1
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Stasevich EM, Simonova AV, Bogomolova EA, Murashko MM, Uvarova AN, Zheremyan EA, Korneev KV, Schwartz AM, Kuprash DV, Demin DE. Cut from the same cloth: RNAs transcribed from regulatory elements. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195049. [PMID: 38964653 DOI: 10.1016/j.bbagrm.2024.195049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases.
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Affiliation(s)
- E M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A V Simonova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Bogomolova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - M M Murashko
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - A N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - K V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A M Schwartz
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - D V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D E Demin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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2
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Fosseprez O, Cuvier O. Uncovering the functions and mechanisms of regulatory elements-associated non-coding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195059. [PMID: 39226990 DOI: 10.1016/j.bbagrm.2024.195059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/12/2024] [Accepted: 08/23/2024] [Indexed: 09/05/2024]
Abstract
Over the past decade, regulatory non-coding RNAs (ncRNAs) produced by RNA Pol II have been revealed as meaningful players in various essential cellular functions. In particular, thousands of ncRNAs are produced at transcriptional regulatory elements such as enhancers and promoters, where they may exert multiple functions to regulate proper development, cellular programming, transcription or genomic stability. Here, we review the mechanisms involving these regulatory element-associated ncRNAs, and particularly enhancer RNAs (eRNAs) and PROMoter uPstream Transcripts (PROMPTs). We contextualize the mechanisms described to the processing and degradation of these short lived RNAs. We summarize recent findings explaining how ncRNAs operate locally at promoters and enhancers, or further away, either shortly after their production by RNA Pol II, or through post-transcriptional stabilization. Such discoveries lead to a converging model accounting for how ncRNAs influence cellular fate, by acting on transcription and chromatin structure, which may further involve factors participating to 3D nuclear organization.
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Affiliation(s)
- Olivier Fosseprez
- Chromatin Dynamics and Cell Proliferation team; Center of Integrative Biology (CBI), Molecular Cellular and Developmental Biology Unit (MCD/UMR5077) Center of Integrative Biology (CBI-CNRS), Université de Toulouse (UPS), F-31000, France.
| | - Olivier Cuvier
- Chromatin Dynamics and Cell Proliferation team; Center of Integrative Biology (CBI), Molecular Cellular and Developmental Biology Unit (MCD/UMR5077) Center of Integrative Biology (CBI-CNRS), Université de Toulouse (UPS), F-31000, France.
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3
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Kim S, Liu TT, Ou F, Murphy TL, Murphy KM. Anatomy of a superenhancer. Adv Immunol 2024; 163:51-96. [PMID: 39271259 DOI: 10.1016/bs.ai.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
Interferon regulatory factor-8 (IRF8) is the lineage determining transcription factor for the type one classical dendritic cell (cDC1) subset, a terminal selector for plasmacytoid dendritic cells and important for the function of monocytes. Studies of Irf8 gene regulation have identified several enhancers controlling its activity during development of progenitors in the bone marrow that precisely regulate expression at distinct developmental stages. Each enhancer responds to distinct transcription factors that are expressed at each stage. IRF8 is first expressed in early progenitors that form the monocyte dendritic cell progenitor (MDP) in response to induction of the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) acting at the Irf8 +56 kb enhancer. IRF8 levels increase further as the MDP transits into the common dendritic cell progenitor (CDP) in response to E protein activity at the Irf8 +41 kb enhancer. Upon Nfil3-induction in CDPs leading to specification of the cDC1 progenitor, abrupt induction of BATF3 forms the JUN/BATF3/IRF8 heterotrimer that activates the Irf8 +32 kb enhancer that sustains Irf8 autoactivation throughout the cDC1 lifetime. Deletions of each of these enhancers has revealed their stage dependent activation. Surprisingly, studies of compound heterozygotes for each combination of enhancer deletions revealed that activation of each subsequent enhancer requires the successful activation of the previous enhancer in strictly cis-dependent mechanism. Successful progression of enhancer activation is finely tuned to alter the functional accessibility of subsequent enhancers to factors active in the next stage of development. The molecular basis for these phenomenon is still obscure but could have implications for genomic regulation in a broader developmental context.
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Affiliation(s)
- Sunkyung Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Tian-Tian Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Feiya Ou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States.
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4
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Refael T, Sudman M, Golan G, Pnueli L, Naik S, Preger-Ben Noon E, Henn A, Kaplan A, Melamed P. An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context. Cell Mol Life Sci 2024; 81:361. [PMID: 39158745 PMCID: PMC11335282 DOI: 10.1007/s00018-024-05398-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/21/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Genome-wide studies have demonstrated regulatory roles for diverse non-coding elements, but their precise and interrelated functions have often remained enigmatic. Addressing the need for mechanistic insight, we studied their roles in expression of Lhb which encodes the pituitary gonadotropic hormone that controls reproduction. We identified a bi-directional enhancer in gonadotrope-specific open chromatin, whose functional eRNA (eRNA2) supports permissive chromatin at the Lhb locus. The central untranscribed region of the enhancer contains an iMotif (iM), and is bound by Hmgb2 which stabilizes the iM and directs transcription specifically towards the functional eRNA2. A distinct downstream lncRNA, associated with an inducible G-quadruplex (G4) and iM, also facilitates Lhb expression, following its splicing in situ. GnRH activates Lhb transcription and increased levels of all three RNAs, eRNA2 showing the highest response, while estradiol, which inhibits Lhb, repressed levels of eRNA2 and the lncRNA. The levels of these regulatory RNAs and Lhb mRNA correlate highly in female mice, though strikingly not in males, suggesting a female-specific function. Our findings, which shed new light on the workings of non-coding elements and non-canonical DNA structures, reveal novel mechanisms regulating transcription which have implications not only in the central control of reproduction but also for other inducible genes.
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Affiliation(s)
- Tal Refael
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maya Sudman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gil Golan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sujay Naik
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Arnon Henn
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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5
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McDonald BR, Picard CL, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. NATURE PLANTS 2024; 10:1246-1257. [PMID: 39080503 PMCID: PMC11335568 DOI: 10.1038/s41477-024-01741-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 06/13/2024] [Indexed: 08/07/2024]
Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many 'distal' elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans.
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Affiliation(s)
- Bayley R McDonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Colette L Picard
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ian M Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Marina I Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | | | - Steven E Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.
