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Zhu J, Zhu X, Xu Y, Chen X, Ge X, Huang Y, Wang Z. The role of noncoding RNAs in beta cell biology and tissue engineering. Life Sci 2024; 348:122717. [PMID: 38744419 DOI: 10.1016/j.lfs.2024.122717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/29/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024]
Abstract
The loss or dysfunction of pancreatic β-cells, which are responsible for insulin secretion, constitutes the foundation of all forms of diabetes, a widely prevalent disease worldwide. The replacement of damaged β-cells with regenerated or transplanted cells derived from stem cells is a promising therapeutic strategy. However, inducing the differentiation of stem cells into fully functional glucose-responsive β-cells in vitro has proven to be challenging. Noncoding RNAs (ncRNAs) have emerged as critical regulatory factors governing the differentiation, identity, and function of β-cells. Furthermore, engineered hydrogel systems, biomaterials, and organ-like structures possess engineering characteristics that can provide a three-dimensional (3D) microenvironment that supports stem cell differentiation. This review summarizes the roles and contributions of ncRNAs in maintaining the differentiation, identity, and function of β-cells. And it focuses on regulating the levels of ncRNAs in stem cells to activate β-cell genetic programs for generating alternative β-cells and discusses how to manipulate ncRNA expression by combining hydrogel systems and other tissue engineering materials. Elucidating the patterns of ncRNA-mediated regulation in β-cell biology and utilizing this knowledge to control stem cell differentiation may offer promising therapeutic strategies for generating functional insulin-producing cells in diabetes cell replacement therapy and tissue engineering.
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Affiliation(s)
- Jiaqi Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Xiaoren Zhu
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Yang Xu
- Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xingyou Chen
- Medical School of Nantong University, Nantong 226001, China
| | - Xinqi Ge
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yan Huang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
| | - Zhiwei Wang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China.
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2
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Lee YH, Hass EP, Campodonico W, Lee YK, Lasda E, Shah J, Rinn J, Hwang T. Massively parallel dissection of RNA in RNA-protein interactions in vivo. Nucleic Acids Res 2024; 52:e48. [PMID: 38726866 PMCID: PMC11162807 DOI: 10.1093/nar/gkae334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to biology. Here, we present massively parallel RNA assay combined with immunoprecipitation (MPRNA-IP) for in vivo high-throughput dissection of RNA-protein interactions and describe statistical models for identifying RNA domains and parsing the structural contributions of RNA. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, MPRNA-IP is able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest, including the long noncoding RNA NORAD, bacteriophage MS2 RNA, and human telomerase RNA, and we use it to interrogate the hitherto unknown sequence or structural RNA-binding preferences of the DNA-looping factor CTCF. By integrating systematic mutation analysis with crosslinking immunoprecipitation, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions in vivo.
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Affiliation(s)
- Yu Hsuan Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Evan P Hass
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Will Campodonico
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Erika Lasda
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Jaynish S Shah
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - John L Rinn
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Taeyoung Hwang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Huber J, Tanasie NL, Zernia S, Stigler J. Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment. Nucleic Acids Res 2024:gkae391. [PMID: 38742641 DOI: 10.1093/nar/gkae391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
CTCF is a zinc finger protein associated with transcription regulation that also acts as a barrier factor for topologically associated domains (TADs) generated by cohesin via loop extrusion. These processes require different properties of CTCF-DNA interaction, and it is still unclear how CTCF's structural features may modulate its diverse roles. Here, we employ single-molecule imaging to study both full-length CTCF and truncation mutants. We show that CTCF enriches at CTCF binding sites (CBSs), displaying a longer lifetime than observed previously. We demonstrate that the zinc finger domains mediate CTCF clustering and that clustering enables RNA recruitment, possibly creating a scaffold for interaction with RNA-binding proteins like cohesin's subunit SA. We further reveal a direct recruitment and an increase of SA residence time by CTCF bound at CBSs, suggesting that CTCF-SA interactions are crucial for cohesin stability on chromatin at TAD borders. Furthermore, we establish a single-molecule T7 transcription assay and show that although a transcribing polymerase can remove CTCF from CBSs, transcription is impaired. Our study shows that context-dependent nucleic acid binding determines the multifaceted CTCF roles in genome organization and transcription regulation.
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Affiliation(s)
- Jonas Huber
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Sarah Zernia
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
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Lizana L, Schwartz YB. The scales, mechanisms, and dynamics of the genome architecture. SCIENCE ADVANCES 2024; 10:eadm8167. [PMID: 38598632 PMCID: PMC11006219 DOI: 10.1126/sciadv.adm8167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Even when split into several chromosomes, DNA molecules that make up our genome are too long to fit into the cell nuclei unless massively folded. Such folding must accommodate the need for timely access to selected parts of the genome by transcription factors, RNA polymerases, and DNA replication machinery. Here, we review our current understanding of the genome folding inside the interphase nuclei. We consider the resulting genome architecture at three scales with a particular focus on the intermediate (meso) scale and summarize the insights gained from recent experimental observations and diverse computational models.
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Affiliation(s)
- Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
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Liu Y, Liu F, Li Y, Li Y, Feng Y, Zhao J, Zhou C, Li C, Shen J, Zhang Y. LncRNA Anxa10-203 enhances Mc1r mRNA stability to promote neuropathic pain by recruiting DHX30 in the trigeminal ganglion. J Headache Pain 2024; 25:28. [PMID: 38433184 PMCID: PMC10910797 DOI: 10.1186/s10194-024-01733-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Trigeminal nerve injury is one of the most serious complications in oral clinics, and the subsequent chronic orofacial pain is a consumptive disease. Increasing evidence demonstrates long non-coding RNAs (lncRNAs) play an important role in the pathological process of neuropathic pain. This study aims to explore the function and mechanism of LncRNA Anxa10-203 in the development of orofacial neuropathic pain. METHODS A mouse model of orofacial neuropathic pain was established by chronic constriction injury of the infraorbital nerve (CCI-ION). The Von Frey test was applied to evaluate hypersensitivity of mice. RT-qPCR and/or Western Blot were performed to analyze the expression of Anxa10-203, DHX30, and MC1R. Cellular localization of target genes was verified by immunofluorescence and RNA fluorescence in situ hybridization. RNA pull-down and RNA immunoprecipitation were used to detect the interaction between the target molecules. Electrophysiology was employed to assess the intrinsic excitability of TG neurons (TGNs) in vitro. RESULTS Anxa10-203 was upregulated in the TG of CCI-ION mice, and knockdown of Anxa10-203 relieved neuropathic pain. Structurally, Anxa10-203 was located in the cytoplasm of TGNs. Mechanistically, Mc1r expression was positively correlated with Anxa10-203 and was identified as the functional target of Anxa10-203. Besides, Anxa10-203 recruited RNA binding protein DHX30 and formed the Anxa10-203/DHX30 complex to enhance the stability of Mc1r mRNA, resulting in the upregulation of MC1R, which contributed to the enhancement of the intrinsic activity of TGNs in vitro and orofacial neuropathic pain in vivo. CONCLUSIONS LncRNA Anxa10-203 in the TG played an important role in orofacial neuropathic pain and mediated mechanical allodynia in CCI-ION mice by binding with DHX30 to upregulate MC1R expression.
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Affiliation(s)
- YaJing Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Fei Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - YiKe Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - YueLing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - YuHeng Feng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - JiaShuo Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Cheng Zhou
- Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - ChunJie Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - JieFei Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China.
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - YanYan Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China School of Stomatology, Sichuan University, Chengdu, 610041, China.
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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Hazazi A, AlShehah AA, Khan FR, Hakami MA, Almarshadi F, Abalkhail A, Nassar SA, Almasoudi HH, Ali AA, Abu-Alghayth MH, Kukreti N, Binshaya AS. From diagnosis to therapy: The transformative role of lncRNAs in eye cancer management. Pathol Res Pract 2024; 254:155081. [PMID: 38211388 DOI: 10.1016/j.prp.2023.155081] [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: 11/16/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
The genomic era has brought about a transformative shift in our comprehension of cancer, unveiling the intricate molecular landscape underlying disease development. Eye cancers (ECs), encompassing diverse malignancies affecting ocular tissues, pose distinctive challenges in diagnosis and management. Long non-coding RNAs (lncRNAs), an emerging category of non-coding RNAs, are pivotal actors in the genomic intricacies of eye cancers. LncRNAs have garnered recognition for their multifaceted roles in gene expression regulation and influence on many cellular processes. Many studies support that the lncRNAs have a role in developing various cancers. Recent investigations have pinpointed specific lncRNAs associated with ECs, including retinoblastoma and uveal melanoma. These lncRNAs exert control over critical pathways governing tumor initiation, progression, and metastasis, endowing them with the ability to function as evaluation, predictive, and therapeutic indicators. The article aims to synthesize the existing information concerning the functions of lncRNAs in ECs, elucidating their regulatory mechanisms and clinical significance. By delving into the lncRNAs' expanding relevance in the modulation of oncogenic and tumor-suppressive networks, we gain a deeper understanding of the molecular complexities intrinsic to these diseases. In our exploration of the genomic intricacies of ECs, lncRNAs introduce a fresh perspective, providing an opportunity to function as clinical and therapeutic indicators, and they also have therapeutic benefits that show promise for advancing the treatment of ECs. This comprehensive review bridges the intricate relationship between lncRNAs and ECs within the context of the genomic era.
