1
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Dhaka B, Zimmerli M, Hanhart D, Moser M, Guillen-Ramirez H, Mishra S, Esposito R, Polidori T, Widmer M, García-Pérez R, Julio MKD, Pervouchine D, Melé M, Chouvardas P, Johnson R. Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates. Nucleic Acids Res 2024; 52:2821-2835. [PMID: 38348970 PMCID: PMC11014264 DOI: 10.1093/nar/gkae075] [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: 05/31/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such 'cis-lncRNAs' are presently defined using ad hoc criteria that, we show, are prone to false-positive predictions. The resulting lack of cis-lncRNA catalogues hinders our understanding of their extent, characteristics and mechanisms. Here, we introduce TransCistor, a framework for defining and identifying cis-lncRNAs based on enrichment of targets amongst proximal genes. TransCistor's simple and conservative statistical models are compatible with functionally defined target gene maps generated by existing and future technologies. Using transcriptome-wide perturbation experiments for 268 human and 134 mouse lncRNAs, we provide the first large-scale survey of cis-lncRNAs. Known cis-lncRNAs are correctly identified, including XIST, LINC00240 and UMLILO, and predictions are consistent across analysis methods, perturbation types and independent experiments. We detect cis-activity in a minority of lncRNAs, primarily involving activators over repressors. Cis-lncRNAs are detected by both RNA interference and antisense oligonucleotide perturbations. Mechanistically, cis-lncRNA transcripts are observed to physically associate with their target genes and are weakly enriched with enhancer elements. In summary, TransCistor establishes a quantitative foundation for cis-lncRNAs, opening a path to elucidating their molecular mechanisms and biological significance.
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Affiliation(s)
- Bhavya Dhaka
- School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
| | - Marc Zimmerli
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Daniel Hanhart
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Mario B Moser
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Hugo Guillen-Ramirez
- School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Sanat Mishra
- Indian Institute of Science Education and Research, Mohali, India
| | - Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Maro Widmer
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Centre, Barcelona 08034, Spain
| | - Marianna Kruithof-de Julio
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Dmitri Pervouchine
- Center for Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Centre, Barcelona 08034, Spain
| | - Panagiotis Chouvardas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- FutureNeuro SFI Research Centre, University College Dublin, Dublin D04 V1W8, Ireland
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2
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Luchsinger-Morcelle SJ, Gribnau J, Mira-Bontenbal H. Orchestrating Asymmetric Expression: Mechanisms behind Xist Regulation. EPIGENOMES 2024; 8:6. [PMID: 38390897 PMCID: PMC10885031 DOI: 10.3390/epigenomes8010006] [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: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Compensation for the gene dosage disequilibrium between sex chromosomes in mammals is achieved in female cells by repressing one of its X chromosomes through a process called X chromosome inactivation (XCI), exemplifying the control of gene expression by epigenetic mechanisms. A critical player in this mechanism is Xist, a long, non-coding RNA upregulated from a single X chromosome during early embryonic development in female cells. Over the past few decades, many factors involved at different levels in the regulation of Xist have been discovered. In this review, we hierarchically describe and analyze the different layers of Xist regulation operating concurrently and intricately interacting with each other to achieve asymmetric and monoallelic upregulation of Xist in murine female cells. We categorize these into five different classes: DNA elements, transcription factors, other regulatory proteins, long non-coding RNAs, and the chromatin and topological landscape surrounding Xist.
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Affiliation(s)
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Hegias Mira-Bontenbal
- Department of Developmental Biology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
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3
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Rosspopoff O, Cazottes E, Huret C, Loda A, Collier A, Casanova M, Rugg-Gunn P, Heard E, Ouimette JF, Rougeulle C. Species-specific regulation of XIST by the JPX/FTX orthologs. Nucleic Acids Res 2023; 51:2177-2194. [PMID: 36727460 PMCID: PMC10018341 DOI: 10.1093/nar/gkad029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/08/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolved concomitantly to XIST and have orthologues across all placental mammals. Here, we addressed the functional conservation of human orthologues of two such LRGs, FTX and JPX. By combining analysis of single-cell RNA-seq data from early human embryogenesis with various functional assays in matched human and mouse pluripotent stem- or differentiated post-XCI cells, we demonstrate major functional differences for these orthologues between species, independently of primary sequence conservation. While the function of FTX is not conserved in humans, JPX stands as a major regulator of XIST expression in both species. However, we show that different entities of JPX control the production of XIST at various steps depending on the species. Altogether, our study highlights the functional versatility of LRGs across evolution, and reveals that functional conservation of orthologous LRGs may involve diversified mechanisms of action. These findings represent a striking example of how the evolvability of LRGs can provide adaptative flexibility to constrained gene regulatory networks.
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Affiliation(s)
- Olga Rosspopoff
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Emmanuel Cazottes
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Christophe Huret
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Agnese Loda
- Directors' research, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Amanda J Collier
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Miguel Casanova
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Edith Heard
- Directors' research, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collège de France, Paris, France
| | | | - Claire Rougeulle
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
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4
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Ye Y, Fan X, Long Q, Wang J, Zhang W, Cai Z, Sun M, Gu X, Zou P, Chen D, Guo R. Comprehensive investigation and regulatory function of lncRNAs engaged in western honey bee larval immune response to Ascosphaera apis invasion. Front Physiol 2022; 13:1082522. [PMID: 36589426 PMCID: PMC9800914 DOI: 10.3389/fphys.2022.1082522] [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: 10/28/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Ascosphaera apis is a fungal pathogen that exclusively infects bee larvae, causing chalkbrood disease, which results in severe damage for beekeeping industry. Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes such as immune defense and host-pathogen interaction. However, expression pattern and regulatory role of lncRNAs involved in immune response of bee host to A. apis invasion is still very limited. Here, the gut tissues of Apis mellifera ligustica 4-, 5-, and 6-day-old larvae inoculated by A. apis spores (AmT1, AmT2, and AmT3 groups) and corresponding un-inoculated larval guts (AmCK1, AmCK2, and AmCK3 groups) were prepared and subjected to deep sequencing, followed by identification of lncRNAs, analysis of differentially expressed lncRNAs (DElncRNAs), and investigation of competing endogenous RNA (ceRNA) network. In total, 3,746 A. m. ligustica lncRNAs were identified, including 78 sense lncRNAs, 891 antisense lncRNAs, 1,893 intergenic lncRNAs, 346 bidirectional lncRNAs, and 210 intronic lncRNAs. In the 4-, 5-, and 6- comparison groups, 357, 236, and 505 DElncRNAs were discovered. Additionally, 217, 129, and 272 DElncRNAs were respectively predicted to regulate neighboring genes via cis-acting manner, and these targets were associated with a series of GO terms and KEGG pathways of great importance, such as response to stimulus and Jak-STAT signaling pathway. Moreover, 197, 95, and 356 DElncRNAs were observed to target 10, eight, and 21 DEmiRNAs and further target 147, 79, and 315 DEmRNAs, forming complex regulatory networks. Further investigation suggested that these targets were engaged in several key cellular and humoral immune pathways, such as phagosome and MAPK signaling pathway. Ultimately, the expression trends of nine randomly selected DElncRNAs were verified by RT-qPCR, confirming the authenticity and reliability of our transcriptome data. Findings in this current work not only provide candidate DElncRNAs for functional study, but also lay a foundation for unclosing the mechanism underlying DElncRNA-regulated larval immune responses to A. apis invasion.
