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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.
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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
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2
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Moelling K. Epigenetics and transgenerational inheritance. J Physiol 2024; 602:2537-2545. [PMID: 37772441 DOI: 10.1113/jp284424] [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: 07/10/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Epigenetic modifications can alter the function of genes. The epigenetics changes are caused by environmental effects, which lead to chemical modifications of the DNA or the chromatin. The mechanisms involve the influence of small interfering siRNAs on gene silencing. Epigenetic changes normally last only during the life-time of an individual and are erased in embryos and eggs for a naive progeny. The genomes are reprogrammed and the chemical modifications removed to restart the next generation. However, there are mechanisms that allow the genome to escape from such a clearing effect so that modifications can be transmitted to one or more subsequent generations. In the germline of animal cells small RNAs, including piRNAs, have evolved which guarantee a higher degree of fidelity for transmission of genetic information, guarding especially against the detrimental effect caused by transposon activity. piRNA is essential for transposon silencing for survival of a species and protection of subsequent generations. Inactivation of piRNA results in abundant transposon activity and sperm infertility. The effect in humans has been described but is less distinct. Some stress-induced epigenetic changes are transitory in mice and can be reversed by a change of environment or lifestyle.
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Affiliation(s)
- Karin Moelling
- Institute Medical Microbiology, University Zürich, Zurich, Switzerland
- Max Planck Institute of Molecular Genetics, Berlin, Germany
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3
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Wen Y, Liu Y, Li Q, Tan J, Fu X, Liang Y, Tuo Y, Liu L, Zhou X, LiuFu D, Fan X, Chen C, Chen Z, Wang Z, Fan S, Liu R, Pan L, Zhang Y, Tang WH. Spatiotemporal ATF3 Expression Determines VSMC Fate in Abdominal Aortic Aneurysm. Circ Res 2024; 134:1495-1511. [PMID: 38686580 DOI: 10.1161/circresaha.124.324323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) is a catastrophic disease with little effective therapy, likely due to the limited understanding of the mechanisms underlying AAA development and progression. ATF3 (activating transcription factor 3) has been increasingly recognized as a key regulator of cardiovascular diseases. However, the role of ATF3 in AAA development and progression remains elusive. METHODS Genome-wide RNA sequencing analysis was performed on the aorta isolated from saline or Ang II (angiotensin II)-induced AAA mice, and ATF3 was identified as the potential key gene for AAA development. To examine the role of ATF3 in AAA development, vascular smooth muscle cell-specific ATF3 knockdown or overexpressed mice by recombinant adeno-associated virus serotype 9 vectors carrying ATF3, or shRNA-ATF3 with SM22α (smooth muscle protein 22-α) promoter were used in Ang II-induced AAA mice. In human and murine vascular smooth muscle cells, gain or loss of function experiments were performed to investigate the role of ATF3 in vascular smooth muscle cell proliferation and apoptosis. RESULTS In both Ang II-induced AAA mice and patients with AAA, the expression of ATF3 was reduced in aneurysm tissues but increased in aortic lesion tissues. The deficiency of ATF3 in vascular smooth muscle cell promoted AAA formation in Ang II-induced AAA mice. PDGFRB (platelet-derived growth factor receptor β) was identified as the target of ATF3, which mediated vascular smooth muscle cell proliferation in response to TNF-alpha (tumor necrosis factor-α) at the early stage of AAA. ATF3 suppressed the mitochondria-dependent apoptosis at the advanced stage by upregulating its direct target BCL2. Our chromatin immunoprecipitation results also demonstrated that the recruitment of NFκB1 and P300/BAF/H3K27ac complex to the ATF3 promoter induces ATF3 transcription via enhancer activation. NFKB1 inhibitor (andrographolide) inhibits the expression of ATF3 by blocking the recruiters NFKB1 and ATF3-enhancer to the ATF3-promoter region, ultimately leading to AAA development. CONCLUSIONS Our results demonstrate a previously unrecognized role of ATF3 in AAA development and progression, and ATF3 may serve as a novel therapeutic and prognostic marker for AAA.
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MESH Headings
- Activating Transcription Factor 3/genetics
- Activating Transcription Factor 3/metabolism
- Animals
- Aortic Aneurysm, Abdominal/metabolism
- Aortic Aneurysm, Abdominal/pathology
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/chemically induced
- Humans
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Mice
- Male
- Mice, Inbred C57BL
- Apoptosis
- Cells, Cultured
- Angiotensin II
- Cell Proliferation
- Aorta, Abdominal/pathology
- Aorta, Abdominal/metabolism
- Disease Models, Animal
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Affiliation(s)
- Ying Wen
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Yingying Liu
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Qiang Li
- Department of Vascular Surgery (Q.L.), the Second Affiliated Hospital of Guangzhou Medical University, China
| | - Jinlin Tan
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Xing Fu
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Yiwen Liang
- Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, China (Y. Liang)
| | - Yonghua Tuo
- Department of Neurosurgery (Y.T.), the Second Affiliated Hospital of Guangzhou Medical University, China
| | - Luhao Liu
- Department of Organ Transplantation (L.L., Z.C.), the Second Affiliated Hospital of Guangzhou Medical University, China
| | - Xueqiong Zhou
- Department of Occupational Health and Medicine, School of Public Health, Southern Medical University, China (X.Z.)
| | - Dongkai LiuFu
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Xuejiao Fan
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Chaofei Chen
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Zheng Chen
- Department of Organ Transplantation (L.L., Z.C.), the Second Affiliated Hospital of Guangzhou Medical University, China
| | - Zhouping Wang
- Department of Cardiology (Z.W.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Shunyang Fan
- Heart Center, The Third Affiliated Hospital of Zhengzhou University, China (S.F., W.H.T.)
| | - Renjing Liu
- Victor Chang Cardiac Research Institute, Sydney, Australia (R.L.)
| | - Lei Pan
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, China (L.P.)
| | - Yuan Zhang
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
| | - Wai Ho Tang
- Institute of Pediatrics (Y.W., Y. Liu, J.T., X.F., D.L., X.F., C.C., Y.Z., W.H.T.), Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, China
- Heart Center, The Third Affiliated Hospital of Zhengzhou University, China (S.F., W.H.T.)
- School of Nursing and Health Studies, Hong Kong Metropolitan University, Kowloon, Hong Kong SAR, China (W.H.T.)
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Mukhopadhyay P, Miller H, Stoja A, Bishop AJR. Approaches for Mapping and Analysis of R-loops. Curr Protoc 2024; 4:e1037. [PMID: 38666626 DOI: 10.1002/cpz1.1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
R-loops are nucleic acid structures composed of a DNA:RNA hybrid with a displaced non-template single-stranded DNA. Current approaches to identify and map R-loop formation across the genome employ either an antibody targeted against R-loops (S9.6) or a catalytically inactivated form of RNase H1 (dRNH1), a nuclease that can bind and resolve DNA:RNA hybrids via RNA exonuclease activity. This overview article outlines several ways to map R-loops using either methodology, explaining the differences and similarities among the approaches. Bioinformatic analysis of R-loops involves several layers of quality control and processing before visualizing the data. This article provides resources and tools that can be used to accurately process R-loop mapping data and explains the advantages and disadvantages of the resources as compared to one another. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Pramiti Mukhopadhyay
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | | | - Aiola Stoja
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, Texas
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5
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Tan J, Tan YY, Ngian ZK, Chong SY, Rao VK, Wang JW, Zeng X, Ong CT. ApoE maintains neuronal integrity via microRNA and H3K27me3-mediated repression. iScience 2024; 27:109231. [PMID: 38439966 PMCID: PMC10909902 DOI: 10.1016/j.isci.2024.109231] [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: 05/01/2023] [Revised: 12/15/2023] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
ApoE regulates neurogenesis, although how it influences genetic programs remains elusive. Cortical neurons induced from isogenic control and ApoE-/- human neural stem cells (NSCs) recapitulated key transcriptomic signatures of in vivo counterparts identified from single-cell human midbrain. Surprisingly, ApoE expression in NSC and neural progenitor cells (NPCs) is not required for differentiation. Instead, ApoE prevents the over-proliferation of non-neuronal cells during extended neuronal culture when it is not expressed. Elevated miR-199a-5p level in ApoE-/- cells lowers the EZH1 protein and the repressive H3K27me3 mark, a phenotype rescued by miR-199a-5p steric inhibitor. Reduced H3K27me3 at genes linked to extracellular matrix organization and angiogenesis in ApoE-/- NPC correlates with their aberrant expression and phenotypes in neurons. Interestingly, the ApoE coding sequence, which contains many predicted miR-199a-5p binding sites, can repress miR-199a-5p without translating into protein. This suggests that ApoE maintains neurons integrity through the target-directed miRNA degradation of miR-199a-5p, imparting the H3K27me3-mediated repression of non-neuronal genes during differentiation.
