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Forsyth KS, Jiwrajka N, Lovell CD, Toothacre NE, Anguera MC. The conneXion between sex and immune responses. Nat Rev Immunol 2024; 24:487-502. [PMID: 38383754 PMCID: PMC11216897 DOI: 10.1038/s41577-024-00996-9] [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] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
There are notable sex-based differences in immune responses to pathogens and self-antigens, with female individuals exhibiting increased susceptibility to various autoimmune diseases, and male individuals displaying preferential susceptibility to some viral, bacterial, parasitic and fungal infections. Although sex hormones clearly contribute to sex differences in immune cell composition and function, the presence of two X chromosomes in female individuals suggests that differential gene expression of numerous X chromosome-linked immune-related genes may also influence sex-biased innate and adaptive immune cell function in health and disease. Here, we review the sex differences in immune system composition and function, examining how hormones and genetics influence the immune system. We focus on the genetic and epigenetic contributions responsible for altered X chromosome-linked gene expression, and how this impacts sex-biased immune responses in the context of pathogen infection and systemic autoimmunity.
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Affiliation(s)
- Katherine S Forsyth
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikhil Jiwrajka
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Claudia D Lovell
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natalie E Toothacre
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Bohrer C, Varon E, Peretz E, Reinitz G, Kinor N, Halle D, Nissan A, Shav-Tal Y. CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced. Histochem Cell Biol 2024; 162:91-107. [PMID: 38763947 PMCID: PMC11227459 DOI: 10.1007/s00418-024-02294-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Super-enhancers are unique gene expression regulators widely involved in cancer development. Spread over large DNA segments, they tend to be found next to oncogenes. The super-enhancer c-MYC locus forms long-range chromatin looping with nearby genes, which brings the enhancer and the genes into proximity, to promote gene activation. The colon cancer-associated transcript 1 (CCAT1) gene, which is part of the MYC locus, transcribes a lncRNA that is overexpressed in colon cancer cells through activation by MYC. Comparing different types of cancer cell lines using RNA fluorescence in situ hybridization (RNA FISH), we detected very prominent CCAT1 expression in HeLa cells, observed as several large CCAT1 nuclear foci. We found that dozens of CCAT1 transcripts accumulate on the gene locus, in addition to active transcription occurring from the gene. The accumulating transcripts are released from the chromatin during cell division. Examination of CCAT1 lncRNA expression patterns on the single-RNA level showed that unspliced CCAT1 transcripts are released from the gene into the nucleoplasm. Most of these unspliced transcripts were observed in proximity to the active gene but were not associated with nuclear speckles in which unspliced RNAs usually accumulate. At larger distances from the gene, the CCAT1 transcripts appeared spliced, implying that most CCAT1 transcripts undergo post-transcriptional splicing in the zone of the active gene. Finally, we show that unspliced CCAT1 transcripts can be detected in the cytoplasm during splicing inhibition, which suggests that there are several CCAT1 variants, spliced and unspliced, that the cell can recognize as suitable for export.
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Affiliation(s)
- Chaya Bohrer
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Varon
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eldar Peretz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Gita Reinitz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Kinor
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - David Halle
- Biochemistry Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Aviram Nissan
- Ziv Medical Center, Safed, Israel
- Surgical Innovation Laboratory, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel.
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3
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Zeinelabdeen Y, Abaza T, Yasser MB, Elemam NM, Youness RA. MIAT LncRNA: A multifunctional key player in non-oncological pathological conditions. Noncoding RNA Res 2024; 9:447-462. [PMID: 38511054 PMCID: PMC10950597 DOI: 10.1016/j.ncrna.2024.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/22/2024] Open
Abstract
The discovery of non-coding RNAs (ncRNAs) has unveiled a wide range of transcripts that do not encode proteins but play key roles in several cellular and molecular processes. Long noncoding RNAs (lncRNAs) are specific class of ncRNAs that are longer than 200 nucleotides and have gained significant attention due to their diverse mechanisms of action and potential involvement in various pathological conditions. In the current review, the authors focus on the role of lncRNAs, specifically highlighting the Myocardial Infarction Associated Transcript (MIAT), in non-oncological context. MIAT is a nuclear lncRNA that has been directly linked to myocardial infarction and is reported to control post-transcriptional processes as a competitive endogenous RNA (ceRNA) molecule. It interacts with microRNAs (miRNAs), thereby limiting the translation and expression of their respective target messenger RNA (mRNA) and regulating protein expression. Yet, MIAT has been implicated in other numerous pathological conditions such as other cardiovascular diseases, autoimmune disease, neurodegenerative diseases, metabolic diseases, and many others. In this review, the authors emphasize that MIAT exhibits distinct expression patterns and functions across different pathological conditions and is emerging as potential diagnostic, prognostic, and therapeutic agent. Additionally, the authors highlight the regulatory role of MIAT and shed light on the involvement of lncRNAs and specifically MIAT in various non-oncological pathological conditions.
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Affiliation(s)
- Yousra Zeinelabdeen
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
- Faculty of Medical Sciences/UMCG, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, the Netherlands
| | - Tasneem Abaza
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
- Biotechnology and Biomolecular Biochemistry Program, Faculty of Science, Cairo University, Cairo, Egypt
| | - Montaser Bellah Yasser
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
| | - Noha M. Elemam
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Rana A. Youness
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
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4
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [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: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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5
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Liang X, Di F, Wei H, Liu N, Chen C, Wang X, Sun M, Zhang M, Li M, Zhang J, Zhang S. Functional identification of long non-coding RNAs induced by PM 2.5 in microglia through microarray analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116136. [PMID: 38387142 DOI: 10.1016/j.ecoenv.2024.116136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
As a dominating air pollutant, atmospheric fine particulate matter within 2.5 μm in diameter (PM2.5) has attracted increasing attention from the researchers all over the world, which will lead to various adverse effects on the central nervous system (CNS), yet the potential mechanism is unclear. In this study, the microglia (BV2 cell line) were exposed to different concentrations of PM2.5 (5, 10 and 20 μg/cm2) for 24 h. It was found that PM2.5 could result in adverse effects on microglia such as decreased cell viability, structural damage and even cell death. And it was reported that long non-coding RNAs (lncRNAs) could participate in multitudinous neurological diseases. Therefore, the microarray analysis was conducted in order to disclose the underlying neurotoxicity mechanism of PM2.5 by ascertaining the differentially expressed lncRNAs (DElncRNAs). The consequences indicated that the DElncRNAs were enriched in various biological pathways, including ferroptosis, IL-17 signaling pathway and NOD-like receptor signaling pathway. Moreover, the cis- and trans-regulated mRNAs by DElncRNAs as well as the corresponding transcriptional factors (TFs) were observed, such as CEBPA, MYC, MEIS1 and KLF4. In summary, our study supplies some candidate libraries and potential preventive target against PM2.5-induced toxicity through targeting lncRNAs. Furthermore, the post-transcriptional regulation will contribute to the future research on PM2.5-induced neurotoxicity.
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Affiliation(s)
- Xue Liang
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China; Medical Science and Technology Innovation Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China.
| | - Fanglin Di
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Haiyun Wei
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Natong Liu
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Chao Chen
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Xinzhi Wang
- School of Public Health, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Meng Sun
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China
| | - Min Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Meng Li
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, China
| | - Jie Zhang
- Medical Science and Technology Innovation Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China; Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
| | - Shuping Zhang
- Medical Science and Technology Innovation Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China; Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan, Shandong 250117, China
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6
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Gupta K, Czerminski JT, Lawrence JB. Trisomy silencing by XIST: translational prospects and challenges. Hum Genet 2024:10.1007/s00439-024-02651-8. [PMID: 38459355 DOI: 10.1007/s00439-024-02651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/25/2024] [Indexed: 03/10/2024]
Abstract
XIST RNA is heavily studied for its role in fundamental epigenetics and X-chromosome inactivation; however, the translational potential of this singular RNA has been much less explored. This article combines elements of a review on XIST biology with our perspective on the translational prospects and challenges of XIST transgenics. We first briefly review aspects of XIST RNA basic biology that are key to its translational relevance, and then discuss recent efforts to develop translational utility of XIST for chromosome dosage disorders, particularly Down syndrome (DS). Remarkably, it was shown in vitro that expression of an XIST transgene inserted into one chromosome 21 can comprehensively silence that chromosome and "dosage compensate" Trisomy 21, the cause of DS. Here we summarize recent findings and discuss potential paths whereby ability to induce "trisomy silencing" can advance translational research for new therapeutic strategies. Despite its common nature, the underlying biology for various aspects of DS, including cell types and pathways impacted (and when), is poorly understood. Recent studies show that an inducible iPSC system to dosage-correct chromosome 21 can provide a powerful approach to unravel the cells and pathways directly impacted, and the developmental timing, information key to design pharmacotherapeutics. In addition, we discuss prospects of a more far-reaching and challenging possibility that XIST itself could be developed into a therapeutic agent, for targeted cellular "chromosome therapy". A few rare case studies of imbalanced X;autosome translocations indicate that natural XIST can rescue an otherwise lethal trisomy. The potential efficacy of XIST transgenes later in development faces substantial biological and technical challenges, although recent findings are encouraging, and technology is rapidly evolving. Hence, it is compelling to consider the transformative possibility that XIST-mediated chromosome therapy may ultimately be developed, for specific pathologies seen in DS, or other duplication disorders.
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Affiliation(s)
- Khusali Gupta
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Jan T Czerminski
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA.
