA, leaving a displaced single-stranded non-template DNA loop. Previously, we demonstrated that R-loop and subsequent G-quadruplex formation upregulate transcription. However, the mechanistic basis of how transcription activity generates R-loop formation is unknown. Here, we investigate the kinetics of transcription and its impact on R-loop formation using single-molecule FRET and EMSA. We show that R-loop formation is tuned by the frequency and the rate of transcription, controlled by the RNA polymerase and NTP concentrations, respectively. We provide a plausible mechanism in which gradually increasing the duration of the promoter opening leads to the R-loop formation. Through stochastic simulation, we demonstrate that the frequency of transcription primarily governs R-loop formation. This work highlights the intricate balance between transcription dynamics and R-loop formation, providing new insights into the structure-function relationship.
Collapse
Affiliation(s)
- Bradleigh Palmer
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Chun-Ying Lee
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Leya Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Tapas Paul
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.
| |
Collapse
|
8
|
Hwang J, Lee CY, Brahmachari S, Tripathi S, Paul T, Lee H, Craig A, Ha T, Myong S. DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase. Nat Commun 2025; 16:3363. [PMID: 40204744 PMCID: PMC11982182 DOI: 10.1038/s41467-025-58479-x] [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: 05/21/2024] [Accepted: 03/24/2025] [Indexed: 04/11/2025] Open
Abstract
RNA polymerase (RNAP) is a processive motor that modulates DNA supercoiling and reshapes DNA structures. The feedback loop between the DNA topology and transcription remains elusive. Here, we investigate the impact of potential G-quadruplex forming sequences (PQS) on transcription in response to DNA supercoiling. We find that supercoiled DNA increases transcription frequency 10-fold higher than relaxed DNA, which lead to an abrupt formation of G-quadruplex (G4) and R-loop structures. Moreover, the stable R-loop relieves topological strain, facilitated by G4 formation. The cooperative formation of G4/R-loop effectively alters the DNA topology around the promoter and suppresses transcriptional activity by impeding RNAP loading. These findings highlight negative supercoiling as a built-in spring that triggers a transcriptional burst followed by a rapid suppression upon G4/R-loop formation. This study sheds light on the intricate interplay between DNA topology and structural change in transcriptional regulation, with implications for understanding gene expression dynamics.
Collapse
Affiliation(s)
- Jihee Hwang
- Programs in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Chun-Ying Lee
- Programs in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Shubham Tripathi
- Yale Center for Systems and Engineering Immunology & Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tapas Paul
- Programs in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Huijin Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alanna Craig
- Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Taekjip Ha
- Programs in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biophysics, Johns Hopkins University, Baltimore, MD, USA
- Program in Cellular Molecular Developmental Biology, Johns Hopkins University, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Sua Myong
- Programs in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Biophysics, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
9
|
Mangione RM, Pierce S, Zheng M, Martin RM, Goncalves C, Kumar A, Scaglione S, de Sousa Morgado C, Penzo A, Lancrey A, Reid RJD, Lautier O, Gaillard PH, Stirling PC, de Almeida SF, Rothstein R, Palancade B. DNA lesions can frequently precede DNA:RNA hybrid accumulation. Nat Commun 2025; 16:2401. [PMID: 40064914 PMCID: PMC11893903 DOI: 10.1038/s41467-025-57588-x] [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: 06/10/2024] [Accepted: 02/26/2025] [Indexed: 03/14/2025] Open
Abstract
While DNA:RNA hybrids contribute to multiple genomic transactions, their unscheduled formation is a recognized source of DNA lesions. Here, through a suite of systematic screens, we rather observed that a wide range of yeast mutant situations primarily triggering DNA damage actually leads to hybrid accumulation. Focusing on Okazaki fragment processing, we establish that genic hybrids can actually form as a consequence of replication-born discontinuities such as unprocessed flaps or unligated Okazaki fragments. Strikingly, such "post-lesion" DNA:RNA hybrids neither detectably contribute to genetic instability, nor disturb gene expression, as opposed to "pre-lesion" hybrids formed upon defective mRNA biogenesis, e.g., in THO complex mutants. Post-lesion hybrids similarly arise in distinct genomic instability situations, triggered by pharmacological or genetic manipulation of DNA-dependent processes, both in yeast and human cells. Altogether, our data establish that the accumulation of transcription-born DNA:RNA hybrids can occur as a consequence of various types of natural or pathological DNA lesions, yet do not necessarily aggravate their genotoxicity.
Collapse
Affiliation(s)
| | - Steven Pierce
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Myriam Zheng
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert M Martin
- GIMM-Gulbenkian Institute for Molecular Medicine, Lisbon, Portugal
- Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | | | - Arun Kumar
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sarah Scaglione
- Centre de Recherche en Cancérologie de Marseille (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Cristiana de Sousa Morgado
- GIMM-Gulbenkian Institute for Molecular Medicine, Lisbon, Portugal
- Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Astrid Lancrey
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Robert J D Reid
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Ophélie Lautier
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Pierre-Henri Gaillard
- Centre de Recherche en Cancérologie de Marseille (CRCM), U1068 Inserm, UMR7258 CNRS, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sérgio F de Almeida
- GIMM-Gulbenkian Institute for Molecular Medicine, Lisbon, Portugal
- Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France.
| |
Collapse
|
10
|
Batra S, Allwein B, Kumar C, Devbhandari S, Brüning JG, Bahng S, Lee CM, Marians KJ, Hite RK, Remus D. G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation. Science 2025; 387:eadt1978. [PMID: 40048517 DOI: 10.1126/science.adt1978] [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: 09/23/2024] [Accepted: 12/15/2024] [Indexed: 03/15/2025]
Abstract
DNA G-quadruplexes (G4s) are non-B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we characterized fork collisions with preformed G4s in the parental DNA using reconstituted yeast and human replisomes. We demonstrate that a single G4 in the leading strand template is sufficient to stall replisomes by arresting the CMG helicase. Cryo-electron microscopy structures of stalled yeast and human CMG complexes reveal that the folded G4 is lodged inside the central CMG channel, arresting translocation. The G4 stabilizes the CMG at distinct translocation intermediates, suggesting an unprecedented helical inchworm mechanism for DNA translocation. These findings illuminate the eukaryotic replication fork mechanism under normal and perturbed conditions.
Collapse
Affiliation(s)
- Sahil Batra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Allwein
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- BCMB Allied PhD Program, Weill Cornell Medical Graduate School, Weill Cornell Medicine, New York, NY, USA
| | - Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sujan Devbhandari
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jan-Gert Brüning
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soon Bahng
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chong M Lee
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth J Marians
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
11
|
Chen X, Mai Z, Zheng Y, Lin P, Lu Y, Zheng J, Lin Y, Zhou Z, Xu R, Zhao X, Cui L. The hidden weavers: A review of DNA/RNA R-loops in stem cell biology and therapeutic potential. Int J Biol Macromol 2025; 297:139895. [PMID: 39818393 DOI: 10.1016/j.ijbiomac.2025.139895] [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: 07/22/2024] [Revised: 12/28/2024] [Accepted: 01/13/2025] [Indexed: 01/18/2025]
Abstract
R-loops, three-stranded nucleic acid structures composed of RNA-DNA hybrids, are increasingly recognized as central regulators of genomic stability and transcription. These structures play critical roles across various cellular processes, including DNA replication, repair, and gene regulation, with significant implications for stem cell biology and disease pathogenesis. This review comprehensively explores the molecular underpinnings of R-loop formation, emphasizing the dual nature of R-loops in both facilitating normal cellular functions and contributing to genomic instability. We critically evaluate the current methodologies for R-loop detection, highlighting the need for more precise and higher-resolution techniques to enhance our understanding of R-loop dynamics and their biological consequences. Importantly, the review provides novel insights into the pivotal role of R-loops in stem cell biology, suggesting that manipulating R-loop dynamics could substantially improve the efficacy of stem cell-based therapies. Additionally, we discuss the challenges and future prospects in R-loop research, particularly within the realm of stem cell biology, and underscore the potential therapeutic avenues for targeting R-loop dysregulation. Our findings suggest that a deeper understanding of R-loop biology could lead to novel strategies for enhancing the stability and functionality of stem cells, thereby maximizing their therapeutic outcomes in regenerative medicine and disease treatment.
Collapse
Affiliation(s)
- Xu Chen
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Zizhao Mai
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Yucheng Zheng
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Pei Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Ye Lu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Yunfan Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Zihao Zhou
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Rongwei Xu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China
| | - Xinyuan Zhao
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China.
| | - Li Cui
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou 510280, Guangdong, China.
| |
Collapse
|
12
|
de Klein B, Eickhoff N, Zwart W. The emerging regulatory interface between DNA repair and steroid hormone receptors in cancer. Trends Mol Med 2025:S1471-4914(25)00006-1. [PMID: 39934021 DOI: 10.1016/j.molmed.2025.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 01/10/2025] [Accepted: 01/15/2025] [Indexed: 02/13/2025]
Abstract
Human cells potentiate highly diverse functions through tight transcriptional regulation and maintenance of genome integrity. While the DNA damage response (DDR) safeguards the genome, ligand-activated transcription factors, such as steroid hormone receptors (SHRs), provide complex transcriptional outputs. Interestingly, an increasing body of evidence reveals a direct biological and functional interplay between DDR factors and SHR cascades in cancer. SHRs can directly affect DDR gene expression, but DDR factors in turn act as transcriptional coregulators, enabling oncogenic SHR-mediated signaling, which has the potential for novel therapeutic interventions. With a focus on breast and prostate cancer, we describe in this review recent developments in, and insights into, the complex interplay between SHR signaling and the DDR, highlighting opportunities for future clinical interventions.