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Affiliation(s)
- Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | | | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Fahad Almarshadi
- Department of Public Health, College of Public Health and Health Informatics, University of Ha'il, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Qassim, Saudi Arabia
| | - Somia A Nassar
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia; Department of Parasitology & Animal Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Amer Al Ali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Mohammed H Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Abdulkarim S Binshaya
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
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Ning D, Jin J, Fang Y, Du P, Yuan C, Chen J, Huang Q, Cheng K, Mo J, Xu L, Guo H, Yang MJ, Chen X, Liang H, Zhang B, Zhang W. DEAD-Box Helicase 17 exacerbates non-alcoholic steatohepatitis via transcriptional repression of cyp2c29, inducing hepatic lipid metabolism disorder and eliciting the activation of M1 macrophages. Clin Transl Med 2024; 14:e1529. [PMID: 38303609 PMCID: PMC10835191 DOI: 10.1002/ctm2.1529] [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: 01/17/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 02/03/2024] Open
Abstract
OBJECTIVE Our study was to elucidate the role of RNA helicase DEAD-Box Helicase 17 (DDX17) in NAFLD and to explore its underlying mechanisms. METHODS We created hepatocyte-specific Ddx17-deficient mice aim to investigate the impact of Ddx17 on NAFLD induced by a high-fat diet (HFD) as well as methionine and choline-deficient l-amino acid diet (MCD) in adult male mice. RNA-seq and lipidomic analyses were conducted to depict the metabolic landscape, and CUT&Tag combined with chromatin immunoprecipitation (ChIP) and luciferase reporter assays were conducted. RESULTS In this work, we observed a notable increase in DDX17 expression in the livers of patients with NASH and in murine models of NASH induced by HFD or MCD. After introducing lentiviruses into hepatocyte L02 for DDX17 knockdown or overexpression, we found that lipid accumulation induced by palmitic acid/oleic acid (PAOA) in L02 cells was noticeably weakened by DDX17 knockdown but augmented by DDX17 overexpression. Furthermore, hepatocyte-specific DDX17 knockout significantly alleviated hepatic steatosis, inflammatory response and fibrosis in mice after the administration of MCD and HFD. Mechanistically, our analysis of RNA-seq and CUT&Tag results combined with ChIP and luciferase reporter assays indicated that DDX17 transcriptionally represses Cyp2c29 gene expression by cooperating with CCCTC binding factor (CTCF) and DEAD-Box Helicase 5 (DDX5). Using absolute quantitative lipidomics analysis, we identified a hepatocyte-specific DDX17 deficiency that decreased lipid accumulation and altered lipid composition in the livers of mice after MCD administration. Based on the RNA-seq analysis, our findings suggest that DDX17 could potentially have an impact on the modulation of lipid metabolism and the activation of M1 macrophages in murine NASH models. CONCLUSION These results imply that DDX17 is involved in NASH development by promoting lipid accumulation in hepatocytes, inducing the activation of M1 macrophages, subsequent inflammatory responses and fibrosis through the transcriptional repression of Cyp2c29 in mice. Therefore, DDX17 holds promise as a potential drug target for the treatment of NASH.
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Affiliation(s)
- Deng Ning
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Department of Hepatobiliary SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jie Jin
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Yuanyuan Fang
- Department of NeurologyTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Pengcheng Du
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Chaoyi Yuan
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Jin Chen
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Qibo Huang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Kun Cheng
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Jie Mo
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Lei Xu
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
| | - Hui Guo
- Institute of Organ TransplantationTongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanChina
| | - Mia Jiming Yang
- Institute for Management in Medicine and Health SciencesUniversity of BayreuthBayreuthGermany
| | - Xiaoping Chen
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
| | - Huifang Liang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
| | - Bixiang Zhang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
| | - Wanguang Zhang
- Department of Hepatic Surgery CenterTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Hepato‐Pancreato‐Biliary DiseasesWuhanChina
- Key Laboratory of Organ TransplantationMinistry of Education and Ministry of HealthWuhanChina
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Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
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Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
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Banerjee S, Sarkar R, Mukherjee A, Mitra S, Gope A, Chawla-Sarkar M. Rotavirus-induced lncRNA SLC7A11-AS1 promotes ferroptosis by targeting cystine/glutamate antiporter xCT (SLC7A11) to facilitate virus infection. Virus Res 2024; 339:199261. [PMID: 37923170 PMCID: PMC10684390 DOI: 10.1016/j.virusres.2023.199261] [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: 08/23/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Rotavirus (RV) is the primary etiological agent of virus-associated gastroenteritis in infants, causing 200,000 childhood death annually. Despite the availability of vaccines, rotaviral diarrhea continues to be a severe issue in underdeveloped nations in Asia and Africa. The situation demands continual studies on host-rotavirus interactions to understand disease pathogenesis and develop effective antiviral therapeutics. Long non-coding RNAs (lncRNAs), which are a subset of non-coding RNAs of more than 200 nucleotides in length, are reported to play a regulatory function in numerous viral infections. Virus infection often alters the host transcriptome including lncRNA that are differentially expressed either to play an antiviral role or to be advantageous towards virus propagation. In the current study, qPCR array-based expression profiling of host lncRNAs was performed in rotavirus-infected HT-29 cells that identified the lncRNA SLC7A11-AS1 to be upregulated during RV infection. Knockdown of SLC7A11-AS1 conspicuously reduced RV titers implying its pro-viral significance. RV-induced SLC7A11-AS1 downregulates the gene SLC7A11/xCT that encodes the light chain subunit of the system XC- cystine-glutamate exchange transporter, leading to decrease in intracellular glutathione level and increase in lipid peroxidation, which are signature features of ferroptotic pathway. Ectopic expression of xCT also abrogated RV infection by reversing the virus optimized levels of intracellular GSH and lipid ROS levels. Cumulatively, the study reveals that RV infection triggers ferroptotic cell death via SLC7A11-AS1/xCT axis to facilitate its own propagation.
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Affiliation(s)
- Shreya Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rakesh Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Arpita Mukherjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Animesh Gope
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India.
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10
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Chen X, Pillay S, Lohmann F, Bieker JJ. Association of DDX5/p68 protein with the upstream erythroid enhancer element (EHS1) of the gene encoding the KLF1 transcription factor. J Biol Chem 2023; 299:105489. [PMID: 38000658 PMCID: PMC10750184 DOI: 10.1016/j.jbc.2023.105489] [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: 03/06/2023] [Revised: 10/28/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
EKLF/KLF1 is an essential transcription factor that plays a global role in erythroid transcriptional activation. Regulation of KLF1 is of interest, as it displays a highly restricted expression pattern, limited to erythroid cells and its progenitors. Here we use biochemical affinity purification to identify the DDX5/p68 protein as an activator of KLF1 by virtue of its interaction with the erythroid-specific DNAse hypersensitive site upstream enhancer element (EHS1). We further show that this protein associates with DEK and CTCF. We postulate that the range of interactions of DDX5/p68 with these and other proteins known to interact with this element render it part of the enhanseosome complex critical for optimal expression of KLF1 and enables the formation of a proper chromatin configuration at the Klf1 locus. These individual interactions provide quantitative contributions that, in sum, establish the high-level activity of the Klf1 promoter and suggest they can be selectively manipulated for clinical benefit.
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Affiliation(s)
- Xiaoyong Chen
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - Sanjana Pillay
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - Felix Lohmann
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA
| | - James J Bieker
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, New York, New York, USA; Black Familly Stem Cell Institute, Mount Sinai School of Medicine, New York, New York, USA; Tisch Cancer Institute, Mount Sinai School of Medicine, New York, New York, USA; Mindich Child Health and Development Institute, Mount Sinai School of Medicine, New York, New York, USA.
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11
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Yang ZY, Yan XC, Zhang JYL, Liang L, Gao CC, Zhang PR, Liu Y, Sun JX, Ruan B, Duan JL, Wang RN, Feng XX, Che B, Xiao T, Han H. Repression of rRNA gene transcription by endothelial SPEN deficiency normalizes tumor vasculature via nucleolar stress. J Clin Invest 2023; 133:e159860. [PMID: 37607001 PMCID: PMC10575731 DOI: 10.1172/jci159860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
Human cancers induce a chaotic, dysfunctional vasculature that promotes tumor growth and blunts most current therapies; however, the mechanisms underlying the induction of a dysfunctional vasculature have been unclear. Here, we show that split end (SPEN), a transcription repressor, coordinates rRNA synthesis in endothelial cells (ECs) and is required for physiological and tumor angiogenesis. SPEN deficiency attenuated EC proliferation and blunted retinal angiogenesis, which was attributed to p53 activation. Furthermore, SPEN knockdown activated p53 by upregulating noncoding promoter RNA (pRNA), which represses rRNA transcription and triggers p53-mediated nucleolar stress. In human cancer biopsies, a low endothelial SPEN level correlated with extended overall survival. In mice, endothelial SPEN deficiency compromised rRNA expression and repressed tumor growth and metastasis by normalizing tumor vessels, and this was abrogated by p53 haploinsufficiency. rRNA gene transcription is driven by RNA polymerase I (RNPI). We found that CX-5461, an RNPI inhibitor, recapitulated the effect of Spen ablation on tumor vessel normalization and combining CX-5461 with cisplatin substantially improved the efficacy of treating tumors in mice. Together, these results demonstrate that SPEN is required for angiogenesis by repressing pRNA to enable rRNA gene transcription and ribosomal biogenesis and that RNPI represents a target for tumor vessel normalization therapy of cancer.