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7
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Hall LL, Creamer KM, Byron M, Lawrence JB. Differences in Alu vs L1-rich chromosome bands underpin architectural reorganization of the inactive-X chromosome and SAHFs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574742. [PMID: 38260534 PMCID: PMC10802495 DOI: 10.1101/2024.01.09.574742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The linear DNA sequence of mammalian chromosomes is organized in large blocks of DNA with similar sequence properties, producing a pattern of dark and light staining bands on mitotic chromosomes. Cytogenetic banding is essentially invariant between people and cell-types and thus may be assumed unrelated to genome regulation. We investigate whether large blocks of Alu-rich R-bands and L1-rich G-bands provide a framework upon which functional genome architecture is built. We examine two models of large-scale chromatin condensation: X-chromosome inactivation and formation of senescence-associated heterochromatin foci (SAHFs). XIST RNA triggers gene silencing but also formation of the condensed Barr Body (BB), thought to reflect cumulative gene silencing. However, we find Alu-rich regions are depleted from the L1-rich BB, supporting it is a dense core but not the entire chromosome. Alu-rich bands are also gene-rich, affirming our earlier findings that genes localize at the outer periphery of the BB. SAHFs similarly form within each territory by coalescence of syntenic L1 regions depleted for highly Alu-rich DNA. Analysis of senescent cell Hi-C data also shows large contiguous blocks of G-band and R-band DNA remodel as a segmental unit. Entire dark-bands gain distal intrachromosomal interactions as L1-rich regions form the SAHF. Most striking is that sharp Alu peaks within R-bands resist these changes in condensation. We further show that Chr19, which is exceptionally Alu rich, fails to form a SAHF. Collective results show regulation of genome architecture corresponding to large blocks of DNA and demonstrate resistance of segments with high Alu to chromosome condensation.
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Affiliation(s)
- Lisa L. Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Kevin M. Creamer
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
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8
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Dror I, Chitiashvili T, Tan SYX, Cano CT, Sahakyan A, Markaki Y, Chronis C, Collier AJ, Deng W, Liang G, Sun Y, Afasizheva A, Miller J, Xiao W, Black DL, Ding F, Plath K. XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells. Cell 2024; 187:110-129.e31. [PMID: 38181737 PMCID: PMC10783549 DOI: 10.1016/j.cell.2023.11.033] [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: 12/21/2020] [Revised: 04/01/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024]
Abstract
X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
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Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tsotne Chitiashvili
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Y X Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Clara T Cano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Sahakyan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yolanda Markaki
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Amanda J Collier
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guohao Liang
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anna Afasizheva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jarrett Miller
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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9
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Sabikunnahar B, Caldwell S, Varnum S, Hogan T, Lahue KG, Rathkolb B, Gerlini R, Dragano NRV, Aguilar‐Pimentel A, Irmler M, Sanz‐Moreno A, da Silva‐Buttkus P, Beckers J, Wolf E, Gailus‐Durner V, Fuchs H, Hrabe de Angelis M, Ather JL, Poynter ME, Krementsov DN. LncRNA U90926 is dispensable for the development of obesity-associated phenotypes in vivo. Physiol Rep 2024; 12:e15901. [PMID: 38171546 PMCID: PMC10764201 DOI: 10.14814/phy2.15901] [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: 08/26/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Obesity is a global health problem characterized by excessive fat accumulation, driven by adipogenesis and lipid accumulation. Long non-coding RNAs (lncRNAs) have recently been implicated in regulating adipogenesis and adipose tissue function. Mouse lncRNA U90926 was previously identified as a repressor of in vitro adipogenesis in 3T3-L1 preadipocytes. Consequently, we hypothesized that, in vivo, U90926 may repress adipogenesis, and hence its deletion would increase weight gain and adiposity. We tested the hypothesis by applying U90926-deficient (U9-KO) mice to a high-throughput phenotyping pipeline. Compared with WT, U9-KO mice showed no major differences across a wide range of behavioral, neurological, and other physiological parameters. In mice fed a standard diet, we have found no differences in obesity-related phenotypes, including weight gain, fat mass, and plasma concentrations of glucose, insulin, triglycerides, and free fatty acids, in U9-KO mice compared to WT. U90926 deficiency lacked a major effect on white adipose tissue morphology and gene expression profile. Furthermore, in mice fed a high-fat diet, we found increased expression of U90926 in adipose tissue stromal vascular cell fraction, yet observed no effect of U90926 deficiency on weight gain, fat mass, adipogenesis marker expression, and immune cell infiltration into the adipose tissue. These data suggest that the U90926 lacks an essential role in obesity-related phenotypes and adipose tissue biology in vivo.
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Affiliation(s)
- Bristy Sabikunnahar
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Sydney Caldwell
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Stella Varnum
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Tyler Hogan
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Karolyn G. Lahue
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Birgit Rathkolb
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Institute of Molecular Animal Breeding and Biotechnology, Gene CenterLudwig‐Maximilians‐University MünchenMunichGermany
| | - Raffaele Gerlini
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Nathalia R. V. Dragano
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
| | - Antonio Aguilar‐Pimentel
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Martin Irmler
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Adrián Sanz‐Moreno
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Patricia da Silva‐Buttkus
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Johannes Beckers
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- TUM School of Life SciencesTechnische Universität MünchenFreisingGermany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene CenterLudwig‐Maximilians‐University MünchenMunichGermany
| | - Valerie Gailus‐Durner
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Helmut Fuchs
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- TUM School of Life SciencesTechnische Universität MünchenFreisingGermany
| | | | | | - Dimitry N. Krementsov
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
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10
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Sen S, Dhuppar S, Mazumder A. Combined 3D DNA FISH, Single-Molecule RNA FISH, and Immunofluorescence. Methods Mol Biol 2024; 2784:203-214. [PMID: 38502488 DOI: 10.1007/978-1-0716-3766-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Nuclear architecture is a potential regulator of gene expression in eukaryotic cells. Studies connecting nuclear architecture to gene expression are often population-averaged and do not report on the cell-level heterogeneity in genome organization and associated gene expression. In this report we present a simple way to combine fluorescence in situ hybridization (FISH)-based detection of DNA, with single-molecule RNA FISH (smFISH) and immunofluorescence (IF), while also preserving the three-dimensional (3D) nuclear architecture of a cell. Recently developed smFISH techniques enable the detection of individual RNA molecules; while using 3D DNA FISH, copy numbers and positions of genes inside the nucleus can be interrogated without interfering with 3D nuclear architecture. Our method to combine 3D DNA FISH with smFISH and IF enables a unique quantitative handle on the central dogma of molecular biology.
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Affiliation(s)
- Souvik Sen
- Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana, India
| | - Shivnarayan Dhuppar
- Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana, India
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aprotim Mazumder
- Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana, India.
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11
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Bravo‐Estupiñan DM, Aguilar‐Guerrero K, Quirós S, Acón M, Marín‐Müller C, Ibáñez‐Hernández M, Mora‐Rodríguez RA. Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems-level property in cancer. Cancer Med 2023; 12:22130-22155. [PMID: 37987212 PMCID: PMC10757140 DOI: 10.1002/cam4.6719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The gene dosage compensation hypothesis presents a mechanism through which the expression of certain genes is modulated to compensate for differences in the dose of genes when additional chromosomes are present. It is one of the means through which cancer cells actively cope with the potential damaging effects of aneuploidy, a hallmark of most cancers. Dosage compensation arises through several processes, including downregulation or overexpression of specific genes and the relocation of dosage-sensitive genes. In cancer, a majority of compensated genes are generally thought to be regulated at the translational or post-translational level, and include the basic components of a compensation loop, including sensors of gene dosage and modulators of gene expression. Post-translational regulation is mostly undertaken by a general degradation or aggregation of remaining protein subunits of macromolecular complexes. An increasingly important role has also been observed for transcriptional level regulation. This article reviews the process of targeted gene dosage compensation in cancer and other biological conditions, along with the mechanisms by which cells regulate specific genes to restore cellular homeostasis. These mechanisms represent potential targets for the inhibition of dosage compensation of specific genes in aneuploid cancers. This article critically examines the process of targeted gene dosage compensation in cancer and other biological contexts, alongside the criteria for identifying genes subject to dosage compensation and the intricate mechanisms by which cells orchestrate the regulation of specific genes to reinstate cellular homeostasis. Ultimately, our aim is to gain a comprehensive understanding of the intricate nature of a systems-level property. This property hinges upon the kinetic parameters of regulatory motifs, which we have termed "gene dosage sensor loops." These loops have the potential to operate at both the transcriptional and translational levels, thus emerging as promising candidates for the inhibition of dosage compensation in specific genes. Additionally, they represent novel and highly specific therapeutic targets in the context of aneuploid cancer.
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Affiliation(s)
- Diana M. Bravo‐Estupiñan
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Programa de Doctorado en Ciencias, Sistema de Estudios de Posgrado (SEP)Universidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Karol Aguilar‐Guerrero
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Maestría académica en Microbiología, Programa de Posgrado en Microbiología, Parasitología, Química Clínica e InmunologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Steve Quirós
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Man‐Sai Acón
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
| | - Christian Marín‐Müller
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Miguel Ibáñez‐Hernández
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
| | - Rodrigo A. Mora‐Rodríguez
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
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12
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Huschner F, Głowacka-Walas J, Mills JD, Klonowska K, Lasseter K, Asara JM, Moavero R, Hertzberg C, Weschke B, Riney K, Feucht M, Scholl T, Krsek P, Nabbout R, Jansen AC, Petrák B, van Scheppingen J, Zamecnik J, Iyer A, Anink JJ, Mühlebner A, Mijnsbergen C, Lagae L, Curatolo P, Borkowska J, Sadowski K, Domańska-Pakieła D, Blazejczyk M, Jansen FE, Janson S, Urbanska M, Tempes A, Janssen B, Sijko K, Wojdan K, Jozwiak S, Kotulska K, Lehmann K, Aronica E, Jaworski J, Kwiatkowski DJ. Molecular EPISTOP, a comprehensive multi-omic analysis of blood from Tuberous Sclerosis Complex infants age birth to two years. Nat Commun 2023; 14:7664. [PMID: 37996417 PMCID: PMC10667269 DOI: 10.1038/s41467-023-42855-6] [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: 02/23/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023] Open
Abstract
We present a comprehensive multi-omic analysis of the EPISTOP prospective clinical trial of early intervention with vigabatrin for pre-symptomatic epilepsy treatment in Tuberous Sclerosis Complex (TSC), in which 93 infants with TSC were followed from birth to age 2 years, seeking biomarkers of epilepsy development. Vigabatrin had profound effects on many metabolites, increasing serum deoxycytidine monophosphate (dCMP) levels 52-fold. Most serum proteins and metabolites, and blood RNA species showed significant change with age. Thirty-nine proteins, metabolites, and genes showed significant differences between age-matched control and TSC infants. Six also showed a progressive difference in expression between control, TSC without epilepsy, and TSC with epilepsy groups. A multivariate approach using enrollment samples identified multiple 3-variable predictors of epilepsy, with the best having a positive predictive value of 0.987. This rich dataset will enable further discovery and analysis of developmental effects, and associations with seizure development in TSC.