Collapse
Affiliation(s)
- Bim de Klein
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nils Eickhoff
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, 5600, MB, Eindhoven, The Netherlands.
| |
Collapse
|
13
|
Damasceno JD, Briggs EM, Krasilnikova M, Marques CA, Lapsley C, McCulloch R. R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania. Nat Commun 2025; 16:1470. [PMID: 39922816 PMCID: PMC11807225 DOI: 10.1038/s41467-025-56785-y] [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: 05/16/2024] [Accepted: 01/31/2025] [Indexed: 02/10/2025] Open
Abstract
Genomes in eukaryotes normally undergo DNA replication in a choreographed temporal order, resulting in early and late replicating chromosome compartments. Leishmania, a human protozoan parasite, displays an unconventional DNA replication program in which the timing of DNA replication completion is chromosome size-dependent: larger chromosomes complete replication later then smaller ones. Here we show that both R-loops and RNase H1, a ribonuclease that resolves RNA-DNA hybrids, accumulate in Leishmania major chromosomes in a pattern that reflects their replication timing. Furthermore, we demonstrate that such differential organisation of R-loops, RNase H1 and DNA replication timing across the parasite's chromosomes correlates with size-dependent differences in chromatin accessibility, G quadruplex distribution and sequence content. Using conditional gene excision, we show that loss of RNase H1 leads to transient growth perturbation and permanently abrogates the differences in DNA replication timing across chromosomes, as well as altering levels of aneuploidy and increasing chromosome instability in a size-dependent manner. This work provides a link between R-loop homeostasis and DNA replication timing in a eukaryotic parasite and demonstrates that orchestration of DNA replication dictates levels of genome plasticity in Leishmania.
Collapse
Affiliation(s)
- Jeziel D Damasceno
- The University of Glasgow Centre for Parasitology, The Wellcome Centre for Integrative Parasitology, University of Glasgow, School of Infection and Immunity, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
| | - Emma M Briggs
- University of Edinburgh, Institute for Immunology and Infection Research, School of Biological Sciences, Edinburgh, UK
- Biosciences Institute, Cookson Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Marija Krasilnikova
- The University of Glasgow Centre for Parasitology, The Wellcome Centre for Integrative Parasitology, University of Glasgow, School of Infection and Immunity, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Catarina A Marques
- The University of Glasgow Centre for Parasitology, The Wellcome Centre for Integrative Parasitology, University of Glasgow, School of Infection and Immunity, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Craig Lapsley
- The University of Glasgow Centre for Parasitology, The Wellcome Centre for Integrative Parasitology, University of Glasgow, School of Infection and Immunity, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Richard McCulloch
- The University of Glasgow Centre for Parasitology, The Wellcome Centre for Integrative Parasitology, University of Glasgow, School of Infection and Immunity, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
| |
Collapse
|
14
|
Kang Z, Xu C, Lu S, Gong J, Yan R, Luo G, Wang Y, He Q, Wu Y, Yan Y, Qian B, Han S, Bu Z, Zhang J, Xia X, Chen L, Hu Z, Lin M, Sun Z, Gu Y, Ye L. NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit. Nat Commun 2025; 16:791. [PMID: 39824811 PMCID: PMC11742055 DOI: 10.1038/s41467-024-55579-y] [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: 07/04/2023] [Accepted: 12/16/2024] [Indexed: 01/20/2025] Open
Abstract
Transcription elongation, especially RNA polymerase II (Pol II) pause-release, is less studied than transcription initiation in regulating gene expression during meiosis. It is also unclear how transcription elongation interplays with transcription initiation. Here, we show that depletion of NKAPL, a testis-specific protein distantly related to RNA splicing factors, causes male infertility in mice by blocking the meiotic exit and downregulating haploid genes. NKAPL binds to promoter-associated nascent transcripts and co-localizes with DNA-RNA hybrid R-loop structures at GAA-rich loci to enhance R-loop formation and facilitate Pol II pause-release. NKAPL depletion prolongs Pol II pauses and stalls the SOX30/HDAC3 transcription initiation complex on the chromatin. Genetic variants in NKAPL are associated with azoospermia in humans, while mice carrying an NKAPL frameshift mutation (M349fs) show defective meiotic exit and transcriptomic changes similar to NKAPL depletion. These findings identify NKAPL as an R-loop-recognizing factor that regulates transcription elongation, which coordinates the meiotic-to-postmeiotic transcriptome switch in alliance with the SOX30/HDAC3-mediated transcription initiation.
Collapse
Affiliation(s)
- Zhenlong Kang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Chen Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Shuai Lu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Nanjing, China
| | - Jie Gong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Ruoyu Yan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Gan Luo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Yuanyuan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Qing He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Yifei Wu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Yitong Yan
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing, People's Republic of China
| | - Baomei Qian
- Reproductive and Genetic Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Shenglin Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Zhiwen Bu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
| | - Xian Xia
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mingyan Lin
- Department of Neurobiology, School of Basic Medical Science, Nanjing Medical University, Nanjing, People's Republic of China.
| | - Zheng Sun
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Yayun Gu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China.
- Reproductive Genetic Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Suzhou, Jiangsu, China.
- Innovation Center of Suzhou Nanjing Medical University, Suzhou, Jiangsu, China.
- National Center of Technology Innovation for Biopharmaceuticals, Suzhou, Jiangsu, China.
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, China.
- Innovation Center of Suzhou Nanjing Medical University, Suzhou, Jiangsu, China.
- National Center of Technology Innovation for Biopharmaceuticals, Suzhou, Jiangsu, China.
| |
Collapse
|
15
|
Sun C, Wang Z, Li Q, Sun Q, Xu W. mDRIP-seq is a high-throughput method for quantitative profiling of R-loop landscape. Sci Bull (Beijing) 2025; 70:38-41. [PMID: 38821747 DOI: 10.1016/j.scib.2024.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/07/2024] [Accepted: 05/11/2024] [Indexed: 06/02/2024]
Affiliation(s)
- Changbin Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhenzhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qin Li
- Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, Tsinghua University, Beijing 100084, China
| | - Wei Xu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| |
Collapse
|
16
|
Guo XL, Wang YD, Liu YJ, Chu L, Zhu H, Hu Y, Wu RY, Xie HY, Yu J, Li SP, Xiong CY, Li RY, Ke F, Chen L, Chen GQ, Chen L, Bai F, Enver T, Li GH, Li HF, Hong DL. Fetal hepatocytes protect the HSPC genome via fetuin-A. Nature 2025; 637:402-411. [PMID: 39633051 PMCID: PMC11711094 DOI: 10.1038/s41586-024-08307-x] [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: 01/04/2023] [Accepted: 10/30/2024] [Indexed: 12/07/2024]
Abstract
The maintenance of genomic integrity in rapidly proliferating cells is a substantial challenge during embryonic development1-3. Although numerous cell-intrinsic mechanisms have been revealed4-7, little is known about genome-protective effects and influences of developmental tissue microenvironments on tissue-forming cells. Here we show that fetal liver hepatocytes provide protection to haematopoietic stem and progenitor cell (HSPC) genomes. Lineage tracing and depletion in mice demonstrated that delayed hepatocyte development in early fetal livers increased the chromosomal instability of newly colonizing HSPCs. In addition, HSPCs developed tolerance to genotoxins in hepatocyte-conditioned medium, suggesting that hepatocytes protect the HSPC genome in a paracrine manner. Proteomic analyses demonstrated the enrichment of fetuin-A in hepatocyte-conditioned medium but not in early fetal livers. Fetuin-A activates a Toll-like receptor pathway to prevent pathogenic R-loop accumulation in HSPCs undergoing DNA replication and gene transcription in the fetal liver. Numerous haematopoietic regulatory genes frequently involved in leukaemogenic mutations are associated with R-loop-enriched regions. In Fetua-knockout mice, HSPCs showed increased genome instability and susceptibility to malignancy induction. Moreover, low concentrations of fetuin-A correlated with the oncogenesis of childhood leukaemia. Therefore, we uncover a mechanism operating in developmental tissues that offers tissue-forming cell genome protection and is implicated in developmental-related diseases.
Collapse
Affiliation(s)
- Xiao-Lin Guo
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Ding Wang
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan-Jun Liu
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Chu
- Department of Obstetrics and Gynecology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hua Zhu
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye Hu
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ren-Yan Wu
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong-Yu Xie
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Juan Yu
- National laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shui-Ping Li
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao-Yang Xiong
- National laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ruo-Yan Li
- Biomedical Pioneering Innovation Centre (BIOPIC) and Translational Cancer Research Centre, School of Life Sciences, First Hospital, Peking University, Beijing, China
| | - Fang Ke
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Chen
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo-Qiang Chen
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Units of Stress and Tumor, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Hainan Academy of Medical Sciences, School of Basic Medicine and Life Science, Hainan Medical University, Haikou, China
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fan Bai
- Biomedical Pioneering Innovation Centre (BIOPIC) and Translational Cancer Research Centre, School of Life Sciences, First Hospital, Peking University, Beijing, China
| | - Tariq Enver
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK
| | - Guo-Hong Li
- National laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huai-Fang Li
- Department of Obstetrics and Gynecology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Deng-Li Hong
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Institute of Haematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Research Units of Stress and Tumor, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Innovative Research Team of High-level Local Universities in Shanghai, Shanghai, China.