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12
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Sachs P, Bergmaier P, Treutwein K, Mermoud JE. The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse. Genes (Basel) 2023; 14:1793. [PMID: 37761933 PMCID: PMC10530723 DOI: 10.3390/genes14091793] [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: 08/23/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
In vertebrates, SMARCAD1 participates in transcriptional regulation, heterochromatin maintenance, DNA repair, and replication. The molecular basis underlying its involvement in these processes is not well understood. We identified the RNA polymerase III general transcription factor TFIIIC as an interaction partner of native SMARCAD1 in mouse and human models using endogenous co-immunoprecipitations. TFIIIC has dual functionality, acting as a general transcription factor and as a genome organizer separating chromatin domains. We found that its partnership with SMARCAD1 is conserved across different mammalian cell types, from somatic to pluripotent cells. Using purified proteins, we confirmed that their interaction is direct. A gene expression analysis suggested that SMARCAD1 is dispensable for TFIIIC function as an RNA polymerase III transcription factor in mouse ESCs. The distribution of TFIIIC and SMARCAD1 in the ESC genome is distinct, and unlike in yeast, SMARCAD1 is not enriched at active tRNA genes. Further analysis of SMARCAD1-binding partners in pluripotent and differentiated mammalian cells reveals that SMARCAD1 associates with several factors that have key regulatory roles in chromatin organization, such as cohesin, laminB, and DDX5. Together, our work suggests for the first time that the SMARCAD1 enzyme participates in genome organization in mammalian nuclei through interactions with architectural proteins.
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Affiliation(s)
- Parysatis Sachs
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
- CMC Development, R&D, Sanofi, 65926 Frankfurt, Germany
| | - Philipp Bergmaier
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
- Global Development Operations, R&D, Merck Healthcare, 64293 Darmstadt, Germany
| | - Katrin Treutwein
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
| | - Jacqueline E. Mermoud
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, 35043 Marburg, Germany
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13
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Del Moral-Morales A, Salgado-Albarrán M, Sánchez-Pérez Y, Wenke NK, Baumbach J, Soto-Reyes E. CTCF and Its Multi-Partner Network for Chromatin Regulation. Cells 2023; 12:1357. [PMID: 37408191 DOI: 10.3390/cells12101357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Architectural proteins are essential epigenetic regulators that play a critical role in organizing chromatin and controlling gene expression. CTCF (CCCTC-binding factor) is a key architectural protein responsible for maintaining the intricate 3D structure of chromatin. Because of its multivalent properties and plasticity to bind various sequences, CTCF is similar to a Swiss knife for genome organization. Despite the importance of this protein, its mechanisms of action are not fully elucidated. It has been hypothesized that its versatility is achieved through interaction with multiple partners, forming a complex network that regulates chromatin folding within the nucleus. In this review, we delve into CTCF's interactions with other molecules involved in epigenetic processes, particularly histone and DNA demethylases, as well as several long non-coding RNAs (lncRNAs) that are able to recruit CTCF. Our review highlights the importance of CTCF partners to shed light on chromatin regulation and pave the way for future exploration of the mechanisms that enable the finely-tuned role of CTCF as a master regulator of chromatin.
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Affiliation(s)
- Aylin Del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, D-22607 Hamburg, Germany
- Computational BioMedicine Lab., University of Southern Denmark, DK-5230 Odense, Denmark
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City 05348, Mexico
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14
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Porter H, Li Y, Neguembor MV, Beltran M, Varsally W, Martin L, Cornejo MT, Pezić D, Bhamra A, Surinova S, Jenner RG, Cosma MP, Hadjur S. Cohesin-independent STAG proteins interact with RNA and R-loops and promote complex loading. eLife 2023; 12:e79386. [PMID: 37010886 PMCID: PMC10238091 DOI: 10.7554/elife.79386] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Most studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in the localization of cohesin to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin, cluster in 3D and interact with CTCF, as well as with a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA, and R-loops, even in the absence of cohesin. Our results place SA1 on chromatin upstream of the cohesin ring and reveal a role for SA1 in cohesin loading which is independent of NIPBL, the canonical cohesin loader. We propose that SA1 takes advantage of structural R-loop platforms to link cohesin loading and chromatin structure with diverse functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease.
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Affiliation(s)
- Hayley Porter
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Yang Li
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Manuel Beltran
- Regulatory Genomics Group, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Wazeer Varsally
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Laura Martin
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Manuel Tavares Cornejo
- Regulatory Genomics Group, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Dubravka Pezić
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Amandeep Bhamra
- Proteomics Research Translational Technology Platform, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Silvia Surinova
- Proteomics Research Translational Technology Platform, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Richard G Jenner
- Regulatory Genomics Group, Cancer Institute, University College LondonLondonUnited Kingdom
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College LondonLondonUnited Kingdom
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15
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Yeo SJ, Ying C, Fullwood MJ, Tergaonkar V. Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains. Trends Genet 2023; 39:217-232. [PMID: 36642680 DOI: 10.1016/j.tig.2022.12.003] [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: 08/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.
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Affiliation(s)
- Samuel Jianjie Yeo
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Singapore 308232, Singapore
| | - Chen Ying
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Pathology and the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore.
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16
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Sarfaraz N, Somarowthu S, Bouchard MJ. The interplay of long noncoding RNAs and hepatitis B virus. J Med Virol 2023; 95:e28058. [PMID: 35946066 DOI: 10.1002/jmv.28058] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 01/11/2023]
Abstract
Hepatitis B Virus (HBV) infections remain a major global health burden with an estimated 296 million people living with a chronic infection and 884,000 HBV-related deaths annually. Notably, patients with a chronic hepatitis B (CHB) infection are at a 30-fold greater risk of developing hepatocellular carcinoma (HCC), the most common type of primary liver cancer, which is the 3rd deadliest cancer worldwide. Several groups have assessed HBV-related aberrant expression of host-cell long noncoding RNAs (lncRNAs) and how altered expression of specific lncRNAs affects HBV replication and progression to associated disease states. Given the challenges in establishing effective HBV models and analyzing transcriptomic data, this review focuses on lncRNA expression data primarily collected from clinical patient samples and primary human hepatocytes, with the subsequent mechanism of action analysis in cell lines or other model systems. Ultimately, understanding HBV-induced lncRNA-expression dysregulation could lead to new treatments and biomarkers for HBV infection and its associated diseases.
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Affiliation(s)
- Nima Sarfaraz
- Graduate Program in Molecular and Cell Biology and Genetics, Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Srinivas Somarowthu
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
| | - Michael J Bouchard
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA
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17
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Valton AL, Venev SV, Mair B, Khokhar ES, Tong AHY, Usaj M, Chan K, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. Nat Struct Mol Biol 2022; 29:1239-1251. [PMID: 36482254 PMCID: PMC10228515 DOI: 10.1038/s41594-022-00890-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 11/01/2022] [Indexed: 12/13/2022]
Abstract
Cohesin-mediated loop extrusion has been shown to be blocked at specific cis-elements, including CTCF sites, producing patterns of loops and domain boundaries along chromosomes. Here we explore such cis-elements, and their role in gene regulation. We find that transcription termination sites of active genes form cohesin- and RNA polymerase II-dependent domain boundaries that do not accumulate cohesin. At these sites, cohesin is first stalled and then rapidly unloaded. Start sites of transcriptionally active genes form cohesin-bound boundaries, as shown before, but are cohesin-independent. Together with cohesin loading, possibly at enhancers, these sites create a pattern of cohesin traffic that guides enhancer-promoter interactions. Disrupting this traffic pattern, by removing CTCF, renders cells sensitive to knockout of genes involved in transcription initiation, such as the SAGA complexes, and RNA processing such DEAD/H-Box RNA helicases. Without CTCF, these factors are less efficiently recruited to active promoters.
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Affiliation(s)
- Anne-Laure Valton
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sergey V Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Barbara Mair
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Eraj Shafiq Khokhar
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amy H Y Tong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Matej Usaj
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Chan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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18
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Battistelli C, Garbo S, Maione R. MyoD-Induced Trans-Differentiation: A Paradigm for Dissecting the Molecular Mechanisms of Cell Commitment, Differentiation and Reprogramming. Cells 2022; 11:3435. [PMID: 36359831 PMCID: PMC9654159 DOI: 10.3390/cells11213435] [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] [Received: 10/09/2022] [Revised: 10/23/2022] [Accepted: 10/28/2022] [Indexed: 10/20/2023] Open
Abstract
The discovery of the skeletal muscle-specific transcription factor MyoD represents a milestone in the field of transcriptional regulation during differentiation and cell-fate reprogramming. MyoD was the first tissue-specific factor found capable of converting non-muscle somatic cells into skeletal muscle cells. A unique feature of MyoD, with respect to other lineage-specific factors able to drive trans-differentiation processes, is its ability to dramatically change the cell fate even when expressed alone. The present review will outline the molecular strategies by which MyoD reprograms the transcriptional regulation of the cell of origin during the myogenic conversion, focusing on the activation and coordination of a complex network of co-factors and epigenetic mechanisms. Some molecular roadblocks, found to restrain MyoD-dependent trans-differentiation, and the possible ways for overcoming these barriers, will also be discussed. Indeed, they are of critical importance not only to expand our knowledge of basic muscle biology but also to improve the generation skeletal muscle cells for translational research.
