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p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis. Mol Cell 2020; 77:761-774.e8. [PMID: 31973890 DOI: 10.1016/j.molcel.2019.12.014] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/20/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
The tumor suppressor p53 transcriptionally activates target genes to suppress cellular proliferation during stress. p53 has also been implicated in the repression of the proto-oncogene Myc, but the mechanism has remained unclear. Here, we identify Pvt1b, a p53-dependent isoform of the long noncoding RNA (lncRNA) Pvt1, expressed 50 kb downstream of Myc, which becomes induced by DNA damage or oncogenic signaling and accumulates near its site of transcription. We show that production of the Pvt1b RNA is necessary and sufficient to suppress Myc transcription in cis without altering the chromatin organization of the locus. Inhibition of Pvt1b increases Myc levels and transcriptional activity and promotes cellular proliferation. Furthermore, Pvt1b loss accelerates tumor growth, but not tumor progression, in an autochthonous mouse model of lung cancer. These findings demonstrate that Pvt1b acts at the intersection of the p53 and Myc transcriptional networks to reinforce the anti-proliferative activities of p53.
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Abstract
Long noncoding RNAs (lncRNAs) have emerged as important regulators of gene expression networks. Over 50,000 lncRNA loci have been annotated in the human genome, but only a subset has been involved in regulation of key cellular processes, organismal development, and diseases. Hence, the functional role for the majority of the lncRNA genes remains unknown. With the recent developments of different CRISPR/Cas9 technologies, the function of lncRNAs can now be examined. CRISPR interference (CRISPRi) is one of these methods that can be used to inhibit the expression of any genomic locus including lncRNAs. This system utilizes catalytically inactive (d)Cas9 fused to KRAB repression domain and single guide RNA against targeted genomic locus. Since CRISPRi has negligible off-target effects and does not involve changes in the underlying genomic DNA sequence, it represents a valuable addition to the existing armamentarium used to investigate lncRNA biology.
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Affiliation(s)
- Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, London, UK.
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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53
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Overcoming challenges and dogmas to understand the functions of pseudogenes. Nat Rev Genet 2019; 21:191-201. [DOI: 10.1038/s41576-019-0196-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 01/08/2023]
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54
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Awwad DA. Beyond classic editing: innovative CRISPR approaches for functional studies of long non-coding RNA. Biol Methods Protoc 2019; 4:bpz017. [PMID: 32161809 PMCID: PMC6994087 DOI: 10.1093/biomethods/bpz017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 09/06/2019] [Accepted: 11/19/2019] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) makeup a considerable part of the non-coding human genome and had been well-established as crucial players in an array of biological processes. In spite of their abundance and versatile roles, their functional characteristics remain largely undiscovered mainly due to the lack of suitable genetic manipulation tools. The emerging CRISPR/Cas9 technology has been widely adapted in several studies that aim to screen and identify novel lncRNAs as well as interrogate the functional properties of specific lncRNAs. However, the complexity of lncRNAs genes and the regulatory mechanisms that govern their transcription, as well as their unique functionality pose several limitations the utilization of classic CRISPR methods in lncRNAs functional studies. Here, we overview the unique characteristics of lncRNAs transcription and function and the suitability of the CRISPR toolbox for applications in functional characterization of lncRNAs. We discuss some of the novel variations to the classic CRISPR/Cas9 system that have been tailored and applied previously to study several aspects of lncRNAs functionality. Finally, we share perspectives on the potential applications of various CRISPR systems, including RNA-targeting, in the direct editing and manipulation of lncRNAs.
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Affiliation(s)
- Dahlia A Awwad
- Center of X-Ray Determination of Structure of Matter (CXDS), Helmi Institute of Biomedical Research, Zewail City of Science and Technology, Giza, Cairo, Egypt
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55
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McDonel P, Guttman M. Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression. Cold Spring Harb Perspect Biol 2019; 11:11/12/a032151. [PMID: 31791999 DOI: 10.1101/cshperspect.a032151] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammalian genomes encode tens of thousands of long noncoding RNAs (lncRNAs) that have been implicated in a diverse array of biological processes and human diseases. In recent years, the development of new tools for studying lncRNAs has enabled important progress in defining the mechanisms by which Xist and other lncRNAs function. This collective work provides a framework for how to define the mechanisms by which lncRNAs act. This includes defining lncRNA function, identifying and characterizing lncRNA-protein interactions, and lncRNA localization in the cell. In this review, we discuss various experimental approaches for deciphering lncRNA mechanisms and discuss issues and limitations in interpreting these results. We explore what these data can reveal about lncRNA function and mechanism as well as emerging insights into lncRNA biology that have been derived from these studies.