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6
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Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [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] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
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Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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7
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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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8
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Ben-Tov Perry R, Tsoory M, Tolmasov M, Ulitsky I. Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation. Cell Rep 2023; 42:113168. [PMID: 37742186 PMCID: PMC10636608 DOI: 10.1016/j.celrep.2023.113168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are expressed in many brain circuits and types of neurons; nevertheless, their functional significance for normal brain functions remains elusive. Here, we study the functions in the central nervous system of Silc1, an lncRNA we have shown previously to be important for neuronal regeneration in the peripheral nervous system. We found that Silc1 is rapidly and strongly induced in the hippocampus upon exposure to novelty and is required for efficient spatial learning. Silc1 production is important for induction of Sox11 (its cis-regulated target gene) throughout the CA1-CA3 regions and proper expression of key Sox11 target genes. Consistent with its role in neuronal plasticity, Silc1 levels decline during aging and in models of Alzheimer's disease. Overall, we describe a plasticity pathway in which Silc1 acts as an immediate-early gene to activate Sox11 and induce a neuronal growth-associated transcriptional program important for learning.
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Affiliation(s)
- Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Michael Tsoory
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael Tolmasov
- Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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9
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Ntini E, Budach S, Vang Ørom UA, Marsico A. Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs. Cell Syst 2023; 14:906-922.e6. [PMID: 37857083 DOI: 10.1016/j.cels.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in gene expression regulation in cis. Although enriched in the cell chromatin fraction, to what degree this defines their regulatory potential remains unclear. Furthermore, the factors underlying lncRNA chromatin tethering, as well as the molecular basis of efficient lncRNA chromatin dissociation and its impact on enhancer activity and target gene expression, remain to be resolved. Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. By incorporating genomic, transcriptomic, and epigenetic metrics, as well as RNA-binding protein propensities, in machine learning models, we identify features that define transcript groups of different chromatin dissociation dynamics. Notably, lncRNAs transcribed from enhancers display reduced chromatin retention, suggesting that, in addition to splicing, their chromatin dissociation may shape enhancer activity.
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Affiliation(s)
- Evgenia Ntini
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Institute of Molecular Biology and Biotechnology, IMBB-FORTH, 70013 Heraklio, Greece.
| | - Stefan Budach
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany
| | - Ulf A Vang Ørom
- Aarhus University, Department of Molecular Biology and Genetics, 8000 Aarhus, Denmark
| | - Annalisa Marsico
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Computational Health Center, Helmholtz Center Munich, Munich, Germany.
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10
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Mcdonald BR, Picard C, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559415. [PMID: 37808859 PMCID: PMC10557634 DOI: 10.1101/2023.09.25.559415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating ("nascent") transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many "distal" elements in plants initiate tissue-specific stable transcripts and are likely bone fide promoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer "enhancers" or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.
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Affiliation(s)
- Bayley R. Mcdonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Colette Picard
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ian M. Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Marina I. Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | | | - Steven E. Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sascha H. Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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11
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Mattick JS. A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs. Bioessays 2023; 45:e2300080. [PMID: 37318305 DOI: 10.1002/bies.202300080] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of 'normal science'. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in 'noncoding' sequences with developmental complexity; genetic loci termed 'enhancers' that control spatiotemporal gene expression patterns during development; and a plethora of 'intergenic', overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. Also see the video abstract here: https://youtu.be/qxeGwahBANw.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, New South Wales, Australia
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12
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Gil N, Perry RBT, Mukamel Z, Tuck A, Bühler M, Ulitsky I. Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus. Cell Rep 2023; 42:112569. [PMID: 37256750 PMCID: PMC10320833 DOI: 10.1016/j.celrep.2023.112569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.
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Affiliation(s)
- Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Mukamel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alex Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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13
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 521] [Impact Index Per Article: 521.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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14
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Li F, Zhou J. G-quadruplexes from non-coding RNAs. J Mol Med (Berl) 2023:10.1007/s00109-023-02314-7. [PMID: 37069370 DOI: 10.1007/s00109-023-02314-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
Non-coding RNAs (ncRNAs) are significant regulators of gene expression in a wide range of biological processes, such as transcription, RNA maturation, or translation. ncRNAs interplay with proteins or other RNAs through not only classical sequence-based mechanisms but also unique higher-order structures such as RNA G-quadruplexes (rG4s). rG4s are predictably formed in guanine-rich sequences and are closely related to various human diseases, such as tumors, neurodegenerative diseases, and infections. This review focuses on the vital role of rG4s in ncRNAs, particularly lncRNAs and miRNAs. We outline the dynamic balance between rG4s and RNA stem-loop/hairpin structures and the interplay between ncRNAs and interactors, thereby modulating gene expression and disease progression. A complete understanding of the biological regulatory role and mechanism of rG4s in ncRNAs affirms the critical importance of folding into the appropriate three-dimensional structure in maintaining or modulating the functions of ncRNAs. It makes them novel therapeutic targets for adjusting potential-G4-containing-ncRNAs-associated diseases.
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Affiliation(s)
- Fangyuan Li
- Department Medical Research Central, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
- Clinical Biobank, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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15
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Liu TT, Ou F, Belk JA, Bagadia P, Anderson DA, Durai V, Yao W, Satpathy AT, Murphy TL, Murphy KM. Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation. Genes Dev 2023; 37:291-302. [PMID: 36990511 PMCID: PMC10153461 DOI: 10.1101/gad.350339.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
Abstract
Individual elements within a superenhancer can act in a cooperative or temporal manner, but the underlying mechanisms remain obscure. We recently identified an Irf8 superenhancer, within which different elements act at distinct stages of type 1 classical dendritic cell (cDC1) development. The +41-kb Irf8 enhancer is required for pre-cDC1 specification, while the +32-kb Irf8 enhancer acts to support subsequent cDC1 maturation. Here, we found that compound heterozygous Δ32/Δ41 mice, lacking the +32- and +41-kb enhancers on different chromosomes, show normal pre-cDC1 specification but, surprisingly, completely lack mature cDC1 development, suggesting cis dependence of the +32-kb enhancer on the +41-kb enhancer. Transcription of the +32-kb Irf8 enhancer-associated long noncoding RNA (lncRNA) Gm39266 is also dependent on the +41-kb enhancer. However, cDC1 development in mice remained intact when Gm39266 transcripts were eliminated by CRISPR/Cas9-mediated deletion of lncRNA promoters and when transcription across the +32-kb enhancer was blocked by premature polyadenylation. We showed that chromatin accessibility and BATF3 binding at the +32-kb enhancer were dependent on a functional +41-kb enhancer located in cis Thus, the +41-kb Irf8 enhancer controls the subsequent activation of the +32-kb Irf8 enhancer in a manner that is independent of associated lncRNA transcription.