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
17
|
Stratigi K, Siametis A, Garinis GA. Looping forward: exploring R-loop processing and therapeutic potential. FEBS Lett 2025; 599:244-266. [PMID: 38844597 PMCID: PMC11771710 DOI: 10.1002/1873-3468.14947] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 01/28/2025]
Abstract
Recently, there has been increasing interest in the complex relationship between transcription and genome stability, with specific attention directed toward the physiological significance of molecular structures known as R-loops. These structures arise when an RNA strand invades into the DNA duplex, and their formation is involved in a wide range of regulatory functions affecting gene expression, DNA repair processes or cell homeostasis. The persistent presence of R-loops, if not effectively removed, contributes to genome instability, underscoring the significance of the factors responsible for their resolution and modification. In this review, we provide a comprehensive overview of how R-loop processing can drive either a beneficial or a harmful outcome. Additionally, we explore the potential for manipulating such structures to devise rationalized therapeutic strategies targeting the aberrant accumulation of R-loops.
Collapse
Affiliation(s)
- Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology‐HellasHeraklionCreteGreece
| | - Athanasios Siametis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology‐HellasHeraklionCreteGreece
- Department of BiologyUniversity of CreteHeraklionCreteGreece
| | - George A. Garinis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology‐HellasHeraklionCreteGreece
- Department of BiologyUniversity of CreteHeraklionCreteGreece
| |
Collapse
|
18
|
Zhao W, Luo Q, Zhan H, Du Z, Deng T, Duan H. DDX18 influences chemotherapy sensitivity in colorectal cancer by regulating genomic stability. Exp Cell Res 2025; 444:114344. [PMID: 39577603 DOI: 10.1016/j.yexcr.2024.114344] [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: 09/29/2024] [Revised: 11/18/2024] [Accepted: 11/18/2024] [Indexed: 11/24/2024]
Abstract
Chromosomal Instability (CIN) encompasses approximately 65 %-70 % of colorectal cancer (CRC) patients, playing a pivotal role in tumor progression. However, controversies persist regarding the molecular characteristics and treatment strategies associated with these patients. Integrative colorectal cancer proteogenomic analysis identified DDX18 in colorectal cancer. We investigated the molecular mechanisms underlying the regulation of colorectal cancer by the R-loop binding protein DDX18 using colon cancer tissues, cell lines and patient-derived organoids. Our findings revealed that DDX18 expression positively correlates with the expression of genomic instability marker R-loops. Moreover, heightened DDX18 expression delays the completion of DNA damage repair, leading to an increase in double-strand DNA breaks, thereby promoting genomic instability. Notably, the upregulation of DDX18 enhances sensitivity to DNA-damaging. This study elucidated DDX18 beyond participating in fundamental physiological functions, may play a crucial role in the regulation of genomic stability, and also provides a powerful resource for further functional exploration of DDX18 in cancer progression and therapeutic application.
Collapse
Affiliation(s)
- Wenchao Zhao
- Department of Oncology, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410000, China; Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, China; Hunan Hepatobiliary and Pancreatic Cancer Clinical Medical Research Center, China.
| | - Qingqing Luo
- Department of Oncology, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410000, China; Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, China; Hunan Hepatobiliary and Pancreatic Cancer Clinical Medical Research Center, China
| | - Han Zhan
- 921 Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, China
| | - Zhen Du
- Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410000, China
| | - Tan Deng
- Department of Oncology, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410000, China; Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, China; Hunan Hepatobiliary and Pancreatic Cancer Clinical Medical Research Center, China.
| | - Huaxin Duan
- Department of Oncology, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410000, China; Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, China; Hunan Hepatobiliary and Pancreatic Cancer Clinical Medical Research Center, China.
| |
Collapse
|
19
|
Ouyang J. Transcription as a double-edged sword in genome maintenance. FEBS Lett 2025; 599:147-156. [PMID: 39704019 DOI: 10.1002/1873-3468.15080] [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: 02/16/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 12/21/2024]
Abstract
Genome maintenance is essential for the integrity of the genetic blueprint, of which only a small fraction is transcribed in higher eukaryotes. DNA lesions occurring in the transcribed genome trigger transcription pausing and transcription-coupled DNA repair. There are two major transcription-coupled DNA repair pathways. The transcription-coupled nucleotide excision repair (TC-NER) pathway has been well studied for decades, while the transcription-coupled homologous recombination repair (TC-HR) pathway has recently gained attention. Importantly, recent studies have uncovered crucial roles of RNA transcripts in TC-HR, opening exciting directions for future research. Transcription also plays pivotal roles in regulating the stability of highly specialized genomic structures such as telomeres, centromeres, and fragile sites. Despite their positive function in genome maintenance, transcription and RNA transcripts can also be the sources of genomic instability, especially when colliding with DNA replication and forming unscheduled pathological RNA:DNA hybrids (R-loops), respectively. Pathological R-loops can result from transcriptional stress, which may be induced by transcription dysregulation. Future investigation into the interplay between transcription and DNA repair will reveal novel molecular bases for genome maintenance and transcriptional stress-associated genomic instability, providing therapeutic targets for human disease intervention.
Collapse
Affiliation(s)
- Jian Ouyang
- Department of Biochemistry and Molecular Biology
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| |
Collapse
|
20
|
Akiki RM, Cornbrooks RG, Magami K, Greige A, Snyder KK, Wood DJ, Herrington MC, Mace P, Blidy K, Koike N, Berto S, Cowan CW, Taniguchi M. A long noncoding eRNA forms R-loops to shape emotional experience-induced behavioral adaptation. Science 2024; 386:1282-1289. [PMID: 39666799 PMCID: PMC12071198 DOI: 10.1126/science.adp1562] [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: 03/19/2024] [Accepted: 10/09/2024] [Indexed: 12/14/2024]
Abstract
Emotional experiences often evoke neural plasticity that supports adaptive changes in behavior, including maladaptive plasticity associated with mood and substance use disorders. These adaptations are supported in part by experience-dependent activation of immediate-early response genes, such as Npas4 (neuronal PAS domain protein 4). Here we show that a conserved long noncoding enhancer RNA (lnc-eRNA), transcribed from an activity-sensitive enhancer, produces DNA:RNA hybrid R-loop structures that support three-dimensional chromatin looping between enhancer and proximal promoter and rapid Npas4 gene induction. Furthermore, in mouse models, Npas4 lnc-eRNA and its R-loop are required for the development of behavioral adaptations produced by chronic psychosocial stress or cocaine exposure, revealing a potential role for this regulatory mechanism in the transmission of emotional experiences.
Collapse
MESH Headings
- Animals
- Male
- Mice
- Adaptation, Psychological/drug effects
- Adaptation, Psychological/physiology
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Behavior, Animal
- Chromatin/metabolism
- Cocaine/pharmacology
- Emotions/drug effects
- Emotions/physiology
- Enhancer Elements, Genetic
- Mice, Inbred C57BL
- Neuronal Plasticity
- Promoter Regions, Genetic
- R-Loop Structures
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Stress, Psychological/genetics
- Stress, Psychological/psychology
Collapse
Affiliation(s)
- Rose Marie Akiki
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
- Medical Scientist Training Program, Medical University of South Carolina; Charleston, SC, USA
| | - Rebecca G. Cornbrooks
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| | - Kosuke Magami
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| | - Alain Greige
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
- Medical Scientist Training Program, Medical University of South Carolina; Charleston, SC, USA
| | - Kirsten K. Snyder
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| | - Daniel J. Wood
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
- Medical Scientist Training Program, Medical University of South Carolina; Charleston, SC, USA
| | | | - Philip Mace
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| | - Kyle Blidy
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine; Kyoto, Japan
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| | - Christopher W. Cowan
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| | - Makoto Taniguchi
- Department of Neuroscience, Medical University of South Carolina; Charleston, SC, USA
| |
Collapse
|
21
|
Wu Y, Lin S, Chen H, Zheng X. Cross-regulation of RNA methylation modifications and R-loops: from molecular mechanisms to clinical implications. Cell Mol Life Sci 2024; 82:1. [PMID: 39656315 PMCID: PMC11631829 DOI: 10.1007/s00018-024-05536-1] [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: 09/26/2024] [Revised: 11/08/2024] [Accepted: 11/29/2024] [Indexed: 12/13/2024]
Abstract
R-loops, RNA-DNA hybrid structures, are integral to key cellular processes such as transcriptional regulation, DNA replication, and repair. However, aberrant accumulation of R-loops can compromise genomic integrity, leading to the development of various diseases. Emerging evidence underscores the pivotal role of RNA methylation modifications, particularly N6-methyladenosine (m6A) and 5-methylcytosine (m5C), in orchestrating the formation, resolution, and stabilization of R-loops. These modifications dynamically regulate R-loop metabolism, exerting bidirectional control by either facilitating or resolving R-loop structures during gene expression regulation and DNA damage repair. Dysregulation of RNA methylation and the resultant imbalance in R-loop homeostasis are closely linked to the pathogenesis of diseases such as cancer and neurodegenerative disorders. Thus, deciphering the cross-talk between RNA methylation and R-loops is essential for understanding the mechanisms underlying genomic stability and identifying novel therapeutic targets. This review provides a comprehensive analysis of the role of RNA methylation in R-loop dynamics, examines their physiological and pathological implications, and proposes future directions for therapeutic intervention targeting these processes.
Collapse
Affiliation(s)
- Yuqing Wu
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shen Lin
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Urology, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, 322000, Yiwu, People's Republic of China
| | - Hong Chen
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiangyi Zheng
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| |
Collapse
|
22
|
Puzzo F, Crossley MP, Goswami A, Zhang F, Pekrun K, Garzon JL, Cimprich KA, Kay MA. AAV-mediated genome editing is influenced by the formation of R-loops. Mol Ther 2024; 32:4256-4271. [PMID: 39369271 PMCID: PMC11638834 DOI: 10.1016/j.ymthe.2024.09.035] [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: 05/22/2024] [Revised: 08/05/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024] Open
Abstract
Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for in vivo gene therapy. However, rAAVs also integrate throughout the genome. Here, we describe DNA-RNA immunoprecipitation sequencing (DRIP-seq) in murine HEPA1-6 hepatoma cells and whole murine liver to establish the similarities and differences in genomic R-loop formation in a transformed cell line and intact tissue. We show enhanced AAV-HR in mice upon genetic and pharmacological upregulation of R-loops. Selecting the highly expressed Albumin gene as a model locus for genome editing in both in vitro and in vivo experiments showed that the R-loop prone 3' end of Albumin was efficiently edited by AAV-HR, whereas the upstream R-loop-deficient region did not result in detectable vector integration. In addition, we found a positive correlation between previously reported off-target rAAV integration sites and R-loop enriched genomic regions. Thus, we conclude that high levels of R-loops, present in highly transcribed genes, may promote rAAV vector genome integration. These findings may shed light on potential mechanisms for improving the safety and efficacy of genome editing by modulating R-loops and may enhance our ability to predict regions most susceptible to off-target insertional mutagenesis by rAAV vectors.