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Affiliation(s)
- Jiazi Tan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Yow-Yong Tan
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Zhen-Kai Ngian
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Suet-Yen Chong
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Vinay Kumar Rao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- Department of Medical Genetics, JSS Medical College, JSS Academy of Higher Education and Research, Mysore 570015, India
| | - Jiong-Wei Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Nanomedicine Translational Research Programme, Centre for NanoMedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117609, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Xianmin Zeng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- RxCell Inc, Novato, CA 94945, USA
| | - Chin-Tong Ong
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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6
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Salguero-Aranda C, Di Blasi E, Galán L, Zaldumbide L, Civantos G, Marcilla D, de Álava E, Díaz-Martín J. Identification of Novel/Rare EWSR1 Fusion Partners in Undifferentiated Mesenchymal Neoplasms. Int J Mol Sci 2024; 25:1735. [PMID: 38339014 PMCID: PMC10855420 DOI: 10.3390/ijms25031735] [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: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Recurrent gene fusions (GFs) in translocated sarcomas are recognized as major oncogenic drivers of the disease, as well as diagnostic markers whose identification is necessary for differential diagnosis. EWSR1 is a 'promiscuous' gene that can fuse with many different partner genes, defining different entities among a broad range of mesenchymal neoplasms. Molecular testing of EWSR1 translocation traditionally relies on FISH assays with break-apart probes, which are unable to identify the fusion partner. Therefore, other ancillary molecular diagnostic modalities are being increasingly adopted for accurate classification of these neoplasms. Herein, we report three cases with rare GFs involving EWSR1 in undifferentiated mesenchymal neoplasms with uncertain differential diagnoses, using targeted RNA-seq and confirming with RT-PCR and Sanger sequencing. Two GFs involved hormone nuclear receptors as 3' partners, NR4A2 and RORB, which have not been previously reported. NR4A2 may functionally replace NR4A3, the usual 3' partner in extraskeletal myxoid chondrosarcoma. The third GF, EWSR1::BEND2, has previously been reported in a subtype of astroblastoma and other rare entities, including a single case of a soft-tissue tumor that we discuss in this work. In conclusion, our findings indicate that the catalogue of mesenchymal neoplasm-bearing EWSR1 fusions continues to grow, underscoring the value of using molecular ancillary techniques with higher diagnostic abilities in the routine clinical setting.
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Affiliation(s)
- Carmen Salguero-Aranda
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
- Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III (CB16/12/00361; CIBERONC-ISCIII), 28029 Madrid, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41004 Seville, Spain
| | - Elena Di Blasi
- Istituto Nazionale dei Tumori, Università degli Studi di Milano, 20133 Milan, Italy
| | - Lourdes Galán
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
| | - Laura Zaldumbide
- Department of Pathology, Hospital Universitario Cruces, 48903 Barakaldo, Spain
| | - Gema Civantos
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
| | - David Marcilla
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
| | - Enrique de Álava
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
- Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III (CB16/12/00361; CIBERONC-ISCIII), 28029 Madrid, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41004 Seville, Spain
| | - Juan Díaz-Martín
- Instituto de Biomedicina de Sevilla, Department of Pathology, Hospital Universitario Virgen del Rocío, CSIC-Universidad de Sevilla, 41013 Seville, Spain; (C.S.-A.)
- Centro de Investigación Biomédica en Red de Cáncer, Instituto de Salud Carlos III (CB16/12/00361; CIBERONC-ISCIII), 28029 Madrid, Spain
- Department of Normal and Pathological Cytology and Histology, School of Medicine, University of Seville, 41004 Seville, Spain
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7
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Hou Y, Li Y, Xiang JF, Tilahun K, Jiang J, Corces VG, Yao B. TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk. Cell Rep 2024; 43:113662. [PMID: 38184854 PMCID: PMC10857847 DOI: 10.1016/j.celrep.2023.113662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
TDP-43 is an RNA/DNA-binding protein that forms aggregates in various brain disorders. TDP-43 engages in many aspects of RNA metabolism, but its molecular roles in regulating genes and transposable elements (TEs) have not been extensively explored. Chronic TDP-43 knockdown impairs cell proliferation and cellular responses to DNA damage. At the molecular level, TDP-43 chronic deficiency affects gene expression either locally or distally by concomitantly altering the crosstalk between R-loops and 5-hydroxymethylcytosine (5hmC) in gene bodies and long-range enhancer/promoter interactions. Furthermore, TDP-43 knockdown induces substantial disease-relevant TE activation by influencing their R-loop and 5hmC homeostasis in a locus-specific manner. Together, our findings highlight the genomic roles of TDP-43 in modulating R-loop-5hmC coordination in coding genes, distal regulatory elements, and TEs, presenting a general and broad molecular mechanism underlying the contributions of proteinopathies to the etiology of neurodegenerative disorders.
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Affiliation(s)
- Yingzi Hou
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jian-Feng Xiang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kedamawit Tilahun
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jie Jiang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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8
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Wu Z, Qu J, Zhang W, Liu GH. Stress, epigenetics, and aging: Unraveling the intricate crosstalk. Mol Cell 2024; 84:34-54. [PMID: 37963471 DOI: 10.1016/j.molcel.2023.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023]
Abstract
Aging, as a complex process involving multiple cellular and molecular pathways, is known to be exacerbated by various stresses. Because responses to these stresses, such as oxidative stress and genotoxic stress, are known to interplay with the epigenome and thereby contribute to the development of age-related diseases, investigations into how such epigenetic mechanisms alter gene expression and maintenance of cellular homeostasis is an active research area. In this review, we highlight recent studies investigating the intricate relationship between stress and aging, including its underlying epigenetic basis; describe different types of stresses that originate from both internal and external stimuli; and discuss potential interventions aimed at alleviating stress and restoring epigenetic patterns to combat aging or age-related diseases. Additionally, we address the challenges currently limiting advancement in this burgeoning field.
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Affiliation(s)
- Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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9
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Jing Y, Jiang X, Ji Q, Wu Z, Wang W, Liu Z, Guillen-Garcia P, Esteban CR, Reddy P, Horvath S, Li J, Geng L, Hu Q, Wang S, Belmonte JCI, Ren J, Zhang W, Qu J, Liu GH. Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation. Cell Stem Cell 2023; 30:1452-1471.e10. [PMID: 37832549 DOI: 10.1016/j.stem.2023.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Our understanding of the molecular basis for cellular senescence remains incomplete, limiting the development of strategies to ameliorate age-related pathologies by preventing stem cell senescence. Here, we performed a genome-wide CRISPR activation (CRISPRa) screening using a human mesenchymal precursor cell (hMPC) model of the progeroid syndrome. We evaluated targets whose activation antagonizes cellular senescence, among which SOX5 outperformed as a top hit. Through decoding the epigenomic landscapes remodeled by overexpressing SOX5, we uncovered its role in resetting the transcription network for geroprotective genes, including HMGB2. Mechanistically, SOX5 binding elevated the enhancer activity of HMGB2 with increased levels of H3K27ac and H3K4me1, raising HMGB2 expression so as to promote rejuvenation. Furthermore, gene therapy with lentiviruses carrying SOX5 or HMGB2 rejuvenated cartilage and alleviated osteoarthritis in aged mice. Our study generated a comprehensive list of rejuvenators, pinpointing SOX5 as a potent driver for rejuvenation both in vitro and in vivo.