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Affiliation(s)
- Tian-Tian Liu
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Feiya Ou
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - David A Anderson
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Winnie Yao
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA;
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16
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Welsh SA, Gardini A. Genomic regulation of transcription and RNA processing by the multitasking Integrator complex. Nat Rev Mol Cell Biol 2023; 24:204-220. [PMID: 36180603 PMCID: PMC9974566 DOI: 10.1038/s41580-022-00534-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2022] [Indexed: 11/09/2022]
Abstract
In higher eukaryotes, fine-tuned activation of protein-coding genes and many non-coding RNAs pivots around the regulated activity of RNA polymerase II (Pol II). The Integrator complex is the only Pol II-associated large multiprotein complex that is metazoan specific, and has therefore been understudied for years. Integrator comprises at least 14 subunits, which are grouped into distinct functional modules. The phosphodiesterase activity of the core catalytic module is co-transcriptionally directed against several RNA species, including long non-coding RNAs (lncRNAs), U small nuclear RNAs (U snRNAs), PIWI-interacting RNAs (piRNAs), enhancer RNAs and nascent pre-mRNAs. Processing of non-coding RNAs by Integrator is essential for their biogenesis, and at protein-coding genes, Integrator is a key modulator of Pol II promoter-proximal pausing and transcript elongation. Recent studies have identified an Integrator-specific serine/threonine-protein phosphatase 2A (PP2A) module, which targets Pol II and other components of the basal transcription machinery. In this Review, we discuss how the activity of Integrator regulates transcription, RNA processing, chromatin landscape and DNA repair. We also discuss the diverse roles of Integrator in development and tumorigenesis.
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17
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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18
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Ponting CP, Haerty W. Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review. Annu Rev Genomics Hum Genet 2022; 23:153-172. [PMID: 35395170 DOI: 10.1146/annurev-genom-112921-123710] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims. We discuss pitfalls of lncRNA experimental and computational methods as well as opposing interpretations of their results. The majority of evidence, we argue, indicates that most lncRNA transcript models reflect transcriptional noise or provide minor regulatory roles, leaving relatively few human lncRNAs that contribute centrally to human development, physiology, or behavior. These important few tend to be spliced and better conserved but lack a simple syntax relating sequence to structure and mechanism, and so resist simple categorization. This genome-wide view should help investigators prioritize individual lncRNAs based on their likely contribution to human biology.
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Affiliation(s)
- Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom;
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19
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Subtype and cell type specific expression of lncRNAs provide insight into breast cancer. Commun Biol 2022; 5:834. [PMID: 35982125 PMCID: PMC9388662 DOI: 10.1038/s42003-022-03559-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in breast cancer pathogenesis through chromatin remodeling, transcriptional and post-transcriptional gene regulation. We report robust associations between lncRNA expression and breast cancer clinicopathological features in two population-based cohorts: SCAN-B and TCGA. Using co-expression analysis of lncRNAs with protein coding genes, we discovered three distinct clusters of lncRNAs. In silico cell type deconvolution coupled with single-cell RNA-seq analyses revealed that these three clusters were driven by cell type specific expression of lncRNAs. In one cluster lncRNAs were expressed by cancer cells and were mostly associated with the estrogen signaling pathways. In the two other clusters, lncRNAs were expressed either by immune cells or fibroblasts of the tumor microenvironment. To further investigate the cis-regulatory regions driving lncRNA expression in breast cancer, we identified subtype-specific transcription factor (TF) occupancy at lncRNA promoters. We also integrated lncRNA expression with DNA methylation data to identify long-range regulatory regions for lncRNA which were validated using ChiA-Pet-Pol2 loops. lncRNAs play an important role in shaping the gene regulatory landscape in breast cancer. We provide a detailed subtype and cell type-specific expression of lncRNA, which improves the understanding of underlying transcriptional regulation in breast cancer.
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20
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Zamani M, Foroughmand AM, Hajjari MR, Bakhshinejad B, Johnson R, Galehdari H. CASC11 and PVT1 spliced transcripts play an oncogenic role in colorectal carcinogenesis. Front Oncol 2022; 12:954634. [PMID: 36052265 PMCID: PMC9424822 DOI: 10.3389/fonc.2022.954634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer is fundamentally a genetic disorder that alters cellular information flow toward aberrant growth. The coding part accounts for less than 2% of the human genome, and it has become apparent that aberrations within the noncoding genome drive important cancer phenotypes. The numerous carcinogenesis-related genomic variations in the 8q24 region include single nucleotide variations (SNVs), copy number variations (CNVs), and viral integrations occur in the neighboring areas of the MYC locus. It seems that MYC is not the only target of these alterations. The MYC-proximal mutations may act via regulatory noncoding RNAs (ncRNAs). In this study, gene expression analyses indicated that the expression of some PVT1 spliced linear transcripts, CircPVT1, CASC11, and MYC is increased in colorectal cancer (CRC). Moreover, the expression of these genes is associated with some clinicopathological characteristics of CRC. Also, in vitro studies in CRC cell lines demonstrated that CASC11 is mostly detected in the nucleus, and different transcripts of PVT1 have different preferences for nuclear and cytoplasmic parts. Furthermore, perturbation of PVT1 expression and concomitant perturbation in PVT1 and CASC11 expression caused MYC overexpression. It seems that transcription of MYC is under regulatory control at the transcriptional level, i.e., initiation and elongation of transcription by its neighboring genes. Altogether, the current data provide evidence for the notion that these noncoding transcripts can significantly participate in the MYC regulation network and in the carcinogenesis of colorectal cells.