Collapse
Affiliation(s)
- Francesco Puzzo
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Aranyak Goswami
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Feijie Zhang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Katja Pekrun
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Jada L Garzon
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Mark A Kay
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
23
|
Anczukow O, Allain FHT, Angarola BL, Black DL, Brooks AN, Cheng C, Conesa A, Crosse EI, Eyras E, Guccione E, Lu SX, Neugebauer KM, Sehgal P, Song X, Tothova Z, Valcárcel J, Weeks KM, Yeo GW, Thomas-Tikhonenko A. Steering research on mRNA splicing in cancer towards clinical translation. Nat Rev Cancer 2024; 24:887-905. [PMID: 39384951 DOI: 10.1038/s41568-024-00750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/11/2024]
Abstract
Splicing factors are affected by recurrent somatic mutations and copy number variations in several types of haematologic and solid malignancies, which is often seen as prima facie evidence that splicing aberrations can drive cancer initiation and progression. However, numerous spliceosome components also 'moonlight' in DNA repair and other cellular processes, making their precise role in cancer difficult to pinpoint. Still, few would deny that dysregulated mRNA splicing is a pervasive feature of most cancers. Correctly interpreting these molecular fingerprints can reveal novel tumour vulnerabilities and untapped therapeutic opportunities. Yet multiple technological challenges, lingering misconceptions, and outstanding questions hinder clinical translation. To start with, the general landscape of splicing aberrations in cancer is not well defined, due to limitations of short-read RNA sequencing not adept at resolving complete mRNA isoforms, as well as the shallow read depth inherent in long-read RNA-sequencing, especially at single-cell level. Although individual cancer-associated isoforms are known to contribute to cancer progression, widespread splicing alterations could be an equally important and, perhaps, more readily actionable feature of human cancers. This is to say that in addition to 'repairing' mis-spliced transcripts, possible therapeutic avenues include exacerbating splicing aberration with small-molecule spliceosome inhibitors, targeting recurrent splicing aberrations with synthetic lethal approaches, and training the immune system to recognize splicing-derived neoantigens.
Collapse
Affiliation(s)
- Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| | - Frédéric H-T Allain
- Department of Biology, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | | | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Chonghui Cheng
- Department of Molecular and Human Genetics, Lester & Sue Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Paterna, Spain
| | - Edie I Crosse
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eduardo Eyras
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ernesto Guccione
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY, USA
| | - Sydney X Lu
- Department of Medicine, Stanford Medical School, Palo Alto, CA, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Priyanka Sehgal
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiao Song
- Department of Neurology, Northwestern University, Chicago, IL, USA
| | - Zuzana Tothova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Juan Valcárcel
- Centre for Genomic Regulation, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
24
|
Zhang X, Liang SB, Yi Z, Qiao Z, Xu B, Geng H, Wang H, Yin X, Tang M, Ge W, Xu YZ, Liang K, Fan YJ, Chen L. Global coupling of R-loop dynamics with RNA polymerase II modulates gene expression and early development of Drosophila. Nucleic Acids Res 2024; 52:13110-13127. [PMID: 39470713 PMCID: PMC11602159 DOI: 10.1093/nar/gkae933] [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: 06/28/2024] [Revised: 09/30/2024] [Accepted: 10/08/2024] [Indexed: 10/30/2024] Open
Abstract
R-loops are involved in many biological processes in cells, yet the regulatory principles for R-loops in vivo and their impact on development remain to be explored. Here, we modified the CUT&Tag strategy to profile R-loops in Drosophila at multiple developmental stages. While high GC content promotes R-loop formation in mammalian cells, it is not required in Drosophila. In contrast, RNAPII abundance appears to be a universal inducing factor for R-loop formation, including active promoters and enhancers, and H3K27me3 decorated repressive regions and intergenic repeat sequences. Importantly, such a regulatory relationship is dynamically maintained throughout development, and development-related transcription factors may regulate RNAPII activation and R-loop dynamics. By ablating Spt6, we further showed the global R-loop induction coupled with RNAPII pausing. Importantly, depending on the gene length, genes underwent up- or down-regulation, both of which were largely reversed by rnh1 overexpression, suggesting that R-loops play a significant role in the divergent regulation of transcription by Spt6 ablation. DNA damage, defects in survival, and cuticle development were similarly alleviated by rnh1 overexpression. Altogether, our findings indicate that dynamic R-loop regulation is dictated by RNAPII pausing and transcription activity, and plays a feedback role in gene regulation, genome stability maintenance, and Drosophila development.
Collapse
Affiliation(s)
- Xianhong Zhang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shao-Bo Liang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhuoyun Yi
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhaohui Qiao
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bo Xu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huichao Geng
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Honghong Wang
- Department of Pathophysiology, Hubei Province Key Laboratory of Allergy and Immunology, Research Center for Medicine and Structural Biology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xinhua Yin
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Mingliang Tang
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yong-Zhen Xu
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kaiwei Liang
- Department of Pathophysiology, Hubei Province Key Laboratory of Allergy and Immunology, Research Center for Medicine and Structural Biology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yu-Jie Fan
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Liang Chen
- RNA Institute, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
25
|
Khosraviani N, Yerlici VT, St-Germain J, Hou YY, Cao SB, Ghali C, Bokros M, Krishnan R, Hakem R, Lee S, Raught B, Mekhail K. Nucleolar Pol II interactome reveals TBPL1, PAF1, and Pol I at intergenic rDNA drive rRNA biogenesis. Nat Commun 2024; 15:9603. [PMID: 39505901 PMCID: PMC11541992 DOI: 10.1038/s41467-024-54002-w] [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: 11/23/2023] [Accepted: 10/28/2024] [Indexed: 11/08/2024] Open
Abstract
Ribosomal DNA (rDNA) repeats harbor ribosomal RNA (rRNA) genes and intergenic spacers (IGS). RNA polymerase (Pol) I transcribes rRNA genes yielding rRNA components of ribosomes. IGS-associated Pol II prevents Pol I from excessively synthesizing IGS non-coding RNAs (ncRNAs) that can disrupt nucleoli and rRNA production. Here, compartment-enriched proximity-dependent biotin identification (compBioID) revealed the TATA-less-promoter-binding TBPL1 and transcription-regulatory PAF1 with nucleolar Pol II. TBPL1 localizes to TCT motifs, driving Pol II and Pol I and maintaining its baseline ncRNA levels. PAF1 promotes Pol II elongation, preventing unscheduled R-loops that hyper-restrain IGS Pol I-associated ncRNAs. PAF1 or TBPL1 deficiency disrupts nucleolar organization and rRNA biogenesis. In PAF1-deficient cells, repressing unscheduled IGS R-loops rescues nucleolar organization and rRNA production. Depleting IGS Pol I-dependent ncRNAs is sufficient to compromise nucleoli. We present the nucleolar interactome of Pol II and show that its regulation by TBPL1 and PAF1 ensures IGS Pol I ncRNAs maintaining nucleolar structure and function.
Collapse
Affiliation(s)
- Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - V Talya Yerlici
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Yi Yang Hou
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shi Bo Cao
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Carla Ghali
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Bokros
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Rehna Krishnan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Lee
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Temerty Centre for AI Research and Education in Medicine, University of Toronto, Toronto, Ontario, Canada.
- College of New Scholars, Artists and Scientists, The Royal Society of Canada, Ottawa, Ontario, Canada.
| |
Collapse
|
26
|
Liu A, Wang Y, Zheng S, Bao Z, Zhu H, Yin L, Liu C, Zhao X, Zhao Z, Zhu D, Yu H. Endonuclear Circ-calm4 regulates ferroptosis via a circR-Loop of the COMP gene in pulmonary artery smooth muscle cells. Eur J Pharmacol 2024; 982:176944. [PMID: 39187041 DOI: 10.1016/j.ejphar.2024.176944] [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: 03/31/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
Abstract
Pulmonary hypertension (PH) is a serious pulmonary vascular disease characterized by vascular remodeling. Circular RNAs (CircRNAs) play important roles in pulmonary hypertension, but the mechanism of PH is not fully understood, particularly the roles of circRNAs located in the nucleus. Circ-calmodulin 4 (circ-calm4) is expressed in both the cytoplasm and the nucleus of pulmonary arterial smooth muscle cells (PASMCs). This study aimed to investigate the role of endonuclear circ-calm4 in PH and elucidate its underlying signaling pathway in ferroptosis. Immunoblotting, quantitative real-time polymerase chain reaction (PCR), malondialdehyde (MDA) assay, immunofluorescence, iron assay, dot blot, and chromatin immunoprecipitation (ChIP) were performed to investigate the role of endonuclear circ-calm4 in PASMC ferroptosis. Increased endonuclear circ-calm4 facilitated ferroptosis in PASMCs under hypoxic conditions. We further identified the cartilage oligomeric matrix protein (COMP) as a downstream effector of circ-calm4 that contributed to the occurrence of hypoxia-induced ferroptosis in PASMCs. Importantly, we confirmed that endonuclear circ-calm4 formed circR-loops with the promoter region of the COMP gene and negatively regulated its expression. Inhibition of COMP restored the phenotypes related to ferroptosis under hypoxia stimulation combined with antisense oligonucleotide (ASO)-circ-calm4 treatment. We conclude that the circ-calm4/COMP axis contributed to hypoxia-induced ferroptosis in PASMCs and that circ-calm4 formed circR-loops with the COMP promoter in the nucleus and negatively regulated its expression. The circ-calm4/COMP axis may be useful for the design of therapeutic strategies for protecting cellular functionality against ferroptosis and pulmonary hypertension.