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Affiliation(s)
| | | | - Rossella Maione
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
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19
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Ward Z, Schmeier S, Pearson J, Cameron VA, Frampton CM, Troughton RW, Doughty RN, Richards AM, Pilbrow AP. Identifying Candidate Circulating RNA Markers for Coronary Artery Disease by Deep RNA-Sequencing in Human Plasma. Cells 2022; 11:3191. [PMID: 36291058 PMCID: PMC9599983 DOI: 10.3390/cells11203191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2023] Open
Abstract
Advances in RNA sequencing (RNA-Seq) have facilitated transcriptomic analysis of plasma for the discovery of new diagnostic and prognostic markers for disease. We aimed to develop a short-read RNA-Seq protocol to detect mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in plasma for the discovery of novel markers for coronary artery disease (CAD) and heart failure (HF). Circulating cell-free RNA from 59 patients with stable CAD (half of whom developed HF within 3 years) and 30 controls was sequenced to a median depth of 108 paired reads per sample. We identified fragments from 3986 messenger RNAs (mRNAs), 164 long non-coding RNAs (lncRNAs), 405 putative novel lncRNAs and 227 circular RNAs in plasma. Circulating levels of 160 mRNAs, 10 lncRNAs and 2 putative novel lncRNAs were altered in patients compared with controls (absolute fold change >1.2, p < 0.01 adjusted for multiple comparisons). The most differentially abundant transcripts were enriched in mRNAs encoded by the mitochondrial genome. We did not detect any differences in the plasma RNA profile between patients who developed HF compared with those who did not. In summary, we show that mRNAs, lncRNAs and circular RNAs can be reliably detected in plasma by deep RNA-Seq. Multiple coding and non-coding transcripts were altered in association with CAD, including several mitochondrial mRNAs, which may indicate underlying myocardial ischaemia and oxidative stress. If validated, circulating levels of these transcripts could potentially be used to help identify asymptomatic individuals with established CAD prior to an acute coronary event.
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Affiliation(s)
- Zoe Ward
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Sebastian Schmeier
- School of Natural and Computational Sciences, Massey University, Auckland 0632, New Zealand
- Evotec SE, Essener Bogen 7, 22419 Hamburg, Germany
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Vicky A Cameron
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Chris M Frampton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Richard W Troughton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Rob N Doughty
- Heart Health Research Group, University of Auckland, Auckland 1023, New Zealand
| | - A. Mark Richards
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
- Cardiovascular Research Institute, National University of Singapore, Singapore 119228, Singapore
| | - Anna P Pilbrow
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
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20
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Dehingia B, Milewska M, Janowski M, Pękowska A. CTCF
shapes chromatin structure and gene expression in health and disease. EMBO Rep 2022; 23:e55146. [PMID: 35993175 PMCID: PMC9442299 DOI: 10.15252/embr.202255146] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/31/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bondita Dehingia
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Małgorzata Milewska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Marcin Janowski
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
| | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology Polish Academy of Sciences Warsaw Poland
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21
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Terrone S, Valat J, Fontrodona N, Giraud G, Claude JB, Combe E, Lapendry A, Polvèche H, Ameur LB, Duvermy A, Modolo L, Bernard P, Mortreux F, Auboeuf D, Bourgeois C. RNA helicase-dependent gene looping impacts messenger RNA processing. Nucleic Acids Res 2022; 50:9226-9246. [PMID: 36039747 PMCID: PMC9458439 DOI: 10.1093/nar/gkac717] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022] Open
Abstract
DDX5 and DDX17 are DEAD-box RNA helicase paralogs which regulate several aspects of gene expression, especially transcription and splicing, through incompletely understood mechanisms. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed the large impact of these RNA helicases on splicing and revealed a widespread deregulation of 3' end processing. In silico analyses and experiments in cultured cells showed the binding and functional contribution of the genome organizing factor CTCF to chromatin sites at or near a subset of DDX5/DDX17-dependent exons that are characterized by a high GC content and a high density of RNA Polymerase II. We propose the existence of an RNA helicase-dependent relationship between CTCF and the dynamics of transcription across DNA and/or RNA structured regions, that contributes to the processing of internal and terminal exons. Moreover, local DDX5/DDX17-dependent chromatin loops spatially connect RNA helicase-regulated exons with their cognate promoter, and we provide the first direct evidence that de novo gene looping modifies alternative splicing and polyadenylation. Overall our findings uncover the impact of DDX5/DDX17-dependent chromatin folding on pre-messenger RNA processing.
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Affiliation(s)
| | | | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Jean-Baptiste Claude
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Hélène Polvèche
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France,CECS/AFM, I-STEM, 28 rue Henri Desbruères, F-91100, Corbeil-Essonnes, France
| | - Lamya Ben Ameur
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Arnaud Duvermy
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Laurent Modolo
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Pascal Bernard
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Cyril F Bourgeois
- To whom correspondence should be addressed. Tel: +33 47272 8663; Fax: +33 47272 8674;
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22
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Bag I, Chen Y, D'Orazio K, Lopez P, Wenzel S, Takagi Y, Lei EP. Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function. G3 (BETHESDA, MD.) 2022; 12:jkac152. [PMID: 35708663 PMCID: PMC9434307 DOI: 10.1093/g3journal/jkac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Chromatin insulators are DNA-protein complexes localized throughout the genome capable of establishing independent transcriptional domains. It was previously reported that the Drosophila su(Hw) mRNA physically associates with the gypsy chromatin insulator protein complex within the nucleus and may serve a noncoding function to affect insulator activity. However, how this mRNA is recruited to the gypsy complex is not known. Here, we utilized RNA-affinity pulldown coupled with mass spectrometry to identify a novel RNA-binding protein, Isha (CG4266), that associates with su(Hw) mRNA in vitro and in vivo. Isha harbors a conserved RNA recognition motif and RNA Polymerase II C-terminal domain-interacting domain (CID). We found that Isha physically interacts with total and elongating Polymerase II and associates with chromatin at the 5' end of genes in an RNA-dependent manner. Furthermore, ChIP-seq analysis reveals Isha overlaps particularly with the core gypsy insulator component CP190 on chromatin. Depletion of Isha reduces enhancer-blocking and barrier activities of the gypsy insulator and disrupts the nuclear localization of insulator bodies. Our results reveal a novel factor Isha that promotes gypsy insulator activity that may act as a nuclear RNA-binding protein adapter for su(Hw) noncoding mRNA.
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Affiliation(s)
- Indira Bag
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yang Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karole D'Orazio
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prisma Lopez
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elissa P Lei
- Corresponding author: Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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23
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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24
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Zhou R, Tian K, Huang J, Duan W, Fu H, Feng Y, Wang H, Jiang Y, Li Y, Wang R, Hu J, Ma H, Qi Z, Ji X. CTCF DNA binding domain undergoes dynamic and selective protein–protein interactions. iScience 2022; 25:105011. [PMID: 36117989 PMCID: PMC9474293 DOI: 10.1016/j.isci.2022.105011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/13/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
CTCF is a predominant insulator protein required for three-dimensional chromatin organization. However, the roles of its insulation of enhancers in a 3D nuclear organization have not been fully explained. Here, we found that the CTCF DNA-binding domain (DBD) forms dynamic self-interacting clusters. Strikingly, CTCF DBD clusters were found to incorporate other insulator proteins but are not coenriched with transcriptional activators in the nucleus. This property is not observed in other domains of CTCF or the DBDs of other transcription factors. Moreover, endogenous CTCF shows a phenotype consistent with the DBD by forming small protein clusters and interacting with CTCF motif arrays that have fewer transcriptional activators bound. Our results reveal an interesting phenomenon in which CTCF DBD interacts with insulator proteins and selectively localizes to nuclear positions with lower concentrations of transcriptional activators, providing insights into the insulation function of CTCF. The CTCF DNA-binding domain forms protein clusters in vivo and in vitro CTCF DBD clusters colocalize with insulator proteins but not with activators Arginine residues of CTCF DBD are frequently mutated in cancers Multiple transcription factor DBDs form protein clusters
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25
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Regulation of Sox8 through lncRNA Mrhl-Mediated Chromatin Looping in Mouse Spermatogonia. Mol Cell Biol 2022; 42:e0047521. [PMID: 35412350 DOI: 10.1128/mcb.00475-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sox8 is a developmentally important transcription factor that plays an important role in sex maintenance and fertility of adult mice. In the B-type spermatogonial cells, Sox8 is regulated by the long noncoding RNAs (lncRNA) Mrhl in a p68-dependant manner under the control of the Wnt signaling pathway. The downregulation of Mrhl leads to the meiotic commitment of the spermatogonial cells in a Sox8-dependant manner. While the molecular players involved in the regulation of transcription at the Sox8 promoter have been worked out, our current study points to the involvement of the architectural proteins CTCF and cohesin in mediating a chromatin loop that brings the Sox8 promoter in contact with a silencer element present within the gene body in the presence of lncRNA Mrhl concomitant with transcriptional repression. Further, lncRNA Mrhl interacts with the Sox8 locus through the formation of a DNA:DNA:RNA triplex, which is necessary for the recruitment of PRC2 to the locus. The downregulation of lncRNA Mrhl results in the promoter-silencer loop giving way to a promoter-enhancer loop. This active transcription-associated chromatin loop is mediated by YY1 and brings the promoter in contact with the enhancer present downstream of the gene.