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Affiliation(s)
- Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Mohammad-Reza Hajjari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Babak Bakhshinejad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- *Correspondence: Hamid Galehdari,
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21
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Abstract
Enhancers confer precise spatiotemporal patterns of gene expression in response to developmental and environmental stimuli. Over the last decade, the transcription of enhancer RNAs (eRNAs) – nascent RNAs transcribed from active enhancers – has emerged as a key factor regulating enhancer activity. eRNAs are relatively short-lived RNA species that are transcribed at very high rates but also quickly degraded. Nevertheless, eRNAs are deeply intertwined within enhancer regulatory networks and are implicated in a number of transcriptional control mechanisms. Enhancers show changes in function and sequence over evolutionary time, raising questions about the relationship between enhancer sequences and eRNA function. Moreover, the vast majority of single nucleotide polymorphisms associated with human complex diseases map to the non-coding genome, with causal disease variants enriched within enhancers. In this Primer, we survey the diverse roles played by eRNAs in enhancer-dependent gene expression, evaluating different models for eRNA function. We also explore questions surrounding the genetic conservation of enhancers and how this relates to eRNA function and dysfunction. Summary: This Primer evaluates the ideas that underpin developing models for eRNA function, exploring cases in which perturbed eRNA function contributes to disease.
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Affiliation(s)
- Laura J. Harrison
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
| | - Daniel Bose
- Molecular and Cellular Biology, School of Biosciences, Sheffield Institute For Nucleic Acids, The University of Sheffield, Firth Court, Western Bank , Sheffield S10 2TN , UK
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22
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Ross CJ, Ulitsky I. Discovering functional motifs in long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1708. [PMID: 34981665 DOI: 10.1002/wrna.1708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Caroline Jane Ross
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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23
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Neyazi S, Ng M, Heckl D, Klusmann JH. Long noncoding RNAs as regulators of pediatric acute myeloid leukemia. Mol Cell Pediatr 2022; 9:10. [PMID: 35596093 PMCID: PMC9123150 DOI: 10.1186/s40348-022-00142-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/30/2022] [Indexed: 11/10/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly emerging as regulators across human development and disease, and many have been described in the context of hematopoiesis and leukemogenesis. These studies have yielded new molecular insights into the contribution of lncRNAs to AML development and revealed connections between lncRNA expression and clinical parameters in AML patients. In this mini review, we illustrate the versatile functions of lncRNAs in AML, with a focus on pediatric AML, and present examples that may serve as future therapeutic targets or predictive factors.
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Affiliation(s)
- Sina Neyazi
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Michelle Ng
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dirk Heckl
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
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24
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Engelhard CA, Huang C, Khani S, Kasparek P, Prochazka J, Rozman J, Reguera DP, Sedlacek R, Kornfeld JW. Comprehensive Transcriptional Profiling and Mouse Phenotyping Reveals Dispensable Role for Adipose Tissue Selective Long Noncoding RNA Gm15551. Noncoding RNA 2022; 8:ncrna8030032. [PMID: 35645339 PMCID: PMC9149892 DOI: 10.3390/ncrna8030032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 12/20/2022] Open
Abstract
Cold and nutrient-activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via the uncoupled respiration and secretion of endocrine factors, thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine-tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to interscapular brown adipose tissue (iBAT) function in a high fat diet (HFD) and cold stressed mice. We focused on Gm15551, which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis, and downregulated by β-adrenergic activation in mature adipocytes. Although we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551.
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Affiliation(s)
- Christoph Andreas Engelhard
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (C.A.E.); (C.H.)
| | - Chien Huang
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (C.A.E.); (C.H.)
- Laboratory of Animal Physiology, Department of Animal Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Sajjad Khani
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Köln, Germany;
- Institute for Diabetes and Cancer (IDC), Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, University Hospital of Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Petr Kasparek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; (P.K.); (J.P.); (J.R.); (D.P.R.); (R.S.)
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; (P.K.); (J.P.); (J.R.); (D.P.R.); (R.S.)
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; (P.K.); (J.P.); (J.R.); (D.P.R.); (R.S.)
| | - David Pajuelo Reguera
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; (P.K.); (J.P.); (J.R.); (D.P.R.); (R.S.)
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prumyslova 595, 25250 Vestec, Czech Republic; (P.K.); (J.P.); (J.R.); (D.P.R.); (R.S.)
| | - Jan-Wilhelm Kornfeld
- Department for Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (C.A.E.); (C.H.)
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Köln, Germany;
- Correspondence:
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25
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Long non-coding RNAs are involved in alternative splicing and promote cancer progression. Br J Cancer 2022; 126:1113-1124. [PMID: 34750493 PMCID: PMC9023592 DOI: 10.1038/s41416-021-01600-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 09/14/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS) is a key process in which precursor RNAs produce different mature RNAs, and the disorder of AS is a key factor in promoting cancer development. Compared with coding RNA, studies on the functions of long non-coding RNAs (lncRNAs) are far from enough. In fact, lncRNA is an important participant and regulator in the process of AS. On the one hand, lncRNAs regulate cancer progression as AS products of precursor messenger RNA (mRNA), but on the other hand, precursor lncRNA generates cancer-related abnormal splicing variants through AS. In addition, lncRNAs directly or indirectly regulate the AS events of downstream target genes, thus affecting the occurrence and development of cancer. Here, we reviewed how lncRNAs regulate AS and influence oncogenesis in different ways.
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26
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Mkandawire TT, Sateriale A. The Long and Short of Next Generation Sequencing for Cryptosporidium Research. Front Cell Infect Microbiol 2022; 12:871860. [PMID: 35419299 PMCID: PMC8995782 DOI: 10.3389/fcimb.2022.871860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
The intestinal parasite Cryptosporidium is a significant cause of severe diarrhoeal disease that can have long term effects. Therapeutic options remain limited despite a significant impact on public health, partly due to various challenges in the field of Cryptosporidium research, including the availability of genomic and transcriptomic data from environmental and clinical isolates. In this review we explore how long read DNA and RNA sequencing technologies have begun to provide novel insights into the biology of the parasite. The increased deployment of these technologies will help researchers address key gaps in the understanding of Cryptosporidium biology, and ultimately drive translational research and better parasite control.