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Affiliation(s)
- Patrick McDonel
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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56
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Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL. The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun 2019; 10:5137. [PMID: 31723143 PMCID: PMC6853988 DOI: 10.1038/s41467-019-12970-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis.
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Affiliation(s)
- Jordan P Lewandowski
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - James C Lee
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Taeyoung Hwang
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Hongjae Sunwoo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Jill M Goldstein
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA, USA
| | - Abigail F Groff
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nydia P Chang
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - William Mallard
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Adam Williams
- The Jackson Laboratory, JAX Genomic Medicine, Farmington, CT, USA
| | - Jorge Henao-Meija
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA
| | - Richard A Flavell
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University, School of Medicine, New Haven, CT, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA, USA
- Joslin Diabetes Center, Boston, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
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57
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Liu JQ, Li T. CRISPR-Cas9-mediated loss-of-function screens. FRONTIERS IN LIFE SCIENCE 2019. [DOI: 10.1080/21553769.2019.1670739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Jia-qing Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Tao Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
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58
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Lewis MW, Li S, Franco HL. Transcriptional control by enhancers and enhancer RNAs. Transcription 2019; 10:171-186. [PMID: 31791217 PMCID: PMC6948965 DOI: 10.1080/21541264.2019.1695492] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/02/2022] Open
Abstract
The regulation of gene expression is a fundamental cellular process and its misregulation is a key component of disease. Enhancers are one of the most salient regulatory elements in the genome and help orchestrate proper spatiotemporal gene expression during development, in homeostasis, and in response to signaling. Notably, molecular aberrations at enhancers, such as translocations and single nucleotide polymorphisms, are emerging as an important source of human variation and susceptibility to disease. Herein we discuss emerging paradigms addressing how genes are regulated by enhancers, common features of active enhancers, and how non-coding enhancer RNAs (eRNAs) can direct gene expression programs that underlie cellular phenotypes. We survey the current evidence, which suggests that eRNAs can bind to transcription factors, mediate enhancer-promoter interactions, influence RNA Pol II elongation, and act as decoys for repressive cofactors. Furthermore, we discuss current methodologies for the identification of eRNAs and novel approaches to elucidate their functions.
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Affiliation(s)
- Michael W. Lewis
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Shen Li
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hector L. Franco
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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59
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Kopp F. Molecular functions and biological roles of long non‐coding RNAs in human physiology and disease. J Gene Med 2019; 21:e3104. [DOI: 10.1002/jgm.3104] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Florian Kopp
- Department of Molecular BiologyUniversity of Texas Southwestern Medical Center Dallas TX USA
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60
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Wang P, Yang X, Zhao L, Liu D, Liu J, Ding Y. A novel long non-coding RNA TONSL-AS1 regulates progression of gastric cancer via activating TONSL. Exp Cell Res 2019; 382:111453. [PMID: 31158361 DOI: 10.1016/j.yexcr.2019.05.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 01/17/2023]
Abstract
Long non-coding RNAs (lncRNAs) are reported to play a significant role in various malignant tumors, yet their potential functions in gastric cancer are not clear. In this study, we found a novel lncRNA, named TONSL-AS1, was downregulated in gastric cancer tissues and cell lines compared with the normal. TONSL-AS1 inhibited cell migration, invasion and proliferation in SGC-7901, MGC-803 cells. Furthermore, TONSL-AS1 could suppress cell tumorigenesis in vivo. Mechanistically, TONSL-AS1's genomic neighboring gene TONSL, which was reported as a tumor suppress gene, was upregulated by TONSL. Additionally, the TONSL-AS1 was positively associated with TONSL in cancer tissues. Our study revealed that the tumor-inhibiting effect of TONSL-AS1 in gastric cancer cells was associated with TONSL. In general, our results indicated that TONSL-AS1 works as a tumor suppressor lncRNA, which may be a new therapeutic target for gastric cancer.
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Affiliation(s)
- Peng Wang
- Department of General Surgery, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University. No.1399, Shichang Road, Shengze Town, Suzhou City, Jiangsu, China; Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Xi Yang
- Department of Gastroenterology, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University. No. 1399, Shichang Road, Shengze Town, Suzhou City, Jiangsu, China
| | - Liang Zhao
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Dongxiao Liu
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Junmao Liu
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine. No.1-1, Zhongfu Road, Nanjing, Jiangsu, China
| | - Yongbin Ding
- Department of General Surgery, The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University. No.1399, Shichang Road, Shengze Town, Suzhou City, Jiangsu, China; Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University. No. 300, Guangzhou Road, Nanjing, Jiangsu, China.