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Affiliation(s)
- Yaping Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wende Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zongbing Cai
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoyu Gu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,*Correspondence: Rui Guo,
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5
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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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6
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Transcriptome analysis from muscle biopsy tissues in late-onset myopathies identifies potential biomarkers correlating to muscle pathology. Neuromuscul Disord 2022; 32:643-653. [DOI: 10.1016/j.nmd.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 11/22/2022]
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7
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Ishihara T, Griffith OW, Suzuki S, Renfree MB. Presence of H3K4me3 on Paternally Expressed Genes of the Paternal Genome From Sperm to Implantation. Front Cell Dev Biol 2022; 10:838684. [PMID: 35359448 PMCID: PMC8960379 DOI: 10.3389/fcell.2022.838684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting, parent-of-origin-specific gene expression, is controlled by differential epigenetic status of the parental chromosomes. While DNA methylation and suppressive histone modifications established during gametogenesis suppress imprinted genes on the inactive allele, how and when the expressed allele gains its active status is not clear. In this study, we asked whether the active histone-3 lysine-4 trimethylation (H3K4me3) marks remain at paternally expressed genes (PEGs) in sperm and embryos before and after fertilization using published data. Here we show that mouse sperm had the active H3K4me3 at more than half of known PEGs, and these genes were present even after fertilization. Using reciprocal cross data, we identified 13 new transient PEGs during zygotic genome activation. Next, we confirmed that the 12 out of the 13 new transient PEGs were associated with the paternal H3K4me3 in sperm. Nine out of the 12 genes were associated with the paternal H3K4me3 in zygotes. Our results show that paternal H3K4me3 marks escape inactivation during the histone-to-protamine transition that occurs during sperm maturation and are present in embryos from early zygotic stages up to implantation.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Oliver W. Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, Nagano, Japan
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Marilyn B. Renfree,
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8
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Marasca F, Sinha S, Vadalà R, Polimeni B, Ranzani V, Paraboschi EM, Burattin FV, Ghilotti M, Crosti M, Negri ML, Campagnoli S, Notarbartolo S, Sartore-Bianchi A, Siena S, Prati D, Montini G, Viale G, Torre O, Harari S, Grifantini R, Soldà G, Biffo S, Abrignani S, Bodega B. LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion. Nat Genet 2022; 54:180-193. [PMID: 35039641 DOI: 10.1038/s41588-021-00989-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
How gene expression is controlled to preserve human T cell quiescence is poorly understood. Here we show that non-canonical splicing variants containing long interspersed nuclear element 1 (LINE1) enforce naive CD4+ T cell quiescence. LINE1-containing transcripts are derived from CD4+ T cell-specific genes upregulated during T cell activation. In naive CD4+ T cells, LINE1-containing transcripts are regulated by the transcription factor IRF4 and kept at chromatin by nucleolin; these transcripts act in cis, hampering levels of histone 3 (H3) lysine 36 trimethyl (H3K36me3) and stalling gene expression. T cell activation induces LINE1-containing transcript downregulation by the splicing suppressor PTBP1 and promotes expression of the corresponding protein-coding genes by the elongating factor GTF2F1 through mTORC1. Dysfunctional T cells, exhausted in vitro or tumor-infiltrating lymphocytes (TILs), accumulate LINE1-containing transcripts at chromatin. Remarkably, depletion of LINE1-containing transcripts restores TIL effector function. Our study identifies a role for LINE1 elements in maintaining T cell quiescence and suggests that an abundance of LINE1-containing transcripts is critical for T cell effector function and exhaustion.
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Affiliation(s)
- Federica Marasca
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Shruti Sinha
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Rebecca Vadalà
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Ph.D. Program in Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, Monza, Italy
| | - Benedetto Polimeni
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Ph.D. Program in Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, Monza, Italy
| | - Valeria Ranzani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | | | - Marco Ghilotti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Mariacristina Crosti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Maria Luce Negri
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | | | - Samuele Notarbartolo
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Montini
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Pediatric Nephrology and Dialysis Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giuseppe Viale
- University of Milan, European Institute of Oncology IRCCS, Milan, Italy
| | - Olga Torre
- Department of Medical Sciences, San Giuseppe Hospital MultiMedica IRCCS, Milan, Italy
| | - Sergio Harari
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Department of Medical Sciences, San Giuseppe Hospital MultiMedica IRCCS, Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- CheckmAb Srl, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.
| | - Beatrice Bodega
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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9
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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10
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The lncRNAs at X Chromosome Inactivation Center: Not Just a Matter of Sex Dosage Compensation. Int J Mol Sci 2022; 23:ijms23020611. [PMID: 35054794 PMCID: PMC8775829 DOI: 10.3390/ijms23020611] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) constitute the majority of the transcriptome, as the result of pervasive transcription of the mammalian genome. Different RNA species, such as lncRNAs, miRNAs, circRNA, mRNAs, engage in regulatory networks based on their reciprocal interactions, often in a competitive manner, in a way denominated “competing endogenous RNA (ceRNA) networks” (“ceRNET”): miRNAs and other ncRNAs modulate each other, since miRNAs can regulate the expression of lncRNAs, which in turn regulate miRNAs, titrating their availability and thus competing with the binding to other RNA targets. The unbalancing of any network component can derail the entire regulatory circuit acting as a driving force for human diseases, thus assigning “new” functions to “old” molecules. This is the case of XIST, the lncRNA characterized in the early 1990s and well known as the essential molecule for X chromosome inactivation in mammalian females, thus preventing an imbalance of X-linked gene expression between females and males. Currently, literature concerning XIST biology is becoming dominated by miRNA associations and they are also gaining prominence for other lncRNAs produced by the X-inactivation center. This review discusses the available literature to explore possible novel functions related to ceRNA activity of lncRNAs produced by the X-inactivation center, beyond their role in dosage compensation, with prospective implications for emerging gender-biased functions and pathological mechanisms.
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11
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Oh HJ, Aguilar R, Kesner B, Lee HG, Kriz AJ, Chu HP, Lee JT. Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops. Cell 2021; 184:6157-6173.e24. [PMID: 34856126 DOI: 10.1016/j.cell.2021.11.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 01/24/2023]
Abstract
Chromosome loops shift dynamically during development, homeostasis, and disease. CCCTC-binding factor (CTCF) is known to anchor loops and construct 3D genomes, but how anchor sites are selected is not yet understood. Here, we unveil Jpx RNA as a determinant of anchor selectivity. Jpx RNA targets thousands of genomic sites, preferentially binding promoters of active genes. Depleting Jpx RNA causes ectopic CTCF binding, massive shifts in chromosome looping, and downregulation of >700 Jpx target genes. Without Jpx, thousands of lost loops are replaced by de novo loops anchored by ectopic CTCF sites. Although Jpx controls CTCF binding on a genome-wide basis, it acts selectively at the subset of developmentally sensitive CTCF sites. Specifically, Jpx targets low-affinity CTCF motifs and displaces CTCF protein through competitive inhibition. We conclude that Jpx acts as a CTCF release factor and shapes the 3D genome by regulating anchor site usage.