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Tan JY, Marques AC. The activity of human enhancers is modulated by the splicing of their associated lncRNAs. PLoS Comput Biol 2022; 18:e1009722. [PMID: 35015755 PMCID: PMC8803168 DOI: 10.1371/journal.pcbi.1009722] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/31/2022] [Accepted: 12/05/2021] [Indexed: 11/19/2022] Open
Abstract
Pervasive enhancer transcription is at the origin of more than half of all long noncoding RNAs in humans. Transcription of enhancer-associated long noncoding RNAs (elncRNA) contribute to their cognate enhancer activity and gene expression regulation in cis. Recently, splicing of elncRNAs was shown to be associated with elevated enhancer activity. However, whether splicing of elncRNA transcripts is a mere consequence of accessibility at highly active enhancers or if elncRNA splicing directly impacts enhancer function, remains unanswered. We analysed genetically driven changes in elncRNA splicing, in humans, to address this outstanding question. We showed that splicing related motifs within multi-exonic elncRNAs evolved under selective constraints during human evolution, suggesting the processing of these transcripts is unlikely to have resulted from transcription across spurious splice sites. Using a genome-wide and unbiased approach, we used nucleotide variants as independent genetic factors to directly assess the causal relationship that underpin elncRNA splicing and their cognate enhancer activity. We found that the splicing of most elncRNAs is associated with changes in chromatin signatures at cognate enhancers and target mRNA expression. We provide evidence that efficient and conserved processing of enhancer-associated elncRNAs contributes to enhancer activity. Most, if not all, active enhancers are transcribed, giving rise to a plethora of transcripts, including enhancer-associated long noncoding RNAs (elncRNAs). Changes in elncRNA levels impacts cognate enhancer activity. Recently splicing of elncRNA has also been found to associate with enhancer activity. Whether this associations reflects a contribution of elncRNA splicing to increased enhancer activity or else is simply the consequence of increased chromatin accessibility that promotes transcriptional elongation and allows for spurious splicing events remains unknown. We show that natural selection has acted, at the species and population level, to preserve DNA elements required for frequent and efficient elncRNA splicing Importantly, using a genome-wide and unbiased statistical population genomics approach, we demonstrate that elncRNA splicing is associated with cognate enhancer function, contributing to chromatin status and enhancer activity. Our results provides strong evidence that efficient elncRNA splicing contributes to enhancer activity genome-wide.
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Affiliation(s)
- Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- * E-mail: (JYT); (ACM)
| | - Ana Claudia Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- * E-mail: (JYT); (ACM)
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28
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Gjaltema RAF, Schwämmle T, Kautz P, Robson M, Schöpflin R, Ravid Lustig L, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus. Mol Cell 2022; 82:190-208.e17. [PMID: 34932975 DOI: 10.1016/j.molcel.2021.11.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
Developmental genes such as Xist, which initiates X chromosome inactivation, are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatiotemporal expression patterns. Xist integrates information on X chromosome dosage and developmental stage to trigger X inactivation in the epiblast specifically in female embryos. Through a pooled CRISPR screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist at the onset of random X inactivation. Chromatin profiling reveals that X-dosage controls the promoter-proximal region, while differentiation cues activate several distal enhancers. The strongest distal element lies in an enhancer cluster associated with a previously unannotated Xist-enhancing regulatory transcript, which we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. With this study, we start to disentangle how multiple, functionally distinct regulatory elements interact to generate complex expression patterns in mammals.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Till Schwämmle
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Pauline Kautz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Michael Robson
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, Edinburgh, UK
| | - Robert Schöpflin
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Liat Ravid Lustig
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Lennart Brandenburg
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Carolina Vechiatto
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Evgenia Ntini
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vera Schmiedel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center München, 85764 Neuherberg, Germany
| | - Stefan Mundlos
- Development and Disease Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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29
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2223-2235. [DOI: 10.1093/hmg/ddac023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/11/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
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Chen Y, Li H, Lai L, Huang Y, Shen J. Discovery of new long noncoding RNAs associated with ulcerative colitis with a novel general microarray expression data. Life Sci 2021; 287:120090. [PMID: 34715141 DOI: 10.1016/j.lfs.2021.120090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 01/01/2023]
Abstract
UC is a chronic, nonspecific disease and characterized by a chronic relapsing intestinal inflammation, which puts a person at a higher risk of developing bowel cancer, while the causes of UC are unknown. Recently, with the development of microarray technology, more and more studies are focusing on the potential roles of long noncoding RNAs (lncRNAs) in the pathogenesis of diseases. The purpose of this study is to devise a method, based on cDNA microarray probe genomics data, to computationally determine the potential function of evolutionary conserved lncRNAs in ulcerative colitis (UC). We analysed a total of 12,593 microarray probes present in the Ensembl, OMIM, UniGene, and Gene Ontology databases. We found that lncRNA n385775 was significantly higher (P < 0.001) in patients with active UC, while n336281 (P = 0.017), n341081 (P = 0.041), and n387236 (P = 0.006) were significantly lower. Then, we validated our findings by measuring the expression of lncRNAs in colon tissue samples from patients affected by UC. Moreover, we validated the expression pattern of the lncRNAs in two cell lines, Caco2/bbe and T84, treated with TNF-α. In Caco2/bbe cells, lncRNA n385775 was significantly upregulated after TNF-α treatment (P = 0.002). This study reports a novel method to re- annotate the transcriptome expression profile from existing cDNA microarray data as a potential approach to investigate the function of lncRNAs in UC.
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Affiliation(s)
- Yueying Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China
| | - HanyangLi Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China
| | - Lijie Lai
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China
| | - Yong Huang
- INMD Pulmonary, University of Virginia, 81 Hospital Dr CHARLOTTESVILLE, VA 22903, USA.
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China.
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31
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He Y, Wang W, Jiang P, Yang L, Guo Q, Xiang J, Gao Y, Wang Y, Chen R. Long Non-Coding RNAs in Oral Submucous Fibrosis: Their Functional Mechanisms and Recent Research Progress. J Inflamm Res 2021; 14:5787-5800. [PMID: 34764671 PMCID: PMC8578048 DOI: 10.2147/jir.s337014] [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: 08/31/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022] Open
Abstract
Many studies have shown that most genomes are transcribed into non-coding RNAs (ncRNAs), including microRNAs (miRs) and long non-coding RNAs (lncRNAs), which can affect different cell characteristics. LncRNAs are long heterologous RNAs that regulate gene expression and various signaling pathways during homeostasis and development. Studies have shown that a lncRNA is an important regulatory molecule that can be targeted to change the physiology and function of cells. Expression or dysfunction of lncRNAs is closely related to various genetic, autoimmune, and metabolic diseases. The importance of ncRNAs in oral submucosal fibrosis (OSF) has garnered much attention in recent years. However, most research has focused on miRs. The role of these molecules in OSF is incompletely understood. This review focuses on the emerging role and function of lncRNAs in OSF as novel regulators. Finally, the potential functional role of lncRNAs as biomarkers for OSF diagnosis is also described. LncRNAs are expected to become a new therapeutic target, but more research is needed to understand their biological functions more deeply.
