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Zhang S, Wen X, Zhou L, Li H, Li W, Hoffman AR, Hu JF, Cui J. Chromatin-RNA in situ Reverse Transcription Sequencing (CRIST-seq) Approach to Profile the Non-coding RNA Interaction Network. Bio Protoc 2023; 13:e4718. [PMID: 37497457 PMCID: PMC10366681 DOI: 10.21769/bioprotoc.4718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/02/2023] [Accepted: 04/28/2023] [Indexed: 07/28/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are defined as RNAs that do not encode proteins, but many ncRNAs do have the ability to regulate gene expression. These ncRNAs play a critical role in the epigenetic regulation of various physiological and pathological processes through diverse biochemical mechanisms. However, the existing screening methods to identify regulatory ncRNAs only focus on whole-cell expression levels and do not capture every ncRNA that targets certain genes. We describe a new method, chromatin-RNA in situ reverse transcription sequencing (CRIST-seq), that can identify all the ncRNAs that are associated with the regulation of any given gene. In this article, we targeted the ncRNAs that are associated with pluripotent gene Sox2, allowing us to catalog the ncRNA regulation network of pluripotency maintenance. This methodology is universally applicable for the study of epigenetic regulation of any genes by making simple changes on the CRISPR-dCas9 gRNAs. Key features This method provides a new technique for screening ncRNAs and establishing chromatin interaction networks. The target gene for this method can be any gene of interest and any site in the entire genome. This method can be further extended to detect RNAs, DNAs, and proteins that interact with target genes. Graphical overview.
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Affiliation(s)
- Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Hui Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
| | - Andrew R. Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin 130061, China
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Zhu Y, Yan Z, Fu C, Wen X, Jia L, Zhou L, Du Z, Wang C, Wang Y, Chen J, Nie Y, Wang W, Cui J, Wang G, Hoffman AR, Hu JF, Li W. LncRNA Osilr9 coordinates promoter DNA demethylation and the intrachromosomal loop structure required for maintaining stem cell pluripotency. Mol Ther 2023; 31:1791-1806. [PMID: 36523163 PMCID: PMC10278046 DOI: 10.1016/j.ymthe.2022.12.010] [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: 01/03/2020] [Revised: 06/08/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Nuclear reprogramming of somatic cells into a pluripotent status has the potential to create patient-specific induced pluripotent stem cells for regenerative medicine. Currently, however, the epigenetic mechanisms underlying this pluripotent reprogramming are poorly understood. To delineate this epigenetic regulatory network, we utilized a chromatin RNA in situ reverse transcription sequencing (CRIST-seq) approach to identify long noncoding RNAs (lncRNAs) embedded in the 3-dimensional intrachromosomal architecture of stem cell core factor genes. By combining CRIST-seq and RNA sequencing, we identified Oct4-Sox2 interacting lncRNA 9 (Osilr9) as a pluripotency-associated lncRNA. Osilr9 expression was associated with the status of stem cell pluripotency in reprogramming. Using short hairpin RNA (shRNA) knockdown, we showed that this lncRNA was required for the optimal maintenance of stem cell pluripotency. Overexpression of Osilr9 induced robust activation of endogenous stem cell core factor genes in fibroblasts. Osilr9 participated in the formation of the intrachromosomal looping required for the maintenance of pluripotency. After binding to the Oct4 promoter, Osilr9 recruited the DNA demethylase ten-eleven translocation 1, leading to promoter demethylation. These data demonstrate that Osilr9 is a critical chromatin epigenetic modulator that coordinates the promoter activity of core stem cell factor genes, highlighting the critical role of pluripotency-associated lncRNAs in stem cell pluripotency and reprogramming.
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Affiliation(s)
- Yanbo Zhu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Zi Yan
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun 130021, Jilin, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Changhao Fu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jingcheng Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yuanyuan Nie
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Wenjun Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
| | - Guixia Wang
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun 130021, Jilin, China.
| | - Andrew R Hoffman
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China; Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China.
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Li S, Liu H, Liu W, Shi N, Zhao M, Wanggou S, Luo W, Wang L, Zhu B, Zuo X, Xie W, Zhao C, Zhou Y, Luo L, Gao X, Jiang X, Ren C. ESRG is critical to maintain the cell survival and self-renewal/pluripotency of hPSCs by collaborating with MCM2 to suppress p53 pathway. Int J Biol Sci 2023; 19:916-935. [PMID: 36778110 PMCID: PMC9909993 DOI: 10.7150/ijbs.79095] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
The mechanisms of self-renewal and pluripotency maintenance of human pluripotent stem cells (hPSCs) have not been fully elucidated, especially for the role of those poorly characterized long noncoding RNAs (lncRNAs). ESRG is a lncRNA highly expressed in hPSCs, and its functional roles are being extensively explored in the field. Here, we identified that the transcription of ESRG can be directly regulated by OCT4, a key self-renewal factor in hPSCs. Knockdown of ESRG induces hPSC differentiation, cell cycle arrest, and apoptosis. ESRG binds to MCM2, a replication-licensing factor, to sustain its steady-state level and nuclear location, safeguarding error-free DNA replication. Further study showed that ESRG knockdown leads to MCM2 abnormalities, resulting in DNA damage and activation of the p53 pathway, ultimately impairs hPSC self-renewal and pluripotency, and induces cell apoptosis. In summary, our study suggests that ESRG, as a novel target of OCT4, plays an essential role in maintaining the cell survival and self-renewal/pluripotency of hPSCs in collaboration with MCM2 to suppress p53 signaling. These findings provide critical insights into the mechanisms underlying the maintenance of self-renewal and pluripotency in hPSCs by lncRNAs.