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Affiliation(s)
| | - Jagoda Głowacka-Walas
- Transition Technologies Science, Warsaw, Poland
- Warsaw University of Technology, The Institute of Computer Science, Warsaw, Poland
| | - James D Mills
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | | | - Kathryn Lasseter
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John M Asara
- Department of Medicine, Harvard Medical School and Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Romina Moavero
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
- Developmental Neurology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Christoph Hertzberg
- Diagnose- und Behandlungszentrum für Kinder, Vivantes-Klinikum Neukölln, Berlin, Germany
| | - Bernhard Weschke
- Department of Child Neurology, Charité University Medicine Berlin, Berlin, Germany
| | - Kate Riney
- Neurosciences Unit, Queensland Children's Hospital, South Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Martha Feucht
- Epilepsy Service, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Member of ERN EpiCARE, Vienna, Austria
| | - Theresa Scholl
- Epilepsy Service, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Member of ERN EpiCARE, Vienna, Austria
| | - Pavel Krsek
- Department of Paediatric Neurology, Motol University Hospital, 2nd Medical Faculty, Charles University, Prague, Czech Republic
| | - Rima Nabbout
- Department of Pediatric Neurology, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Université Paris cité, Imagine Institute, Paris, France
| | - Anna C Jansen
- Neurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bořivoj Petrák
- Department of Paediatric Neurology, Motol University Hospital, 2nd Medical Faculty, Charles University, Prague, Czech Republic
| | - Jackelien van Scheppingen
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Josef Zamecnik
- Department. of Pathology and Molecular Medicine, Motol University Hospital, 2nd Medical Faculty, Charles University, Prague, Czech Republic
| | - Anand Iyer
- Department of Internal Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Jasper J Anink
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Angelika Mühlebner
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline Mijnsbergen
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Lieven Lagae
- Department of Development and Regeneration Section Pediatric Neurology, University Hospitals KU Leuven, Leuven, Belgium
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, Rome, Italy
| | - Julita Borkowska
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Krzysztof Sadowski
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Dorota Domańska-Pakieła
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Magdalena Blazejczyk
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Floor E Jansen
- Department of Child Neurology, Brain Center University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Malgorzata Urbanska
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | - Aleksandra Tempes
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Kamil Sijko
- Transition Technologies Science, Warsaw, Poland
| | - Konrad Wojdan
- Transition Technologies Science, Warsaw, Poland
- Warsaw University of Technology, Institute of Heat Engineering, Warsaw, Poland
| | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
- Department of Child Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, member of ERN EPICARE, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Department of (Neuro)Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede the Netherlands, Utrecht, The Netherlands
| | - Jacek Jaworski
- International Institute of Molecular and Cell Biology, Warsaw, Poland
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13
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Prozzillo Y, Santopietro MV, Messina G, Dimitri P. Unconventional roles of chromatin remodelers and long non-coding RNAs in cell division. Cell Mol Life Sci 2023; 80:365. [PMID: 37982870 PMCID: PMC10661750 DOI: 10.1007/s00018-023-04949-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 11/21/2023]
Abstract
The aim of this review article is to focus on the unconventional roles of epigenetic players (chromatin remodelers and long non-coding RNAs) in cell division, beyond their well-characterized functions in chromatin regulation during cell differentiation and development. In the last two decades, diverse experimental evidence has shown that subunits of SRCAP and p400/TIP60 chromatin remodeling complexes in humans relocate from interphase nuclei to centrosomes, spindle or midbody, with their depletion yielding an array of aberrant outcomes of mitosis and cytokinesis. Remarkably, this behavior is shared by orthologous subunits of the Drosophila melanogaster DOM/TIP60 complex, despite fruit flies and humans diverged over 700 million years ago. In short, the available data support the view that subunits of these complexes are a new class of moonlighting proteins, in that they lead a "double life": during the interphase, they function in chromatin regulation within the nucleus, but as the cell progresses through mitosis, they interact with established mitotic factors, thus becoming integral components of the cell division apparatus. By doing so, they contribute to ensuring the correct distribution of chromosomes in the two daughter cells and, when dysfunctional, can cause genomic instability, a condition that can trigger tumorigenesis and developmental diseases. Research over the past few years has unveiled a major contribution of long non-coding RNAs (lncRNAs) in the epigenetics regulation of gene expression which also impacts on cell division control. Here, we focus on possible structural roles of lncRNAs in the execution of cytokinesis: in particular, we suggest that specific classes of lncRNAs relocate to the midbody to form an architectural scaffold ensuring its proper assembly and function during abscission. Drawing attention to experimental evidence for non-canonical extranuclear roles of chromatin factors and lncRNAs has direct implications on important and novel aspects concerning both the epigenetic regulation and the evolutionary dynamics of cell division with a significant impact on differentiation, development, and diseases.
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Affiliation(s)
- Yuri Prozzillo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | | | - Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.
- Universita degli Studi di Milano-Bicocca, Piazza dell' Ateneo Nuovo, 1, 20126, Milano, Italy.
| | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.
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14
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Hu Q, Xia X, Lian Z, Tian H, Li Z. Regulatory mechanism of LncRNAs in gonadal differentiation of hermaphroditic fish, Monopterus albus. Biol Sex Differ 2023; 14:74. [PMID: 37880697 PMCID: PMC10598917 DOI: 10.1186/s13293-023-00559-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Monopterus albus is a hermaphroditic fish with sex reversal from ovaries to testes via the ovotestes in the process of gonadal development, but the molecular mechanism of the sex reversal was unknown. METHODS We produced transcriptomes containing mRNAs and lncRNAs in the crucial stages of the gonad, including the ovary, ovotestis and testis. The expression of the crucial lncRNAs and their target genes was detected using qRT‒PCR and in situ hybridization. The methylation level and activity of the lncRNA promoter were analysed by applying bisulfite sequencing PCR and dual-luciferase reporter assays, respectively. RESULTS This effort revealed that gonadal development was a dynamic expression change. Regulatory networks of lncRNAs and their target genes were constructed through integrated analysis of lncRNA and mRNA data. The expression and DNA methylation of the lncRNAs MSTRG.38036 and MSTRG.12998 and their target genes Psmβ8 and Ptk2β were detected in developing gonads and sex reversal gonads. The results showed that lncRNAs and their target genes exhibited consistent expression profiles and that the DNA methylation levels were negatively regulated lncRNA expression. Furthermore, we found that Ptk2β probably regulates cyp19a1 expression via the Ptk2β/EGFR/STAT3 pathway to reprogram sex differentiation. CONCLUSIONS This study provides novel insight from lncRNA to explore the potential molecular mechanism by which DNA methylation regulates lncRNA expression to facilitate target gene transcription to reprogram sex differentiation in M. albus, which will also enrich the sex differentiation mechanism of teleosts.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China.
| | - Xueping Xia
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Zitong Lian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wudayuan First Road 8, Wuhan, 430223, China.
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15
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McVeigh P, McCammick E, Robb E, Brophy P, Morphew RM, Marks NJ, Maule AG. Discovery of long non-coding RNAs in the liver fluke, Fasciola hepatica. PLoS Negl Trop Dis 2023; 17:e0011663. [PMID: 37769025 PMCID: PMC10564125 DOI: 10.1371/journal.pntd.0011663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 10/10/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Long non-coding (lnc)RNAs are a class of eukaryotic RNA that do not code for protein and are linked with transcriptional regulation, amongst a myriad of other functions. Using a custom in silico pipeline we have identified 6,436 putative lncRNA transcripts in the liver fluke parasite, Fasciola hepatica, none of which are conserved with those previously described from Schistosoma mansoni. F. hepatica lncRNAs were distinct from F. hepatica mRNAs in transcript length, coding probability, exon/intron composition, expression patterns, and genome distribution. RNA-Seq and digital droplet PCR measurements demonstrated developmentally regulated expression of lncRNAs between intra-mammalian life stages; a similar proportion of lncRNAs (14.2%) and mRNAs (12.8%) were differentially expressed (p<0.001), supporting a functional role for lncRNAs in F. hepatica life stages. While most lncRNAs (81%) were intergenic, we identified some that overlapped protein coding loci in antisense (13%) or intronic (6%) configurations. We found no unequivocal evidence for correlated developmental expression within positionally correlated lncRNA:mRNA pairs, but global co-expression analysis identified five lncRNA that were inversely co-regulated with 89 mRNAs, including a large number of functionally essential proteases. The presence of micro (mi)RNA binding sites in 3135 lncRNAs indicates the potential for miRNA-based post-transcriptional regulation of lncRNA, and/or their function as competing endogenous (ce)RNAs. The same annotation pipeline identified 24,141 putative lncRNAs in F. gigantica. This first description of lncRNAs in F. hepatica provides an avenue to future functional and comparative genomics studies that will provide a new perspective on a poorly understood aspect of parasite biology.