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Affiliation(s)
- Hyun Jung Oh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Rodrigo Aguilar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hun-Goo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Andrea J Kriz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hsueh-Ping Chu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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12
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Dong K, Shen J, He X, Hu G, Wang L, Osman I, Bunting KM, Dixon-Melvin R, Zheng Z, Xin H, Xiang M, Vazdarjanova A, Fulton DJR, Zhou J. CARMN Is an Evolutionarily Conserved Smooth Muscle Cell-Specific LncRNA That Maintains Contractile Phenotype by Binding Myocardin. Circulation 2021; 144:1856-1875. [PMID: 34694145 PMCID: PMC8726016 DOI: 10.1161/circulationaha.121.055949] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Vascular homeostasis is maintained by the differentiated phenotype of vascular smooth muscle cells (VSMCs). The landscape of protein coding genes comprising the transcriptome of differentiated VSMCs has been intensively investigated but many gaps remain including the emerging roles of noncoding genes. METHODS We reanalyzed large-scale, publicly available bulk and single-cell RNA sequencing datasets from multiple tissues and cell types to identify VSMC-enriched long noncoding RNAs. The in vivo expression pattern of a novel smooth muscle cell (SMC)-expressed long noncoding RNA, Carmn (cardiac mesoderm enhancer-associated noncoding RNA), was investigated using a novel Carmn green fluorescent protein knock-in reporter mouse model. Bioinformatics and quantitative real-time polymerase chain reaction analysis were used to assess CARMN expression changes during VSMC phenotypic modulation in human and murine vascular disease models. In vitro, functional assays were performed by knocking down CARMN with antisense oligonucleotides and overexpressing Carmn by adenovirus in human coronary artery SMCs. Carotid artery injury was performed in SMC-specific Carmn knockout mice to assess neointima formation and the therapeutic potential of reversing CARMN loss was tested in a rat carotid artery balloon injury model. The molecular mechanisms underlying CARMN function were investigated using RNA pull-down, RNA immunoprecipitation, and luciferase reporter assays. RESULTS We identified CARMN, which was initially annotated as the host gene of the MIR143/145 cluster and recently reported to play a role in cardiac differentiation, as a highly abundant and conserved, SMC-specific long noncoding RNA. Analysis of the Carmn GFP knock-in mouse model confirmed that Carmn is transiently expressed in embryonic cardiomyocytes and thereafter becomes restricted to SMCs. We also found that Carmn is transcribed independently of Mir143/145. CARMN expression is dramatically decreased by vascular disease in humans and murine models and regulates the contractile phenotype of VSMCs in vitro. In vivo, SMC-specific deletion of Carmn significantly exacerbated, whereas overexpression of Carmn markedly attenuated, injury-induced neointima formation in mouse and rat, respectively. Mechanistically, we found that Carmn physically binds to the key transcriptional cofactor myocardin, facilitating its activity and thereby maintaining the contractile phenotype of VSMCs. CONCLUSIONS CARMN is an evolutionarily conserved SMC-specific long noncoding RNA with a previously unappreciated role in maintaining the contractile phenotype of VSMCs and is the first noncoding RNA discovered to interact with myocardin.
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Affiliation(s)
- Kunzhe Dong
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Jian Shen
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Xiangqin He
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Guoqing Hu
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Liang Wang
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Islam Osman
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Kristopher M. Bunting
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Rachael Dixon-Melvin
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Zeqi Zheng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Hongbo Xin
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, 330031, China
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China
| | - Meixiang Xiang
- Department of Cardiology, The Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Almira Vazdarjanova
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - David J. R. Fulton
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
| | - Jiliang Zhou
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, Georgia, 30912, USA
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13
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Winkler L, Dimitrova N. A mechanistic view of long noncoding RNAs in cancer. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1699. [PMID: 34668345 PMCID: PMC9016092 DOI: 10.1002/wrna.1699] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important modulators of a wide range of biological processes in normal and disease states. In particular, lncRNAs have garnered significant interest as novel players in the molecular pathology of cancer, spurring efforts to define the functions, and elucidate the mechanisms through which cancer‐associated lncRNAs operate. In this review, we discuss the prevalent mechanisms employed by lncRNAs, with a critical assessment of the methodologies used to determine each molecular function. We survey the abilities of cancer‐associated lncRNAs to enact diverse trans functions throughout the nucleus and in the cytoplasm and examine the local roles of cis‐acting lncRNAs in modulating the expression of neighboring genes. In linking lncRNA functions and mechanisms to their roles in cancer biology, we contend that a detailed molecular understanding of lncRNA functionality is key to elucidating their contributions to tumorigenesis and to unlocking their therapeutic potential. This article is categorized under:Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Lauren Winkler
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
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14
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Chowdhary A, Satagopam V, Schneider R. Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer. Front Genet 2021; 12:649619. [PMID: 34276764 PMCID: PMC8281131 DOI: 10.3389/fgene.2021.649619] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023] Open
Abstract
Long non-coding RNAs are diverse class of non-coding RNA molecules >200 base pairs of length having various functions like gene regulation, dosage compensation, epigenetic regulation. Dysregulation and genomic variations of several lncRNAs have been implicated in several diseases. Their tissue and developmental specific expression are contributing factors for them to be viable indicators of physiological states of the cells. Here we present an comprehensive review the molecular mechanisms and functions, state of the art experimental and computational pipelines and challenges involved in the identification and functional annotation of lncRNAs and their prospects as biomarkers. We also illustrate the application of co-expression networks on the TCGA-LIHC dataset for putative functional predictions of lncRNAs having a therapeutic potential in Hepatocellular carcinoma (HCC).
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Affiliation(s)
- Anshika Chowdhary
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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15
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Yin H, Wei C, Lee JT. Revisiting the consequences of deleting the X inactivation center. Proc Natl Acad Sci U S A 2021; 118:e2102683118. [PMID: 34161282 PMCID: PMC8237661 DOI: 10.1073/pnas.2102683118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian cells equalize X-linked dosages between the male (XY) and female (XX) sexes by silencing one X chromosome in the female sex. This process, known as "X chromosome inactivation" (XCI), requires a master switch within the X inactivation center (Xic). The Xic spans several hundred kilobases in the mouse and includes a number of regulatory noncoding genes that produce functional transcripts. Over three decades, transgenic and deletional analyses have demonstrated both the necessity and sufficiency of the Xic to induce XCI, including the steps of X chromosome counting, choice, and initiation of whole-chromosome silencing. One recent study, however, reported that deleting the noncoding sequences of the Xic surprisingly had no effect for XCI and attributed a sufficiency to drive counting to the coding gene, Rnf12/Rlim Here, we revisit the question by creating independent Xic deletion cell lines. Multiple independent clones carrying heterozygous deletions of the Xic display an inability to up-regulate Xist expression, consistent with a counting defect. This defect is rescued by a second site mutation in Tsix occurring in trans, bypassing the defect in counting. These findings reaffirm the essential nature of noncoding Xic elements for the initiation of XCI.