Collapse
MESH Headings
- Animals
- Male
- Mice
- Cartilage Oligomeric Matrix Protein/genetics
- Cartilage Oligomeric Matrix Protein/metabolism
- Cell Hypoxia/genetics
- Cell Nucleus/metabolism
- Cells, Cultured
- Ferroptosis/genetics
- Hypertension, Pulmonary/genetics
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/cytology
- Myocytes, Smooth Muscle/metabolism
- Pulmonary Artery/cytology
- Pulmonary Artery/metabolism
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Signal Transduction
Collapse
Affiliation(s)
- Aijing Liu
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China
| | - Yingqi Wang
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China
| | - Shuang Zheng
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China
| | - Zhitu Bao
- Department of Chest Surgery, the Fifth Affiliated Hospital of Harbin Medical University, Daqing, Heilongjiang Province, China
| | - He Zhu
- Department of Oncology, the Fifth Affiliated Hospital of Harbin Medical University, Daqing, Heilongjiang Province, China
| | - Lulu Yin
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China
| | - Chunmiao Liu
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China
| | - Xiaoxu Zhao
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China
| | - Ziru Zhao
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China
| | - Daling Zhu
- Central Laboratory of Harbin Medical University (Daqing), China; College of Pharmacy, Harbin Medical University, China.
| | - Hang Yu
- Department of Basic Medicine, Harbin Medical University (Daqing), Heilongjiang Province, China.
| |
Collapse
|
27
|
Ferrero L, Zhang W, Benhamed M, Crespi M, Ariel F. Non-B DNA in plant genomes: prediction, mapping, and emerging roles. TRENDS IN PLANT SCIENCE 2024; 29:1224-1244. [PMID: 39079769 DOI: 10.1016/j.tplants.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 11/09/2024]
Abstract
Regulating gene expression in plant development and environmental responses is vital for mitigating the effects of climate change on crop growth and productivity. The eukaryotic genome largely shows the canonical B-DNA structure that is organized into nucleosomes with histone modifications shaping the epigenome. Nuclear proteins and RNA interactions influence chromatin conformations and dynamically modulate gene activity. Non-B DNA conformations and their transitions introduce novel aspects to gene expression modulation, particularly in response to environmental shifts. We explore the current understanding of non-B DNA structures in plant genomes, their interplay with epigenomics and gene expression, and advances in methods for their mapping and characterization. The exploration of so far uncharacterized non-B DNA structures remains an intriguing area in plant chromatin research and offers insights into their potential role in gene regulation.
Collapse
Affiliation(s)
- Lucía Ferrero
- APOLO Biotech, Santa Fe de la Vera Cruz, Santa Fe, Argentina
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Bâtiment 630, 91192 Gif-sur-Yvette, France
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Bâtiment 630, 91192 Gif-sur-Yvette, France
| | - Federico Ariel
- APOLO Biotech, Santa Fe de la Vera Cruz, Santa Fe, Argentina; Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA Buenos Aires, Argentina.
| |
Collapse
|
28
|
Sagi T, Sadato D, Takayasu K, Sasanuma H, Kanoh Y, Masai H. RNA-DNA hybrids on protein coding genes are stabilized by loss of RNase H and are associated with DNA damages during S-phase in fission yeast. Genes Cells 2024; 29:966-982. [PMID: 39252397 DOI: 10.1111/gtc.13157] [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: 07/13/2024] [Revised: 08/15/2024] [Accepted: 08/23/2024] [Indexed: 09/11/2024]
Abstract
RNA-DNA hybrid is a part of the R-loop which is an important non-standard nucleic acid structure. RNA-DNA hybrid/R-loop causes genomic instability by inducing DNA damages or inhibiting DNA replication. It also plays biologically important roles in regulation of transcription, replication, recombination and repair. Here, we have employed catalytically inactive human RNase H1 mutant (D145N) to visualize RNA-DNA hybrids and map their genomic locations in fission yeast cells. The RNA-DNA hybrids appear as multiple nuclear foci in rnh1∆rnh201∆ cells lacking cellular RNase H activity, but not in the wild-type. The majority of RNA-DNA hybrid loci are detected at the protein coding regions and tRNA. In rnh1∆rnh201∆ cells, cells with multiple Rad52 foci increase during S-phase and about 20% of the RNA-DNA hybrids overlap with Rad52 loci. During S-phase, more robust association of Rad52 with RNA-DNA hybrids was observed in the protein coding region than in M-phase. These results suggest that persistent RNA-DNA hybrids in the protein coding region in rnh1∆rnh201∆ cells generate DNA damages during S-phase, potentially through collision with DNA replication forks.
Collapse
Affiliation(s)
- Tomoko Sagi
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Daichi Sadato
- Clinical Research and Trials Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Kazuto Takayasu
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Department of Biosciences, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Hiroyuki Sasanuma
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yutaka Kanoh
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| |
Collapse
|
29
|
Choi H, Zhou L, Zhao Y, Dean J. RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility. Nucleic Acids Res 2024; 52:11973-11994. [PMID: 39162228 PMCID: PMC11514495 DOI: 10.1093/nar/gkae712] [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: 06/18/2023] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
During meiosis, RNA polymerase II transcribes pachytene piRNA precursors with unusually long and unspliced transcripts from discrete autosomal loci in the mouse genome. Despite the importance of piRNA for male fertility and a well-defined maturation process, the transcriptional machinery remains poorly understood. Here, we document that D1PAS1, an ATP-dependent RNA helicase, is critical for pachytene piRNA expression from multiple genomic loci and subsequent translocation into the cytoplasm to ensure mature piRNA biogenesis. Depletion of D1PAS1 in gene-edited mice results in the accumulation of R-loops in pachytene spermatocytes, leading to DNA-damage-induced apoptosis, disruption of piRNA biogenesis, spermatogenic arrest, and male infertility. Transcriptome, genome-wide R-loop profiling, and proteomic analyses document that D1PAS1 regulates pachytene piRNA transcript elongation and termination. D1PAS1 subsequently forms a complex with nuclear export components to ensure pachytene piRNA precursor translocation from the nucleus to the cytoplasm for processing into small non-coding RNAs. Thus, our study defines D1PAS1 as a specific transcription activator that promotes R-loop unwinding and is a critical factor in pachytene piRNA biogenesis.
Collapse
Affiliation(s)
- Heejin Choi
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lecong Zhou
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yangu Zhao
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
30
|
Yadav C, Yadav R, Nanda S, Ranga S, Ahuja P. The hidden architects of the genome: a comprehensive review of R-loops. Mol Biol Rep 2024; 51:1095. [PMID: 39460836 DOI: 10.1007/s11033-024-10025-6] [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: 08/08/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024]
Abstract
Three-stranded DNA: RNA hybrids known as R-loops form when the non-template DNA strand is displaced and the mRNA transcript anneals to its template strand. Although R-loop formation controls DNA damage response, mitochondrial and genomic transcription, and physiological R-loop formation, imbalanced formation of R-loop can jeopardize a cell's genomic integrity. Transcription regulation and immunoglobulin class switch recombination are two further specialized functions of genomic R-loops. R-loop formation has a dual role in the development of cancer and disturbed R-loop homeostasis as observed in several malignancies. R-loops transcribe at the telomeric and pericentromeric regions, develop in the space between long non-coding RNAs and telomeric repeats, and shield telomeres. In bacteria and archaea, R-loop development is a natural defence mechanism against viruses which also causes DNA degradation. Their emergence in the mammalian genome is controlled, suggesting that they were formed as an inevitable byproduct of RNA transcription but also co-opted for regulatory functions. R-loops may be engaged in cell physiology by regulating gene expression. R-loop biology is probably going to remain a fascinating field of study for a very long time as it offers many avenues for R-loop research.
Collapse
Affiliation(s)
- Chetna Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Ritu Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
| | - Smiti Nanda
- Department of Gynaecology and Obstetrics, Pt. B.D. Sharma, University of Health Sciences, Rohtak, Haryana, 124001, India
| | - Shalu Ranga
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Parul Ahuja
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| |
Collapse
|
31
|
Qiu Y, Man C, Zhu L, Zhang S, Wang X, Gong D, Fan Y. R-loops' m6A modification and its roles in cancers. Mol Cancer 2024; 23:232. [PMID: 39425197 PMCID: PMC11487993 DOI: 10.1186/s12943-024-02148-y] [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: 07/02/2024] [Accepted: 10/07/2024] [Indexed: 10/21/2024] Open
Abstract
R-loops are three-stranded nucleic acid structures composed of an RNA-DNA hybrid and a displaced DNA strand. They are widespread and play crucial roles in regulating gene expression, DNA replication, and DNA and histone modifications. However, their regulatory mechanisms remain unclear. As R-loop detection technology advances, changes in R-loop levels have been observed in cancer models, often associated with transcription-replication conflicts and genomic instability. N6-methyladenosine (m6A) is an RNA epigenetic modification that regulates gene expression by affecting RNA localization, splicing, translation, and degradation. Upon reviewing the literature, we found that R-loops with m6A modifications are implicated in tumor development and progression. This article summarizes the molecular mechanisms and detection methods of R-loops and m6A modifications in gene regulation, and reviews recent research on m6A-modified R-loops in oncology. Our goal is to provide new insights into the origins of genomic instability in cancer and potential strategies for targeted therapy.