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61
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Esposito R, Bosch N, Lanzós A, Polidori T, Pulido-Quetglas C, Johnson R. Hacking the Cancer Genome: Profiling Therapeutically Actionable Long Non-coding RNAs Using CRISPR-Cas9 Screening. Cancer Cell 2019; 35:545-557. [PMID: 30827888 DOI: 10.1016/j.ccell.2019.01.019] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/20/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) represent a huge reservoir of potential cancer targets. Such "onco-lncRNAs" have resisted traditional RNAi methods, but CRISPR-Cas9 genome editing now promises functional screens at high throughput and low cost. The unique biology of lncRNAs demands screening strategies distinct from protein-coding genes. The first such screens have identified hundreds of onco-lncRNAs promoting cell proliferation and drug resistance. Ongoing developments will further improve screen performance and translational relevance. This Review aims to highlight the potential of CRISPR screening technology for discovering new onco-lncRNAs, and to guide molecular oncologists wishing to apply it to their cancer of interest.
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Affiliation(s)
- Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Núria Bosch
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Andrés Lanzós
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
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62
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Bink DI, Lozano-Vidal N, Boon RA. Long Non-Coding RNA in Vascular Disease and Aging. Noncoding RNA 2019; 5:ncrna5010026. [PMID: 30893946 PMCID: PMC6468806 DOI: 10.3390/ncrna5010026] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases are the most prominent cause of death in Western society, especially in the elderly. With the increasing life expectancy, the number of patients with cardiovascular diseases will rise in the near future, leading to an increased healthcare burden. There is a need for new therapies to treat this growing number of patients. The discovery of long non-coding RNAs has led to a novel group of molecules that could be considered for their potential as therapeutic targets. This review presents an overview of long non-coding RNAs that are regulated in vascular disease and aging and which might therefore give insight into new pathways that could be targeted to diagnose, prevent, and/or treat vascular diseases.
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Affiliation(s)
- Diewertje I Bink
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, VU University, 1081HV Amsterdam, The Netherlands.
| | - Noelia Lozano-Vidal
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, VU University, 1081HV Amsterdam, The Netherlands.
| | - Reinier A Boon
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, VU University, 1081HV Amsterdam, The Netherlands.
- Institute of Cardiovascular Regeneration, Goethe University, 60596 Frankfurt am Main, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhein-Main, 13347 Berlin, Germany.
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63
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Dangelmaier E, Lazar SB, Lal A. Long noncoding RNAs: p53's secret weapon in the fight against cancer? PLoS Biol 2019; 17:e3000143. [PMID: 30759134 PMCID: PMC6391031 DOI: 10.1371/journal.pbio.3000143] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
p53 regulates the expression of hundreds of genes. Recent surprising observations indicate that no single protein-coding gene controls the tumor suppressor effects of p53. This raises the possibility that a subset of these genes, regulated by a p53-induced long noncoding RNA (lncRNA), could control p53’s tumor suppressor function. We propose molecular mechanisms through which lncRNAs could regulate this subset of genes and hypothesize an exciting, direct role of lncRNAs in p53’s genome stability maintenance function. Exploring these mechanisms could reveal lncRNAs as indispensable mediators of p53 and lay the foundation for understanding how other transcription factors could act via lncRNAs. Transcription factors regulate hundreds of genes, a subset of which could mediate its effects in a given context. This Unsolved Mystery article explores mechanisms by which long noncoding RNAs might regulate such a subset downstream of p53, a well-studied transcription factor and major tumor suppressor.
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Affiliation(s)
- Emily Dangelmaier
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sarah B. Lazar
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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64
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Kopp F, Mendell JT. Functional Classification and Experimental Dissection of Long Noncoding RNAs. Cell 2019; 172:393-407. [PMID: 29373828 DOI: 10.1016/j.cell.2018.01.011] [Citation(s) in RCA: 2413] [Impact Index Per Article: 482.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/22/2017] [Accepted: 01/04/2018] [Indexed: 12/11/2022]
Abstract
Over the last decade, it has been increasingly demonstrated that the genomes of many species are pervasively transcribed, resulting in the production of numerous long noncoding RNAs (lncRNAs). At the same time, it is now appreciated that many types of DNA regulatory elements, such as enhancers and promoters, regularly initiate bi-directional transcription. Thus, discerning functional noncoding transcripts from a vast transcriptome is a paramount priority, and challenge, for the lncRNA field. In this review, we aim to provide a conceptual and experimental framework for classifying and elucidating lncRNA function. We categorize lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and propose an experimental approach to dissect lncRNA activity based on these classifications. These strategies to further understand lncRNAs promise to reveal new and unanticipated biology with great potential to advance our understanding of normal physiology and disease.