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Affiliation(s)
- Paul McVeigh
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Erin McCammick
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Emily Robb
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Peter Brophy
- Department of Life Sciences, Aberystwyth University, Wales, United Kingdom
| | - Russell M. Morphew
- Department of Life Sciences, Aberystwyth University, Wales, United Kingdom
| | - Nikki J. Marks
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Aaron G. Maule
- School of Biological Sciences, Queen’s University Belfast, Northern Ireland, United Kingdom
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16
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis. Genes Dev 2023; 37:829-843. [PMID: 37821107 PMCID: PMC10620047 DOI: 10.1101/gad.350896.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brains from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we showed that imprinted chromatin structure precedes imprinted expression at the locus. Additionally, activation of a distal enhancer induced imprinted expression of Kcnk9 in an allelic chromatin structure-dependent manner. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Courtney M Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Amanda J Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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17
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Valledor M, Byron M, Dumas B, Carone DM, Hall LL, Lawrence JB. Early chromosome condensation by XIST builds A-repeat RNA density that facilitates gene silencing. Cell Rep 2023; 42:112686. [PMID: 37384527 PMCID: PMC10461597 DOI: 10.1016/j.celrep.2023.112686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 10/31/2022] [Accepted: 06/08/2023] [Indexed: 07/01/2023] Open
Abstract
XIST RNA triggers chromosome-wide gene silencing and condenses an active chromosome into a Barr body. Here, we use inducible human XIST to examine early steps in the process, showing that XIST modifies cytoarchitecture before widespread gene silencing. In just 2-4 h, barely visible transcripts populate the large "sparse zone" surrounding the smaller "dense zone"; importantly, density zones exhibit different chromatin impacts. Sparse transcripts immediately trigger immunofluorescence for H2AK119ub and CIZ1, a matrix protein. H3K27me3 appears hours later in the dense zone, which enlarges with chromosome condensation. Genes examined are silenced after compaction of the RNA/DNA territory. Insights into this come from the findings that the A-repeat alone can silence genes and rapidly, but only where dense RNA supports sustained histone deacetylation. We propose that sparse XIST RNA quickly impacts architectural elements to condense the largely non-coding chromosome, coalescing RNA density that facilitates an unstable, A-repeat-dependent step required for gene silencing.
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Affiliation(s)
- Melvys Valledor
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Brett Dumas
- Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Dawn M Carone
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Lisa L Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
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18
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544389. [PMID: 37333073 PMCID: PMC10274912 DOI: 10.1101/2023.06.09.544389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele enhancer-promoter contacts formed early in development prime the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, these enhancer-promoter contacts are blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Courtney M. Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Amanda J. Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
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Kudo R, Yoshida I, Matiz Ceron L, Mizushima S, Kuroki Y, Jogahara T, Kuroiwa A. The Neo-X Does Not Form a Barr Body but Shows a Slightly Condensed Structure in the Okinawa Spiny Rat (Tokudaia muenninki). Cytogenet Genome Res 2023; 162:632-643. [PMID: 37271129 DOI: 10.1159/000531275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/27/2023] [Indexed: 06/06/2023] Open
Abstract
X chromosome inactivation (XCI) is an essential mechanism for gene dosage compensation between male and female cells in mammals. The Okinawa spiny rat (Tokudaia muenninki) is a native rodent in Japan with XX/XY sex chromosomes, like most mammals; however, the X chromosome has acquired a neo-X region (Xp) by fusion with an autosome. We previously reported that dosage compensation has not yet evolved in the neo-X region; however, X-inactive-specific transcript (Xist) RNA (long non-coding RNA required for the initiation of XCI) is partially localized in the region. Here, we show that the neo-X region represents an early chromosomal state in the acquisition of XCI by analyses of heterochromatin and Barr body formation. We found no evidence for heterochromatin formation in the neo-X region by R-banding by acridine orange (RBA) assays and immunostaining of H3K27me3. Double-immunostaining of H3K27me3 and HP1, a component of the Barr body, revealed that the entire ancestral X chromosome region (Xq) showed a bipartite folded structure. By contrast, HP1 was not localized to the neo-X region. However, BAC-FISH revealed that the signals of genes on the neo-X region of the inactive X chromosome were concentrated in a narrow region. These findings indicated that although the neo-X region of the inactive X chromosome does not form a complete Barr body structure (e.g., it lacks HP1), it forms a slightly condensed structure. These findings combined with the previously reported partial binding of Xist RNA suggest that the neo-X region exhibits incomplete inactivation. This may represent an early chromosomal state in the acquisition of the XCI mechanism.
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Affiliation(s)
- Ryoma Kudo
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Ikuya Yoshida
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Luisa Matiz Ceron
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shusei Mizushima
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Center for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takamichi Jogahara
- Faculty of Law, Economics and Management, Okinawa University, Naha, Japan
| | - Asato Kuroiwa
- Reproductive and Developmental Sciences, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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Saxena S, Das A, Kaila T, Ramakrishna G, Sharma S, Gaikwad K. Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea. Genes Genomics 2023; 45:783-811. [PMID: 37115379 DOI: 10.1007/s13258-023-01383-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/21/2022] [Indexed: 04/29/2023]
Abstract
BACKGROUND Long-intergenic non-coding RNAs (lincRNAs) originate from intergenic regions and have no coding potential. LincRNAs have emerged as key players in the regulation of various biological processes in plant development. Cytoplasmic male-sterility (CMS) in association with restorer-of-fertility (Rf) systems makes it a highly reliable tool for exploring heterosis for producing commercial hybrid seeds. To date, there have been no reports of lincRNAs during pollen development in CMS and fertility restorer lines in pigeon pea. OBJECTIVE Identification of lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines. METHODS We employed a computational approach to identify lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines using RNA-Seq data. RESULTS We predicted a total of 2145 potential lincRNAs of which 966 were observed to be differentially expressed between the sterile and fertile pollen. We identified, 927 cis-regulated and 383 trans-regulated target genes of the lincRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the target genes revealed that these genes were specifically enriched in pathways like pollen and pollen tube development, oxidative phosphorylation, etc. We detected 23 lincRNAs that were co-expressed with 17 pollen-related genes with known functions. Fifty-nine lincRNAs were predicted to be endogenous target mimics (eTMs) for 25 miRNAs, and found to be associated with pollen development. The, lincRNA regulatory networks revealed that different lincRNA-miRNA-mRNA networks might be associated with CMS and fertility restoration. CONCLUSION Thus, this study provides valuable information by highlighting the functions of lincRNAs as regulators during pollen development in pigeon pea and utilization in hybrid seed production.
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Affiliation(s)
- Swati Saxena
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Antara Das
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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Nandi S, Mondal A, Ghosh A, Mukherjee S, Das C. Lnc-ing epigenetic mechanisms with autophagy and cancer drug resistance. Adv Cancer Res 2023; 160:133-203. [PMID: 37704287 DOI: 10.1016/bs.acr.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) comprise a diverse class of RNA molecules that regulate various physiological processes and have been reported to be involved in several human pathologies ranging from neurodegenerative disease to cancer. Therapeutic resistance is a major hurdle for cancer treatment. Over the past decade, several studies has emerged on the role of lncRNAs in cancer drug resistance and many trials have been conducted employing them. LncRNAs also regulate different cell death pathways thereby maintaining a fine balance of cell survival and death. Autophagy is a complex cell-killing mechanism that has both cytoprotective and cytotoxic roles. Similarly, autophagy can lead to the induction of both chemosensitization and chemoresistance in cancer cells upon therapeutic intervention. Recently the role of lncRNAs in the regulation of autophagy has also surfaced. Thus, lncRNAs can be used in cancer therapeutics to alleviate the challenges of chemoresistance by targeting the autophagosomal axis. In this chapter, we discuss about the role of lncRNAs in autophagy-mediated cancer drug resistance and its implication in targeted cancer therapy.
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Affiliation(s)
- Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Aritra Ghosh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Indian Institute of Science Education and Research, Kolkata, India
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India.
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22
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Jali I, Vanamamalai VK, Garg P, Navarrete P, Gutiérrez-Adán A, Sharma S. Identification and differential expression of long non-coding RNAs and their association with XIST gene during early embryonic developmental stages of Bos taurus. Int J Biol Macromol 2023; 229:896-908. [PMID: 36572076 DOI: 10.1016/j.ijbiomac.2022.12.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/07/2022] [Accepted: 12/20/2022] [Indexed: 12/26/2022]
Abstract
X-chromosomes inactivation (XCI) is a phenomenon that aims to equalize the dosage of X-linked gene products between XY males and XX females in mammals. XIST gene is the master regulator of X chromosome inactivation during early embryonic developmental stages of Bos taurus. Biological molecule such as lncRNA plays significant role in the control of XCI, by RNA-based regulatory mechanisms and are non-coding regions of the genome. In our study, using in-silico transcriptome data analysis approach, we analysed RNA-seq data of E35, E39 and E43 samples from bovine genital ridges of early embryonic stages, and identified lncRNA transcripts. More than 7 lakh lncRNA transcripts were identified. Further, our study identified DE-lncRNAs and genes between male and female and studied their co-expression. More than four thousand differentially expressed lncRNAs identified. The co-expression and RT-PCR study in the result showed that there exists an association between the XIST and DE-lncRNAs in early embryonic gonads of bovine at E35. In this study, the association between DE-lncRNAs and XIST gene indicates, the potentially important role of DE-lncRNAs during embryo development in bovine. In conclusion, this study shows there exist an interplay between genes and lncRNAs at transcriptome level of bovine during early embryonic days.
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Affiliation(s)
- Itishree Jali
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India; DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, Haryana, India
| | - Venkata Krishna Vanamamalai
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India; DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, Haryana, India
| | - Priyanka Garg
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India
| | - Paula Navarrete
- INIA-CSIC Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Alfonso Gutiérrez-Adán
- INIA-CSIC Centro Nacional Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Opp. Journalist Colony, Near Gowlidoddi, Extended Q City Road, Gachibowli, Hyderabad 500 032, Telangana, India; DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, Haryana, India.