Collapse
Affiliation(s)
- Yue Qiu
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China
| | - Changfeng Man
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China
| | - Luyu Zhu
- Department of Gastroenterology, The Suqian Clinical College of Xuzhou Medical University, No 120, Suzhi Road, Suqian, Jiangsu Province, 223812, People's Republic of China
| | - Shiqi Zhang
- Department of Gastroenterology, The Suqian Clinical College of Xuzhou Medical University, No 120, Suzhi Road, Suqian, Jiangsu Province, 223812, People's Republic of China
| | - Xiaoyan Wang
- Department of Gastroenterology, The Suqian Clinical College of Xuzhou Medical University, No 120, Suzhi Road, Suqian, Jiangsu Province, 223812, People's Republic of China.
| | - Dandan Gong
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China.
| | - Yu Fan
- Cancer Institute, Affiliated People's Hospital of Jiangsu University, No 8, Dianli Road, Zhenjiang, Jiangsu Province, 212002, People's Republic of China.
| |
Collapse
|
32
|
Liu T, Shen X, Ren Y, Lu H, Liu Y, Chen C, Yu L, Xue Z. Genome-wide mapping of native co-localized G4s and R-loops in living cells. eLife 2024; 13:RP99026. [PMID: 39392462 PMCID: PMC11469684 DOI: 10.7554/elife.99026] [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: 10/12/2024] Open
Abstract
The interplay between G4s and R-loops are emerging in regulating DNA repair, replication, and transcription. A comprehensive picture of native co-localized G4s and R-loops in living cells is currently lacking. Here, we describe the development of HepG4-seq and an optimized HBD-seq methods, which robustly capture native G4s and R-loops, respectively, in living cells. We successfully employed these methods to establish comprehensive maps of native co-localized G4s and R-loops in human HEK293 cells and mouse embryonic stem cells (mESCs). We discovered that co-localized G4s and R-loops are dynamically altered in a cell type-dependent manner and are largely localized at active promoters and enhancers of transcriptional active genes. We further demonstrated the helicase Dhx9 as a direct and major regulator that modulates the formation and resolution of co-localized G4s and R-loops. Depletion of Dhx9 impaired the self-renewal and differentiation capacities of mESCs by altering the transcription of co-localized G4s and R-loops -associated genes. Taken together, our work established that the endogenous co-localized G4s and R-loops are prevalently persisted in the regulatory regions of active genes and are involved in the transcriptional regulation of their linked genes, opening the door for exploring broader roles of co-localized G4s and R-loops in development and disease.
Collapse
Affiliation(s)
- Ting Liu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Xing Shen
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Yijia Ren
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Hongyu Lu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Yu Liu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Chong Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan UniversityChengduChina
| | - Lin Yu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
| | - Zhihong Xue
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan UniversityChengduChina
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan ProvinceChengduChina
| |
Collapse
|
33
|
Crowner A, Smith K, DeSmet M. Regulation of R-Loops in DNA Tumor Viruses. Pathogens 2024; 13:863. [PMID: 39452734 PMCID: PMC11510693 DOI: 10.3390/pathogens13100863] [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: 09/11/2024] [Revised: 09/25/2024] [Accepted: 09/30/2024] [Indexed: 10/26/2024] Open
Abstract
R-loops are triple-stranded nucleic acid structures that occur when newly synthesized single-stranded RNA anneals to duplex DNA upon the collision of replication forks with transcription complexes. These RNA-DNA hybrids facilitate several transcriptional processes in the cell and have been described extensively in the literature. Recently, evidence has emerged that R-loops are key regulators of DNA tumor virus transcription and the replication of their lifecycle. Studies have demonstrated that R-loops on the Human Papillomavirus (HPV) genome must be resolved to maintain genome maintenance and avoid viral integration, a hallmark of HPV cancers. For Epstein-Barr virus (EBV), R-loops are formed at the oriLyt to establish lytic replication. Structural maintenance of chromosome proteins 5/6 (SMC5/6) bind to these viral R-loops to repress EBV lytic replication. Most viruses in the herpesvirales order, such as KSHV, contain R-loop-forming sequences. In this perspective, we will describe the current, although limited, literature demonstrating the importance of RNA-DNA hybrids to regulate DNA virus transcription. We will also detail potential new areas of R-loop research and how these viruses can be used as tools to study the growing field of R-loops.
Collapse
Affiliation(s)
- Anaiya Crowner
- Indiana University Simon Comprehensive Cancer Center American Cancer Society Post-Baccalaureate Diversity in Cancer Research Education Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Keely Smith
- Indiana University Simon Comprehensive Cancer Center American Cancer Society Post-Baccalaureate Diversity in Cancer Research Education Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Marsha DeSmet
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Yu Z, Wang Q, Zhang Q, Tian Y, Yan G, Zhu J, Zhu G, Zhang Y. Decoding the genomic landscape of chromatin-associated biomolecular condensates. Nat Commun 2024; 15:6952. [PMID: 39138204 PMCID: PMC11322608 DOI: 10.1038/s41467-024-51426-2] [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: 07/28/2023] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Biomolecular condensates play a significant role in chromatin activities, primarily by concentrating and compartmentalizing proteins and/or nucleic acids. However, their genomic landscapes and compositions remain largely unexplored due to a lack of dedicated computational tools for systematic identification in vivo. To address this, we develop CondSigDetector, a computational framework designed to detect condensate-like chromatin-associated protein co-occupancy signatures (CondSigs), to predict genomic loci and component proteins of distinct chromatin-associated biomolecular condensates. Applying this framework to mouse embryonic stem cells (mESC) and human K562 cells enable us to depict the high-resolution genomic landscape of chromatin-associated biomolecular condensates, and uncover both known and potentially unknown biomolecular condensates. Multi-omics analysis and experimental validation further verify the condensation properties of CondSigs. Additionally, our investigation sheds light on the impact of chromatin-associated biomolecular condensates on chromatin activities. Collectively, CondSigDetector provides an approach to decode the genomic landscape of chromatin-associated condensates, facilitating a deeper understanding of their biological functions and underlying mechanisms in cells.
Collapse
Affiliation(s)
- Zhaowei Yu
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qi Wang
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qichen Zhang
- Pancreatic Intensive Care Unit, Changhai hospital, Naval Medical University, Shanghai, 200433, China
- Lingang Laboratory, Shanghai, 200031, China
| | - Yawen Tian
- Lingang Laboratory, Shanghai, 200031, China
| | - Guo Yan
- Lingang Laboratory, Shanghai, 200031, China
| | - Jidong Zhu
- Etern Biopharma, Shanghai, 201203, China
| | - Guangya Zhu
- Lingang Laboratory, Shanghai, 200031, China.
| | - Yong Zhang
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Institute for Regenerative Medicine, Department of Neurosurgery, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| |
Collapse
|
36
|
Xu W, Liu X, Li J, Sun C, Chen L, Zhou J, Li K, Li Q, Meng A, Sun Q. ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis. CELL INSIGHT 2024; 3:100179. [PMID: 38974143 PMCID: PMC11225018 DOI: 10.1016/j.cellin.2024.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
R-loop, a chromatin structure containing one RNA:DNA hybrid and one unpaired single-stranded DNA, plays multiple biological roles. However, due to technical limitations, the landscapes and potential functions of R-loops during embryogenesis remain elusive. Here, we developed a quantitative and high-resolution ultra-low input R-loop profiling method, named ULI-ssDRIP-seq, which can map global R-loops with as few as 1000 cells. By using ULI-ssDRIP-seq, we reveal the R-loop dynamics in the zebrafish from gametes to early embryos. In oocytes, the R-loop level is relatively low in most regions of the nuclear genome, except maternal-inherited rDNA and mitochondrial genome. The correlation between R-loop and CG methylation dynamics during early development is relatively weak. Furthermore, either up- or down-regulation of global R-loops by knockdown or overexpression of RNase H1 causes a delay of embryonic development with dramatic expression changes in zygotic and maternal genes. This study provides comprehensive R-loop landscapes during early vertebrate embryogenesis and demonstrates the implication of R-loops in embryonic development.
Collapse
Affiliation(s)
- Wei Xu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xin Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jinjin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Changbin Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Luxi Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jincong Zhou
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Kuan Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qin Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qianwen Sun
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| |
Collapse
|
37
|
Peixoto ML, Madan E. Unraveling the complexity: Advanced methods in analyzing DNA, RNA, and protein interactions. Adv Cancer Res 2024; 163:251-302. [PMID: 39271265 DOI: 10.1016/bs.acr.2024.06.010] [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: 09/15/2024]
Abstract
Exploring the intricate interplay within and between nucleic acids, as well as their interactions with proteins, holds pivotal significance in unraveling the molecular complexities steering cancer initiation and progression. To investigate these interactions, a diverse array of highly specific and sensitive molecular techniques has been developed. The selection of a particular technique depends on the specific nature of the interactions. Typically, researchers employ an amalgamation of these different techniques to obtain a comprehensive and holistic understanding of inter- and intramolecular interactions involving DNA-DNA, RNA-RNA, DNA-RNA, or protein-DNA/RNA. Examining nucleic acid conformation reveals alternative secondary structures beyond conventional ones that have implications for cancer pathways. Mutational hotspots in cancer often lie within sequences prone to adopting these alternative structures, highlighting the importance of investigating intra-genomic and intra-transcriptomic interactions, especially in the context of mutations, to deepen our understanding of oncology. Beyond these intramolecular interactions, the interplay between DNA and RNA leads to formations like DNA:RNA hybrids (known as R-loops) or even DNA:DNA:RNA triplex structures, both influencing biological processes that ultimately impact cancer. Protein-nucleic acid interactions are intrinsic cellular phenomena crucial in both normal and pathological conditions. In particular, genetic mutations or single amino acid variations can alter a protein's structure, function, and binding affinity, thus influencing cancer progression. It is thus, imperative to understand the differences between wild-type (WT) and mutated (MT) genes, transcripts, and proteins. The review aims to summarize the frequently employed methods and techniques for investigating interactions involving nucleic acids and proteins, highlighting recent advancements and diverse adaptations of each technique.