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Affiliation(s)
- Shasha Li
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Hui Liu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Weidong Liu
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Ning Shi
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100039, China
| | - Ming Zhao
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Siyi Wanggou
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Weiren Luo
- Cancer Research Institute, Shenzhen Third People's Hospital, the Second Affiliated Hospital of Southern University of Science and technology, Shenzhen, Guangdong 518100 China
| | - Lei Wang
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Bin Zhu
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Xiang Zuo
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Wen Xie
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Cong Zhao
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Yao Zhou
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
| | - Longlong Luo
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100039, China
| | - Xiang Gao
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100039, China
| | - Xingjun Jiang
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Caiping Ren
- NHC Key Laboratory of Carcinogenesis, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan 410078, China
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Zhou RT, Ni YR, Zeng FJ. The roles of long noncoding RNAs in the regulation of OCT4 expression. Stem Cell Res Ther 2022; 13:383. [PMID: 35907897 PMCID: PMC9338536 DOI: 10.1186/s13287-022-03059-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/19/2022] [Indexed: 12/13/2022] Open
Abstract
OCT4 is a major transcription factor that maintains the pluripotency of stem cells, including embryonic stem cells, induced pluripotent stem cells and cancer stem cells. An increasing number of long noncoding RNAs have been reported to participate in the regulation of OCT4 expression through various mechanisms, including binding with the OCT4 gene promoter to regulate local methylation; promoting chromosomal spatial folding to form an inner ring, thereby aggregating OCT4 cis-acting elements scattered in discontinuous sites of the chromosome; competitively binding microRNAs with OCT4 to upregulate OCT4 expression at the posttranscriptional level; and sharing a promoter with OCT4. Moreover, the transcription of some long noncoding RNAs is regulated by OCT4, and certain long noncoding RNAs form feedback regulatory loops with OCT4. In this review, we summarized the research progress of the long noncoding RNAs involved in the regulation of OCT4 expression.
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Affiliation(s)
- Rui-Ting Zhou
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443003, Hubei, China.,Yichang Central People's Hospital, Yichang, 443003, Hubei, China.,Medical College, China Three Gorges University, Yichang, 443002, Hubei, China
| | - Yi-Ran Ni
- Medical College, China Three Gorges University, Yichang, 443002, Hubei, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, Hubei, China
| | - Fan-Jun Zeng
- The First College of Clinical Medical Science, China Three Gorges University, Yichang, 443003, Hubei, China. .,Yichang Central People's Hospital, Yichang, 443003, Hubei, China.
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5
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Wang Y, Jia L, Wang C, Du Z, Zhang S, Zhou L, Wen X, Li H, Chen H, Nie Y, Li D, Liu S, Figueroa DS, Ay F, Xu W, Zhang S, Li W, Cui J, Hoffman AR, Guo H, Hu JF. Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. J Cell Biol 2022; 221:213009. [PMID: 35171230 PMCID: PMC8855478 DOI: 10.1083/jcb.202009134] [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: 09/24/2020] [Revised: 12/01/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
The molecular circuitry that causes stem cells to exit from pluripotency remains largely uncharacterized. Using chromatin RNA in situ reverse transcription sequencing, we identified Peln1 as a novel chromatin RNA component in the promoter complex of Oct4, a stem cell master transcription factor gene. Peln1 was negatively associated with pluripotent status during somatic reprogramming. Peln1 overexpression caused E14 cells to exit from pluripotency, while Peln1 downregulation induced robust reprogramming. Mechanistically, we discovered that Peln1 interacted with the Oct4 promoter and recruited the DNA methyltransferase DNMT3A. By de novo altering the epigenotype in the Oct4 promoter, Peln1 dismantled the intrachromosomal loop that is required for the maintenance of pluripotency. Using RNA reverse transcription-associated trap sequencing, we showed that Peln1 targets multiple pathway genes that are associated with stem cell self-renewal. These findings demonstrate that Peln1 can act as a new epigenetic player and use a trans mechanism to induce an exit from the pluripotent state in stem cells.
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Affiliation(s)
- Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Zhonghua Du
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Xue Wen
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Li
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Yuanyuan Nie
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | | | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Andrew R Hoffman
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Guo
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
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Dehghani H. Regulation of Chromatin Organization in Cell Stemness: The Emerging Role of Long Non-coding RNAs. Stem Cell Rev Rep 2021; 17:2042-2053. [PMID: 34181184 DOI: 10.1007/s12015-021-10209-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 12/27/2022]
Abstract
Chromatin is organized as chromosome territories in the nucleus of an interphase cell. The cell-type- and cell-state-specific organization of chromatin including the location, volume, compaction level, and spatial arrangement of chromosome territories are the major determinants of genome function. In addition, in response to different signaling stimuli and regulatory cues, it is the dynamic adaptation of chromatin structure that establishes and organizes transcriptional programs. It is known that varying levels of stemness are defined by gene regulatory networks. Accordingly, chromatin is the main milieu to host the transcriptional programs and gene regulatory networks responsible for the stemness status of a cell. In this review, our current understanding of the spatial organization of chromatin and the ways by which it defines stemness are discussed. In particular, the role of lncRNAs that regulate and affect chromatin organization and stemness properties are delineated. These roles can be categorized into the topics of specific binding to and epigenetic regulation of the promoter of pluripotency genes, their interaction with transcription factors, coordinating the intra- and inter-chromosomal looping of pluripotency-related genes, and their RNA-independent functions. This review brings together the results of studies that have begun to clarify the emerging roles of lncRNAs in the regulation of chromatin organization adapted for stemness and cancer plasticity.
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Affiliation(s)
- Hesam Dehghani
- Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.
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