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Czerminski JT, King OD, Lawrence JB. Large-scale organoid study suggests effects of trisomy 21 on early fetal neurodevelopment are more subtle than variability between isogenic lines and experiments. Front Neurosci 2023; 16:972201. [PMID: 36817096 PMCID: PMC9935940 DOI: 10.3389/fnins.2022.972201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/08/2022] [Indexed: 02/05/2023] Open
Abstract
This study examines cortical organoids generated from a panel of isogenic trisomic and disomic iPSC lines (subclones) as a model of early fetal brain development in Down syndrome (DS). An initial experiment comparing organoids from one trisomic and one disomic line showed many genome-wide transcriptomic differences and modest differences in cell-type proportions, suggesting there may be a neurodevelopmental phenotype that is due to trisomy of chr21. To better control for multiple sources of variation, we undertook a highly robust study of ∼1,200 organoids using an expanded panel of six all-isogenic lines, three disomic, and three trisomic. The power of this experimental design was indicated by strong detection of the ∼1.5-fold difference in chr21 genes. However, the numerous expression differences in non-chr21 genes seen in the smaller experiment fell away, and the differences in cell-type representation between lines did not correlate with trisomy 21. Results suggest that the initial smaller experiment picked up differences between small organoid samples and individual isogenic lines, which "averaged out" in the larger panel of isogenic lines. Our results indicate that even when organoid and batch variability are better controlled for, variation between isogenic cell lines (even subclones) may obscure, or be conflated with, subtle neurodevelopmental phenotypes that may be present in ∼2nd trimester DS brain development. Interestingly, despite this variability between organoid batches and lines, and the "fetal stage" of these organoids, an increase in secreted Aβ40 peptide levels-an Alzheimer-related cellular phenotype-was more strongly associated with trisomy 21 status than were neurodevelopmental shifts in cell-type composition.
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Affiliation(s)
- Jan T. Czerminski
- Medical Scientist Training Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Oliver D. King
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States,Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States,*Correspondence: Jeanne B. Lawrence,
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Ma Y, Shi J, Zhang Y, Chen Z, Jia G. Titanium Dioxide Nanoparticles Altered the lncRNA Expression Profile in Human Lung Cells. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1059. [PMID: 36673815 PMCID: PMC9858630 DOI: 10.3390/ijerph20021059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Respiration is considered to be the main occupational or environmental exposure pathway of titanium dioxide nanoparticles (TiO2 NPs), and the lung is considered to be the target organ of respiratory exposure; however, the mechanism of respiratory toxicity is not fully understood. In this study, the effect of TiO2 NPs on the expression profile of long non-coding RNA (lncRNA) in bronchial epithelial cells (BEAS-2B) was investigated to understand their potential toxic mechanism. BEAS-2B cells were treated with 100 μg/mL TiO2 NPs for 48 h, then RNA sequencing was performed to screen the differential lncRNAs compared with the control group, and the enrichment pathways of the differentially expressed lncRNAs were further analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG). The results identified a total of 45,769 lncRNAs, and 277 different lncRNAs were screened. KEGG pathway analysis showed that the targeted mRNAs of these different lncRNAs were enriched in the pyrimidine metabolism pathway. This work demonstrates that TiO2 NPs could alter the lncRNA expression profile in BEAS-2B cells, and epigenetics may play a role in the mechanism of respiratory toxicity induced by TiO2 NPs.
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Affiliation(s)
- Ying Ma
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Jiaqi Shi
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Yi Zhang
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Zhangjian Chen
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
| | - Guang Jia
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing 100191, China
- Beijing Key Laboratory of Toxicological Research and Risk Assessment for Food Safety, School of Public Health, Peking University, Beijing 100191, China
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25
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Motosugi N, Sugiyama A, Okada C, Otomo A, Umezawa A, Akutsu H, Hadano S, Fukuda A. De-erosion of X chromosome dosage compensation by the editing of XIST regulatory regions restores the differentiation potential in hPSCs. CELL REPORTS METHODS 2022; 2:100352. [PMID: 36590687 PMCID: PMC9795333 DOI: 10.1016/j.crmeth.2022.100352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/29/2022] [Accepted: 10/28/2022] [Indexed: 12/02/2022]
Abstract
Human pluripotent stem cells (hPSCs) regularly and irreversibly show the erosion of X chromosome inactivation (XCI) by long non-coding RNA (lncRNA) XIST silencing, causing challenges in various applications of female hPSCs. Here, we report reliable methods to reactivate XIST with monoallelic expression in female hPSCs. Surprisingly, we find that the editing of XIST regulatory regions by Cas9-mediated non-homologous end joining is sufficient for the reactivation of XIST by endogenous systems. Proliferated hPSCs with XIST reactivation show XCI from an eroded X chromosome, suggesting that hPSCs with normal dosage compensation might lead to a growth advantage. Furthermore, the use of targeting vectors, including the XIST regulatory region sequences and selection cassette, enables XIST reactivation in hPSCs with high efficiency. XIST-reactivated hPSCs can show the restoration of differentiation potential. Thus, our findings demonstrate that XIST re-expression is a beneficial method to maximize the use of female hPSCs in various applications, such as proper disease modeling.
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Affiliation(s)
- Nami Motosugi
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Akiko Sugiyama
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chisa Okada
- Support Center for Medical Research and Education, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Asako Otomo
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Shinji Hadano
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan
| | - Atsushi Fukuda
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
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RNA-Mediated Regulation of Meiosis in Budding Yeast. Noncoding RNA 2022; 8:ncrna8060077. [PMID: 36412912 PMCID: PMC9680404 DOI: 10.3390/ncrna8060077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cells change their physiological state in response to environmental cues. In the absence of nutrients, unicellular fungi such as budding yeast exit mitotic proliferation and enter the meiotic cycle, leading to the production of haploid cells that are encased within spore walls. These cell state transitions are orchestrated in a developmentally coordinated manner. Execution of the meiotic cell cycle program in budding yeast, Saccharomyces cerevisiae, is regulated by the key transcription factor, Ime1. Recent developments have uncovered the role of non-coding RNA in the regulation of Ime1 and meiosis. In this review, we summarize the role of ncRNA-mediated and RNA homeostasis-based processes in the regulation of meiosis in Saccharomyces cerevisiae.
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Circulating Long Non-Coding RNAs Could Be the Potential Prognostic Biomarker for Liquid Biopsy for the Clinical Management of Oral Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14225590. [PMID: 36428681 PMCID: PMC9688117 DOI: 10.3390/cancers14225590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) have little or no coding potential. These transcripts are longer than 200 nucleotides. Since lncRNAs are master regulators of almost all biological processes, recent evidence proves that aberrantly expressed lncRNAs are pathogenic for oral squamous cell carcinoma (OSCC) and other diseases. LncRNAs influence chromatin modifications, transcriptional modifications, post-transcriptional modifications, genomic imprinting, cell proliferation, invasion, metastasis, and apoptosis. Consequently, they have an impact on the disease transformation, progression, and morbidity in OSCC. Therefore, circulating lncRNAs could be the potential cancer biomarker for the better clinical management (diagnosis, prognosis, and monitoring) of OSCC to provide advanced treatment strategies and clinical decisions. In this review, we report and discuss the recent understandings and perceptions of dysregulated lncRNAs with a focus on their clinical significance in OSCC-disease monitoring and treatment. Evidence clearly indicates that a specific lncRNA expression signature could act as an indicator for the early prediction of diagnosis and prognosis for the initiation, progression, recurrence, metastasis and other clinical prognostic-factors (overall survival, disease-free survival, etc.) in OSCC. The present review demonstrates the current knowledge that all potential lncRNA expression signatures are molecular biomarkers for the early prediction of prognosis in OSCC. Finally, the review provides information about the clinical significance, challenges and limitations of the clinical usage of circulating lncRNAs in a liquid biopsy method in early, pre-symptomatic, sub-clinical, accurate OSCC prognostication. More studies on lncRNA are required to unveil the biology of the inherent mechanisms involved in the process of the development of differential prognostic outcomes in OSCC.
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Li J, Wu X, Ma H, Sun G, Ding P, Lu S, Zhang L, Yang P, Peng Y, Fu J, Wang L. New developments in non-exosomal and exosomal ncRNAs in coronary artery disease. Epigenomics 2022; 14:1355-1372. [PMID: 36514887 DOI: 10.2217/epi-2022-0201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim & methods: Non-exosomal and exosomal ncRNAs have been reported to be involved in the regulation of coronary artery disease (CAD). Therefore, to explore the biological effects of non-exosomal/exosomal ncRNAs in CAD, the authors searched for studies published in the last 3 years on these ncRNAs in CAD and summarized their functions and mechanisms. Results: The authors summarized 120 non-exosomal ncRNAs capable of regulating CAD progression. In clinical studies, 47 non-exosomal and nine exosomal ncRNAs were able to serve as biomarkers for the diagnosis of CAD. Conclusion: Non-exosomal/exosomal ncRNAs are not only able to serve as biomarkers for CAD diagnosis but can also regulate CAD progression through ceRNA mechanisms and are a potential target for early clinical intervention in CAD.