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Affiliation(s)
- Hao Yin
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02114
| | - Chunyao Wei
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
- Department of Genetics, Harvard Medical School, Boston, MA 02114
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114;
- Department of Genetics, Harvard Medical School, Boston, MA 02114
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16
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Naciri I, Lin B, Webb CH, Jiang S, Carmona S, Liu W, Mortazavi A, Sun S. Linking Chromosomal Silencing With Xist Expression From Autosomal Integrated Transgenes. Front Cell Dev Biol 2021; 9:693154. [PMID: 34222260 PMCID: PMC8250153 DOI: 10.3389/fcell.2021.693154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Xist is the master regulator of X-Chromosome Inactivation (XCI), the mammalian dosage compensation mechanism that silences one of the two X chromosomes in a female cell. XCI is established during early embryonic development. Xist transgene (Tg) integrated into an autosome can induce transcriptional silencing of flanking genes; however, the effect and mechanism of Xist RNA on autosomal sequence silencing remain elusive. In this study, we investigate an autosomal integration of Xist Tg that is compatible with mouse viability but causes male sterility in homozygous transgenic mice. We observed ectopic Xist expression in the transgenic male cells along with a transcriptional reduction of genes clustered in four segments on the mouse chromosome 1 (Chr 1). RNA/DNA Fluorescent in situ Hybridization (FISH) and chromosome painting confirmed that Xist Tg is associated with chromosome 1. To determine the spreading mechanism of autosomal silencing induced by Xist Tg on Chr 1, we analyzed the positions of the transcriptionally repressed chromosomal sequences relative to the Xist Tg location inside the cell nucleus. Our results show that the transcriptionally repressed chromosomal segments are closely proximal to Xist Tg in the three-dimensional nucleus space. Our findings therefore support a model that Xist directs and maintains long-range transcriptional silencing facilitated by the three-dimensional chromosome organization.
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Affiliation(s)
- Ikrame Naciri
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Benjamin Lin
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Chiu-Ho Webb
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Shan Jiang
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Sarah Carmona
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Wenzhu Liu
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Sha Sun
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States
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17
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Jiao H, Shuai X, Luo Y, Zhou Z, Zhao Y, Li B, Gu G, Li W, Li M, Zeng H, Guo X, Xiao Y, Song Z, Gan L, Huang Q. Deep Insight Into Long Non-coding RNA and mRNA Transcriptome Profiling in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3. Front Vet Sci 2021; 8:625609. [PMID: 33996960 PMCID: PMC8116512 DOI: 10.3389/fvets.2021.625609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Swine hepatitis E (swine HE) is a new type of zoonotic infectious disease caused by the swine hepatitis E virus (swine HEV). Open reading frame 3 (ORF3) is an important virulent protein of swine HEV, but its function still is mainly unclear. In this study, we generated adenoviruses ADV4-ORF3 and ADV4 negative control (ADV4-NC), which successfully mediated overexpression of enhanced green fluorescent protein (EGFP)-ORF3 and EGFP, respectively, in HepG2 cells. High-throughput sequencing was used to screen for differentially expressed long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs). The cis-target genes of lncRNAs were predicted, functional enrichment (Gene Ontology [GO] and Kyoto Encyclopedia of Genes and Genomes [KEGG]) was performed, and 12 lncRNAs with statistically significant different expressions (p ≤ 0.05 and q ≤ 1) were selected for further quantitative real-time reverse transcription (qRT-PCR) validation. In HepG2 cells, we identified 62 significantly differentially expressed genes (DEGs) (6,564 transcripts) and 319 lncRNAs (124 known lncRNAs and 195 novel lncRNAs) that were affected by ORF3, which were involved in systemic lupus erythematosus, Staphylococcus aureus infection, signaling pathways pluripotency regulation of stem cells, the peroxisome proliferator-activated receptor (PPAR) signaling pathway, and platinum drug resistance pathways. Cis-target gene prediction identified 45 lncRNAs corresponding to candidate mRNAs, among which eight were validated by qRT-PCR: LINC02476 (two transcripts), RAP2C-AS1, AC016526, AL139099, and ZNF337-AS1 (3 transcripts). Our results revealed that the lncRNA profile in host cells affected by ORF3, swine HEV ORF3, might affect the pentose and glucuronate interconversions and mediate the formation of obstructive jaundice by influencing bile secretion, which will help to determine the function of ORF3 and the infection mechanism and treatment of swine HE.
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Affiliation(s)
- Hanwei Jiao
- College of Veterinary Medicine, Southwest University, Chongqing, China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing, China.,Chongqing Veterinary Scientific Engineering Research Center, Southwest University, Chongqing, China
| | - Xuehong Shuai
- College of Veterinary Medicine, Southwest University, Chongqing, China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing, China.,Chongqing Veterinary Scientific Engineering Research Center, Southwest University, Chongqing, China
| | - Yichen Luo
- College of Veterinary Medicine, Southwest University, Chongqing, China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing, China.,Chongqing Veterinary Scientific Engineering Research Center, Southwest University, Chongqing, China
| | - Zhixiong Zhou
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Yu Zhao
- College of Veterinary Medicine, Southwest University, Chongqing, China.,Institute of Animal Husbandry and Veterinary Medicine of Guizhou Academy of Agricultural Science, Guiyang, China
| | - Bowen Li
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Guojing Gu
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Wenjie Li
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Mengjuan Li
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Hui Zeng
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Xiaoyi Guo
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Yu Xiao
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Zhenhui Song
- College of Veterinary Medicine, Southwest University, Chongqing, China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing, China.,Chongqing Veterinary Scientific Engineering Research Center, Southwest University, Chongqing, China
| | - Ling Gan
- College of Veterinary Medicine, Southwest University, Chongqing, China.,Immunology Research Center, Medical Research Institute, Southwest University, Chongqing, China.,Chongqing Veterinary Scientific Engineering Research Center, Southwest University, Chongqing, China
| | - Qingzhou Huang
- College of Veterinary Medicine, Southwest University, Chongqing, China.,Chongqing Veterinary Scientific Engineering Research Center, Southwest University, Chongqing, China
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18
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Li G, Li X, Yuan C, Zhou C, Li X, Li J, Guo B. Long Non-Coding RNA JPX Contributes to Tumorigenesis by Regulating miR-5195-3p/VEGFA in Non-Small Cell Lung Cancer. Cancer Manag Res 2021; 13:1477-1489. [PMID: 33613033 PMCID: PMC7886111 DOI: 10.2147/cmar.s255317] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 01/12/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung cancer is the most frequently diagnosed cancer. Of all lung cancers, 80-85% are verified as non-small-cell lung cancer (NSCLC). Just proximal to X-inactive specific transcript (JPX), functions as lncRNA, contributed to tumor progression and suggested a poor prognosis in NSCLC. However, the pathogenesis of JPX involved in NSCLC is still unclear. METHODS The expressions of JPX, miR-5195-3p, and Vascular endothelial growth factor A (VEGFA) were detected by real-time quantitative polymerase chain reaction (RT-qPCR). Proliferation, colony number, apoptosis, invasion, and migration were analyzed by Cell Counting Kit-8 (CCK-8), colony formation, flow cytometry, transwell, and wound healing assays, severally. The protein levels of VEGFA, E-cadherin, N-cadherin, and Vimentin were detected by Western blot assay. The interaction between JPX, miR-5195-3p and VEGFA was predicted by starBase, and then verified by the dual-luciferase reporter, RNA Immunoprecipitation (RIP) and RNA pull-down assay. The biological role of JPX on NSCLC tumor growth was assessed by the xenograft tumor model in vivo. RESULTS JPX and VEGFA were upregulated, and miR-5195-3p was downregulated in NSCLC. JPX induced proliferation, colony number, invasion, migration, epithelial-mesenchymal transition (EMT), and inhibited apoptosis of NSCLC cells. JPX is directly bound to miR-5195-3p. JPX regulated NSCLC cell proliferation, apoptosis and EMT by modulating miR-5195-3p. miR-5195-3p hindered NSCLC cells proliferation, EMT and accelerated apoptosis by directly targeting VEGFA. JPX silencing hindered the cell growth of NSCLC in vivo. CONCLUSION JPX facilitated proliferation, colony number, invasion, migration, EMT, and repressed apoptosis by miR-5195-3p/VEGFA axis, offering a possible therapeutic strategy for NSCLC.