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Affiliation(s)
- Yaobin Jing
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Pedro Guillen-Garcia
- Department of Traumatology and Research Unit, Clinica CEMTRO, 28035 Madrid, Spain
| | - Concepcion Rodriguez Esteban
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Pradeep Reddy
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve Horvath
- Altos Labs, Inc., San Diego, CA 94022, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 10833, USA
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Lingling Geng
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Qinchao Hu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510060, China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Chongqing Renji Hospital, University of Chinese Academy of Sciences, Chongqing 400062, China
| | - Juan Carlos Izpisua Belmonte
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jie Ren
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Weiqi Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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10
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Bradley L, Savage KI. 'From R-lupus to cancer': Reviewing the role of R-loops in innate immune responses. DNA Repair (Amst) 2023; 131:103581. [PMID: 37832251 DOI: 10.1016/j.dnarep.2023.103581] [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: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
Cells possess an inherent and evolutionarily conserved ability to detect and respond to the presence of foreign and pathological 'self' nucleic acids. The result is the stimulation of innate immune responses, signalling to the host immune system that defence mechanisms are necessary to protect the organism. To date, there is a vast body of literature describing innate immune responses to various nucleic acid species, including dsDNA, ssDNA and ssRNA etc., however, there is limited information available on responses to R-loops. R-loops are 3-stranded nucleic acid structures that form during transcription, upon DNA damage and in various other settings. Emerging evidence suggests that innate immune responses may also exist for the detection of R-loop related nucleic acid structures, implicating R-loops as drivers of inflammatory states. In this review, we aim to summarise the evidence indicating that R-loops are immunogenic species that can trigger innate immune responses in physiological and pathological settings and discuss the implications of this in the study of various diseases and therapeutic development.
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Affiliation(s)
- Leanne Bradley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Rd, Belfast, United Kingdom
| | - Kienan I Savage
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Rd, Belfast, United Kingdom.
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11
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Vujovic F, Shepherd CE, Witting PK, Hunter N, Farahani RM. Redox-Mediated Rewiring of Signalling Pathways: The Role of a Cellular Clock in Brain Health and Disease. Antioxidants (Basel) 2023; 12:1873. [PMID: 37891951 PMCID: PMC10604469 DOI: 10.3390/antiox12101873] [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: 09/11/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Metazoan signalling pathways can be rewired to dampen or amplify the rate of events, such as those that occur in development and aging. Given that a linear network topology restricts the capacity to rewire signalling pathways, such scalability of the pace of biological events suggests the existence of programmable non-linear elements in the underlying signalling pathways. Here, we review the network topology of key signalling pathways with a focus on redox-sensitive proteins, including PTEN and Ras GTPase, that reshape the connectivity profile of signalling pathways in response to an altered redox state. While this network-level impact of redox is achieved by the modulation of individual redox-sensitive proteins, it is the population by these proteins of critical nodes in a network topology of signal transduction pathways that amplifies the impact of redox-mediated reprogramming. We propose that redox-mediated rewiring is essential to regulate the rate of transmission of biological signals, giving rise to a programmable cellular clock that orchestrates the pace of biological phenomena such as development and aging. We further review the evidence that an aberrant redox-mediated modulation of output of the cellular clock contributes to the emergence of pathological conditions affecting the human brain.
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Affiliation(s)
- Filip Vujovic
- IDR/Westmead Institute for Medical Research, Sydney, NSW 2145, Australia; (F.V.); (N.H.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Paul K. Witting
- Redox Biology Group, Charles Perkins Centre, Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Sydney, NSW 2145, Australia; (F.V.); (N.H.)
| | - Ramin M. Farahani
- IDR/Westmead Institute for Medical Research, Sydney, NSW 2145, Australia; (F.V.); (N.H.)
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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12
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Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K. G-quadruplexes associated with R-loops promote CTCF binding. Mol Cell 2023; 83:3064-3079.e5. [PMID: 37552993 PMCID: PMC10529333 DOI: 10.1016/j.molcel.2023.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/24/2023] [Accepted: 07/07/2023] [Indexed: 08/10/2023]
Abstract
CTCF is a critical regulator of genome architecture and gene expression that binds thousands of sites on chromatin. CTCF genomic localization is controlled by the recognition of a DNA sequence motif and regulated by DNA modifications. However, CTCF does not bind to all its potential sites in all cell types, raising the question of whether the underlying chromatin structure can regulate CTCF occupancy. Here, we report that R-loops facilitate CTCF binding through the formation of associated G-quadruplex (G4) structures. R-loops and G4s co-localize with CTCF at many genomic regions in mouse embryonic stem cells and promote CTCF binding to its cognate DNA motif in vitro. R-loop attenuation reduces CTCF binding in vivo. Deletion of a specific G4-forming motif in a gene reduces CTCF binding and alters gene expression. Conversely, chemical stabilization of G4s results in CTCF gains and accompanying alterations in chromatin organization, suggesting a pivotal role for G4 structures in reinforcing long-range genome interactions through CTCF.
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Affiliation(s)
- Phillip Wulfridge
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qingqing Yan
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel Rell
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Doherty
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Skye Jacobson
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Offley
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandra Deliard
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kelly Feng
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer E Phillips-Cremins
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Kavitha Sarma
- Gene expression and Regulation program, The Wistar Institute, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Xu C, Li C, Chen J, Xiong Y, Qiao Z, Fan P, Li C, Ma S, Liu J, Song A, Tao B, Xu T, Xu W, Chi Y, Xue J, Wang P, Ye D, Gu H, Zhang P, Wang Q, Xiao R, Cheng J, Zheng H, Yu X, Zhang Z, Wu J, Liang K, Liu YJ, Lu H, Chen FX. R-loop-dependent promoter-proximal termination ensures genome stability. Nature 2023; 621:610-619. [PMID: 37557913 PMCID: PMC10511320 DOI: 10.1038/s41586-023-06515-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 08/03/2023] [Indexed: 08/11/2023]
Abstract
The proper regulation of transcription is essential for maintaining genome integrity and executing other downstream cellular functions1,2. Here we identify a stable association between the genome-stability regulator sensor of single-stranded DNA (SOSS)3 and the transcription regulator Integrator-PP2A (INTAC)4-6. Through SSB1-mediated recognition of single-stranded DNA, SOSS-INTAC stimulates promoter-proximal termination of transcription and attenuates R-loops associated with paused RNA polymerase II to prevent R-loop-induced genome instability. SOSS-INTAC-dependent attenuation of R-loops is enhanced by the ability of SSB1 to form liquid-like condensates. Deletion of NABP2 (encoding SSB1) or introduction of cancer-associated mutations into its intrinsically disordered region leads to a pervasive accumulation of R-loops, highlighting a genome surveillance function of SOSS-INTAC that enables timely termination of transcription at promoters to constrain R-loop accumulation and ensure genome stability.
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Affiliation(s)
- Congling Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jiwei Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yan Xiong
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhibin Qiao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Pengyu Fan
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Shuangyu Ma
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Aixia Song
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Bolin Tao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Wei Xu
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yayun Chi
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jingyan Xue
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Pu Wang
- Huashan Hospital, Fudan University, Shanghai Key Laboratory of Medical Epigenetics, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Dan Ye
- Huashan Hospital, Fudan University, Shanghai Key Laboratory of Medical Epigenetics, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiong Wang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruijing Xiao
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jingdong Cheng
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Hai Zheng
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoli Yu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jiong Wu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yan-Jun Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China.
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.
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14
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Zhou J, Lei X, Shafiq S, Zhang W, Li Q, Li K, Zhu J, Dong Z, He XJ, Sun Q. DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis. SCIENCE ADVANCES 2023; 9:eadg2699. [PMID: 37566662 PMCID: PMC10421056 DOI: 10.1126/sciadv.adg2699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find that DDM1 (decrease in DNA methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 cotranscriptionally can facilitate constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the cotranscriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.