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Affiliation(s)
- Jingru Li
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Xinyu Wu
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Haocheng Ma
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Guihu Sun
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Peng Ding
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Si Lu
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Lijiao Zhang
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Ping Yang
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Yunzhu Peng
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Jingyun Fu
- Department of Endocrinology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Luqiao Wang
- Department of Cardiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
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Zhang T, Wang WL, Liu TJ, Lu S, Bian YC, Xiao R, Zhang CL. LncRNA <i>Gm16638-201</i> Inhibits the 14-3-3Ɛ Pathway in the Murine Prefrontal Cortex to Induce Depressive Behaviors. Biol Pharm Bull 2022; 45:1616-1626. [DOI: 10.1248/bpb.b22-00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ting Zhang
- Inner Mongolia Key Laboratory of Molecular Pathology, Inner Mongolia Medical University
| | - Wan Lun Wang
- Inner Mongolia Key Laboratory of Molecular Pathology, Inner Mongolia Medical University
| | - Tong Jia Liu
- Inner Mongolia Key Laboratory of Molecular Pathology, Inner Mongolia Medical University
| | - Shuang Lu
- Inner Mongolia Key Laboratory of Molecular Pathology, Inner Mongolia Medical University
| | - Yan Chao Bian
- Inner Mongolia Key Laboratory of Molecular Pathology, Inner Mongolia Medical University
| | - Rui Xiao
- Inner Mongolia Key Laboratory of Molecular Pathology, Inner Mongolia Medical University
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30
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31
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Bondhus L, Wei A, Arboleda VA. DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features. BMC Bioinformatics 2022; 23:364. [PMID: 36064314 PMCID: PMC9447346 DOI: 10.1186/s12859-022-04899-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 08/22/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Pathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers exhibit extraordinary diversity in the scale of the epigenetic changes they affect, from single basepair modifications by DNMT1 to whole genome structural changes by PRM1/2. Patterns of DNA methylation are related to a diverse set of epigenetic features across this full range of epigenetic scale, making DNA methylation valuable for mapping regions of general epigenetic dysregulation. However, existing methods are unable to accurately identify regions of differential methylation across this full range of epigenetic scale directly from DNA methylation data. RESULTS To address this, we developed DMRscaler, a novel method that uses an iterative windowing procedure to capture regions of differential DNA methylation (DMRs) ranging in size from single basepairs to whole chromosomes. We benchmarked DMRscaler against several DMR callers in simulated and natural data comparing XX and XY peripheral blood samples. DMRscaler was the only method that accurately called DMRs ranging in size from 100 bp to 1 Mb (pearson's r = 0.94) and up to 152 Mb on the X-chromosome. We then analyzed methylation data from rare-disease cohorts that harbor chromatin modifier gene mutations in NSD1, EZH2, and KAT6A where DMRscaler identified novel DMRs spanning gene clusters involved in development. CONCLUSION Taken together, our results show DMRscaler is uniquely able to capture the size of DMR features across the full range of epigenetic scale and identify novel, co-regulated regions that drive epigenetic dysregulation in human disease.
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Affiliation(s)
- Leroy Bondhus
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Angela Wei
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA
| | - Valerie A. Arboleda
- grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, UCLA, 615 Charles E. Young Drive South, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Bioinformatics Interdepartmental PhD Program, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Molecular Biology Institute, UCLA, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095 USA
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Transcriptome-Wide Detection of Intron/Exon Definition in the Endogenous Pre-mRNA Transcripts of Mammalian Cells and Its Regulation by Depolarization. Int J Mol Sci 2022; 23:ijms231710157. [PMID: 36077555 PMCID: PMC9456152 DOI: 10.3390/ijms231710157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
Pairing of splice sites across an intron or exon is the central point of intron or exon definition in pre-mRNA splicing with the latter mode proposed for most mammalian exons. However, transcriptome-wide pairing within endogenous transcripts has not been examined for the prevalence of each mode in mammalian cells. Here we report such pairings in rat GH3 pituitary cells by measuring the relative abundance of nuclear RNA-Seq reads at the intron start or end (RISE). Interestingly, RISE indexes are positively correlated between 5′ and 3′ splice sites specifically across introns or exons but inversely correlated with the usage of adjacent exons. Moreover, the ratios between the paired indexes were globally modulated by depolarization, which was disruptible by 5-aza-Cytidine. The nucleotide matrices of the RISE-positive splice sites deviate significantly from the rat consensus, and short introns or exons are enriched with the cross-intron or -exon RISE pairs, respectively. Functionally, the RISE-positive genes cluster for basic cellular processes including RNA binding/splicing, or more specifically, hormone production if regulated by depolarization. Together, the RISE analysis identified the transcriptome-wide regulation of either intron or exon definition between weak splice sites of short introns/exons in mammalian cells. The analysis also provides a way to further track the splicing intermediates and intron/exon definition during the dynamic regulation of alternative splicing by extracellular factors.
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Lovell CD, Anguera MC. Long Noncoding RNAs That Function in Nutrition: Lnc-ing Nutritional Cues to Metabolic Pathways. Annu Rev Nutr 2022; 42:251-274. [PMID: 35436418 DOI: 10.1146/annurev-nutr-062220-030244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Long noncoding RNAs (lncRNAs) are sensitive to changing environments and play key roles in health and disease. Emerging evidence indicates that lncRNAs regulate gene expression to shape metabolic processes in response to changing nutritional cues. Here we review various lncRNAs sensitive to fasting, feeding, and high-fat diet in key metabolic tissues (liver, adipose, and muscle), highlighting regulatory mechanisms that trigger expression changes of lncRNAs themselves, and how these lncRNAs regulate gene expression of key metabolic genes in specific cell types or across tissues. Determining how lncRNAs respond to changes in nutrition is critical for our understanding of the complex downstream cascades following dietary changes and can shape how we treat metabolic disease. Furthermore, investigating sex biases that might influence lncRNA-regulated responses will likely reveal contributions toward the observed disparities between the sexes in metabolic diseases.
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Affiliation(s)
- Claudia D Lovell
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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34
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Moon JE, Lawrence JB. Chromosome silencing in vitro reveals trisomy 21 causes cell-autonomous deficits in angiogenesis and early dysregulation in Notch signaling. Cell Rep 2022; 40:111174. [PMID: 35947952 PMCID: PMC9505374 DOI: 10.1016/j.celrep.2022.111174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 12/24/2021] [Accepted: 07/18/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the prevalence of Down syndrome (DS), little is known regarding the specific cell pathologies that underlie this multi-system disorder. To understand which cell types and pathways are more directly affected by trisomy 21 (T21), we used an inducible-XIST system to silence one chromosome 21 in vitro. T21 caused the dysregulation of Notch signaling in iPSCs, potentially affecting cell-type programming. Further analyses identified dysregulation of pathways important for two cell types: neurogenesis and angiogenesis. Angiogenesis is essential to many bodily systems, yet is understudied in DS; therefore, we focused next on whether T21 affects endothelial cells. An in vitro assay for microvasculature formation revealed a cellular pathology involving delayed tube formation in response to angiogenic signals. Parallel transcriptomic analysis of endothelia further showed deficits in angiogenesis regulators. Results indicate a direct cell-autonomous impact of T21 on endothelial function, highlighting the importance of angiogenesis, with wide-reaching implications for development and disease progression. Moon and Lawrence examine the immediate effects of trisomy 21 silencing and find angiogenesis and neurogenesis pathways, including Notch signaling, affected as early as pluripotency. In endothelial cells, functional analyses show that trisomy delays the angiogenic response for microvessel formation and transcriptomics show a parallel impact on angiogenic regulators and signal-response and cytoskeleton processes.
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Affiliation(s)
- Jennifer E Moon
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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35
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Wang S, Tan B, Xiao L, Zeng J, Zhao X, Hong L, Li Z, Cai G, Zheng E, Gu T, Wu Z. Long non-coding RNA Gm10561 promotes myogenesis by sponging miR-432. Epigenetics 2022; 17:2039-2055. [PMID: 35899799 DOI: 10.1080/15592294.2022.2105052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Skeletal myogenesis is a highly ordered process finely regulated by various factors. Long non-coding RNAs play an important regulatory role in myogenesis via multiple mechanisms. In this study, we identified the lncRNA Gm10561, which was upregulated during myogenic differentiation and is highly expressed in skeletal muscle. Knockdown of Gm10561 inhibited the proliferation and differentiation of C2C12 myoblasts in vitro and muscle growth in vivo. Overexpression of Gm10561 promoted the proliferation and differentiation of both C2C12 myoblasts and porcine muscle satellite cells. Notably, lncRNA Gm10561 is localized in the cytoplasm and competitively bound to miR-432, which directly targets MEF2C and E2F3. It was confirmed that lncRNA Gm10561 regulates the proliferation and differentiation of myoblasts by acting as a sponge of miR-432 to modulate MEF2C and E2F3 expression. Thus, the lncRNA-Gm10561-miR-432-MEF2C/E2F3 axis plays an important role in myogenesis.
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Affiliation(s)
- Shanshan Wang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Baohua Tan
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liyao Xiao
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jiekang Zeng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xinming Zhao
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, Guangdong, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangzhou, Guangdong, China
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36
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Fatema K, Larson Z, Barrott J. Navigating the genomic instability mine field of osteosarcoma to better understand implications of non-coding RNAs. BIOCELL 2022; 46:2177-2193. [PMID: 35755302 PMCID: PMC9224338 DOI: 10.32604/biocell.2022.020141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Osteosarcoma is one of the most genomically complex cancers and as result, it has been difficult to assign genomic aberrations that contribute to disease progression and patient outcome consistently across samples. One potential source for correlating osteosarcoma and genomic biomarkers is within the non-coding regions of RNA that are differentially expressed. However, it is unsurprising that a cancer classification that is fraught with genomic instability is likely to have numerous studies correlating non-coding RNA expression and function have been published on the subject. This review undertakes the formidable task of evaluating the published literature of noncoding RNAs in osteosarcoma. This is not the first review on this topic and will certainly not be the last. The review is organized with an introduction into osteosarcoma and the epigenetic control of gene expression before reviewing the molecular function and expression of long non-coding RNAs, circular RNAs, and short non-coding RNAs such as microRNAs, piwi RNAs, and short-interfering RNAs. The review concludes with a review of the literature and how the biology of non-coding RNAs can be used therapeutically to treat cancers, especially osteosarcoma. We conclude that non-coding RNA expression and function in osteosarcoma is equally complex to understanding the expression differences and function of coding RNA and proteins; however, with the added lens of both coding and non-coding genomic sequence, researchers can begin to identify the patterns that consistently associate with aggressive osteosarcoma.