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Affiliation(s)
- Guanglian Li
- Department of Oncology, The People’s Hospital of Shouguang, Weifang, People’s Republic of China
| | - Xinrui Li
- Department of Oncology, The People’s Hospital of Shouguang, Weifang, People’s Republic of China
| | - Chao Yuan
- Department of Oncology, The People’s Hospital of Shouguang, Weifang, People’s Republic of China
| | - Caifeng Zhou
- Department of Oncology, The People’s Hospital of Shouguang, Weifang, People’s Republic of China
| | - Xinxin Li
- Department of Oncology, The People’s Hospital of Shouguang, Weifang, People’s Republic of China
| | - Jinfang Li
- Department of Oncology, The People’s Hospital of Shouguang, Weifang, People’s Republic of China
| | - Bin Guo
- Department of Oncology, The People’s Hospital of Shouguang, Weifang, People’s Republic of China
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19
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Zhang X, Zhou T, Chen B, Bai H, Bai Y, Zhao J, Pu F, Wu Y, Chen L, Shi Y, Ke Q, Zheng W, Chen J, Xu P. Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker ( Larimichthys crocea) in Response to Cryptocaryon irritans Infection. Front Genet 2020; 11:590475. [PMID: 33281881 PMCID: PMC7689269 DOI: 10.3389/fgene.2020.590475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Large-scale transcription studies have revealed numerous lncRNAs (long non-coding RNAs). lncRNAs have been proposed to participate in the regulation of a diverse range of biological processes, including transcriptional regulation. Although lncRNAs have attracted increasing attention, the studies in large yellow croaker (Larimichthys crocea) are still rare, and they lack systematic analysis. In this study, 101 RNA-seq datasets varied in ages, sexes, and tissues were retrieved from the NCBI database to generate a comprehensive catalog of large yellow croaker transcriptome database. A set of 14,599 high-confidence lncRNAs from 13,673 loci were identified and characterized. Furthermore, RNA-seq datasets obtained from the infection of C. irritans were employed to investigate the differential expression pattern of lncRNAs and analyze potential biological functions. A total of 77 differentially expressed lncRNAs targeting to 567 protein-coding genes were identified by using expression analysis. Several immune genes, including TLR5, CD2AP, and MMP9, were highlighted. With GO enrichment and KEGG pathway analysis, the immune-related terms or pathways were enriched. This study created a comprehensive dataset of lncRNAs for large yellow croaker, which would be helpful for the researches of functional roles of lncRNAs in large yellow croaker.
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Affiliation(s)
- Xinyi Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Tao Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yulin Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ji Zhao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yidi Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiaozhen Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Weiqiang Zheng
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Jia Chen
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen, China
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20
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Jin M, Ren J, Luo M, You Z, Fang Y, Han Y, Li G, Liu H. Long non-coding RNA JPX correlates with poor prognosis and tumor progression in non-small-cell lung cancer by interacting with miR-145-5p and CCND2. Carcinogenesis 2020; 41:634-645. [PMID: 31253987 DOI: 10.1093/carcin/bgz125] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/03/2019] [Accepted: 06/26/2019] [Indexed: 01/27/2023] Open
Abstract
Emerging studies have shown that the aberrant expression and function of long non-coding RNAs (lncRNAs) are involved in carcinogenesis and the development of various cancers. The long noncoding RNA JPX (lncRNA JPX) on the X chromosome is an activator of X-inactive-specific transcript (XIST) and is a molecular switch for X-chromosome inactivation. However, the exact mechanism by which JPX acts in non-small-cell lung cancer (NSCLC) is not well studied. Here, through integrating clinical data and a series of functional experiments, we found that lncRNA JPX expression is significantly upregulated in NSCLC tissues compared with that in paired adjacent normal tissues from two independent datasets and significantly associated with a poor survival and other malignant phenotypes (tumor stage, tumor volume) of NSCLC. Furthermore, we elucidated that JPX functions as an oncogene in NSCLC-promoting cell proliferation and cell migration by affecting cell-cycle progression. Mechanistically, JPX upregulates cyclin D2 (CCND2) expression in a competing endogenous RNA mechanism by interacting with miR-145-5p, thus provoking the development and progression of NSCLC. These findings reveal the mechanism of X-chromosome lncRNA JPX and its core regulatory circuitry JPX/miR-145-5p/CCND2 in the development and progression of NSCLC, which bring us closer to an understanding of the molecular drivers of NSCLC.
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Affiliation(s)
- Meng Jin
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Jie Ren
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Miao Luo
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Zhenxi You
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yuanyuan Fang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yin Han
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Guangcai Li
- Department of Respiratory Medicine, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Huiguo Liu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
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21
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Hu H, Jia Q, Xi J, Zhou B, Li Z. Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows. BMC Genomics 2020; 21:636. [PMID: 32928107 PMCID: PMC7490888 DOI: 10.1186/s12864-020-07055-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/06/2020] [Indexed: 01/20/2023] Open
Abstract
Background Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data. Conclusions These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.
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Affiliation(s)
- Huiyan Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Qing Jia
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China. .,Engineering Research Center for Agriculture in Hebei Mountainous Areas, Baoding, 071000, Hebei, China.
| | - Jianzhong Xi
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Bo Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
| | - Zhiqiang Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Hebei Agricultural University, Lekai South Street No. 2596, Baoding, 071000, Hebei, China
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22
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Chen X, Yang J, Wang Y. LncRNA JPX promotes cervical cancer progression by modulating miR-25-3p/SOX4 axis. Cancer Cell Int 2020; 20:441. [PMID: 32943989 PMCID: PMC7487936 DOI: 10.1186/s12935-020-01486-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 08/07/2020] [Indexed: 02/02/2023] Open
Abstract
Background The long noncoding RNA (lncRNA) JPX is a molecular switch for X-chromosome inactivation. Accumulating studies have shown that the aberrant expression and function of lncRNAs are involved in the occurrence and development of tumors. However, the functional importance and mechanism of the action of lncRNA JPX in cervical cancer (CC) remain unknown. Method In this study, qRT-PCR and western blotting were used to evaluate the mRNA or protein expression of JPX, miR-25-3p and SOX4 in CC tissues and cell lines. StarBase v2.0 database, luciferase reporter assay and RNA immunoprecipitation assay were used to explore the relationship between JPX and miR-25-3p. EdU assay, CCK-8 assay and transwell assay were utilized to evaluate the proliferation, migration and invasion of CC cells. The tumor xenograft assay in nude mice was performed to demonstrate the role of the JPX/miR-25-3p/SOX4 axis in CC. Results We found that JPX was markedly upregulated, whereas miR-25-3p was markedly downregulated in CC tissues and cell lines, and the expression of JPX was negatively correlated with miR-25-3p in CC tissues. Moreover, overexpression of JPX increased proliferation, migration and invasion of HeLa cells, whereas knockdown of JPX decreased proliferation, migration and invasion of HeLa cells. In contrast to JPX, overexpression of miR-25-3p decreased proliferation, migration and invasion of HeLa cells. In addition, knockdown of JPX was found to inhibit HeLa cell viability and tumor development via up-regulating the expression of miR-25-3p and inhibiting the expression of SOX4. Conclusions Our study demonstrates that JPX promotes cervical cancer progression through modulating the miR-25-3p/SOX4 axis, and may serve as a potential target for CC therapy.