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26
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Song Y, Liang Z, Zhang J, Hu G, Wang J, Li Y, Guo R, Dong X, Babarinde IA, Ping W, Sheng YL, Li H, Chen Z, Gao M, Chen Y, Shan G, Zhang MQ, Hutchins AP, Fu XD, Yao H. CTCF functions as an insulator for somatic genes and a chromatin remodeler for pluripotency genes during reprogramming. Cell Rep 2022; 39:110626. [PMID: 35385732 DOI: 10.1016/j.celrep.2022.110626] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/13/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
CTCF mediates chromatin insulation and long-distance enhancer-promoter (EP) interactions; however, little is known about how these regulatory functions are partitioned among target genes in key biological processes. Here, we show that Ctcf expression is progressively increased during induced pluripotency. In this process, CTCF first functions as a chromatin insulator responsible for direct silencing of the somatic gene expression program and, interestingly, elevated Ctcf expression next ensures chromatin accessibility and contributes to increased EP interactions for a fraction of pluripotency-associated genes. Therefore, CTCF functions in a context-specific manner to modulate the 3D genome to enable cellular reprogramming. We further discover that these context-specific CTCF functions also enlist SMARCA5, an imitation switch (ISWI) chromatin remodeler, together rewiring the epigenome to facilitate cell-fate switch. These findings reveal the dual functions of CTCF in conjunction with a key chromatin remodeler to drive reprogramming toward pluripotency.
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Affiliation(s)
- Yawei Song
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jie Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Juehan Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyi Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Isaac A Babarinde
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wangfang Ping
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Liang Sheng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Huanhuan Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
| | - Zhaoming Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China
| | - Minghui Gao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ge Shan
- Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing 100084, China; Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX 75080-3021, USA
| | - Andrew P Hutchins
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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27
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Cummings CT, Rowley MJ. Implications of Dosage Deficiencies in CTCF and Cohesin on Genome Organization, Gene Expression, and Human Neurodevelopment. Genes (Basel) 2022; 13:583. [PMID: 35456389 PMCID: PMC9030571 DOI: 10.3390/genes13040583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Properly organizing DNA within the nucleus is critical to ensure normal downstream nuclear functions. CTCF and cohesin act as major architectural proteins, working in concert to generate thousands of high-intensity chromatin loops. Due to their central role in loop formation, a massive research effort has been dedicated to investigating the mechanism by which CTCF and cohesin create these loops. Recent results lead to questioning the direct impact of CTCF loops on gene expression. Additionally, results of controlled depletion experiments in cell lines has indicated that genome architecture may be somewhat resistant to incomplete deficiencies in CTCF or cohesin. However, heterozygous human genetic deficiencies in CTCF and cohesin have illustrated the importance of their dosage in genome architecture, cellular processes, animal behavior, and disease phenotypes. Thus, the importance of considering CTCF or cohesin levels is especially made clear by these heterozygous germline variants that characterize genetic syndromes, which are increasingly recognized in clinical practice. Defined primarily by developmental delay and intellectual disability, the phenotypes of CTCF and cohesin deficiency illustrate the importance of architectural proteins particularly in neurodevelopment. We discuss the distinct roles of CTCF and cohesin in forming chromatin loops, highlight the major role that dosage of each protein plays in the amplitude of observed effects on gene expression, and contrast these results to heterozygous mutation phenotypes in murine models and clinical patients. Insights highlighted by this comparison have implications for future research into these newly emerging genetic syndromes.
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Affiliation(s)
- Christopher T. Cummings
- Munroe-Meyer Institute, Department of Genetic Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - M. Jordan Rowley
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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28
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Luo H, Zhu G, Eshelman MA, Fung TK, Lai Q, Wang F, Zeisig BB, Lesperance J, Ma X, Chen S, Cesari N, Cogle C, Chen B, Xu B, Yang FC, So CWE, Qiu Y, Xu M, Huang S. HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia. Mol Cell 2022; 82:833-851.e11. [PMID: 35180428 PMCID: PMC8985430 DOI: 10.1016/j.molcel.2022.01.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/29/2021] [Accepted: 01/19/2022] [Indexed: 01/09/2023]
Abstract
HOTTIP lncRNA is highly expressed in acute myeloid leukemia (AML) driven by MLL rearrangements or NPM1 mutations to mediate HOXA topologically associated domain (TAD) formation and drive aberrant transcription. However, the mechanism through which HOTTIP accesses CCCTC-binding factor (CTCF) chromatin boundaries and regulates CTCF-mediated genome topology remains unknown. Here, we show that HOTTIP directly interacts with and regulates a fraction of CTCF-binding sites (CBSs) in the AML genome by recruiting CTCF/cohesin complex and R-loop-associated regulators to form R-loops. HOTTIP-mediated R-loops reinforce the CTCF boundary and facilitate formation of TADs to drive gene transcription. Either deleting CBS or targeting RNase H to eliminate R-loops in the boundary CBS of β-catenin TAD impaired CTCF boundary activity, inhibited promoter/enhancer interactions, reduced β-catenin target expression, and mitigated leukemogenesis in xenograft mouse models with aberrant HOTTIP expression. Thus, HOTTIP-mediated R-loop formation directly reinforces CTCF chromatin boundary activity and TAD integrity to drive oncogene transcription and leukemia development.
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MESH Headings
- Animals
- CCCTC-Binding Factor/genetics
- CCCTC-Binding Factor/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Line, Tumor
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Gene Expression Regulation, Leukemic
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice, Transgenic
- R-Loop Structures
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Structure-Activity Relationship
- Transcription, Genetic
- Transcriptional Activation
- beta Catenin/genetics
- beta Catenin/metabolism
- Cohesins
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Affiliation(s)
- Huacheng Luo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ganqian Zhu
- Department of Molecular Medicine, the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3904, USA
| | - Melanie A Eshelman
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Tsz Kan Fung
- School of Cancer and Pharmaceutical Science, King's College London, London SE5 9NU, UK; Department of Haematological Medicine, King's College Hospital, London SE5 9RS, UK
| | - Qian Lai
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Fei Wang
- Department of Hematology and Oncology, The Affiliated Zhongda Hospital, Southeast University Medical School, Nanjing 21009, China
| | - Bernd B Zeisig
- School of Cancer and Pharmaceutical Science, King's College London, London SE5 9NU, UK; Department of Haematological Medicine, King's College Hospital, London SE5 9RS, UK
| | - Julia Lesperance
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Xiaoyan Ma
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Department of Hematology and Oncology, The Affiliated Zhongda Hospital, Southeast University Medical School, Nanjing 21009, China
| | - Shi Chen
- Department of Molecular Medicine, the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3904, USA
| | - Nicholas Cesari
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Christopher Cogle
- Division of Hematology/Oncology, Department of Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Baoan Chen
- Department of Hematology and Oncology, The Affiliated Zhongda Hospital, Southeast University Medical School, Nanjing 21009, China
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Feng-Chun Yang
- Department of Cell System & Anatomy, the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3904, USA; Mays Cancer Center, Joe R. & Teresa Lozano Long School of Medicine, the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3904, USA
| | - Chi Wai Eric So
- School of Cancer and Pharmaceutical Science, King's College London, London SE5 9NU, UK; Department of Haematological Medicine, King's College Hospital, London SE5 9RS, UK.
| | - Yi Qiu
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Mingjiang Xu
- Department of Molecular Medicine, the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3904, USA; Department of Cell System & Anatomy, the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3904, USA.
| | - Suming Huang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
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Suthapot P, Xiao T, Felsenfeld G, Hongeng S, Wongtrakoongate P. The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2. Life Sci 2022; 291:120298. [PMID: 35007564 DOI: 10.1016/j.lfs.2021.120298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 12/31/2022]
Abstract
AIMS Understanding human neurogenesis is critical toward regenerative medicine for neurodegeneration. However, little is known how neural differentiation is regulated by DEAD box-containing RNA helicases, which comprise a diverse class of RNA remodeling enzymes. MATERIALS AND METHODS ChIP-seq was utilized to identify binding sites of DDX5 and DDX17 in both human pluripotent stem cell (hPSC) line NTERA2 and their retinoic acid-induced neural derivatives. RNA-seq was used to elucidate genes differentially expressed upon depletion of DDX5 and DDX17. Neurosphere assay, flow cytometry, and immunofluorescence staining were performed to test the effect of depletion of the two RNA helicases in neural differentiation. KEY FINDINGS We show here that expression of DDX5 and DDX17 is abundant throughout neural differentiation of NTERA2, and is mostly localized within the nucleus. The two RNA helicases occupy chromatin genome-wide at regions associated with neurogenesis-related genes in both hPSCs and their neural derivatives. Further, both DDX5 and DDX17 are mutually required for controlling transcriptional expression of these genes, but are not important for maintenance of stem cell state of hPSCs. In contrast, they facilitate early neural differentiation of hPSCs, generation of neurospheres from the stem cells, and transcriptional expression of key neurogenic transcription factors such as SOX1 and PAX6 during neural differentiation. Importantly, DDX5 and DDX17 are critical for differentiation of hPSCs toward NESTIN- and TUBB3-positive cells, which represent neural progenitors and mature neurons, respectively. SIGNIFICANCE Collectively, our findings suggest the role of DDX5 and DDX17 in transcriptional regulation of genes involved in neurogenesis, and hence in neural differentiation of hPSCs.