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Affiliation(s)
- Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xue Lei
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Sarfraz Shafiq
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qin Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jiafu Zhu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xin-jian He
- National Institute of Biological Sciences, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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15
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Xu YJ, Dai SK, Duan CH, Zhang ZH, Liu PP, Liu C, Du HZ, Lu XK, Hu S, Li L, Teng ZQ, Liu CM. ASH2L regulates postnatal neurogenesis through Onecut2-mediated inhibition of TGF-β signaling pathway. Cell Death Differ 2023; 30:1943-1956. [PMID: 37433907 PMCID: PMC10406892 DOI: 10.1038/s41418-023-01189-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: 08/20/2021] [Revised: 06/18/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023] Open
Abstract
The ability of neural stem/progenitor cells (NSPCs) to proliferate and differentiate is required through different stages of neurogenesis. Disturbance in the regulation of neurogenesis causes many neurological diseases, such as intellectual disability, autism, and schizophrenia. However, the intrinsic mechanisms of this regulation in neurogenesis remain poorly understood. Here, we report that Ash2l (Absent, small or homeotic discs-like 2), one core component of a multimeric histone methyltransferase complex, is essential for NSPC fate determination during postnatal neurogenesis. Deletion of Ash2l in NSPCs impairs their capacity for proliferation and differentiation, leading to simplified dendritic arbors in adult-born hippocampal neurons and deficits in cognitive abilities. RNA sequencing data reveal that Ash2l primarily regulates cell fate specification and neuron commitment. Furthermore, we identified Onecut2, a major downstream target of ASH2L characterized by bivalent histone modifications, and demonstrated that constitutive expression of Onecut2 restores defective proliferation and differentiation of NSPCs in adult Ash2l-deficient mice. Importantly, we identified that Onecut2 modulates TGF-β signaling in NSPCs and that treatment with a TGF-β inhibitor rectifies the phenotype of Ash2l-deficient NSPCs. Collectively, our findings reveal the ASH2L-Onecut2-TGF-β signaling axis that mediates postnatal neurogenesis to maintain proper forebrain function.
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Affiliation(s)
- Ya-Jie Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Chun-Hui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Zi-Han Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Cong Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Hong-Zhen Du
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Xu-Kun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Medical College, Soochow University, 215000, Suzhou, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China.
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16
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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17
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Kaneko H, Kaitsuka T, Tomizawa K. Artificial induction of circadian rhythm by combining exogenous BMAL1 expression and polycomb repressive complex 2 inhibition in human induced pluripotent stem cells. Cell Mol Life Sci 2023; 80:200. [PMID: 37421441 PMCID: PMC11072008 DOI: 10.1007/s00018-023-04847-z] [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: 03/15/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
Understanding the physiology of human-induced pluripotent stem cells (iPSCs) is necessary for directed differentiation, mimicking embryonic development, and regenerative medicine applications. Pluripotent stem cells (PSCs) exhibit unique abilities such as self-renewal and pluripotency, but they lack some functions that are associated with normal somatic cells. One such function is the circadian oscillation of clock genes; however, whether or not PSCs demonstrate this capability remains unclear. In this study, the reason why circadian rhythm does not oscillate in human iPSCs was examined. This phenomenon may be due to the transcriptional repression of clock genes resulting from the hypermethylation of histone H3 at lysine 27 (H3K27), or it may be due to the low levels of brain and muscle ARNT-like 1 (BMAL1) protein. Therefore, BMAL1-overexpressing cells were generated and pre-treated with GSK126, an inhibitor of enhancer of zest homologue 2 (EZH2), which is a methyltransferase of H3K27 and a component of polycomb repressive complex 2. Consequently, a significant circadian rhythm following endogenous BMAL1, period 2 (PER2), and other clock gene expression was induced by these two factors, suggesting a candidate mechanism for the lack of rhythmicity of clock gene expression in iPSCs.
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Affiliation(s)
- Hitomi Kaneko
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Taku Kaitsuka
- School of Pharmacy at Fukuoka, International University of Health and Welfare, Enokizu 137-1, Okawa, Fukuoka, 831-8501, Japan.
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan.
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18
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Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. Beyond transcription: compelling open questions in plant RNA biology. THE PLANT CELL 2023; 35:1626-1653. [PMID: 36477566 PMCID: PMC10226580 DOI: 10.1093/plcell/koac346] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 12/06/2022] [Indexed: 05/30/2023]
Abstract
The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
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Affiliation(s)
- Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Micaela A Godoy Herz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Alberto R Kornblihtt
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Reed Sorenson
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Kentaro Nakaminami
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, Orsay 91405, France
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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19
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Liu X, Liu Z, Wu Z, Ren J, Fan Y, Sun L, Cao G, Niu Y, Zhang B, Ji Q, Jiang X, Wang C, Wang Q, Ji Z, Li L, Esteban CR, Yan K, Li W, Cai Y, Wang S, Zheng A, Zhang YE, Tan S, Cai Y, Song M, Lu F, Tang F, Ji W, Zhou Q, Belmonte JCI, Zhang W, Qu J, Liu GH. Resurrection of endogenous retroviruses during aging reinforces senescence. Cell 2023; 186:287-304.e26. [PMID: 36610399 DOI: 10.1016/j.cell.2022.12.017] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/13/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023]
Abstract
Whether and how certain transposable elements with viral origins, such as endogenous retroviruses (ERVs) dormant in our genomes, can become awakened and contribute to the aging process is largely unknown. In human senescent cells, we found that HERVK (HML-2), the most recently integrated human ERVs, are unlocked to transcribe viral genes and produce retrovirus-like particles (RVLPs). These HERVK RVLPs constitute a transmissible message to elicit senescence phenotypes in young cells, which can be blocked by neutralizing antibodies. The activation of ERVs was also observed in organs of aged primates and mice as well as in human tissues and serum from the elderly. Their repression alleviates cellular senescence and tissue degeneration and, to some extent, organismal aging. These findings indicate that the resurrection of ERVs is a hallmark and driving force of cellular senescence and tissue aging.
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Affiliation(s)
- Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Sun
- NHC Beijing Institute of Geriatrics, NHC Key Laboratory of Geriatrics, Institute of Geriatric Medicine of Chinese Academy of Medical Sciences, National Center of Gerontology/Beijing Hospital, Beijing 100730, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Baohu Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cui Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanzhu Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing Municipal Geriatric Medical Research Center, Beijing 100053, China; The Fifth People's Hospital of Chongqing, Chongqing 400062, China
| | - Aihua Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong E Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingao Cai
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Falong Lu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fuchou Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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20
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Polenkowski M, Allister AB, Burbano de Lara S, Pierce A, Geary B, El Bounkari O, Wiehlmann L, Hoffmann A, Whetton AD, Tamura T, Tran DDH. THOC5 complexes with DDX5, DDX17, and CDK12 to regulate R loop structures and transcription elongation rate. iScience 2022; 26:105784. [PMID: 36590164 PMCID: PMC9800341 DOI: 10.1016/j.isci.2022.105784] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/10/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
THOC5, a member of the THO complex, is essential for the 3'processing of some inducible genes, the export of a subset of mRNAs and stem cell survival. Here we show that THOC5 depletion results in altered 3'cleavage of >50% of mRNAs and changes in RNA polymerase II binding across genes. THOC5 is recruited close to high-density polymerase II sites, suggesting that THOC5 is involved in transcriptional elongation. Indeed, measurement of elongation rates in vivo demonstrated decreased rates in THOC5-depleted cells. Furthermore, THOC5 is preferentially recruited to its target genes in slow polymerase II cells compared with fast polymerase II cells. Importantly chromatin-associated THOC5 interacts with CDK12 (a modulator of transcription elongation) and RNA helicases DDX5, DDX17, and THOC6 only in slow polymerase II cells. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate a novel function of THOC5 in transcription elongation.
