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González-Iglesias A, Arcas A, Domingo-Muelas A, Mancini E, Galcerán J, Valcárcel J, Fariñas I, Nieto MA. Intron detention tightly regulates the stemness/differentiation switch in the adult neurogenic niche. Nat Commun 2024; 15:2837. [PMID: 38565566 PMCID: PMC10987655 DOI: 10.1038/s41467-024-47092-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The adult mammalian brain retains some capacity to replenish neurons and glia, holding promise for brain regeneration. Thus, understanding the mechanisms controlling adult neural stem cell (NSC) differentiation is crucial. Paradoxically, adult NSCs in the subependymal zone transcribe genes associated with both multipotency maintenance and neural differentiation, but the mechanism that prevents conflicts in fate decisions due to these opposing transcriptional programmes is unknown. Here we describe intron detention as such control mechanism. In NSCs, while multiple mRNAs from stemness genes are spliced and exported to the cytoplasm, transcripts from differentiation genes remain unspliced and detained in the nucleus, and the opposite is true under neural differentiation conditions. We also show that m6A methylation is the mechanism that releases intron detention and triggers nuclear export, enabling rapid and synchronized responses. m6A RNA methylation operates as an on/off switch for transcripts with antagonistic functions, tightly controlling the timing of NSCs commitment to differentiation.
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Affiliation(s)
| | - Aida Arcas
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
| | - Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
- Carlos Simon Foundation, 46980, Paterna, Valencia, Spain
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Igenomix Foundation, 46980, Paterna, Valencia, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Joan Galcerán
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física and Instituto de Biotecnología y Biomedicina, Universidad de Valencia, Burjassot, 46100, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029, Madrid, Spain
| | - M Angela Nieto
- Instituto de Neurociencias (CSIC-UMH), Sant Joan d'Alacant, 03550, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Raras (CIBERER), 28029, Madrid, Spain.
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Yu B, Qi Y, Li R, Shi Q, Satpathy A, Chang HY. B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33442682 PMCID: PMC7805439 DOI: 10.1101/2021.01.03.425167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The long noncoding RNA (lncRNA) XIST establishes X chromosome inactivation (XCI) in female cells in early development and thereafter is thought to be largely dispensable. Here we show XIST is continually required in adult human B cells to silence a subset of X-linked immune genes such as TLR7 . XIST-dependent genes lack promoter DNA methylation and require continual XIST-dependent histone deacetylation. XIST RNA-directed proteomics and CRISPRi screen reveal distinctive somatic cell-specific XIST complexes, and identify TRIM28 that mediates Pol II pausing at promoters of X-linked genes in B cells. XIST dysregylation, reflected by escape of XIST-dependent genes, occurs in CD11c+ atypical memory B cells across single-cell transcriptome data in patients with female-biased autoimmunity and COVID-19 infection. XIST inactivation with TLR7 agonism suffices to promote isotype-switched atypical B cells. These results suggest cell-type-specific diversification of lncRNA-protein complexes increase lncRNA functionalities, and expand roles for XIST in sex-differences in biology and medicine. HIGHLIGHTS XIST prevents escape of genes with DNA hypomethylated promoters in B cells.XIST maintains X-inactivation through continuous deacetylation of H3K27ac.XIST ChIRP-MS and allelic CRISPRi screen reveal a B cell-specific XIST cofactor TRIM28.XIST loss and TLR7 stimulation promotes CD11c+ atypical B cell formation.
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Zhu W, Zhou BL, Rong LJ, Ye L, Xu HJ, Zhou Y, Yan XJ, Liu WD, Zhu B, Wang L, Jiang XJ, Ren CP. Roles of PTBP1 in alternative splicing, glycolysis, and oncogensis. J Zhejiang Univ Sci B 2020; 21:122-136. [PMID: 32115910 DOI: 10.1631/jzus.b1900422] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) plays an essential role in splicing and is expressed in almost all cell types in humans, unlike the other proteins of the PTBP family. PTBP1 mediates several cellular processes in certain types of cells, including the growth and differentiation of neuronal cells and activation of immune cells. Its function is regulated by various molecules, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and RNA-binding proteins. PTBP1 plays roles in various diseases, particularly in some cancers, including colorectal cancer, renal cell cancer, breast cancer, and glioma. In cancers, it acts mainly as a regulator of glycolysis, apoptosis, proliferation, tumorigenesis, invasion, and migration. The role of PTBP1 in cancer has become a popular research topic in recent years, and this research has contributed greatly to the formulation of a useful therapeutic strategy for cancer. In this review, we summarize recent findings related to PTBP1 and discuss how it regulates the development of cancer cells.
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Affiliation(s)
- Wei Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bo-Lun Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li-Juan Rong
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li Ye
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hong-Juan Xu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yao Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xue-Jun Yan
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wei-Dong Liu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bin Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lei Wang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xing-Jun Jiang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Cai-Ping Ren
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
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Yoon SB, Park YH, Choi SA, Yang HJ, Jeong PS, Cha JJ, Lee S, Lee SH, Lee JH, Sim BW, Koo BS, Park SJ, Lee Y, Kim YH, Hong JJ, Kim JS, Jin YB, Huh JW, Lee SR, Song BS, Kim SU. Real-time PCR quantification of spliced X-box binding protein 1 (XBP1) using a universal primer method. PLoS One 2019; 14:e0219978. [PMID: 31329612 PMCID: PMC6645673 DOI: 10.1371/journal.pone.0219978] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/05/2019] [Indexed: 12/21/2022] Open
Abstract
X-box binding protein 1 (XBP1) mRNA processing plays a crucial role in the unfolded protein response (UPR), which is activated in response to endoplasmic reticulum (ER) stress. Upon accumulation of the UPR-converted XBP1 mRNA splicing from an unspliced (u) XBP1 (inactive) isoform to the spliced (s) XBP1 (active) isoform, inositol-requiring enzyme 1 α (IRE1α) removes a 26-nucleotide intron from uXBP1 mRNA. Recent studies have reported the assessment of ER stress by examining the ratio of sXBP1 to uXBP1 mRNA (s/uXBP1 ratio) via densitometric analysis of PCR bands relative to increased levels of sXBP1 to uXBP1 using a housekeeping gene for normalization. However, this measurement is visualized by gel electrophoresis, making it very difficult to quantify differences between the two XBP1 bands and complicating data interpretation. Moreover, most commonly used housekeeping genes display an unacceptably high variable expression pattern of the s/uXBP1 ratio under different experimental conditions, such as various phases of development and different cell types, limiting their use as internal controls. For a more quantitative determination of XBP1 splicing activity, we measured the expression levels of total XBP1 (tXBP1: common region of s/uXBP1) and sXBP1 via real-time PCR using specific primer sets. We also designed universal real-time PCR primer sets capable of amplifying a portion of each u/s/tXBP1 mRNA that is highly conserved in eukaryotes, including humans, monkeys, cows, pigs, and mice. Therefore, we provide a more convenient and easily approachable quantitative real-time PCR method that can be used in various research fields to assess ER stress.
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Affiliation(s)
- Seung-Bin Yoon
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeollabuk-do, Republic of Korea
| | - Young-Ho Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Seon-A Choi
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Hae-Jun Yang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Pil-Soo Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Jae-Jin Cha
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Sanghoon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Seung Hwan Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Jong-Hee Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Bo-Woong Sim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Bon-Sang Koo
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Ji-Su Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeollabuk-do, Republic of Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Bong-Seok Song
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
- * E-mail: (BSS); (SUK)
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Futuristic Animal Resource & Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
- * E-mail: (BSS); (SUK)
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