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Affiliation(s)
- Kaniz Fatema
- Biomedical and Pharmaceutical Science, Idaho State University, Pocatello, 83209, USA
| | - Zachary Larson
- Biomedical and Pharmaceutical Science, Idaho State University, Pocatello, 83209, USA
| | - Jared Barrott
- Biomedical and Pharmaceutical Science, Idaho State University, Pocatello, 83209, USA
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37
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Abstract
It has long been proposed that nuclear RNAs might play an important role in organizing the structure of the nucleus. Initial experiments performed more than 30 years ago found that global disruption of RNA led to visible rearrangements of nuclear organization. Yet, this idea remained controversial for many years, in large part because it was unclear what specific RNAs might be involved, and which specific nuclear structures might be dependent on RNA. Over the past few years, the contributions of RNA to organizing nuclear structures have become clearer with the discovery that many nuclear bodies are enriched for specific noncoding RNAs (ncRNAs); in specific cases, ncRNAs have been shown to be essential for establishment and maintenance of these nuclear structures. More recently, many different ncRNAs have been shown to play critical roles in initiating the three-dimensional (3D) spatial organization of DNA, RNA, and protein molecules in the nucleus. These examples, combined with global imaging and genomic experiments, have begun to paint a picture of a broader role for RNA in nuclear organization and to uncover a unifying mechanism that may explain why RNA is a uniquely suited molecule for this role. In this review, we provide an overview of the history of RNA and nuclear structure and discuss key examples of RNA-mediated bodies, the global roles of ncRNAs in shaping nuclear structure, and emerging insights into mechanisms of RNA-mediated nuclear organization.
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Affiliation(s)
- Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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38
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Dossin F, Heard E. The Molecular and Nuclear Dynamics of X-Chromosome Inactivation. Cold Spring Harb Perspect Biol 2022; 14:a040196. [PMID: 34312245 PMCID: PMC9121902 DOI: 10.1101/cshperspect.a040196] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In female eutherian mammals, dosage compensation of X-linked gene expression is achieved during development through transcriptional silencing of one of the two X chromosomes. Following X chromosome inactivation (XCI), the inactive X chromosome remains faithfully silenced throughout somatic cell divisions. XCI is dependent on Xist, a long noncoding RNA that coats and silences the X chromosome from which it is transcribed. Xist coating triggers a cascade of chromosome-wide changes occurring at the levels of transcription, chromatin composition, chromosome structure, and spatial organization within the nucleus. XCI has emerged as a paradigm for the study of such crucial nuclear processes and the dissection of their functional interplay. In the past decade, the advent of tools to characterize and perturb these processes have provided an unprecedented understanding into their roles during XCI. The mechanisms orchestrating the initiation of XCI as well as its maintenance are thus being unraveled, although many questions still remain. Here, we introduce key aspects of the XCI process and review the recent discoveries about its molecular basis.
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Affiliation(s)
- François Dossin
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
| | - Edith Heard
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
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39
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Samanta MK, Gayen S, Harris C, Maclary E, Murata-Nakamura Y, Malcore RM, Porter RS, Garay PM, Vallianatos CN, Samollow PB, Iwase S, Kalantry S. Activation of Xist by an evolutionarily conserved function of KDM5C demethylase. Nat Commun 2022; 13:2602. [PMID: 35545632 PMCID: PMC9095838 DOI: 10.1038/s41467-022-30352-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
XX female and XY male therian mammals equalize X-linked gene expression through the mitotically-stable transcriptional inactivation of one of the two X chromosomes in female somatic cells. Here, we describe an essential function of the X-linked homolog of an ancestral X-Y gene pair, Kdm5c-Kdm5d, in the expression of Xist lncRNA, which is required for stable X-inactivation. Ablation of Kdm5c function in females results in a significant reduction in Xist RNA expression. Kdm5c encodes a demethylase that enhances Xist expression by converting histone H3K4me2/3 modifications into H3K4me1. Ectopic expression of mouse and human KDM5C, but not the Y-linked homolog KDM5D, induces Xist in male mouse embryonic stem cells (mESCs). Similarly, marsupial (opossum) Kdm5c but not Kdm5d also upregulates Xist in male mESCs, despite marsupials lacking Xist, suggesting that the KDM5C function that activates Xist in eutherians is strongly conserved and predates the divergence of eutherian and metatherian mammals. In support, prototherian (platypus) Kdm5c also induces Xist in male mESCs. Together, our data suggest that eutherian mammals co-opted the ancestral demethylase KDM5C during sex chromosome evolution to upregulate Xist for the female-specific induction of X-inactivation.
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Affiliation(s)
- Milan Kumar Samanta
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Srimonta Gayen
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Emily Maclary
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Yumie Murata-Nakamura
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Rebecca M Malcore
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Robert S Porter
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Patricia M Garay
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Christina N Vallianatos
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Paul B Samollow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.
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Jara E, Peñagaricano F, Armstrong E, Menezes C, Tardiz L, Rodons G, Iriarte A. Identification of Long Noncoding RNAs Involved in Eyelid Pigmentation of Hereford Cattle. Front Genet 2022; 13:864567. [PMID: 35601493 PMCID: PMC9114348 DOI: 10.3389/fgene.2022.864567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/20/2022] [Indexed: 12/05/2022] Open
Abstract
Several ocular pathologies in cattle, such as ocular squamous cell carcinoma and infectious keratoconjunctivitis, have been associated with low pigmentation of the eyelids. The main objective of this study was to analyze the transcriptome of eyelid skin in Hereford cattle using strand-specific RNA sequencing technology to characterize and identify long noncoding RNAs (lncRNAs). We compared the expression of lncRNAs between pigmented and unpigmented eyelids and analyzed the interaction of lncRNAs and putative target genes to reveal the genetic basis underlying eyelid pigmentation in cattle. We predicted 4,937 putative lncRNAs mapped to the bovine reference genome, enriching the catalog of lncRNAs in Bos taurus. We found 27 differentially expressed lncRNAs between pigmented and unpigmented eyelids, suggesting their involvement in eyelid pigmentation. In addition, we revealed potential links between some significant differentially expressed lncRNAs and target mRNAs involved in the immune response and pigmentation. Overall, this study expands the catalog of lncRNAs in cattle and contributes to a better understanding of the biology of eyelid pigmentation.
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Affiliation(s)
- Eugenio Jara
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Eileen Armstrong
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Claudia Menezes
- Laboratorio de Endocrinología y Metabolismo Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Lucía Tardiz
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Gastón Rodons
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
- *Correspondence: Andrés Iriarte,
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41
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Yu Y, Pang D, Li C, Gu X, Chen Y, Ou R, Wei Q, Shang H. The expression discrepancy and characteristics of long non-coding RNAs in peripheral blood leukocytes from amyotrophic lateral sclerosis patients. Mol Neurobiol 2022; 59:3678-3689. [PMID: 35364800 DOI: 10.1007/s12035-022-02789-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/12/2021] [Indexed: 02/08/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is known to be a progressive neurodegenerative disease that affects upper and lower motor neurons. Less than 10% of ALS patients are defined as familial ALS, and more than 90% are sporadic ALS (SALS). According to the genomic information described in existing databases, up to 98% of the human genome consists of non-coding sequences. Nearly 40% of long non-coding RNAs (lncRNAs) are specifically expressed in the brain. We believe that the discrepancy of lncRNAs expression plays a key role in neurodegenerative diseases. We screened 30 lncRNAs with altered expression from peripheral blood leukocytes of SALS patients by microarray and validated 13 of them in leukocytes of SALS, Parkinson's disease (PD) patients, and healthy controls (HC). We followed the bioinformatics to perform a functional enrichment analysis of co-expressed mRNAs, transcription factors, and lncRNAs for functional prediction. We identified that lnc-DYRYK2-7:1, lnc-ABCA12-3:1, and lnc-POTEM-4:7 show decreased expression in SALS patients, whereas in PD patients, they show increased expression or no change. In addition, expression of lnc-CNTN4-2:1 and lnc-NR3C2-8:1 was decreased in both SALS and PD patients. We found that XIST was only reduced in male patients with SALS and PD, and not in female patients with SALS but was elevated in PD by gender grouping. We also performed GO term enrichment and KEGG pathway analysis for lncRNAs showing differential expression in microarray. We discovered that a significant proportion of differential expressed lncRNAs were associated with various signaling pathways and transcription factors which are consistent with other clinical findings.
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Affiliation(s)
- Yujiao Yu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Xiaojing Gu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Yongping Chen
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Ruwei Ou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No.37, Guoxue Lane, Chengdu, Sichuan, 610041, China.
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42
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From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet 2022; 23:229-243. [PMID: 34837040 DOI: 10.1038/s41576-021-00427-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA (lncRNA) loci in the human genome, but evidence of functional significance has remained controversial for many lncRNAs. Genetically engineered model organisms are considered the gold standard for linking genotype to phenotype. Recent advances in CRISPR-Cas genome editing have led to a rapid increase in the use of mouse models to more readily survey lncRNAs for functional significance. Here, we review strategies to investigate the physiological relevance of lncRNA loci by highlighting studies that have used genetic mouse models to reveal key in vivo roles for lncRNAs, from fertility to brain development. We illustrate how an investigative approach, starting with whole-gene deletion followed by transcription termination and/or transgene rescue strategies, can provide definitive evidence for the in vivo function of mammalian lncRNAs.
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43
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Cao H, Kapranov P. Methods to Analyze the Non-Coding RNA Interactome—Recent Advances and Challenges. Front Genet 2022; 13:857759. [PMID: 35368711 PMCID: PMC8969105 DOI: 10.3389/fgene.2022.857759] [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: 01/19/2022] [Accepted: 02/15/2022] [Indexed: 12/03/2022] Open
Abstract
Most of the human genome is transcribed to generate a multitude of non-coding RNAs. However, while these transcripts have generated an immense amount of scientific interest, their biological function remains a subject of an intense debate. Understanding mechanisms of action of non-coding RNAs is a key to addressing the issue of biological relevance of these transcripts. Based on some well-understood non-coding RNAs that function inside the cell by interacting with other molecules, it is generally believed many other non-coding transcripts could also function in a similar fashion. Therefore, development of methods that can map RNA interactome is the key to understanding functionality of the extensive cellular non-coding transcriptome. Here, we review the vast progress that has been made in the past decade in technologies that can map RNA interactions with different sites in DNA, proteins or other RNA molecules; the general approaches used to validate the existence of novel interactions; and the challenges posed by interpreting the data obtained using the interactome mapping methods.