Collapse
Affiliation(s)
- Maria Leonor Peixoto
- Champalimaud Center for the Unknown, Lisbon, Portugal; Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Esha Madan
- Department of Surgery, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA, United States; VCU Institute of Molecular Medicine, Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
| |
Collapse
|
38
|
Ng RR, Lin Z, Zhang Y, Ti SC, Javed A, Wong JWH, Fang Q, Leung JWC, Tang AHN, Huen MSY. R-loop resolution by ARIP4 helicase promotes androgen-mediated transcription induction. SCIENCE ADVANCES 2024; 10:eadm9577. [PMID: 39028815 PMCID: PMC11259169 DOI: 10.1126/sciadv.adm9577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
Pausing of RNA polymerase II (Pol II) at transcription start sites (TSSs) primes target genes for productive elongation. Coincidentally, DNA double-strand breaks (DSBs) enrich at highly transcribed and Pol II-paused genes, although their interplay remains undefined. Using androgen receptor (AR) signaling as a model, we have uncovered AR-interacting protein 4 (ARIP4) helicase as a driver of androgen-dependent transcription induction. Chromatin immunoprecipitation sequencing analysis revealed that ARIP4 preferentially co-occupies TSSs with paused Pol II. Moreover, we found that ARIP4 complexes with topoisomerase II beta and mediates transient DSB formation upon hormone stimulation. Accordingly, ARIP4 deficiency compromised release of paused Pol II and resulted in R-loop accumulation at a panel of highly transcribed AR target genes. Last, we showed that ARIP4 binds and unwinds R-loops in vitro and that its expression positively correlates with prostate cancer progression. We propose that androgen stimulation triggers ARIP4-mediated unwinding of R-loops at TSSs, enforcing Pol II pause release to effectively drive an androgen-dependent expression program.
Collapse
Affiliation(s)
- Raissa Regina Ng
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
| | - Zhongyang Lin
- Department of Biology, Shantou University, Shantou, Guangdong, China
| | - Yanmin Zhang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
| | - Shih Chieh Ti
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
| | - Asif Javed
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
| | - Jason Wing Hon Wong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
| | - Qingming Fang
- Department of Biochemistry and Structural Biology and Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Justin Wai Chung Leung
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Alex Hin Ning Tang
- Department of Pathology, School of Clinical Medicine LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
| | - Michael Shing Yan Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong S.A.R
| |
Collapse
|
39
|
Yang BZ, Liu MY, Chiu KL, Chien YL, Cheng CA, Chen YL, Tsui LY, Lin KR, Chu HPC, Wu CSP. DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability. Nat Commun 2024; 15:6009. [PMID: 39019926 PMCID: PMC11255299 DOI: 10.1038/s41467-024-50428-4] [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: 09/04/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
RNA helicase DHX9 is essential for genome stability by resolving aberrant R-loops. However, its regulatory mechanisms remain unclear. Here we show that SUMOylation at lysine 120 (K120) is crucial for DHX9 function. Preventing SUMOylation at K120 leads to R-loop dysregulation, increased DNA damage, and cell death. Cells expressing DHX9 K120R mutant which cannot be SUMOylated are more sensitive to genotoxic agents and this sensitivity is mitigated by RNase H overexpression. Unlike the mutant, wild-type DHX9 interacts with R-loop-associated proteins such as PARP1 and DDX21 via SUMO-interacting motifs. Fusion of SUMO2 to the DHX9 K120R mutant enhances its association with these proteins, reduces R-loop accumulation, and alleviates survival defects of DHX9 K120R. Our findings highlight the critical role of DHX9 SUMOylation in maintaining genome stability by regulating protein interactions necessary for R-loop balance.
Collapse
Affiliation(s)
- Bing-Ze Yang
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Mei-Yin Liu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Kuan-Lin Chiu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 106319, Taiwan
| | - Yuh-Ling Chien
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Ching-An Cheng
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Yu-Lin Chen
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Li-Yu Tsui
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | - Keng-Ru Lin
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan
| | | | - Ching-Shyi Peter Wu
- Department and Graduate Institute of Pharmacology, College of Medicine, National Taiwan University, Taipei, 100233, Taiwan.
| |
Collapse
|
40
|
Zhang X, Xu J, Hu J, Zhang S, Hao Y, Zhang D, Qian H, Wang D, Fu XD. Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation. Nat Commun 2024; 15:6031. [PMID: 39019869 PMCID: PMC11255242 DOI: 10.1038/s41467-024-50298-w] [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: 04/07/2023] [Accepted: 07/04/2024] [Indexed: 07/19/2024] Open
Abstract
Mutations in the Cockayne Syndrome group B (CSB) gene cause cancer in mice, but premature aging and severe neurodevelopmental defects in humans. CSB, a member of the SWI/SNF family of chromatin remodelers, plays diverse roles in regulating gene expression and transcription-coupled nucleotide excision repair (TC-NER); however, these functions do not explain the distinct phenotypic differences observed between CSB-deficient mice and humans. During investigating Cockayne Syndrome-associated genome instability, we uncover an intrinsic mechanism that involves elongating RNA polymerase II (RNAPII) undergoing transient pauses at internal T-runs where CSB is required to propel RNAPII forward. Consequently, CSB deficiency retards RNAPII elongation in these regions, and when coupled with G-rich sequences upstream, exacerbates genome instability by promoting R-loop formation. These R-loop prone motifs are notably abundant in relatively long genes related to neuronal functions in the human genome, but less prevalent in the mouse genome. These findings provide mechanistic insights into differential impacts of CSB deficiency on mice versus humans and suggest that the manifestation of the Cockayne Syndrome phenotype in humans results from the progressive evolution of mammalian genomes.
Collapse
Affiliation(s)
- Xuan Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Jun Xu
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Genetics and Metabolism Department, The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Hu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Sitao Zhang
- National Institute of Biological Sciences,7 Science Park Road, Beijing, China
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Hao Qian
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Xiang-Dong Fu
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences and School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
| |
Collapse
|
41
|
Kannan A, Gangadharan Leela S, Branzei D, Gangwani L. Role of senataxin in R-loop-mediated neurodegeneration. Brain Commun 2024; 6:fcae239. [PMID: 39070547 PMCID: PMC11277865 DOI: 10.1093/braincomms/fcae239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
Senataxin is an RNA:DNA helicase that plays an important role in the resolution of RNA:DNA hybrids (R-loops) formed during transcription. R-loops are involved in the regulation of biological processes such as immunoglobulin class switching, gene expression and DNA repair. Excessive accumulation of R-loops results in DNA damage and loss of genomic integrity. Senataxin is critical for maintaining optimal levels of R-loops to prevent DNA damage and acts as a genome guardian. Within the nucleus, senataxin interacts with various RNA processing factors and DNA damage response and repair proteins. Senataxin interactors include survival motor neuron and zinc finger protein 1, with whom it co-localizes in sub-nuclear bodies. Despite its ubiquitous expression, mutations in senataxin specifically affect neurons and result in distinct neurodegenerative diseases such as amyotrophic lateral sclerosis type 4 and ataxia with oculomotor apraxia type 2, which are attributed to the gain-of-function and the loss-of-function mutations in senataxin, respectively. In addition, low levels of senataxin (loss-of-function) in spinal muscular atrophy result in the accumulation of R-loops causing DNA damage and motor neuron degeneration. Senataxin may play multiple functions in diverse cellular processes; however, its emerging role in R-loop resolution and maintenance of genomic integrity is gaining attention in the field of neurodegenerative diseases. In this review, we highlight the role of senataxin in R-loop resolution and its potential as a therapeutic target to treat neurodegenerative diseases.
Collapse
Affiliation(s)
| | - Shyni Gangadharan Leela
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Dana Branzei
- The AIRC Institute of Molecular Oncology Foundation, IFOM ETS, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
| | - Laxman Gangwani
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
42
|
Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024; 223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [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: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
Collapse
Affiliation(s)
- Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hengyi Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Phillip R. Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Olivia M. Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Alan M. Lambowitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
43
|
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 PMCID: PMC12044674 DOI: 10.1038/s41556-024-01437-4] [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: 12/18/2023] [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.
Collapse
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.
| |
Collapse
|
44
|
Machitani M, Nomura A, Yamashita T, Yasukawa M, Ueki S, Fujita KI, Ueno T, Yamashita A, Tanzawa Y, Watanabe M, Taniguchi T, Saitoh N, Kaneko S, Kato Y, Mano H, Masutomi K. Maintenance of R-loop structures by phosphorylated hTERT preserves genome integrity. Nat Cell Biol 2024; 26:932-945. [PMID: 38806647 DOI: 10.1038/s41556-024-01427-6] [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: 07/18/2023] [Accepted: 04/23/2024] [Indexed: 05/30/2024]
Abstract
As aberrant accumulation of RNA-DNA hybrids (R-loops) causes DNA damage and genome instability, cells express regulators of R-loop structures. Here we report that RNA-dependent RNA polymerase (RdRP) activity of human telomerase reverse transcriptase (hTERT) regulates R-loop formation. We found that the phosphorylated form of hTERT (p-hTERT) exhibits RdRP activity in nuclear speckles both in telomerase-positive cells and telomerase-negative cells with alternative lengthening of telomeres (ALT) activity. The p-hTERT did not associate with telomerase RNA component in nuclear speckles but, instead, with TERRA RNAs to resolve R-loops. Targeting of the TERT gene in ALT cells ablated RdRP activity and impaired tumour growth. Using a genome-scale CRISPR loss-of-function screen, we identified Fanconi anaemia/BRCA genes as synthetic lethal partners of hTERT RdRP. Inactivation of RdRP and Fanconi anaemia/BRCA genes caused accumulation of R-loop structures and DNA damage. These findings indicate that RdRP activity of p-hTERT guards against genome instability by removing R-loop structures.