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Affiliation(s)
- Mareike Polenkowski
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Aldrige Bernardus Allister
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | | | - Andrew Pierce
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Bethany Geary
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Omar El Bounkari
- Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Lutz Wiehlmann
- Pädiatrische Pneumologie Hannover Medical School, Hannover D-30623, Germany
| | - Andrea Hoffmann
- Department of Orthopedic Surgery, Hannover Medical School, Hannover D-30623, Germany
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester M13 9PL, UK
| | - Teruko Tamura
- Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Doan Duy Hai Tran
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany,Corresponding author
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21
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Liu P, Dai S, Mi T, Tang G, Wang Z, Wang H, Du H, Tang Y, Teng Z, Liu C. Acetate supplementation restores cognitive deficits caused by ARID1A haploinsufficiency in excitatory neurons. EMBO Mol Med 2022; 14:e15795. [PMID: 36385502 PMCID: PMC9728054 DOI: 10.15252/emmm.202215795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/18/2022] Open
Abstract
Mutations in AT-rich interactive domain-containing protein 1A (ARID1A) cause Coffin-Siris syndrome (CSS), a rare genetic disorder that results in mild to severe intellectual disabilities. However, the biological role of ARID1A in the brain remains unclear. In this study, we report that the haploinsufficiency of ARID1A in excitatory neurons causes cognitive impairment and defects in hippocampal synaptic transmission and dendritic morphology in mice. Similarly, human embryonic stem cell-derived excitatory neurons with deleted ARID1A exhibit fewer dendritic branches and spines, and abnormal electrophysiological activity. Importantly, supplementation of acetate, an epigenetic metabolite, can ameliorate the morphological and electrophysiological deficits observed in mice with Arid1a haploinsufficiency, as well as in ARID1A-null human excitatory neurons. Mechanistically, transcriptomic and ChIP-seq analyses demonstrate that acetate supplementation can increase the levels of H3K27 acetylation at the promoters of key regulatory genes associated with neural development and synaptic transmission. Collectively, these findings support the essential roles of ARID1A in the excitatory neurons and cognition and suggest that acetate supplementation could be a potential therapeutic intervention for CSS.
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Affiliation(s)
- Pei‐Pei Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Shang‐Kun Dai
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,School of Life Sciences and MedicineShandong University of TechnologyZiboChina
| | - Ting‐Wei Mi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Gang‐Bin Tang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Zhuo Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Hui Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Hong‐Zhen Du
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Yi Tang
- Department of Neurology, Innovation Center for Neurological Disorders, Xuanwu HospitalCapital Medical UniversityBeijingChina
| | - Zhao‐Qian Teng
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Chang‐Mei Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina,University of Chinese Academy of SciencesBeijingChina,Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina,Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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22
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Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
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23
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Kimura N, Takayama KI, Yamada Y, Kume H, Fujimura T, Inoue S. Ribonuclease H2 Subunit A Preserves Genomic Integrity and Promotes Prostate Cancer Progression. CANCER RESEARCH COMMUNICATIONS 2022; 2:870-883. [PMID: 36923313 PMCID: PMC10010380 DOI: 10.1158/2767-9764.crc-22-0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/15/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Homeostasis of genomic integrity should be regulated to promote proliferation and inhibit DNA damage-induced cell death in cancer. Ribonuclease H2 (RNase H2) maintains genome stability by controlling DNA:RNA hybrid and R-loop levels. Here, we identified that RNase H2 subunit A (RNASEH2A), a component of RNase H2, is highly expressed in castration-resistant prostate cancer (CRPC) tissues compared with localized prostate cancer. Interestingly, we showed that RNASEH2A suppressed R-loop levels to prevent cell apoptosis induced by DNA damage in prostate cancer cells. Both in vivo and in vitro studies revealed that RNASEH2A promotes cell growth and migration via the negative regulation of p53 and positive regulation of AR and AR-V7. Mechanistically, epigenetic regulation followed by R-loop accumulation in these promoters was observed for these gene regulations. Importantly, IHC analysis demonstrated that R-loop formation increased in CRPC tissues and correlated with RNASEH2A expression levels. Notably, two small molecules targeting RNase H2 activity were found to suppress CRPC tumor growth with no significant toxic effects. Collectively, we propose that RNASEH2A overexpression is a hallmark of prostate cancer progression by maintaining genomic stability to prevent R-loop-mediated apoptosis induction. Targeting RNase H2 activity could be a potential strategy for treating CRPC tumors. Significance RNASEH2A was demonstrated to be highly upregulated in aggressive prostate cancer to degrade R-loop accumulation and preserve genomic stability for tumor growth, suggesting that RNase H2 activity could be a promising therapeutic target.
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Affiliation(s)
- Naoki Kimura
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ken-Ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Yuta Yamada
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | | | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan.,Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
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24
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Miller HE, Montemayor D, Abdul J, Vines A, Levy SA, Hartono SR, Sharma K, Frost B, Chédin F, Bishop AJR. Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions. Nucleic Acids Res 2022; 50:7260-7286. [PMID: 35758606 PMCID: PMC9303298 DOI: 10.1093/nar/gkac537] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/16/2022] [Indexed: 12/13/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. While the pathological consequences of R-loops have been well-studied to date, the locations, classes, and dynamics of physiological R-loops remain poorly understood. R-loop mapping studies provide insight into R-loop dynamics, but their findings are challenging to generalize. This is due to the narrow biological scope of individual studies, the limitations of each mapping modality, and, in some cases, poor data quality. In this study, we reprocessed 810 R-loop mapping datasets from a wide array of biological conditions and mapping modalities. From this data resource, we developed an accurate R-loop data quality control method, and we reveal the extent of poor-quality data within previously published studies. We then identified a set of high-confidence R-loop mapping samples and used them to define consensus R-loop sites called 'R-loop regions' (RL regions). In the process, we identified a stark divergence between RL regions detected by S9.6 and dRNH-based mapping methods, particularly with respect to R-loop size, location, and colocalization with RNA binding factors. Taken together, this work provides a much-needed method to assess R-loop data quality and offers novel context regarding the differences between dRNH- and S9.6-based R-loop mapping approaches.
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Affiliation(s)
- Henry E Miller
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.,Bioinformatics Research Network, Atlanta, GA, USA
| | - Daniel Montemayor
- Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.,Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Jebriel Abdul
- Bioinformatics Research Network, Atlanta, GA, USA.,Department of Biology, University of Ottawa, Ottawa, Canada
| | - Anna Vines
- Bioinformatics Research Network, Atlanta, GA, USA.,Faculty of Arts, University of Bristol, Bristol, U.K
| | - Simon A Levy
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Bioinformatics Research Network, Atlanta, GA, USA.,Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.,Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA
| | - Kumar Sharma
- Department of Medicine, UT Health San Antonio, San Antonio, TX, USA.,Center for Precision Medicine, UT Health San Antonio, San Antonio, TX, USA
| | - Bess Frost
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Sam & Ann Barshop Institute for Longevity & Aging Studies, UT Health San Antonio, San Antonio, TX, USA.,Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, UC Davis, Davis, CA, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX, USA.,Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX, USA.,May's Cancer Center, UT Health San Antonio, San Antonio, TX, USA
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25
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Liu Z, Chen Q, You X, Wu X, Liu R, Li T, Gao L, Chen X, Lei A, Zeng W, Zheng Y. Sperm-derived RNAs improve the efficiency of somatic cell nuclear transfer (SCNT) through promoting R-loop formation. Mol Reprod Dev 2022; 89:325-336. [PMID: 35734898 DOI: 10.1002/mrd.23627] [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: 01/19/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/10/2022]
Abstract
Mammalian sperm and oocytes are haploid cells that carry parental genetic and epigenetic information for their progeny. The cytoplasm of oocytes is also capable of reprograming somatic cells to establish totipotency through somatic cell nuclear transfer (SCNT). However, epigenetic barriers seriously counteract SCNT reprogramming. Here, we found that sperm-derived RNAs elevated chromatin accessibility of nuclear donor cells concurrent with the appearance of increased RNA amount and decreased cell proliferation, instead of activating DNA damage response. Additionally, tri-methylation of lysine 9 on histone H3 (H3K9me3) and the H3K9 methyltransferase SUV39H2 were significantly downregulated by the sperm-derived RNA treatment. Our findings thus raise a fascinating possibility that sperm RNA-induced R-loops may activate gene expression and chromatin structure, thereby promoting SCNT reprogramming.