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Affiliation(s)
- Praewa Suthapot
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tiaojiang Xiao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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30
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Hu DX, Sun QF, Xu L, Lu HD, Zhang F, Li ZM, Zhang MY. Knockdown of DEAD-box 51 inhibits tumor growth of esophageal squamous cell carcinoma via the PI3K/AKT pathway. World J Gastroenterol 2022; 28:464-478. [PMID: 35125830 PMCID: PMC8790558 DOI: 10.3748/wjg.v28.i4.464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 11/15/2021] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies that seriously threaten people’s health worldwide. DEAD-box helicase 51 (DDX51) is a member of the DEAD-box (DDX) RNA helicase family, and drives or inhibits tumor progression in multiple cancer types.
AIM To determine whether DDX51 affects the biological behavior of ESCC.
METHODS The expression of DDX51 in ESCC tumor tissues and adjacent normal tissues was detected by Immunohistochemistry (IHC) analyses and quantitative PCR (qPCR). We knocked down DDX51 in ESCC cell lines by using a small interfering RNA (siRNA) transfection. The proliferation, apoptosis, and mobility of DDX51 siRNA-transfected cells were detected. The effect of DDX51 on the phosphoinositide 3-kinase (PI3K)/AKT pathway was investigated by western blot analysis. A mouse xenograft model was established to investigate the effects of DDX51 knockdown on ESCC tumor growth.
RESULTS DDX51 exhibited high expression in ESCC tissues compared with normal tissues and represented a poor prognosis in patients with ESCC. Knockdown of DDX51 induced inhibition of ESCC cell proliferation and promoted apoptosis. Moreover, DDX51 siRNA-expressing cells also exhibited lower migration and invasion rates. Investigations into the underlying mechanisms suggested that DDX51 knockdown induced inactivation of the PI3K/AKT pathway, including decreased phosphorylation levels of phosphate and tensin homolog, PI3K, AKT, and mammalian target of rapamycin. Rescue experiments demonstrated that the AKT activator insulin-like growth factor 1 could reverse the inhibitory effects of DDX51 on ESCC malignant development. Finally, we injected DDX51 siRNA-transfected TE-1 cells into an animal model, which resulted in slower tumor growth.
CONCLUSION Our study suggests for the first time that DDX51 promotes cancer cell proliferation by regulating the PI3K/AKT pathway; thus, DDX51 might be a therapeutic target for ESCC.
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Affiliation(s)
- Dong-Xin Hu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Qi-Feng Sun
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Lin Xu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Hong-Da Lu
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Fan Zhang
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Zhen-Miao Li
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Ming-Yan Zhang
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
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Sanbonmatsu K. Towards Molecular Mechanism in Long Non-coding RNAs: Linking Structure and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:23-32. [DOI: 10.1007/978-3-030-92034-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2021; 33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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Long noncoding RNAs: Emerging regulators of normal and malignant hematopoiesis. Blood 2021; 138:2327-2336. [PMID: 34482397 DOI: 10.1182/blood.2021011992] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/13/2021] [Indexed: 11/20/2022] Open
Abstract
Genome wide analyses have revealed that long-noncoding RNAs (lncRNAs) are not only passive transcription products, but also major regulators of genome structure and transcription. In particular, lncRNAs exert profound effects on various biological processes, such as chromatin structure, transcription, RNA stability and translation, and protein degradation and localization, which depend on their localization and interacting partners. Recent studies have revealed that thousands of lncRNAs are aberrantly expressed in various cancer types and some of them are associated with malignant transformation. Despite extensive efforts, the diverse functions of lncRNAs and molecular mechanisms in which they act remain elusive. Many hematological disorders and malignancies are primarily resulted from genetic alterations that lead to the dysregulation of gene regulatory networks required for cellular proliferation and differentiation. Consequently, a growing list of lncRNAs has been reported for their involvement in the modulation of hematopoietic gene expression networks and hematopoietic stem and progenitor cell (HS/PC) function. Dysregulation of some of these lncRNAs has been attributed to pathogenesis of hematological malignancies. In this review, we will summarize current advances and knowledge of lncRNAs in gene regulation, focusing on the recent progresses on the role of lncRNAs in CTCF/cohesin mediated three-dimensional (3D) genome organization, and how such genome folding signals in turn regulate transcription, HS/PC function and transformation. The knowledge will provide mechanistic and translational insights into HS/PC biology and myeloid malignancy pathophysiology.
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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35
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The DEAD-box protein family of RNA helicases: sentinels for a myriad of cellular functions with emerging roles in tumorigenesis. Int J Clin Oncol 2021; 26:795-825. [PMID: 33656655 DOI: 10.1007/s10147-021-01892-1] [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: 12/07/2020] [Accepted: 02/20/2021] [Indexed: 02/06/2023]
Abstract
DEAD-box RNA helicases comprise a family within helicase superfamily 2 and make up the largest group of RNA helicases. They are a profoundly conserved family of RNA-binding proteins, carrying a generic Asp-Glu-Ala-Asp (D-E-A-D) motif that gives the family its name. Members of the DEAD-box family of RNA helicases are engaged in all facets of RNA metabolism from biogenesis to decay. DEAD-box proteins ordinarily function as constituents of enormous multi-protein complexes and it is believed that interactions with other components in the complexes might be answerable for the various capacities ascribed to these proteins. Therefore, their exact function is probably impacted by their interacting partners and to be profoundly context dependent. This may give a clarification to the occasionally inconsistent reports proposing that DEAD-box proteins have both pro- and anti-proliferative functions in cancer. There is emerging evidence that DEAD-box family of RNA helicases play pivotal functions in various cellular processes and in numerous cases have been embroiled in cellular proliferation and/or neoplastic transformation. In various malignancy types, DEAD-box RNA helicases have been reported to possess pro-proliferation or even oncogenic roles as well as anti-proliferative or tumor suppressor functions. Clarifying the exact function of DEAD-box helicases in cancer is probably intricate, and relies upon the cellular milieu and interacting factors. This review aims to summarize the current data on the numerous capacities that have been ascribed to DEAD-box RNA helicases. It also highlights their diverse actions upon malignant transformation in the various tumor types.
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36
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Maksimenko OG, Fursenko DV, Belova EV, Georgiev PG. CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers. Acta Naturae 2021; 13:31-46. [PMID: 33959385 PMCID: PMC8084297 DOI: 10.32607/actanaturae.11206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.
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Affiliation(s)
- O. G. Maksimenko
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
| | | | - E. V. Belova
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
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Ramírez-Colmenero A, Oktaba K, Fernandez-Valverde SL. Evolution of Genome-Organizing Long Non-coding RNAs in Metazoans. Front Genet 2020; 11:589697. [PMID: 33329735 PMCID: PMC7734150 DOI: 10.3389/fgene.2020.589697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 12/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have important regulatory functions across eukarya. It is now clear that many of these functions are related to gene expression regulation through their capacity to recruit epigenetic modifiers and establish chromatin interactions. Several lncRNAs have been recently shown to participate in modulating chromatin within the spatial organization of the genome in the three-dimensional space of the nucleus. The identification of lncRNA candidates is challenging, as it is their functional characterization. Conservation signatures of lncRNAs are different from those of protein-coding genes, making identifying lncRNAs under selection a difficult task, and the homology between lncRNAs may not be readily apparent. Here, we review the evidence for these higher-order genome organization functions of lncRNAs in animals and the evolutionary signatures they display.
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Affiliation(s)
- América Ramírez-Colmenero
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Katarzyna Oktaba
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
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38
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A long noncoding RNA, LncMyoD, modulates chromatin accessibility to regulate muscle stem cell myogenic lineage progression. Proc Natl Acad Sci U S A 2020; 117:32464-32475. [PMID: 33293420 PMCID: PMC7768704 DOI: 10.1073/pnas.2005868117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic regulations control the accessibility of transcription factors to their target regions. Modulation of chromatin accessibility determines which transcripts to be expressed and therefore, defines cell identity. Chromatin modulation during cell fate determination involves a complex regulatory network, yet the comprehensive view remains to be explored. Here, we provide a global view of chromatin accessibility during muscle stem cell activation. We identified a long noncoding RNA (lncRNA), LncMyoD, which regulates lineage determination and progression through modulating chromatin accessibility. Functional analysis showed that loss of LncMyoD strongly impairs reprogramming of fibroblasts into myogenic lineage and causes defects in muscle stem cell differentiation. Our findings provide an epigenetic mechanism for the regulation of muscle stem cell myogenic lineage progression by an lncRNA. Epigenetics regulation plays a critical role in determining cell identity by controlling the accessibility of lineage-specific regulatory regions. In muscle stem cells, epigenetic mechanisms of how chromatin accessibility is modulated during cell fate determination are not fully understood. Here, we identified a long noncoding RNA, LncMyoD, that functions as a chromatin modulator for myogenic lineage determination and progression. The depletion of LncMyoD in muscle stem cells led to the down-regulation of myogenic genes and defects in myogenic differentiation. LncMyoD exclusively binds with MyoD and not with other myogenic regulatory factors and promotes transactivation of target genes. The mechanistic study revealed that loss of LncMyoD prevents the establishment of a permissive chromatin environment at myogenic E-box–containing regions, therefore restricting the binding of MyoD. Furthermore, the depletion of LncMyoD strongly impairs the reprogramming of fibroblasts into the myogenic lineage. Taken together, our study shows that LncMyoD associates with MyoD and promotes myogenic gene expression through modulating MyoD accessibility to chromatin, thereby regulating myogenic lineage determination and progression.