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Affiliation(s)
- Xia Chen
- Department of Gynaecology and Obstetrics, The Affiliated Lianyungang Oriental Hospital of Xuzhou Medical University, No. 57 Zhong'hua Rest Road, Lianyun District, Lianyungang, 222042 Jiangsu China
| | - Jingxiu Yang
- Department of Gynaecology and Obstetrics, The Affiliated Lianyungang Oriental Hospital of Xuzhou Medical University, No. 57 Zhong'hua Rest Road, Lianyun District, Lianyungang, 222042 Jiangsu China
| | - Yuping Wang
- Department of Gynaecology and Obstetrics, The Affiliated Lianyungang Oriental Hospital of Xuzhou Medical University, No. 57 Zhong'hua Rest Road, Lianyun District, Lianyungang, 222042 Jiangsu China
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23
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Li T, Chen B, Yang P, Wang D, Du B, Kang L. Long Non-coding RNA Derived from lncRNA-mRNA Co-expression Networks Modulates the Locust Phase Change. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:664-678. [PMID: 32866667 PMCID: PMC8377017 DOI: 10.1016/j.gpb.2020.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/14/2020] [Accepted: 05/31/2020] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) regulate various biological processes ranging from gene expression to animal behavior. Although protein-coding genes, microRNAs, and neuropeptides play important roles in the regulation of phenotypic plasticity in migratory locust, empirical studies on the function of lncRNAs in this process remain limited. Here, we applied high-throughput RNA-seq to compare the expression patterns of lncRNAs and mRNAs in the time course of locust phase change. We found that lncRNAs responded more rapidly at the early stages of phase transition. Functional annotations demonstrated that early changed lncRNAs employed different pathways in isolation and crowding phases to cope with changes in the population density. Two overlapping hub lncRNA loci in the crowding and isolation networks were screened for functional verification. One of them, LNC1010057, was validated as a potential regulator of locust phase change. This work offers insights into the molecular mechanism underlying locust phase change and expands the scope of lncRNA functions in animal behavior.
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Affiliation(s)
- Ting Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Chen
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Depin Wang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baozhen Du
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Hebei University, Baoding 071002, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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24
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Wang H, Zhong J, Zhang C, Chai Z, Cao H, Wang J, Zhu J, Wang J, Ji Q. The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak. BMC Genomics 2020; 21:347. [PMID: 32381004 PMCID: PMC7203869 DOI: 10.1186/s12864-020-6757-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 04/27/2020] [Indexed: 02/07/2023] Open
Abstract
Background The Intramuscular fat (IMF) content in meat products, which is positively correlated with meat quality, is an important trait considered by consumers. The regulation of IMF deposition is species specific. However, the IMF-deposition-related mRNA and non-coding RNA and their regulatory network in yak (Bos grunniens) remain unknown. High-throughput sequencing technology provides a powerful approach for analyzing the association between transcriptome-related differences and specific traits in animals. Thus, the whole transcriptomes of yak muscle and adipose tissues were screened and analyzed to elucidate the IMF deposition-related genes. The muscle tissues were used for IMF content measurements. Results Significant differences were observed between the 0.5- and 2.5-year-old yaks. Several mRNAs, miRNAs, lncRNAs and circRNAs were generally expressed in both muscle and adipose tissues. Between the 0.5- and 2.5-year-old yaks, 149 mRNAs, 62 miRNAs, 4 lncRNAs, and 223 circRNAs were differentially expressed in muscle tissue, and 72 mRNAs, 15 miRNAs, 9 lncRNAs, and 211 circRNAs were differentially expressed in adipose tissue. KEGG annotation revelved that these differentially expressed genes were related to pathways that maintain normal biological functions of muscle and adipose tissues. Moreover, 16 mRNAs, 5 miRNAs, 3 lncRNAs, and 5 circRNAs were co-differentially expressed in both types of tissue. We suspected that these co-differentially expressed genes were involved in IMF-deposition in the yak. Additionally, LPL, ACADL, SCD, and FASN, which were previously shown to be associated with the IMF content, were identified in the competing endogenous RNA (ceRNA) regulatory network that was constructed on the basis of the IMF deposition-related genes. Three ceRNA subnetworks also revealed that TCONS-00016416 and its target SIRT1 “talk” to each other through the same miR-381-y and miR-208 response elements, whereas TCONS-00061798 and its target PRKCA, and TCONS-00084092 and its target LPL “talk” to each other through miR-122-x and miR-499-y response elements, respectively. Conclusion Taken together, our results reveal the potential mRNA and noncoding RNAs involved in IMF deposition in the yak, providing a useful resource for further research on IMF deposition in this animal species.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China. .,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Chengfu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Hanwen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Qiumei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China.
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25
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Robinson EK, Covarrubias S, Carpenter S. The how and why of lncRNA function: An innate immune perspective. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194419. [PMID: 31487549 PMCID: PMC7185634 DOI: 10.1016/j.bbagrm.2019.194419] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
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Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America.
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26
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Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs. Int J Mol Sci 2020; 21:ijms21051732. [PMID: 32138348 PMCID: PMC7084294 DOI: 10.3390/ijms21051732] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
Intramuscular fat (IMF) content is closely related to various meat traits, such as tenderness, juiciness, and flavor. The IMF content varies considerably among pig breeds with different genetic backgrounds. Long intergenic non-coding RNAs (lincRNAs) have been widely identified in many species and found to be an important class of regulators that can participate in multiple biological processes. However, the mechanism behind lincRNAs regulation of pig IMF content remains unknown and requires further study. In our study, we identified a total of 156 lincRNAs in the longissimus dorsi muscle of Wei (fat-type) and Yorkshire (lean-type) pigs using previously published data. These identified lincRNAs have shorter transcript length, longer exon length, lower exon number, and lower expression level as compared with protein-coding transcripts. We predicted potential target genes (PTGs) that are potentially regulated by lincRNAs in cis or trans regulation. Gene ontology and pathway analyses indicated that many potential lincRNAs target genes are involved in IMF-related processes or pathways, such as fatty acid catabolic process and adipocytokine signaling pathway. In addition, we analyzed quantitative trait locus (QTL) sites that differentially expressed lincRNAs (DE lincRNAs) between Wei and Yorkshire pigs co-localized. The QTL sites where DE lincRNAs co-localize are mostly related to IMF content. Furthermore, we constructed a co-expressed network between DE lincRNAs and their differentially expressed PTGs (DEPTGs). On the basis of their expression levels, we suggest that many DE lincRNAs can affect IMF development by positively or negatively regulating their PTGs. This study identified and analyzed some lincRNAs- and PTGs-related IMF development of the two pig breeds and provided new insight into research on the roles of lincRNAs in the two types of breeds.