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Affiliation(s)
- Zidong Liu
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Qiang Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xueni You
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xiaodong Wu
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Ruifang Liu
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Tao Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Leilei Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xiaoxu Chen
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Anmin Lei
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Wenxian Zeng
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Yi Zheng
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
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26
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Liu Z, Ji Q, Ren J, Yan P, Wu Z, Wang S, Sun L, Wang Z, Li J, Sun G, Liang C, Sun R, Jiang X, Hu J, Ding Y, Wang Q, Bi S, Wei G, Cao G, Zhao G, Wang H, Zhou Q, Belmonte JCI, Qu J, Zhang W, Liu GH. Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging. Dev Cell 2022; 57:1347-1368.e12. [PMID: 35613614 DOI: 10.1016/j.devcel.2022.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/24/2022] [Accepted: 05/02/2022] [Indexed: 01/10/2023]
Abstract
Nuclear deformation, a hallmark frequently observed in senescent cells, is presumed to be associated with the erosion of chromatin organization at the nuclear periphery. However, how such gradual changes in higher-order genome organization impinge on local epigenetic modifications to drive cellular mechanisms of aging has remained enigmatic. Here, through large-scale epigenomic analyses of isogenic young, senescent, and progeroid human mesenchymal progenitor cells (hMPCs), we delineate a hierarchy of integrated structural state changes that manifest as heterochromatin loss in repressive compartments, euchromatin weakening in active compartments, switching in interfacing topological compartments, and increasing epigenetic entropy. We found that the epigenetic de-repression unlocks the expression of pregnancy-specific beta-1 glycoprotein (PSG) genes that exacerbate hMPC aging and serve as potential aging biomarkers. Our analyses provide a rich resource for uncovering the principles of epigenomic landscape organization and its changes in cellular aging and for identifying aging drivers and intervention targets with a genome-topology-based mechanism.
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Affiliation(s)
- Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengze Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Liang Sun
- NHC Beijing Institute of Geriatrics, NHC Key Laboratory of Geriatrics, Institute of Geriatric Medicine of Chinese Academy of Medical Sciences, National Center of Gerontology/ Beijing Hospital, Beijing 100730, China; Department of Clinical Laboratory, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Zehua Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuqian Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Run Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianli Hu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingjie Ding
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijia Bi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoguang Zhao
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
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27
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Munden A, Benton ML, Capra JA, Nordman JT. R-loop mapping and characterization during Drosophila embryogenesis reveals developmental plasticity in R-loop signatures. J Mol Biol 2022; 434:167645. [PMID: 35609632 PMCID: PMC9254486 DOI: 10.1016/j.jmb.2022.167645] [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: 04/20/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022]
Abstract
R-loops are involved in transcriptional regulation, DNA and histone post-translational modifications, genome replication and genome stability. To what extent R-loop abundance and genome-wide localization is actively regulated during metazoan embryogenesis is unknown. Drosophila embryogenesis provides a powerful system to address these questions due to its well-characterized developmental program, the sudden onset of zygotic transcription and available genome-wide data sets. Here, we measure the overall abundance and genome localization of R-loops in early and late-stage embryos relative to Drosophila cultured cells. We demonstrate that absolute R-loop levels change during embryogenesis and that RNaseH1 catalytic activity is critical for embryonic development. R-loop mapping by strand-specific DRIP-seq reveals that R-loop localization is plastic across development, both in the genes which form R-loops and where they localize relative to gene bodies. Importantly, these changes are not driven by changes in the transcriptional program. Negative GC skew and absolute changes in AT skew are associated with R-loop formation in Drosophila. Furthermore, we demonstrate that while some chromatin binding proteins and histone modifications such as H3K27me3 are associated with R-loops throughout development, other chromatin factors associated with R-loops in a developmental specific manner. Our findings highlight the importance and developmental plasticity of R-loops during Drosophila embryogenesis.
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Affiliation(s)
- Alexander Munden
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA
| | | | - John A Capra
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94103, USA
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA.
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28
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Cross-species metabolomic analysis identifies uridine as a potent regeneration promoting factor. Cell Discov 2022; 8:6. [PMID: 35102134 PMCID: PMC8803930 DOI: 10.1038/s41421-021-00361-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/05/2021] [Indexed: 01/07/2023] Open
Abstract
Regenerative capacity declines throughout evolution and with age. In this study, we asked whether metabolic programs underlying regenerative capability might be conserved across species, and if so, whether such metabolic drivers might be harnessed to promote tissue repair. To this end, we conducted metabolomic analyses in two vertebrate organ regeneration models: the axolotl limb blastema and antler stem cells. To further reveal why young individuals have higher regenerative capacity than the elderly, we also constructed metabolic profiles for primate juvenile and aged tissues, as well as young and aged human stem cells. In joint analyses, we uncovered that active pyrimidine metabolism and fatty acid metabolism correlated with higher regenerative capacity. Furthermore, we identified a set of regeneration-related metabolite effectors conserved across species. One such metabolite is uridine, a pyrimidine nucleoside, which can rejuvenate aged human stem cells and promote regeneration of various tissues in vivo. These observations will open new avenues for metabolic intervention in tissue repair and regeneration.
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29
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Neural Pericytes: A genomic archival state programmed by CHromatin topology. Eur J Cell Biol 2022; 101:151211. [DOI: 10.1016/j.ejcb.2022.151211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 11/22/2022] Open
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30
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The Cumulative Formation of R-loop Interacts with Histone Modifications to Shape Cell Reprogramming. Int J Mol Sci 2022; 23:ijms23031567. [PMID: 35163490 PMCID: PMC8835745 DOI: 10.3390/ijms23031567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
R-loop, a three-stranded RNA/DNA structure, plays important roles in modulating genome stability and gene expression, but the molecular mechanism of R-loops in cell reprogramming remains elusive. Here, we comprehensively profiled the genome-wide landscape of R-loops during cell reprogramming. The results showed that the R-loop formation on most different types of repetitive elements is stage-specific in cell reprogramming. We unveiled that the cumulative deposition of an R-loop subset is positively correlated with gene expression during reprogramming. More importantly, the dynamic turnover of this R-loop subset is accompanied by the activation of the pluripotent transcriptional regulatory network (TRN). Moreover, the large accumulation of the active histone marker H3K4me3 and the reduction in H3K27me3 were also observed in these R-loop regions. Finally, we characterized the dynamic network of R-loops that facilitates cell fate transitions in reprogramming. Together, our study provides a new clue for deciphering the interplay mechanism between R-loops and HMs to control cell reprogramming.
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31
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Graham GT, Selvanathan SP, Zöllner SK, Stahl E, Shlien A, Caplen N, Üren A, Toretsky JA. Comprehensive profiling of mRNA splicing indicates that GC content signals altered cassette exon inclusion in Ewing sarcoma. NAR Cancer 2022; 4:zcab052. [PMID: 35047826 PMCID: PMC8759570 DOI: 10.1093/narcan/zcab052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/30/2021] [Accepted: 01/06/2022] [Indexed: 11/29/2022] Open
Abstract
Ewing sarcoma (EwS) is a small round blue cell tumor and is the second most frequent pediatric bone cancer. 85% of EwS tumors express the fusion oncoprotein EWS-FLI1, the product of a t(11;22) reciprocal translocation. Prior work has indicated that transcription regulation alone does not fully describe the oncogenic capacity of EWS-FLI1, nor does it provide an effective means to stratify patient tumors. Research using EwS cell lines and patient samples has suggested that EWS-FLI1 also disrupts mRNA biogenesis. In this work we both describe the underlying characteristics of mRNA that are aberrantly spliced in EwS tumor samples as well as catalogue mRNA splicing events across other pediatric tumor types. Here, we also use short- and long-read sequencing to identify cis-factors that contribute to splicing profiles we observe in Ewing sarcoma. Our analysis suggests that GC content upstream of cassette exons is a defining factor of mRNA splicing in EwS. We also describe specific splicing events that discriminate EwS tumor samples from the assumed cell of origin, human mesenchymal stem cells derived from bone marrow (hMSC-BM). Finally, we identify specific splicing factors PCBP2, RBMX, and SRSF9 by motif enrichment and confirm findings from tumor samples in EwS cell lines.