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Affiliation(s)
- Yaodong He
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
| | - Wei Wang
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
| | - Pingping Jiang
- School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, 230032, People's Republic of China
| | - Lin Yang
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
| | - Qi Guo
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
| | - Junwei Xiang
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
| | - Yuling Gao
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
| | - Yuanyin Wang
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
| | - Ran Chen
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, Anhui Province, 230032, People's Republic of China
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Identification of sheep lncRNAs related to the immune response to vaccines and aluminium adjuvants. BMC Genomics 2021; 22:770. [PMID: 34706639 PMCID: PMC8554944 DOI: 10.1186/s12864-021-08086-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are involved in several immune processes, including the immune response to vaccination, but most of them remain uncharacterised in livestock species. The mechanism of action of aluminium adjuvants as vaccine components is neither not fully understood. Results We built a transcriptome from sheep PBMCs RNA-seq data in order to identify unannotated lncRNAs and analysed their expression patterns along protein coding genes. We found 2284 novel lncRNAs and assessed their conservation in terms of sequence and synteny. Differential expression analysis performed between animals inoculated with commercial vaccines or aluminium adjuvant alone and the co-expression analysis revealed lncRNAs related to the immune response to vaccines and adjuvants. A group of co-expressed genes enriched in cytokine signalling and production highlighted the differences between different treatments. A number of differentially expressed lncRNAs were correlated with a divergently located protein-coding gene, such as the OSM cytokine. Other lncRNAs were predicted to act as sponges of miRNAs involved in immune response regulation. Conclusions This work enlarges the lncRNA catalogue in sheep and puts an accent on their involvement in the immune response to repetitive vaccination, providing a basis for further characterisation of the non-coding sheep transcriptome within different immune cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08086-z.
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33
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Heterogeneity among enhancer RNAs: origins, consequences and perspectives. Essays Biochem 2021; 65:709-721. [PMID: 34414426 DOI: 10.1042/ebc20200064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs transcribed from distal cis-regulatory elements (i.e. enhancers), which are stereotyped as short, rarely spliced and unstable. In fact, a non-negligible fraction of eRNAs seems to be longer, spliced and more stable, and their cognate enhancers are epigenomically and functionally distinguishable from typical enhancers. In this review, we first summarized the genomic and molecular origins underlying the observed heterogeneity among eRNAs. Then, we discussed how their heterogeneous properties (e.g. stability) affect the modes of interaction with their regulatory partners, from promiscuous cis-interactions to specific trans-interactions. Finally, we highlighted the existence of a seemingly continuous spectrum of eRNA properties and its implications in the genomic origins of non-coding RNA genes from an evolutionary perspective.
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34
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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: 24] [Impact Index Per Article: 8.0] [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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35
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Zboril E, Yoo H, Chen L, Liu Z. Dynamic Interactions of Transcription Factors and Enhancer Reprogramming in Cancer Progression. Front Oncol 2021; 11:753051. [PMID: 34616687 PMCID: PMC8488287 DOI: 10.3389/fonc.2021.753051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
While improved tumor treatment has significantly reduced the overall mortality rates, invasive progression including recurrence, therapy resistance and metastasis contributes to the majority of deaths caused by cancer. Enhancers are essential distal DNA regulatory elements that control temporal- or spatial-specific gene expression patterns during development and other biological processes. Genome-wide sequencing has revealed frequent alterations of enhancers in cancers and reprogramming of distal enhancers has emerged as one of the important features for tumors. In this review, we will discuss tumor progression-associated enhancer dynamics, its transcription factor (TF) drivers and how enhancer reprogramming modulates gene expression during cancer invasive progression. Additionally, we will explore recent advancements in contemporary technology including single-cell sequencing, spatial transcriptomics and CUT&RUN, which have permitted integrated studies of enhancer reprogramming in vivo. Given the essential roles of enhancer dynamics and its drivers in controlling cancer progression and treatment outcome, understanding these changes will be paramount in mitigating invasive events and discovering novel therapeutic targets.
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Affiliation(s)
- Emily Zboril
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Hannah Yoo
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Lizhen Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Cell Systems and Anatomy, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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36
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Abstract
The world of long non-coding RNAs (lncRNAs) has opened up massive new prospects in understanding the regulation of gene expression. Not only are there seemingly almost infinite numbers of lncRNAs in the mammalian cell, but they have highly diverse mechanisms of action. In the nucleus, some are chromatin-associated, transcribed from transcriptional enhancers (eRNAs) and/or direct changes in the epigenetic landscape with profound effects on gene expression. The pituitary gonadotrope is responsible for activation of reproduction through production and secretion of appropriate levels of the gonadotropic hormones. As such, it exemplifies a cell whose function is defined through changes in developmental and temporal patterns of gene expression, including those that are hormonally induced. Roles for diverse distal regulatory elements and eRNAs in gonadotrope biology have only just begun to emerge. Here, we will present an overview of the different kinds of lncRNAs that alter gene expression, and what is known about their roles in regulating some of the key gonadotrope genes. We will also review various screens that have detected differentially expressed pituitary lncRNAs associated with changes in reproductive state and those whose expression is found to play a role in gonadotrope-derived nonfunctioning pituitary adenomas. We hope to shed light on this exciting new field, emphasize the open questions, and encourage research to illuminate the roles of lncRNAs in various endocrine systems.
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Affiliation(s)
- Tal Refael
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
- Correspondence: Philippa Melamed, PhD, Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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37
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [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: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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38
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Policarpo R, Sierksma A, De Strooper B, d'Ydewalle C. From Junk to Function: LncRNAs in CNS Health and Disease. Front Mol Neurosci 2021; 14:714768. [PMID: 34349622 PMCID: PMC8327212 DOI: 10.3389/fnmol.2021.714768] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.
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Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,UK Dementia Research Institute, University College London, London, United Kingdom
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
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39
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Long non-coding RNAs and splicing. Essays Biochem 2021; 65:723-729. [PMID: 33835135 DOI: 10.1042/ebc20200087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/05/2021] [Accepted: 03/15/2021] [Indexed: 12/25/2022]
Abstract
In this review I focus on the role of splicing in long non-coding RNA (lncRNA) life. First, I summarize differences between the splicing efficiency of protein-coding genes and lncRNAs and discuss why non-coding RNAs are spliced less efficiently. In the second half of the review, I speculate why splice sites are the most conserved sequences in lncRNAs and what additional roles could splicing play in lncRNA metabolism. I discuss the hypothesis that the splicing machinery can, besides its dominant role in intron removal and exon joining, protect cells from undesired transcripts.