Collapse
Affiliation(s)
- Mitsuhiro Machitani
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Nomura
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Japan
| | - Taro Yamashita
- Department of Gastroenterology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Mami Yasukawa
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Saori Ueki
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Ken-Ichi Fujita
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Akio Yamashita
- Department of Investigative Medicine, University of the Ryukyus Graduate School of Medicine, Nakagami, Japan
| | - Yoshikazu Tanzawa
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Japan
| | - Masahiko Watanabe
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Japan
| | - Toshiyasu Taniguchi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenkichi Masutomi
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan.
| |
Collapse
|
45
|
Bujosa P, Reina O, Caballé A, Casas-Lamesa A, Torras-Llort M, Pérez-Roldán J, Nacht AS, Vicent GP, Bernués J, Azorín F. Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs. Cell Rep 2024; 43:114137. [PMID: 38662543 DOI: 10.1016/j.celrep.2024.114137] [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: 04/14/2023] [Revised: 12/23/2023] [Accepted: 04/08/2024] [Indexed: 06/01/2024] Open
Abstract
Chromatin-associated RNAs (cRNAs) are a poorly characterized fraction of cellular RNAs that co-purify with chromatin. Their full complexity and the mechanisms regulating their packaging and chromatin association remain poorly understood. Here, we address these questions in Drosophila. We find that cRNAs constitute a heterogeneous group of RNA species that is abundant in heterochromatic transcripts. We show that heterochromatic cRNAs interact with the heterogeneous nuclear ribonucleoproteins (hnRNP) hrp36/hrp48 and that depletion of linker histone dH1 impairs this interaction. dH1 depletion induces the accumulation of RNA::DNA hybrids (R-loops) in heterochromatin and, as a consequence, increases retention of heterochromatic cRNAs. These effects correlate with increased RNA polymerase II (RNAPII) occupancy at heterochromatin. Notably, impairing cRNA assembly by depletion of hrp36/hrp48 mimics heterochromatic R-loop accumulation induced by dH1 depletion. We also show that dH1 depletion alters nucleosome organization, increasing accessibility of heterochromatin. Altogether, these perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loop formation and cRNA retention at heterochromatin.
Collapse
Affiliation(s)
- Paula Bujosa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Adrià Caballé
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Anna Casas-Lamesa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Mònica Torras-Llort
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ana Silvina Nacht
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guillermo P Vicent
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
| |
Collapse
|
46
|
Duardo RC, Marinello J, Russo M, Morelli S, Pepe S, Guerra F, Gómez-González B, Aguilera A, Capranico G. Human DNA topoisomerase I poisoning causes R loop-mediated genome instability attenuated by transcription factor IIS. SCIENCE ADVANCES 2024; 10:eadm8196. [PMID: 38787953 PMCID: PMC11122683 DOI: 10.1126/sciadv.adm8196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
Abstract
DNA topoisomerase I can contribute to cancer genome instability. During catalytic activity, topoisomerase I forms a transient intermediate, topoisomerase I-DNA cleavage complex (Top1cc) to allow strand rotation and duplex relaxation, which can lead to elevated levels of DNA-RNA hybrids and micronuclei. To comprehend the underlying mechanisms, we have integrated genomic data of Top1cc-triggered hybrids and DNA double-strand breaks (DSBs) shortly after Top1cc induction, revealing that Top1ccs increase hybrid levels with different mechanisms. DSBs are at highly transcribed genes in early replicating initiation zones and overlap with hybrids downstream of accumulated RNA polymerase II (RNAPII) at gene 5'-ends. A transcription factor IIS mutant impairing transcription elongation further increased RNAPII accumulation likely due to backtracking. Moreover, Top1ccs can trigger micronuclei when occurring during late G1 or early/mid S, but not during late S. As micronuclei and transcription-replication conflicts are attenuated by transcription factor IIS, our results support a role of RNAPII arrest in Top1cc-induced transcription-replication conflicts leading to DSBs and micronuclei.
Collapse
Affiliation(s)
- Renée C. Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Sara Morelli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Universidad de Sevilla–CSIC, Calle Américo Vespucio 24, 41092 Seville, Spain
- Departamento de Genetica, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Universidad de Sevilla–CSIC, Calle Américo Vespucio 24, 41092 Seville, Spain
- Departamento de Genetica, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum–University of Bologna, via Selmi 3, 40126, Bologna, Italy
| |
Collapse
|
47
|
Puzzo F, Crossley MP, Goswami A, Zhang F, Pekrun K, Garzon JL, Cimprich KA, Kay MA. AAV-mediated genome editing is influenced by the formation of R-loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592855. [PMID: 38766176 PMCID: PMC11100726 DOI: 10.1101/2024.05.07.592855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for in vivo gene therapy. However, rAAVs also integrate throughout the genome. Here, we describe DNA-RNA immunoprecipitation sequencing (DRIP-seq) in murine HEPA1-6 hepatoma cells and whole murine liver to establish the similarities and differences in genomic R-loop formation in a transformed cell line and intact tissue. We show enhanced AAV-HR in mice upon genetic and pharmacological upregulation of R-loops. Selecting the highly expressed Albumin gene as a model locus for genome editing in both in vitro and in vivo experiments showed that the R-loop prone, 3' end of Albumin was efficiently edited by AAV-HR, whereas the upstream R-loop-deficient region did not result in detectable vector integration. In addition, we found a positive correlation between previously reported off-target rAAV integration sites and R-loop enriched genomic regions. Thus, we conclude that high levels of R-loops, present in highly transcribed genes, promote rAAV vector genome integration. These findings may shed light on potential mechanisms for improving the safety and efficacy of genome editing by modulating R-loops and may enhance our ability to predict regions most susceptible to off-target insertional mutagenesis by rAAV vectors.
Collapse
Affiliation(s)
- Francesco Puzzo
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | | | - Aranyak Goswami
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Feijie Zhang
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Katja Pekrun
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Jada L Garzon
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Mark A Kay
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| |
Collapse
|
48
|
Galli S, Flint G, Růžičková L, Di Antonio M. Genome-wide mapping of G-quadruplex DNA: a step-by-step guide to select the most effective method. RSC Chem Biol 2024; 5:426-438. [PMID: 38725910 PMCID: PMC11078208 DOI: 10.1039/d4cb00023d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/21/2024] [Indexed: 05/12/2024] Open
Abstract
The development of methods that enabled genome-wide mapping of DNA G-quadruplex structures in chromatin has played a critical role in providing evidence to support the formation of these structures in living cells. Over the past decade, a variety of methods aimed at mapping G-quadruplexes have been reported in the literature. In this critical review, we have sought to provide a technical overview on the relative strengths and weaknesses of the genomics approaches currently available, offering step-by-step guidance to assessing experimental needs and selecting the most appropriate method to achieve effective genome-wide mapping of DNA G-quadruplexes.
Collapse
Affiliation(s)
- Silvia Galli
- Imperial College London, Chemistry Department, Molecular Science Research Hub 82 Wood Lane London UK
| | - Gem Flint
- Imperial College London, Chemistry Department, Molecular Science Research Hub 82 Wood Lane London UK
- Institute of Chemical Biology, Molecular Science Research Hub 82 Wood Lane London UK
| | - Lucie Růžičková
- Imperial College London, Chemistry Department, Molecular Science Research Hub 82 Wood Lane London UK
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Science Research Hub 82 Wood Lane London UK
- Institute of Chemical Biology, Molecular Science Research Hub 82 Wood Lane London UK
- The Francis Crick Institute 1 Midland Road London UK
| |
Collapse
|
49
|
Mérida-Cerro JA, Maraver-Cárdenas P, Rondón AG, Aguilera A. Rat1 promotes premature transcription termination at R-loops. Nucleic Acids Res 2024; 52:3623-3635. [PMID: 38281203 DOI: 10.1093/nar/gkae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid structures formed by a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in yeast. Importantly, we demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such structures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, providing an entry site for Rat1. Thus, we have uncovered an unanticipated function of Rat1 as a transcription restoring factor opening up the possibility that it may also promote transcription through other genomic DNA structures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relieved by Rat1, it will cause genomic instability, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.
Collapse
Affiliation(s)
- José Antonio Mérida-Cerro
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Pablo Maraver-Cárdenas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| |
Collapse
|
50
|
Mukhopadhyay P, Miller H, Stoja A, Bishop AJR. Approaches for Mapping and Analysis of R-loops. Curr Protoc 2024; 4:e1037. [PMID: 38666626 PMCID: PMC11840513 DOI: 10.1002/cpz1.1037] [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: 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, 8403 Floyd Curl Dr, San Antonio, TX 78229
| | - Henry Miller
- Altos Labs, 1300 Island Dr Redwood City, CA 94065
| | - Aiola Stoja
- Greehey Children’s Cancer Research Institute, UT Health San
Antonio, 8403 Floyd Curl Dr, San Antonio, TX 78229
| | - Alexander J. R. Bishop
- Greehey Children’s Cancer Research Institute, UT Health San
Antonio, 8403 Floyd Curl Dr, San Antonio, TX 78229
| |
Collapse
|