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39
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Sawaengdee W, Cui K, Zhao K, Hongeng S, Fucharoen S, Wongtrakoongate P. Genome-Wide Transcriptional Regulation of the Long Non-coding RNA Steroid Receptor RNA Activator in Human Erythroblasts. Front Genet 2020; 11:850. [PMID: 32849830 PMCID: PMC7431964 DOI: 10.3389/fgene.2020.00850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/13/2020] [Indexed: 01/21/2023] Open
Abstract
Erythropoiesis of human hematopoietic stem cells (HSCs) maintains generation of red blood cells throughout life. However, little is known how human erythropoiesis is regulated by long non-coding RNAs (lncRNAs). By using ChIRP-seq, we report here that the lncRNA steroid receptor RNA activator (SRA) occupies chromatin, and co-localizes with CTCF, H3K4me3, and H3K27me3 genome-wide in human erythroblast cell line K562. CTCF binding sites that are also occupied by SRA are enriched for either H3K4me3 or H3K27me3. Transcriptome-wide analyses reveal that SRA facilitates expression of erythroid-associated genes, while repressing leukocyte-associated genes in both K562 and CD36-positive primary human proerythroblasts derived from HSCs. We find that SRA-regulated genes are enriched by both CTCF and SRA bindings. Further, silencing of SRA decreases expression of the erythroid-specific markers TFRC and GYPA, and down-regulates expression of globin genes in both K562 and human proerythroblast cells. Taken together, our findings establish that the lncRNA SRA occupies chromatin, and promotes transcription of erythroid genes, therefore facilitating human erythroid transcriptional program.
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Affiliation(s)
- Waritta Sawaengdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kairong Cui
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, Thailand
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40
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Xing Z, Russon MP, Utturkar SM, Tran EJ. The RNA helicase DDX5 supports mitochondrial function in small cell lung cancer. J Biol Chem 2020; 295:8988-8998. [PMID: 32376686 PMCID: PMC7335798 DOI: 10.1074/jbc.ra120.012600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/23/2020] [Indexed: 11/06/2022] Open
Abstract
DEAD-box helicase 5 (DDX5) is a founding member of the DEAD-box RNA helicase family, a group of enzymes that regulate ribonucleoprotein formation and function in every aspect of RNA metabolism, ranging from synthesis to decay. Our laboratory previously found that DDX5 is involved in energy homeostasis, a process that is altered in many cancers. Small cell lung cancer (SCLC) is an understudied cancer type for which effective treatments are currently unavailable. Using an array of methods, including short hairpin RNA-mediated gene silencing, RNA and ChIP sequencing analyses, and metabolite profiling, we show here that DDX5 is overexpressed in SCLC cell lines and that its down-regulation results in various metabolic and cellular alterations. Depletion of DDX5 resulted in reduced growth and mitochondrial dysfunction in the chemoresistant SCLC cell line H69AR. The latter was evidenced by down-regulation of genes involved in oxidative phosphorylation and by impaired oxygen consumption. Interestingly, DDX5 depletion specifically reduced intracellular succinate, a TCA cycle intermediate that serves as a direct electron donor to mitochondrial complex II. We propose that the oncogenic role of DDX5, at least in part, manifests as up-regulation of respiration supporting the energy demands of cancer cells.
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Affiliation(s)
- Zheng Xing
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Matthew P Russon
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Sagar M Utturkar
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA.
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Ruiz Buendía GA, Leleu M, Marzetta F, Vanzan L, Tan JY, Ythier V, Randall EL, Marques AC, Baubec T, Murr R, Xenarios I, Dion V. Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion. SCIENCE ADVANCES 2020; 6:eaaz4012. [PMID: 32656337 PMCID: PMC7334000 DOI: 10.1126/sciadv.aaz4012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Expanded CAG/CTG repeats underlie 13 neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Upon expansion, disease loci acquire heterochromatic characteristics, which may provoke changes to chromatin conformation and thereby affect both gene expression and repeat instability. Here, we tested this hypothesis by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD-derived cells. We find that allele sizes ranging from 15 to 1700 repeats displayed similar chromatin interaction profiles. This was true for both loci and for alleles with different DNA methylation levels and CTCF binding. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the conformation of the surrounding chromatin. We conclude that CAG/CTG repeat expansions are not enough to alter chromatin conformation in cis. Therefore, it is unlikely that changes in chromatin interactions drive repeat instability or changes in gene expression in these disorders.
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Affiliation(s)
- Gustavo A. Ruiz Buendía
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Flavia Marzetta
- Vital-IT Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ludovica Vanzan
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Jennifer Y. Tan
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Victor Ythier
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Emma L. Randall
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
| | - Ana C. Marques
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Rabih Murr
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Dion
- UK Dementia Research Institute at Cardiff University at Cardiff University, Hadyn Ellis Building, Maindy Road, CF24 4HQ Cardiff, UK
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42
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Qiu Y, Huang S. CTCF-mediated genome organization and leukemogenesis. Leukemia 2020; 34:2295-2304. [PMID: 32518417 DOI: 10.1038/s41375-020-0906-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/13/2022]
Abstract
Recent technological advancements and genome-wide studies provide compelling evidence that dynamic chromatin interaction and three-dimensional genome organization in nuclei play an important role in regulating gene expression. Mammalian genomes consist of many small functional domains termed topologically associated domains (TADs), many of them organized by CCCTC-binding factor (CTCF) and the cohesion complex. Changes in genome TADs might result in inappropriate promoter/enhancer communications leading to activation of oncogenes or suppression of tumor suppressors. During normal hematopoiesis and leukemogenesis, genome structure alters considerably to facilitate normal and malignant hematopoiesis, respectively. Delineating theses normal and abnormal processes will evolve our understanding of disease pathogenesis and development of potential treatment strategies. This review highlights the role of CTCF and its associated protein complexes in three-dimensional genome organization in development and leukemogenesis, as well as the roles of CTCF boundary defined TAD in transcription regulation. We further explore the function of chromatin modulators, such as CTCF, cohesin, and long noncoding RNAs (lncRNAs) in chromosomal interactions and hematopoietic genome organization. Finally, we focus on the implication of 3D genome alteration in the pathogenesis of leukemia and provide a scientific basis for targeted intervention.
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Affiliation(s)
- Yi Qiu
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, 16033, USA. .,Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA, 16033, USA.
| | - Suming Huang
- Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA, 16033, USA. .,Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, 16033, USA.
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43
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Li Y, Liao Z, Luo H, Benyoucef A, Kang Y, Lai Q, Dovat S, Miller B, Chepelev I, Li Y, Zhao K, Brand M, Huang S. Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis. Nucleic Acids Res 2020; 48:3119-3133. [PMID: 32086528 PMCID: PMC7102946 DOI: 10.1093/nar/gkaa098] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/23/2022] Open
Abstract
Aberrant activation of the TAL1 is associated with up to 60% of T-ALL cases and is involved in CTCF-mediated genome organization within the TAL1 locus, suggesting that CTCF boundary plays a pathogenic role in T-ALL. Here, we show that -31-Kb CTCF binding site (-31CBS) serves as chromatin boundary that defines topologically associating domain (TAD) and enhancer/promoter interaction required for TAL1 activation. Deleted or inverted -31CBS impairs TAL1 expression in a context-dependent manner. Deletion of -31CBS reduces chromatin accessibility and blocks long-range interaction between the +51 erythroid enhancer and TAL1 promoter-1 leading to inhibition of TAL1 expression in erythroid cells, but not T-ALL cells. However, in TAL1-expressing T-ALL cells, the leukemia-prone TAL1 promoter-IV specifically interacts with the +19 stem cell enhancer located 19 Kb downstream of TAL1 and this interaction is disrupted by the -31CBS inversion in T-ALL cells. Inversion of -31CBS in Jurkat cells alters chromatin accessibility, histone modifications and CTCF-mediated TAD leading to inhibition of TAL1 expression and TAL1-driven leukemogenesis. Thus, our data reveal that -31CBS acts as critical regulator to define +19-enhancer and the leukemic prone promoter IV interaction for TAL1 activation in T-ALL. Manipulation of CTCF boundary can alter TAL1 TAD and oncogenic transcription networks in leukemogenesis.