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Affiliation(s)
| | | | | | | | | | | | | | - Jeffrey A Toretsky
- To whom correspondence should be addressed. Tel: +1 202 687 8909; Fax: +1 202 687 8909;
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Xu W, Li K, Li Q, Li S, Zhou J, Sun Q. Quantitative, Convenient, and Efficient Genome-Wide R-Loop Profiling by ssDRIP-Seq in Multiple Organisms. Methods Mol Biol 2022; 2528:445-464. [PMID: 35704209 DOI: 10.1007/978-1-0716-2477-7_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
R-loop is a three-stranded chromatin structure, comprising one single-stranded DNA and another DNA:RNA hybrid strand, plays various and essential biological functions in many organisms. Developing a precise, efficient, faithful, and unbiased genome-wide R-loop detection method with extensive adaptability in all organisms is at the top priority for R-loop biology. Here, we provide a straightforward and highly efficient protocol for genome-wide strand-specific R-loop profiling in various organisms. In brief, genomic DNA is extracted and fragmented by the cocktail of restriction enzymes, and then the DNA:RNA hybrids are immunoprecipitated, following by the single-stranded DNA adaptor ligation and next-generation sequencing (named as ssDRIP-seq). Coupling with a straightforward and step-by-step bioinformatic pipeline, this method can provide high resolution and comprehensive strand-specific information for R-loop formation. ssDRIP-seq has been successfully applied for detecting R-loops from prokaryotes such as E. coli, to eukaryotes such as S. cerevisiae, mammalian cell culture and tissues, as well as plants Arabidopsis and rice, with high reproducibility and sensitivity.
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Affiliation(s)
- Wei Xu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 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, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qin Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shuai Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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Rezaei-Lotfi S, Vujovic F, Simonian M, Hunter N, Farahani RM. Programmed genomic instability regulates neural transdifferentiation of human brain microvascular pericytes. Genome Biol 2021; 22:334. [PMID: 34886891 PMCID: PMC8656028 DOI: 10.1186/s13059-021-02555-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Transdifferentiation describes transformation in vivo of specialized cells from one lineage into another. While there is extensive literature on forced induction of lineage reprogramming in vitro, endogenous mechanisms that govern transdifferentiation remain largely unknown. The observation that human microvascular pericytes transdifferentiate into neurons provided an opportunity to explore the endogenous molecular basis for lineage reprogramming. RESULTS We show that abrupt destabilization of the higher-order chromatin topology that chaperones lineage memory of pericytes is driven by transient global transcriptional arrest. This leads within minutes to localized decompression of the repressed competing higher-order chromatin topology and expression of pro-neural genes. Transition to neural lineage is completed by probabilistic induction of R-loops in key myogenic loci upon re-initiation of RNA polymerase activity, leading to depletion of the myogenic transcriptome and emergence of the neurogenic transcriptome. CONCLUSIONS These findings suggest that the global transcriptional landscape not only shapes the functional cellular identity of pericytes, but also stabilizes lineage memory by silencing the competing neural program within a repressed chromatin state.
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Affiliation(s)
- Saba Rezaei-Lotfi
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
| | - Filip Vujovic
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
| | - Mary Simonian
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
| | - Ramin M. Farahani
- IDR/Westmead Institute for Medical Research, Westmead, NSW 2145 Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006 Australia
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R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences. Int J Mol Sci 2021; 22:ijms222312857. [PMID: 34884661 PMCID: PMC8657672 DOI: 10.3390/ijms222312857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 12/02/2022] Open
Abstract
R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes.
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A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements. J Genet Genomics 2021; 48:1007-1019. [PMID: 34531149 DOI: 10.1016/j.jgg.2021.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
Enhancers modulate gene expression by interacting with promoters. Models of enhancer-promoter interactions (EPIs) in the literature involve the activity of many components, including transcription factors and nucleic acid. However, the role that sequence similarity plays in EPIs remains largely unexplored. Herein, we report that Alu-derived sequences dominate sequence similarity between enhancers and promoters. After rejecting alternative DNA:DNA and DNA:RNA triplex models, we propose that enhancer-associated RNAs (eRNAs) may directly contact their targeted promoters by forming trans-acting R-loops at those Alu sequences. We show how the characteristic distribution of functional genomic data, such as RNA-DNA proximate ligation reads, binding of transcription factors, and RNA-binding proteins, all align with the Alu sequences of EPIs. We also show that these aligned Alu sequences may be subject to the constraint of coevolution, further implying the functional significance of these R-loop hybrids. Finally, our results imply that eRNA and Alu elements associate in a manner previously unrecognized in EPIs and the evolution of gene regulation networks in mammals.
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36
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Lin R, Zhong X, Zhou Y, Geng H, Hu Q, Huang Z, Hu J, Fu XD, Chen L, Chen JY. R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. Nucleic Acids Res 2021; 50:D303-D315. [PMID: 34792163 PMCID: PMC8728142 DOI: 10.1093/nar/gkab1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/28/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.
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Affiliation(s)
- Ruoyao Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Yongli Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huichao Geng
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qingxi Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhihao Huang
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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37
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Replication stress: from chromatin to immunity and beyond. Curr Opin Genet Dev 2021; 71:136-142. [PMID: 34455237 DOI: 10.1016/j.gde.2021.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/08/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022]
Abstract
Replication stress (RS) is a hallmark of cancer cells that is associated with increased genomic instability. RS occurs when replication forks encounter obstacles along the DNA. Stalled forks are signaled by checkpoint kinases that prevent fork collapse and coordinate fork repair pathways. Fork restart also depends on chromatin remodelers to increase the accessibility of nascent chromatin to recombination and repair factors. In this review, we discuss recent findings on the causes and consequences of RS, with a focus on endogenous replication impediments and their impact on fork velocity. We also discuss recent studies on the interplay between stalled forks and innate immunity, which extends the RS response beyond cell boundaries and opens new avenues for cancer therapy.
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38
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Sexton CE, Tillett RL, Han MV. The essential but enigmatic regulatory role of HERVH in pluripotency. Trends Genet 2021; 38:12-21. [PMID: 34340871 DOI: 10.1016/j.tig.2021.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 01/09/2023]
Abstract
Human specific endogenous retrovirus H (HERVH) is highly expressed in both naive and primed stem cells and is essential for pluripotency. Despite the proven relationship between HERVH expression and pluripotency, there is no single definitive model for the function of HERVH. Instead, several hypotheses of a regulatory function have been put forward including HERVH acting as enhancers, long noncoding RNAs (lncRNAs), and most recently as markers of topologically associating domain (TAD) boundaries. Recently several enhancer-associated lncRNAs have been characterized, which bind to Mediator and are necessary for promoter-enhancer folding interactions. We propose a synergistic model of HERVH function combining relevant findings and discuss the current limitations for its role in regulation, including the lack of evidence for a pluripotency-associated target gene.
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Affiliation(s)
- Corinne E Sexton
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
| | | | - Mira V Han
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, Las Vegas, NV 89154, USA.
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DNA-RNA Hybrid (R-Loop): From a Unified Picture of the Mammalian Telomere to the Genome-Wide Profile. Cells 2021; 10:cells10061556. [PMID: 34205454 PMCID: PMC8233970 DOI: 10.3390/cells10061556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 01/16/2023] Open
Abstract
Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular extract without antibody that allows their physical isolation and determination of their RNA nucleotide sequence. We then define in the normal mouse and human sperm genomes the notion of stable DNA associated RNA terminal R-loop complexes, including TERRA molecules synthesized from local promoters of every chromosome. Furthermore, the first strong evidence of all telomeric structures, applied additionally to the whole murine sperm genome compared to the testes, showed reproducible R-loop complexes of the whole genome and suggesting a defined profile in the sperm genome for the next generation.