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40
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A first exon termination checkpoint preferentially suppresses extragenic transcription. Nat Struct Mol Biol 2021; 28:337-346. [PMID: 33767452 PMCID: PMC7610630 DOI: 10.1038/s41594-021-00572-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023]
Abstract
Interactions between the splicing machinery and RNA polymerase II increase protein-coding gene transcription. Similarly, exons and splicing signals of enhancer-generated long noncoding RNAs (elncRNAs) augment enhancer activity. However, elncRNAs are inefficiently spliced, suggesting that, compared with protein-coding genes, they contain qualitatively different exons with a limited ability to drive splicing. We show here that the inefficiently spliced first exons of elncRNAs as well as promoter-antisense long noncoding RNAs (pa-lncRNAs) in human and mouse cells trigger a transcription termination checkpoint that requires WDR82, an RNA polymerase II-binding protein, and its RNA-binding partner of previously unknown function, ZC3H4. We propose that the first exons of elncRNAs and pa-lncRNAs are an intrinsic component of a regulatory mechanism that, on the one hand, maximizes the activity of these cis-regulatory elements by recruiting the splicing machinery and, on the other, contains elements that suppress pervasive extragenic transcription.
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41
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Kay MK, Zhang J, Choudhury M. Screening for alternative splicing of lncRNA Dleu2 in the mouse liver cell line AML-12. Biomed Rep 2021; 14:50. [PMID: 33859821 DOI: 10.3892/br.2021.1426] [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: 11/25/2020] [Accepted: 03/19/2021] [Indexed: 11/05/2022] Open
Abstract
The long non coding RNA deleted in leukemia 2 gene (Dleu2) has recently been demonstrated to be an active player in the progression of several types of cancer, including hepatocellular carcinoma. Dleu2 may serve a role in modulating the downstream effects-mediated by alternative splicing of its multiple exons. However, the proportional expression of these alternative splicing populations of the Dleu2 exons is currently unknown. To determine how Dleu2 could be affected by alternative splicing, a series of alternative splicing primer sets were designed to investigate which transcripts were preferentially activated when Dleu2 was targeted for downregulation or upregulation. A specific Dleu2 small interfering RNA that targeted an exon upstream of the tumor suppressor microRNA site significantly knocked down Dleu2 expression across all the primer sets used, which targeted 13 different alternative splicing transcripts over 5 different promoter sites in the mouse liver cell line, AML-12. Similarly, 50 µM Resveratrol led to significant upregulation of Dleu2 in 11 alternative splicing transcripts. These results show that Dleu2 is capable of successful modulation across alternative splicing transcripts that can be screened, and also that Resveratrol can be a potential nutraceutical, which may potentially lead to novel approaches in the use of lncRNA Dleu2 for diagnostics and regulation.
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Affiliation(s)
- Matthew Krivacka Kay
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
| | - Jian Zhang
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
| | - Mahua Choudhury
- Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, Texas, TX 77843, USA
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42
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Gil N, Ulitsky I. Inefficient splicing curbs noncoding RNA transcription. Nat Struct Mol Biol 2021; 28:327-328. [PMID: 33767453 DOI: 10.1038/s41594-021-00582-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Noa Gil
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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43
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Cruciform Formable Sequences within Pou5f1 Enhancer Are Indispensable for Mouse ES Cell Integrity. Int J Mol Sci 2021; 22:ijms22073399. [PMID: 33810223 PMCID: PMC8036336 DOI: 10.3390/ijms22073399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
DNA can adopt various structures besides the B-form. Among them, cruciform structures are formed on inverted repeat (IR) sequences. While cruciform formable IRs (CFIRs) are sometimes found in regulatory regions of transcription, their function in transcription remains elusive, especially in eukaryotes. We found a cluster of CFIRs within the mouse Pou5f1 enhancer. Here, we demonstrate that this cluster or some member(s) plays an active role in the transcriptional regulation of not only Pou5f1, but also Sox2, Nanog, Klf4 and Esrrb. To clarify in vivo function of the cluster, we performed genome editing using mouse ES cells, in which each of the CFIRs was altered to the corresponding mirror repeat sequence. The alterations reduced the level of the Pou5f1 transcript in the genome-edited cell lines, and elevated those of Sox2, Nanog, Klf4 and Esrrb. Furthermore, transcription of non-coding RNAs (ncRNAs) within the enhancer was also upregulated in the genome-edited cell lines, in a similar manner to Sox2, Nanog, Klf4 and Esrrb. These ncRNAs are hypothesized to control the expression of these four pluripotency genes. The CFIRs present in the Pou5f1 enhancer seem to be important to maintain the integrity of ES cells.
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44
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Bennett M, Ulitsky I, Alloza I, Vandenbroeck K, Miscianinov V, Mahmoud AD, Ballantyne M, Rodor J, Baker AH. Novel Transcript Discovery Expands the Repertoire of Pathologically-Associated, Long Non-Coding RNAs in Vascular Smooth Muscle Cells. Int J Mol Sci 2021; 22:1484. [PMID: 33540814 PMCID: PMC7867340 DOI: 10.3390/ijms22031484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 01/23/2023] Open
Abstract
Vascular smooth muscle cells (VSMCs) provide vital contractile force within blood vessel walls, yet can also propagate cardiovascular pathologies through proliferative and pro-inflammatory activities. Such phenotypes are driven, in part, by the diverse effects of long non-coding RNAs (lncRNAs) on gene expression. However, lncRNA characterisation in VSMCs in pathological states is hampered by incomplete lncRNA representation in reference annotation. We aimed to improve lncRNA representation in such contexts by assembling non-reference transcripts in RNA sequencing datasets describing VSMCs stimulated in vitro with cytokines, growth factors, or mechanical stress, as well as those isolated from atherosclerotic plaques. All transcripts were then subjected to a rigorous lncRNA prediction pipeline. We substantially improved coverage of lncRNAs responding to pro-mitogenic stimuli, with non-reference lncRNAs contributing 21-32% for each dataset. We also demonstrate non-reference lncRNAs were biased towards enriched expression within VSMCs, and transcription from enhancer sites, suggesting particular relevance to VSMC processes, and the regulation of neighbouring protein-coding genes. Both VSMC-enriched and enhancer-transcribed lncRNAs were large components of lncRNAs responding to pathological stimuli, yet without novel transcript discovery 33-46% of these lncRNAs would remain hidden. Our comprehensive VSMC lncRNA repertoire allows proper prioritisation of candidates for characterisation and exemplifies a strategy to broaden our knowledge of lncRNA across a range of disease states.