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27
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Ariel F, Lucero L, Christ A, Mammarella MF, Jegu T, Veluchamy A, Mariappan K, Latrasse D, Blein T, Liu C, Benhamed M, Crespi M. R-Loop Mediated trans Action of the APOLO Long Noncoding RNA. Mol Cell 2020; 77:1055-1065.e4. [DOI: 10.1016/j.molcel.2019.12.015] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/30/2019] [Accepted: 12/18/2019] [Indexed: 11/25/2022]
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28
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Abstract
Embryonic Stem cells are widely studied to elucidate the disease and developmental processes because of their capability to differentiate into cells of any lineage, Pervasive transcription is a distinct feature of all multicellular organisms and genomic elements such as enhancers and bidirectional or unidirectional promoters regulate these processes. Thousands of loci in each species produce a class of transcripts called noncoding RNAs (ncRNAs), that are well known for their influential regulatory roles in multiple biological processes including stem cell pluripotency and differentiation. The number of lncRNA species increases in more complex organisms highlighting the importance of RNA-based control in the evolution of multicellular organisms. Over the past decade, numerous studies have shed light on lncRNA biogenesis and functional significance in the cell and the organism. In this review, we focus primarily on lncRNAs affecting the stem cell state and developmental pathways.
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Affiliation(s)
- Meghali Aich
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India; Academy of Scientific & Innovative Research, New Delhi, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, New Delhi, India; Academy of Scientific & Innovative Research, New Delhi, India.
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29
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Liang M, Hu K. Involvement of lncRNA-HOTTIP in the Repair of Ultraviolet Light-Induced DNA Damage in Spermatogenic Cells. Mol Cells 2019; 42:794-803. [PMID: 31697875 PMCID: PMC6883981 DOI: 10.14348/molcells.2019.0121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/21/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022] Open
Abstract
Ultraviolet light (UV)-induced cellular response has been studied by numerous investigators for many years. Long noncoding RNAs (lncRNAs) are emerging as new regulators of diverse cellular process; however, little is known about the role of lncRNAs in the cellular response to UV treatment. Here, we demonstrate that levels of lncRNA-HOTTIP significantly increases after UV stimulation and regulates the UV-mediated cellular response to UV through the coordinate activation of its neighboring gene Hoxa13 in GC-1 cells (spermatogonia germ cell line). UV-induced, G2/M-phase arrest and early apoptosis can be regulated by lncRNA-HOTTIP and Hoxa13. Furthermore, lncRNA-HOTTIP can up-regulate γ-H2AX and p53 expression via Hoxa13 in UV-irradiated GC-1 cells. In addition, p53 has the ability to regulate the expression of both lncRNA-HOTTIP and Hoxa13 in vitro and in vivo. Our results provide new data regarding the role lncRNAs play in the UV response in spermatogenic cells.
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Affiliation(s)
- Meng Liang
- Department of Biotechnology, School of Life Science, Bengbu Medical College, Bengbu 233030,
China
| | - Ke Hu
- Department of Biotechnology, School of Life Science, Bengbu Medical College, Bengbu 233030,
China
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30
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Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton ( Gossypium hirsutum L.). Genes (Basel) 2019; 10:genes10120947. [PMID: 31756984 PMCID: PMC6947465 DOI: 10.3390/genes10120947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022] Open
Abstract
Cotton plays an important role in the economy of many countries. Many studies have revealed that numerous genes and various metabolic pathways are involved in anther development. In this research, we studied the differently expressed mRNA and lncRNA during the anther development of cotton between the cytoplasmic male sterility (CMS) line, C2P5A, and the maintainer line, C2P5B, using RNA-seq analysis. We identified 17,897 known differentially expressed (DE) mRNAs, and 865 DE long noncoding RNAs (lncRNAs) that corresponded to 1172 cis-target genes at three stages of anther development using gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of DE mRNAs; and cis-target genes of DE lncRNAs probably involved in the degradation of tapetum cells, microspore development, pollen development, and in the differentiation, proliferation, and apoptosis of the anther cell wall in cotton. Of these DE genes, LTCONS_00105434, LTCONS_00004262, LTCONS_00126105, LTCONS_00085561, and LTCONS_00085561, correspond to cis-target genes Ghir_A09G011050.1, Ghir_A01G005150.1, Ghir_D05G003710.2, Ghir_A03G016640.1, and Ghir_A12G005100.1, respectively. They participate in oxidative phosphorylation, flavonoid biosynthesis, pentose and glucuronate interconversions, fatty acid biosynthesis, and MAPK signaling pathway in plants, respectively. In summary, the transcriptomic data indicated that DE lncRNAs and DE mRNAs were related to the anther development of cotton at the pollen mother cell stage, tetrad stage, and microspore stage, and abnormal expression could lead to anther abortion, resulting in male sterility of cotton.
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31
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Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet 2019; 21:102-117. [DOI: 10.1038/s41576-019-0184-5] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/14/2022]
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32
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Karner H, Webb CH, Carmona S, Liu Y, Lin B, Erhard M, Chan D, Baldi P, Spitale RC, Sun S. Functional Conservation of LncRNA JPX Despite Sequence and Structural Divergence. J Mol Biol 2019; 432:283-300. [PMID: 31518612 DOI: 10.1016/j.jmb.2019.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 02/02/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been identified in all eukaryotes and are most abundant in the human genome. However, the functional importance and mechanisms of action for human lncRNAs are largely unknown. Using comparative sequence, structural, and functional analyses, we characterize the evolution and molecular function of human lncRNA JPX. We find that human JPX and its mouse homolog, lncRNA Jpx, have deep divergence in their nucleotide sequences and RNA secondary structures. Despite such differences, both lncRNAs demonstrate robust binding to CTCF, a protein that is central to Jpx's role in X chromosome inactivation. In addition, our functional rescue experiment using Jpx-deletion mutant cells shows that human JPX can functionally complement the loss of Jpx in mouse embryonic stem cells. Our findings support a model for functional conservation of lncRNAs independent from sequence and structural divergence. This study provides mechanistic insight into the evolution of lncRNA function.
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Affiliation(s)
- Heather Karner
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Chiu-Ho Webb
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Sarah Carmona
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Yu Liu
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697, USA
| | - Benjamin Lin
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Micaela Erhard
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Dalen Chan
- Department of Pharmaceutical Sciences, College of Health Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, Institute for Genomics and Bioinformatics, University of California Irvine, Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, College of Health Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Sha Sun
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA.
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Talon I, Janiszewski A, Chappell J, Vanheer L, Pasque V. Recent Advances in Understanding the Reversal of Gene Silencing During X Chromosome Reactivation. Front Cell Dev Biol 2019; 7:169. [PMID: 31552244 PMCID: PMC6733891 DOI: 10.3389/fcell.2019.00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022] Open
Abstract
Dosage compensation between XX female and XY male cells is achieved by a process known as X chromosome inactivation (XCI) in mammals. XCI is initiated early during development in female cells and is subsequently stably maintained in most somatic cells. Despite its stability, the robust transcriptional silencing of XCI is reversible, in the embryo and also in a number of reprogramming settings. Although XCI has been intensively studied, the dynamics, factors, and mechanisms of X chromosome reactivation (XCR) remain largely unknown. In this review, we discuss how new sequencing technologies and reprogramming approaches have enabled recent advances that revealed the timing of transcriptional activation during XCR. We also discuss the factors and chromatin features that might be important to understand the dynamics and mechanisms of the erasure of transcriptional gene silencing on the inactive X chromosome (Xi).