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Affiliation(s)
- Ying Li
- Department of Pediatrics and Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ziwei Liao
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA.,Institute of Hematology, Jinan University Medical College, ShiPai, Guangzhou, 510632, China
| | - Huacheng Luo
- Department of Pediatrics and Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Aissa Benyoucef
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada
| | - Yuanyuan Kang
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Qian Lai
- Department of Pediatrics and Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Sinisa Dovat
- Department of Pediatrics and Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Barbara Miller
- Department of Pediatrics and Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Iouri Chepelev
- Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20814, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yangqiu Li
- Institute of Hematology, Jinan University Medical College, ShiPai, Guangzhou, 510632, China
| | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20814, USA
| | - Marjorie Brand
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada
| | - Suming Huang
- Department of Pediatrics and Pharmacology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, FL 32610, USA
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44
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Guay C, Abdulkarim B, Tan JY, Dubuis G, Rütti S, Laybutt DR, Widmann C, Regazzi R, Marques AC. Loss-of-function of the long non-coding RNA A830019P07Rik in mice does not affect insulin expression and secretion. Sci Rep 2020; 10:6413. [PMID: 32286361 PMCID: PMC7156487 DOI: 10.1038/s41598-020-62969-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/19/2020] [Indexed: 12/03/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) contribute to diverse cellular functions and the dysregulation of their expression or function can contribute to diseases, including diabetes. The contributions of lncRNAs to β-cell development, function and survival has been extensively studied in vitro. However, very little is currently known on the in vivo roles of lncRNAs in the regulation of glucose and insulin homeostasis. Here we investigated the impact of loss-of-function in mice of the lncRNA A830019P07Rik, hereafter P07Rik, which was previously reported to be associated with reduced plasma insulin levels. Compared with wild-type littermates, male and female P07Rik mutant mice did not show any defect in glycaemia and plasma insulin levels in both fed and fasted state. Furthermore, P07Rik mutant mice displayed similar glucose and insulin levels in response to an intra-peritoneal glucose tolerance test. Ex vivo, islets from mutant P07Rik released similar amount of insulin in response to increased glucose concentration as wildtype littermates. In contrast with previous reports, our characterization of P07Rik mouse mutants revealed that loss of function of this lncRNA does not affect glucose and insulin homeostasis in mice.
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Affiliation(s)
- Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Baroj Abdulkarim
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Jennifer Y Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Gilles Dubuis
- Department of Physiology, University of Lausanne, Lausanne, Switzerland
| | - Sabine Rütti
- Department of Physiology, University of Lausanne, Lausanne, Switzerland.,Centre Européen d'Etude du Diabète, Strasbourg, France
| | - David Ross Laybutt
- Garvan Institute of Medical Research, St. Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Christian Widmann
- Department of Physiology, University of Lausanne, Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Ana Claudia Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
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45
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Noordermeer D, Feil R. Differential 3D chromatin organization and gene activity in genomic imprinting. Curr Opin Genet Dev 2020; 61:17-24. [PMID: 32299027 DOI: 10.1016/j.gde.2020.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 01/08/2023]
Abstract
Genomic imprinting gives rise to parent-of-origin dependent allelic gene expression. Most imprinted genes cluster in domains where differentially methylated regions (DMRs)-carrying CpG methylation on one parental allele-regulate their activity. Several imprinted DMRs bind CTCF on the non-methylated allele. CTCF structures TADs ('Topologically Associating Domains'), which are structural units of transcriptional regulation. Recent investigations show that imprinted domains are embedded within TADs that are similar on both parental chromosomes. Within these TADs, however, allelic subdomains are structured by combinations of mono-allelic and bi-allelic CTCF binding that guide imprinted expression. This emerging view indicates that imprinted chromosomal domains should be considered at the overarching TAD level, and questions how CTCF integrates with other regulatory proteins and lncRNAs to achieve imprinted transcriptional programs.
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Affiliation(s)
- Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France.
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46
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Guh CY, Hsieh YH, Chu HP. Functions and properties of nuclear lncRNAs-from systematically mapping the interactomes of lncRNAs. J Biomed Sci 2020; 27:44. [PMID: 32183863 PMCID: PMC7079490 DOI: 10.1186/s12929-020-00640-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
Protein and DNA have been considered as the major components of chromatin. But beyond that, an increasing number of studies show that RNA occupies a large amount of chromatin and acts as a regulator of nuclear architecture. A significant fraction of long non-coding RNAs (lncRNAs) prefers to stay in the nucleus and cooperate with protein complexes to modulate epigenetic regulation, phase separation, compartment formation, and nuclear organization. An RNA strand also can invade into double-stranded DNA to form RNA:DNA hybrids (R-loops) in living cells, contributing to the regulation of gene expression and genomic instability. In this review, we discuss how nuclear lncRNAs orchestrate cellular processes through their interactions with proteins and DNA and summarize the recent genome-wide techniques to study the functions of lncRNAs by revealing their interactomes in vivo.
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Affiliation(s)
- Chia-Yu Guh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Yu-Hung Hsieh
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China
| | - Hsueh-Ping Chu
- Institute of Molecular and Cellular Biology, National Taiwan University, No. 1 Sec. 4 Roosevelt Road, Taipei, Taiwan, Republic of China.
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47
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Hansen AS, Hsieh THS, Cattoglio C, Pustova I, Saldaña-Meyer R, Reinberg D, Darzacq X, Tjian R. Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. Mol Cell 2019; 76:395-411.e13. [PMID: 31522987 PMCID: PMC7251926 DOI: 10.1016/j.molcel.2019.07.039] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/16/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Abstract
Mammalian genomes are folded into topologically associating domains (TADs), consisting of chromatin loops anchored by CTCF and cohesin. Some loops are cell-type specific. Here we asked whether CTCF loops are established by a universal or locus-specific mechanism. Investigating the molecular determinants of CTCF clustering, we found that CTCF self-association in vitro is RNase sensitive and that an internal RNA-binding region (RBRi) mediates CTCF clustering and RNA interaction in vivo. Strikingly, deleting the RBRi impairs about half of all chromatin loops in mESCs and causes deregulation of gene expression. Disrupted loop formation correlates with diminished clustering and chromatin binding of RBRi mutant CTCF, which in turn results in a failure to halt cohesin-mediated extrusion. Thus, CTCF loops fall into at least two classes: RBRi-independent and RBRi-dependent loops. We speculate that evidence for RBRi-dependent loops may provide a molecular mechanism for establishing cell-specific CTCF loops, potentially regulated by RNA(s) or other RBRi-interacting partners.
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Affiliation(s)
- Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Tsung-Han S Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Iryna Pustova
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ricardo Saldaña-Meyer
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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48
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Dai X, Kaushik AC, Zhang J. The Emerging Role of Major Regulatory RNAs in Cancer Control. Front Oncol 2019; 9:920. [PMID: 31608229 PMCID: PMC6771296 DOI: 10.3389/fonc.2019.00920] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Alterations and personal variations of RNA interactions have been mechanistically coupled with disease etiology and phenotypical variations. RNA biomarkers, RNA mimics, and RNA antagonists have been developed for diagnostic, prognostic, and therapeutic uses. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are two major types of RNA molecules with regulatory roles, deregulation of which has been implicated in the initiation and progression of many human malignancies. Accumulating evidence indicated the clinical roles of regulatory RNAs in cancer control, stimulating a surge in exploring the functionalities of regulatory RNAs for improved understanding on disease pathogenesis and management. In this review, we highlight the critical roles of lncRNAs and miRNAs played in tumorigenesis, scrutinize their potential functionalities as diagnostic/prognostic biomarkers and/or therapeutic targets in clinics, outline opportunities that ncRNAs may bring to complement current clinical practice for improved cancer management and identify challenges faced by translating frontier knowledge on non-coding RNAs (ncRNAs) to bedside clinics as well as possible solutions.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Aman Chandra Kaushik
- Wuxi School of Medicine, Jiangnan University, Wuxi, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianying Zhang
- Henan Key Laboratory of Tumor Epidemiology, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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49
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DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation. Proc Natl Acad Sci U S A 2019; 116:20453-20461. [PMID: 31548374 DOI: 10.1073/pnas.1909047116] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4) are noncanonical secondary structures formed in guanine-rich DNA and RNA sequences. MYC, one of the most critical oncogenes, forms a DNA G4 in its proximal promoter region (MycG4) that functions as a transcriptional silencer. However, MycG4 is highly stable in vitro and its regulatory role would require active unfolding. Here we report that DDX5, one of the founding members of the DEAD-box RNA helicase family, is extremely proficient at unfolding MycG4-DNA. Our results show that DDX5 is a highly active G4-resolvase that does not require a single-stranded overhang and that ATP hydrolysis is not directly coupled to G4-unfolding of DDX5. The chromatin binding sites of DDX5 are G-rich sequences. In cancer cells, DDX5 is enriched at the MYC promoter and activates MYC transcription. The DDX5 interaction with the MYC promoter and DDX5-mediated MYC activation is inhibited by G4-interactive small molecules. Our results uncover a function of DDX5 in resolving DNA and RNA G4s and suggest a molecular target to suppress MYC for cancer intervention.
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50
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Yamamoto T, Saitoh N. Non-coding RNAs and chromatin domains. Curr Opin Cell Biol 2019; 58:26-33. [PMID: 30682683 DOI: 10.1016/j.ceb.2018.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/19/2018] [Accepted: 12/06/2018] [Indexed: 11/29/2022]
Abstract
Large-scale transcriptome analyses have identified a variety of non-coding RNAs (ncRNAs) that are not translated into proteins. Many of them are in the nucleus, where they associate with chromatin and regulate its structure and function. Interphase chromosomes are intricately folded into multiple layers and composed of domains. Recent studies using Hi-C technologies have identified a mega-base self-associating chromatin domain: the topologically associating domain (TAD). The domain boundaries are demarcated with the chromatin regulatory proteins CTCF and cohesin, which are often bound to or recruited by ncRNAs. Some ncRNAs form RNA clouds in the nucleus and coordinate the transcription of multiple genes in a chromatin domain. In this review, we describe the emerging link between long ncRNAs and chromatin domains in the nucleus.
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Affiliation(s)
- Tatsuro Yamamoto
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo 135-8550, Japan; Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo 135-8550, Japan.
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