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MESH Headings
- Aorta/cytology
- Coronary Vessels/cytology
- Cytokines/pharmacology
- Datasets as Topic
- Enhancer Elements, Genetic
- Gene Expression Profiling
- Humans
- Intercellular Signaling Peptides and Proteins/pharmacology
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Plaque, Atherosclerotic/metabolism
- RNA, Long Noncoding/analysis
- RNA, Long Noncoding/isolation & purification
- RNA-Seq
- Stress, Mechanical
- Transcription, Genetic/drug effects
- Transcriptome
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Affiliation(s)
- Matthew Bennett
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Iraide Alloza
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903 Barakaldo, Spain; (I.A.); (K.V.)
| | - Koen Vandenbroeck
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903 Barakaldo, Spain; (I.A.); (K.V.)
- Ikerbasque, Basque Foundation for Science, 3 María Díaz Haroko Kalea, 48013 Bilbao, Spain
| | - Vladislav Miscianinov
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Amira Dia Mahmoud
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Margaret Ballantyne
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Julie Rodor
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Andrew H. Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
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45
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Abstract
Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
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46
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Ntini E, Marsico A. Functional impacts of non-coding RNA processing on enhancer activity and target gene expression. J Mol Cell Biol 2020; 11:868-879. [PMID: 31169884 PMCID: PMC6884709 DOI: 10.1093/jmcb/mjz047] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 01/06/2023] Open
Abstract
Tight regulation of gene expression is orchestrated by enhancers. Through recent research advancements, it is becoming clear that enhancers are not solely distal regulatory elements harboring transcription factor binding sites and decorated with specific histone marks, but they rather display signatures of active transcription, showing distinct degrees of transcription unit organization. Thereby, a substantial fraction of enhancers give rise to different species of non-coding RNA transcripts with an unprecedented range of potential functions. In this review, we bring together data from recent studies indicating that non-coding RNA transcription from active enhancers, as well as enhancer-produced long non-coding RNA transcripts, may modulate or define the functional regulatory potential of the cognate enhancer. In addition, we summarize supporting evidence that RNA processing of the enhancer-associated long non-coding RNA transcripts may constitute an additional layer of regulation of enhancer activity, which contributes to the control and final outcome of enhancer-targeted gene expression.
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Affiliation(s)
- Evgenia Ntini
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Free University Berlin, Berlin, Germany
| | - Annalisa Marsico
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Free University Berlin, Berlin, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, München, Germany
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47
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Matthews BJ, Waxman DJ. Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver. Epigenetics Chromatin 2020; 13:30. [PMID: 32680543 PMCID: PMC7368777 DOI: 10.1186/s13072-020-00350-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.
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Affiliation(s)
- Bryan J Matthews
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
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48
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Parvathaneni RK, Bertolini E, Shamimuzzaman M, Vera DL, Lung PY, Rice BR, Zhang J, Brown PJ, Lipka AE, Bass HW, Eveland AL. The regulatory landscape of early maize inflorescence development. Genome Biol 2020; 21:165. [PMID: 32631399 PMCID: PMC7336428 DOI: 10.1186/s13059-020-02070-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. RESULT Here, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. CONCLUSIONS These analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.
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Affiliation(s)
| | | | - Md Shamimuzzaman
- Donald Danforth Plant Science Center, St. Louis, MO 63132 USA
- Current address: USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND 58102 USA
| | - Daniel L. Vera
- The Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL 32306 USA
- Current address: Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Pei-Yau Lung
- Department of Statistics, Florida State University, Tallahassee, FL 32306 USA
| | - Brian R. Rice
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306 USA
| | - Patrick J. Brown
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL 32306 USA
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49
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Enhancer RNAs are an important regulatory layer of the epigenome. Nat Struct Mol Biol 2020; 27:521-528. [PMID: 32514177 DOI: 10.1038/s41594-020-0446-0] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 05/07/2020] [Indexed: 12/20/2022]
Abstract
Noncoding RNAs (ncRNAs) direct a remarkable number of diverse functions in development and disease through their regulation of transcription, RNA processing and translation. Leading the charge in the RNA revolution is a class of ncRNAs that are synthesized at active enhancers, called enhancer RNAs (eRNAs). Here, we review recent insights into the biogenesis of eRNAs and the mechanisms underlying their multifaceted functions and consider how these findings could inform future investigations into enhancer transcription and eRNA function.
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50
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Tan JY, Biasini A, Young RS, Marques AC. Splicing of enhancer-associated lincRNAs contributes to enhancer activity. Life Sci Alliance 2020; 3:3/4/e202000663. [PMID: 32086317 PMCID: PMC7035876 DOI: 10.26508/lsa.202000663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
Transcription is common at active mammalian enhancers sometimes giving rise to stable enhancer-associated long intergenic noncoding RNAs (elincRNAs). Expression of elincRNA is associated with changes in neighboring gene product abundance and local chromosomal topology, suggesting that transcription at these loci contributes to gene expression regulation in cis Despite the lack of evidence supporting sequence-dependent functions for most elincRNAs, splicing of these transcripts is unexpectedly common. Whether elincRNA splicing is a mere consequence of cognate enhancer activity or if it directly impacts enhancer function remains unresolved. Here, we investigate the association between elincRNA splicing and enhancer activity in mouse embryonic stem cells. We show that multi-exonic elincRNAs are enriched at conserved enhancers, and the efficient processing of elincRNAs is strongly associated with their cognate enhancer activity. This association is supported by their enrichment in enhancer-specific chromatin signatures; elevated binding of co-transcriptional regulators; increased local intra-chromosomal DNA contacts; and strengthened cis-regulation on target gene expression. Our results support the role of efficient RNA processing of enhancer-associated transcripts to cognate enhancer activity.
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Affiliation(s)
- Jennifer Y Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Adriano Biasini
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Robert S Young
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ana C Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
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