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Affiliation(s)
| | | | | | | | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, KU Leuven, Leuven, Belgium
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The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist. Nat Genet 2019; 51:1024-1034. [PMID: 31133748 PMCID: PMC6551226 DOI: 10.1038/s41588-019-0412-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/04/2019] [Indexed: 01/08/2023]
Abstract
The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions that swap the Xist/Tsix transcriptional unit and place their promoters in each other’s TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically up-regulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X inactivation. Our study illustrates how the genomic architecture of cis-regulatory landscapes can affect the regulation of mammalian developmental processes.
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Being in a loop: how long non-coding RNAs organise genome architecture. Essays Biochem 2019; 63:177-186. [DOI: 10.1042/ebc20180057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
Chromatin architecture has a significant impact on gene expression. Evidence in the last two decades support RNA as an important component of chromatin structure [Genes Dev. (2005) 19, 1635–1655; PLoS ONE (2007) 2, e1182; Nat. Genet. (2002) 30, 329–334]. Long non-coding RNAs (lncRNAs) are able to control chromatin structure through nucleosome positioning, interaction with chromatin re-modellers and chromosome looping. These functions are carried out in cis at the site of lncRNAs transcription or in trans at distant loci. While the evidence for a role in lncRNAs in regulating gene expression through chromatin interactions is increasing, there is still very little conclusive evidence for a potential role in looping organisation. Here, we review models for the involvement of lncRNAs in genome architecture and the experimental evidence to support them.
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Shi G, Chen L, Chen G, Zou C, Li J, Li M, Fang C, Li C. Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs. Front Genet 2019; 10:160. [PMID: 30886630 PMCID: PMC6409335 DOI: 10.3389/fgene.2019.00160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/19/2022] Open
Abstract
An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat development. Here, we used published RNA-seq data from subcutaneous adipose tissue of Italian Large White pigs and identified 252 putative lincRNAs, wherein 34 were unannotated. These lincRNAs had relatively shorter length, lower number of exons, and lower expression level compared with protein-coding transcripts. Gene ontology and pathway analysis indicated that the adjacent genes of lincRNAs were involved in lipid metabolism. In addition, differentially expressed lincRNAs (DELs) between low and high backfat thickness pigs were identified. Through the detection of quantitative trait locus (QTL), DELs were mainly located in QTLs related to adipose development. Based on the expression correlation of DEL genes and their differentially expressed potential target genes, we constructed a co-expression network and a potential pathway of DEL's effect on lipid metabolism. Our study identified and analyzed lincRNAs in subcutaneous adipose tissue, and results suggested that lincRNAs may be involved in the regulation of subcutaneous fat development. Our findings provided new insights into the biological function of porcine lincRNAs.
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Affiliation(s)
- Gaoli Shi
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lin Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jingxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Liu X, Zhang L, Cui J, Che S, Liu Y, Zhang Y, Cao B, Song Y. The mRNA and lncRNA landscape of the non-pregnant endometrium during the oestrus cycle in dairy goat. ANIMAL PRODUCTION SCIENCE 2019. [DOI: 10.1071/an18426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cyclic changes in the endometrium are essential for embryo implantation in mammals; many studies report that such changes constitute a complex process involving numerous molecular mediators. In the present study, goat endometria at oestrus Day 5 and oestrus Day 15 were selected to systematically analyse the transcriptome using strand-specific Ribo-Zero RNA sequencing. Over 120 million high-quality paired-end reads were generated and 440400 transcripts were identified in the endometrial tissue of dairy goats. In total, 489 differentially expressed mRNAs and 854 differentially expressed long non-coding RNAs were identified when comparing the endometrium at goat endometria at oestrus Day 5 and oestrus Day 15. Neurotensin was found to play a potentially important role in the non-pregnant goat endometrium during the oestrus cycle. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses of the cis-target genes of the differentially expressed long non-coding RNAs showed that GO:0005198 (structural molecule activity) and ko04510 (focal adhesion) might be involved in cyclic endometrial changes. Taken together, the resulting transcriptomic profiles elucidate global trends in mRNA and lncRNA expression in non-pregnant endometria during the oestrus cycle in dairy goats.
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Elling R, Robinson EK, Shapleigh B, Liapis SC, Covarrubias S, Katzman S, Groff AF, Jiang Z, Agarwal S, Motwani M, Chan J, Sharma S, Hennessy EJ, FitzGerald GA, McManus MT, Rinn JL, Fitzgerald KA, Carpenter S. Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell Rep 2018; 25:1511-1524.e6. [PMID: 30404006 PMCID: PMC6291222 DOI: 10.1016/j.celrep.2018.10.027] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 09/04/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
An inducible gene expression program is a hallmark of the host inflammatory response. Recently, long intergenic non-coding RNAs (lincRNAs) have been shown to regulate the magnitude, duration, and resolution of these responses. Among these is lincRNA-Cox2, a dynamically regulated gene that broadly controls immune gene expression. To evaluate the in vivo functions of this lincRNA, we characterized multiple models of lincRNA-Cox2-deficient mice. LincRNA-Cox2-deficient macrophages and murine tissues had altered expression of inflammatory genes. Transcriptomic studies from various tissues revealed that deletion of the lincRNA-Cox2 locus also strongly impaired the basal and inducible expression of the neighboring gene prostaglandin-endoperoxide synthase (Ptgs2), encoding cyclooxygenase-2, a key enzyme in the prostaglandin biosynthesis pathway. By utilizing different genetic manipulations in vitro and in vivo, we found that lincRNA-Cox2 functions through an enhancer RNA mechanism to regulate Ptgs2. More importantly, lincRNA-Cox2 also functions in trans, independently of Ptgs2, to regulate critical innate immune genes in vivo.
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Affiliation(s)
- Roland Elling
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA; Center for Pediatrics, Department of General Pediatrics, University of Freiburg, Freiburg, Germany
| | - Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Stephen C Liapis
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sol Katzman
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Abigail F Groff
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Zhaozhao Jiang
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shiuli Agarwal
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mona Motwani
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennie Chan
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shruti Sharma
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Elizabeth J Hennessy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
| | - Garret A FitzGerald
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - John L Rinn
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Department of Biochemistry, BioFrontiers, University of Colorado Boulder, Boulder, CO 80301, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
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Sahakyan A, Yang Y, Plath K. The Role of Xist in X-Chromosome Dosage Compensation. Trends Cell Biol 2018; 28:999-1013. [PMID: 29910081 DOI: 10.1016/j.tcb.2018.05.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 01/15/2023]
Abstract
In each somatic cell of a female mammal one X chromosome is transcriptionally silenced via X-chromosome inactivation (XCI), initiating early in development. Although XCI events are conserved in mouse and human postimplantation development, regulation of X-chromosome dosage in preimplantation development occurs differently. In preimplantation development, mouse embryos undergo imprinted form of XCI, yet humans lack imprinted XCI and instead regulate gene expression of both X chromosomes by dampening transcription. The long non-coding RNA Xist/XIST is expressed in mouse and human preimplantation and postimplantation development to orchestrate XCI, but its role in dampening is unclear. In this review, we discuss recent advances in our understanding of the role of Xist in X chromosome dosage compensation in mouse and human.
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Affiliation(s)
- Anna Sahakyan
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yihao Yang
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- David Geffen School of Medicine, Department of Biological Chemistry, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA.
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