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40
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Weinreb JT, Ghazale N, Pradhan K, Gupta V, Potts KS, Tricomi B, Daniels NJ, Padgett RA, De Oliveira S, Verma A, Bowman TV. Excessive R-loops trigger an inflammatory cascade leading to increased HSPC production. Dev Cell 2021; 56:627-640.e5. [PMID: 33651979 DOI: 10.1016/j.devcel.2021.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/01/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) arise during embryonic development and are essential for sustaining the blood and immune systems throughout life. Tight regulation of HSPC numbers is critical for hematopoietic homeostasis. Here, we identified DEAD-box helicase 41 (Ddx41) as a gatekeeper of HSPC production. Using zebrafish ddx41 mutants, we unveiled a critical role for this helicase in regulating HSPC production at the endothelial-to-hematopoietic transition. We determined that Ddx41 suppresses the accumulation of R-loops, nucleic acid structures consisting of RNA:DNA hybrids and ssDNAs whose equilibrium is essential for cellular fitness. Excess R-loop levels in ddx41 mutants triggered the cGAS-STING inflammatory pathway leading to increased numbers of hemogenic endothelium and HSPCs. Elevated R-loop accumulation and inflammatory signaling were observed in human cells with decreased DDX41, suggesting possible conservation of mechanism. These findings delineate that precise regulation of R-loop levels during development is critical for limiting cGAS-STING activity and HSPC numbers.
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Affiliation(s)
- Joshua T Weinreb
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Noura Ghazale
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kith Pradhan
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kathryn S Potts
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brad Tricomi
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Noah J Daniels
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Richard A Padgett
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sofia De Oliveira
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Hepatology) and Marion Bessin Liver Research Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Amit Verma
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Oncology), Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine (Oncology), Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA.
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41
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Wang K, Wang H, Li C, Yin Z, Xiao R, Li Q, Xiang Y, Wang W, Huang J, Chen L, Fang P, Liang K. Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor. SCIENCE ADVANCES 2021; 7:7/8/eabe3516. [PMID: 33597247 PMCID: PMC7888926 DOI: 10.1126/sciadv.abe3516] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/30/2020] [Indexed: 05/08/2023]
Abstract
An R loop is a unique triple-stranded structure that participates in multiple key biological processes and is relevant to human diseases. Accurate and comprehensive R loop profiling is a prerequisite for R loops studies. However, current R loop mapping methods generate large discrepancies, therefore an independent method is in urgent need. Here, we establish an independent R loop CUT&Tag (Tn5-based cleavage under targets and tagmentation) method by combining CUT&Tag and GST-His6-2×HBD (glutathione S-transferase-hexahistidine-2× hybrid-binding domain), an artificial DNA-RNA hybrid sensor that specifically recognizes the DNA-RNA hybrids. We demonstrate that the R loop CUT&Tag is sensitive, reproducible, and convenient for native R loop mapping with high resolution, and find that the capture strategies, instead of the specificity of sensors, largely contribute to the disparities among different methods. Together, we provide an independent strategy for genomic profiling of native R loops and help resolve discrepancies among multiple R loop mapping methods.
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Affiliation(s)
- Kang Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Honghong Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhinang Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Ruijing Xiao
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Qiuzi Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, P.R. China
| | - Ying Xiang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wen Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jian Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, P.R. China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, P.R. China
| | - Pingping Fang
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China.
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Research Center for Medicine and Structural Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
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42
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Liu C, Dai SK, Shi RX, He XC, Wang YY, He BD, Sun XW, Du HZ, Liu CM, Teng ZQ. Transcriptional profiling of microglia in the injured brain reveals distinct molecular features underlying neurodegeneration. Glia 2021; 69:1292-1306. [PMID: 33492723 DOI: 10.1002/glia.23966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/30/2020] [Accepted: 01/06/2021] [Indexed: 12/30/2022]
Abstract
Neurotrauma has been recognized as a risk factor for neurodegenerative diseases, and sex difference of the incidence and outcome of neurodegenerative diseases has long been recognized. Past studies suggest that microglia could play a versatile role in both health and disease. So far, the microglial mechanisms underlying neurodegeneration and potentially lead to sex-specific therapies are still very open. Here we applied whole transcriptome analysis of microglia acutely isolated at different timepoints after a cortical stab wound injury to gain insight into genes that might be dysregulated and transcriptionally different between males and females after cortical injury. We found that microglia displayed distinct temporal and sexual molecular signatures of transcriptome after cortical injury. Hypotheses and gene candidates that we presented in the present study could be worthy to be examined to explore the roles of microglia in neurotrauma and in sex-biased neurodegenerative diseases.
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Affiliation(s)
- Cong Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ruo-Xi Shi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xuan-Cheng He
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ying-Ying Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Bao-Dong He
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhen Du
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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Liu GH, Bao Y, Qu J, Zhang W, Zhang T, Kang W, Yang F, Ji Q, Jiang X, Ma Y, Ma S, Liu Z, Chen S, Wang S, Sun S, Geng L, Yan K, Yan P, Fan Y, Song M, Ren J, Wang Q, Yang S, Yang Y, Xiong M, Liang C, Li LZ, Cao T, Hu J, Yang P, Ping J, Hu H, Zheng Y, Sun G, Li J, Liu L, Zou Z, Ding Y, Li M, Liu D, Wang M, Ji Q, Sun X, Wang C, Bi S, Shan H, Zhuo X. Aging Atlas: a multi-omics database for aging biology. Nucleic Acids Res 2021; 49:D825-D830. [PMID: 33119753 PMCID: PMC7779027 DOI: 10.1093/nar/gkaa894] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Organismal aging is driven by interconnected molecular changes encompassing internal and extracellular factors. Combinational analysis of high-throughput 'multi-omics' datasets (gathering information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and pharmacogenomics), at either populational or single-cell levels, can provide a multi-dimensional, integrated profile of the heterogeneous aging process with unprecedented throughput and detail. These new strategies allow for the exploration of the molecular profile and regulatory status of gene expression during aging, and in turn, facilitate the development of new aging interventions. With a continually growing volume of valuable aging-related data, it is necessary to establish an open and integrated database to support a wide spectrum of aging research. The Aging Atlas database aims to provide a wide range of life science researchers with valuable resources that allow access to a large-scale of gene expression and regulation datasets created by various high-throughput omics technologies. The current implementation includes five modules: transcriptomics (RNA-seq), single-cell transcriptomics (scRNA-seq), epigenomics (ChIP-seq), proteomics (protein-protein interaction), and pharmacogenomics (geroprotective compounds). Aging Atlas provides user-friendly functionalities to explore age-related changes in gene expression, as well as raw data download services. Aging Atlas is freely available at https://bigd.big.ac.cn/aging/index.
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Yan P, Ren J, Zhang W, Qu J, Liu GH. Protein quality control of cell stemness. CELL REGENERATION (LONDON, ENGLAND) 2020; 9:22. [PMID: 33179756 PMCID: PMC7658286 DOI: 10.1186/s13619-020-00064-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
Protein quality control (PQC) systems play essential roles in the recognition, refolding and clearance of aberrant proteins, thus ensuring cellular protein homeostasis, or proteostasis. Especially, continued proliferation and differentiation of stem cells require a high rate of translation; therefore, accurate PQC systems are essential to maintain stem cell function. Growing evidence suggested crucial roles of PQC systems in regulating the stemness and differentiation of stem cells. This review focuses on current knowledge regarding the components of the proteostasis network in stem cells, and the importance of proteostasis in maintaining stem cell identity and regenerative functions. A complete understanding of this process might uncover potential applications in aging intervention and aging-related diseases.
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Affiliation(s)
- Pengze Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Ren
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing Qu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Brain Disorders, Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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