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44
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Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. Nat Struct Mol Biol 2022; 29:239-249. [PMID: 35301492 DOI: 10.1038/s41594-022-00739-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/28/2022] [Indexed: 11/08/2022]
Abstract
Although thousands of long non-coding RNAs (lncRNAs) are encoded in mammalian genomes, their mechanisms of action are poorly understood, in part because they are often expressed at lower levels than their proposed targets. One such lncRNA is Xist, which mediates chromosome-wide gene silencing on one of the two X chromosomes (X) to achieve gene expression balance between males and females. How a limited number of Xist molecules can mediate robust silencing of a much larger number of target genes while maintaining specificity exclusively to genes on the X within each cell is not well understood. Here, we show that Xist drives non-stoichiometric recruitment of the essential silencing protein SHARP (also known as SPEN) to amplify its abundance across the inactive X, including at regions not directly occupied by Xist. This amplification is achieved through concentration-dependent homotypic assemblies of SHARP on the X and is required for chromosome-wide silencing. Expression of Xist at higher levels leads to increased localization at autosomal regions, demonstrating that low levels of Xist are critical for ensuring its specificity to the X. We show that Xist (through SHARP) acts to suppress production of its own RNA which may act to constrain overall RNA levels and restrict its ability to spread beyond the X. Together, our results demonstrate a spatial amplification mechanism that allows Xist to achieve two essential but countervailing regulatory objectives: chromosome-wide gene silencing and specificity to the X. This suggests a more general mechanism by which other low-abundance lncRNAs could balance specificity to, and robust control of, their regulatory targets.
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45
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Abstract
Recently an explosion in the discovery of long noncoding RNAs (lncRNAs) was obtained by high-throughput sequencing. Genome-wide transcriptome analyses, in conjugation with research for epigenetic modifications of chromatins, identified a novel type of non-protein coding transcripts longer than 200 nucleotides named lncRNAs . They are gradually emerging as functional and critical participants in many physiological processes. Here we gave an overview of the characteristics, biological functions, and working mechanism for this new class of noncoding RNA molecules.
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46
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Liu N, Wang P, Li X, Pei Y, Sun Y, Ma X, Ge X, Zhu Y, Li F, Hou Y. Long Non-Coding RNAs profiling in pathogenesis of Verticillium dahliae: New insights in the host-pathogen interaction. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111098. [PMID: 34895536 DOI: 10.1016/j.plantsci.2021.111098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/29/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
Verticillium dahliae causes vascular wilt disease on cotton (Gossypium hirsutum), resulting in devastating yield loss worldwide. While little is known about the mechanism of long non-coding RNAs (lncRNAs), several lncRNAs have been implicated in numerous physiological processes and diseases. To better understand V. dahliae pathogenesis, lncRNA was conducted in a V. dahliae virulence model. Potential target genes of significantly regulated lncRNAs were predicted using cis/trans-regulatory algorithms. This study provides evidence for lncRNAs' regulatory role in pathogenesis-related genes. Interestingly, lncRNAs were identified and varying in terms of RNA length and nutrient starvation treatments. Efficient pathogen nutrition during the interaction with the host is a requisite factor during infection. Our observations directly link to mutated V. dahliae invasion, explaining infected cotton have lower pathogenicity and lethality compared to V. dahliae. Remarkably, lncRNAs XLOC_006536 and XLOC_000836 involved in the complex regulation of pathogenesis-related genes in V. dahliae were identified. For the first time the regulatory role of lncRNAs in filamentous fungi was uncovered, and it is our contention that elucidation of lncRNAs will advance our understanding in the development and pathogenesis of V. dahliae and offer alternatives in the control of the diseases caused by fungus V. dahliae attack.
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Affiliation(s)
- Nana Liu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Ping Wang
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiancai Li
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Yakun Pei
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Yun Sun
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiaowen Ma
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, People's Republic of China
| | - Yutao Zhu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, People's Republic of China.
| | - Yuxia Hou
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China.
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47
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Hazan J, Bester AC. CRISPR-Based Approaches for the High-Throughput Characterization of Long Non-Coding RNAs. Noncoding RNA 2021; 7:79. [PMID: 34940760 PMCID: PMC8704461 DOI: 10.3390/ncrna7040079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022] Open
Abstract
Over the last decade, tens of thousands of new long non-coding RNAs (lncRNAs) have been identified in the human genome. Nevertheless, except for a handful of genes, the genetic characteristics and functions of most of these lncRNAs remain elusive; this is partially due to their relatively low expression, high tissue specificity, and low conservation across species. A major limitation for determining the function of lncRNAs was the lack of methodologies suitable for studying these genes. The recent development of CRISPR/Cas9 technology has opened unprecedented opportunities to uncover the genetic and functional characteristics of the non-coding genome via targeted and high-throughput approaches. Specific CRISPR/Cas9-based approaches were developed to target lncRNA loci. Some of these approaches involve modifying the sequence, but others were developed to study lncRNAs by inducing transcriptional and epigenetic changes. The discovery of other programable Cas proteins broaden our possibilities to target RNA molecules with greater precision and accuracy. These approaches allow for the knock-down and characterization of lncRNAs. Here, we review how various CRISPR-based strategies have been used to characterize lncRNAs with important functions in different biological contexts and how these approaches can be further utilized to improve our understanding of the non-coding genome.
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48
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Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell 2021; 184:6174-6192.e32. [PMID: 34813726 PMCID: PMC8671326 DOI: 10.1016/j.cell.2021.10.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 02/08/2023]
Abstract
The lncRNA Xist forms ∼50 diffraction-limited foci to transcriptionally silence one X chromosome. How this small number of RNA foci and interacting proteins regulate a much larger number of X-linked genes is unknown. We show that Xist foci are locally confined, contain ∼2 RNA molecules, and nucleate supramolecular complexes (SMACs) that include many copies of the critical silencing protein SPEN. Aggregation and exchange of SMAC proteins generate local protein gradients that regulate broad, proximal chromatin regions. Partitioning of numerous SPEN molecules into SMACs is mediated by their intrinsically disordered regions and essential for transcriptional repression. Polycomb deposition via SMACs induces chromatin compaction and the increase in SMACs density around genes, which propagates silencing across the X chromosome. Our findings introduce a mechanism for functional nuclear compartmentalization whereby crowding of transcriptional and architectural regulators enables the silencing of many target genes by few RNA molecules.
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49
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Kolpa HJ, Creamer KM, Hall LL, Lawrence JB. SAF-A mutants disrupt chromatin structure through dominant negative effects on RNAs associated with chromatin. Mamm Genome 2021; 33:366-381. [PMID: 34859278 PMCID: PMC9114059 DOI: 10.1007/s00335-021-09935-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022]
Abstract
Here we provide a brief review of relevant background before presenting results of our investigation into the interplay between scaffold attachment factor A (SAF-A), chromatin-associated RNAs, and DNA condensation. SAF-A, also termed heterogenous nuclear protein U (hnRNP U), is a ubiquitous nuclear scaffold protein that was implicated in XIST RNA localization to the inactive X-chromosome (Xi) but also reported to maintain open DNA packaging in euchromatin. Here we use several means to perturb SAF-A and examine potential impacts on the broad association of RNAs on euchromatin, and on chromatin compaction. SAF-A has an N-terminal DNA binding domain and C-terminal RNA binding domain, and a prominent model has been that the protein provides a single-molecule bridge between XIST RNA and chromatin. Here analysis of the impact of SAF-A on broad RNA-chromatin interactions indicate greater biological complexity. We focus on SAF-A's role with repeat-rich C0T-1 hnRNA (repeat-rich heterogeneous nuclear RNA), shown recently to comprise mostly intronic sequences of pre-mRNAs and diverse long non-coding RNAs (lncRNAs). Our results show that SAF-A mutants cause dramatic changes to cytological chromatin condensation through dominant negative effects on C0T-1 RNA's association with euchromatin, and likely other nuclear scaffold factors. In contrast, depletion of SAF-A by RNA interference (RNAi) had no discernible impact on C0T-1 RNA, nor did it cause similarly marked chromatin changes as did three different SAF-A mutations. Overall results support the concept that repeat-rich, chromatin-associated RNAs interact with multiple RNA binding proteins (RBPs) in a complex dynamic meshwork that is integral to larger-scale chromatin architecture and collectively influences cytological-scale DNA condensation.
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Affiliation(s)
- Heather J Kolpa
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,Ashfield MedComms, Lyndhurst, NJ, 07071, USA
| | - Kevin M Creamer
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Lisa L Hall
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA. .,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA. .,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
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50
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Matsuura R, Nakajima T, Ichihara S, Sado T. Ectopic Splicing Disturbs the Function of Xist RNA to Establish the Stable Heterochromatin State. Front Cell Dev Biol 2021; 9:751154. [PMID: 34722536 PMCID: PMC8551810 DOI: 10.3389/fcell.2021.751154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Non-coding Xist RNA plays an essential role in X chromosome inactivation (XCI) in female mammals. It coats the X chromosome in cis and mediates the recruitment of many proteins involved in gene silencing and heterochromatinization. The molecular basis of how Xist RNA initiates chromosomal silencing and what proteins participate in this process has been extensively studied and elucidated. Its involvement in the establishment and maintenance of the X-inactivated state is, however, less understood. The XistIVS allele we previously reported is peculiar in that it can initiate XCI but fails to establish the inactive state that is stably maintained and, therefore, may provide an opportunity to explore how Xist RNA contributes to establish a robust heterochromatin state. Here we demonstrate that ectopic splicing taking place to produce XistIVS RNA disturbs its function to properly establish stable XCI state. This finding warrants the potential of XistIVS RNA to provide further insight into our understanding of how Xist RNA contributes to establish sustainable heterochromatin.
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Affiliation(s)
- Ruka Matsuura
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Tatsuro Nakajima
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Saya Ichihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan
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