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Affiliation(s)
- Florian Kopp
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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65
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Sauvageau M. Diverging RNPs: Toward Understanding lncRNA-Protein Interactions and Functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:285-312. [PMID: 31811638 DOI: 10.1007/978-3-030-31434-7_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA-protein interactions are essential to a variety of biological processes. The realization that mammalian genomes are pervasively transcribed brought a tidal wave of tens of thousands of newly identified long noncoding RNAs (lncRNAs) and raised questions about their purpose in cells. The vast majority of lncRNAs have yet to be studied, and it remains to be determined to how many of these transcripts a function can be ascribed. However, results gleaned from studying a handful of these macromolecules have started to reveal common themes of biological function and mechanism of action involving intricate RNA-protein interactions. Some lncRNAs were shown to regulate the chromatin and transcription of distant and neighboring genes in the nucleus, while others regulate the translation or localization of proteins in the cytoplasm. Some lncRNAs were found to be crucial during development, while mutations and aberrant expression of others have been associated with several types of cancer and a plethora of diseases. Over the last few years, the establishment of new technologies has been key in providing the tools to decode the rules governing lncRNA-protein interactions and functions. This chapter will highlight the general characteristics of lncRNAs, their function, and their mode of action, with a special focus on protein interactions. It will also describe the methods at the disposition of scientists to help them cross this next frontier in our understanding of lncRNA biology.
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Affiliation(s)
- Martin Sauvageau
- Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada. .,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada.
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66
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Groff AF, Barutcu AR, Lewandowski JP, Rinn JL. Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Biol 2018; 19:219. [PMID: 30537984 PMCID: PMC6290506 DOI: 10.1186/s13059-018-1589-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/16/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Recently, it has become clear that some promoters function as long-range regulators of gene expression. However, direct and quantitative assessment of enhancer activity at long intergenic noncoding RNA (lincRNA) or mRNA gene bodies has not been performed. To unbiasedly assess the enhancer capacity across lincRNA and mRNA loci, we performed a massively parallel reporter assay (MPRA) on six lincRNA loci and their closest protein-coding neighbors. RESULTS For both gene classes, we find significantly more MPRA activity in promoter regions than in gene bodies. However, three lincRNA loci, Lincp21, LincEnc1, and Peril, and one mRNA locus, Morc2a, display significant enhancer activity within their gene bodies. We hypothesize that such peaks may mark long-range enhancers, and test this in vivo using RNA sequencing from a knockout mouse model and high-throughput chromosome conformation capture (Hi-C). We find that ablation of a high-activity MPRA peak in the Peril gene body leads to consistent dysregulation of Mccc1 and Exosc9 in the neighboring topologically associated domain (TAD). This occurs irrespective of Peril lincRNA expression, demonstrating this regulation is DNA-dependent. Hi-C confirms long-range contacts with the neighboring TAD, and these interactions are altered upon Peril knockout. Surprisingly, we do not observe consistent regulation of genes within the local TAD. Together, these data suggest a long-range enhancer-like function for the Peril gene body. CONCLUSIONS A multi-faceted approach combining high-throughput enhancer discovery with genetic models can connect enhancers to their gene targets and provides evidence of inter-TAD gene regulation.
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Affiliation(s)
- Abigail F Groff
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Jordan P Lewandowski
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Department of Biochemistry, BioFrontiers, University of Colorado Boulder, Boulder, CO, 80301, USA.
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67
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Liu SJ, Lim DA. Modulating the expression of long non-coding RNAs for functional studies. EMBO Rep 2018; 19:embr.201846955. [PMID: 30467236 DOI: 10.15252/embr.201846955] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 01/24/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as important regulators of cell biology. The mechanisms by which lncRNAs function are likely numerous, and most are poorly understood. Currently, the mechanisms of functional lncRNAs include those that directly involve the lncRNA transcript, the process of their own transcription and splicing, and even underlying transcriptional regulatory elements within the genomic DNA that encodes the lncRNA As our understanding of lncRNA biology evolves, so have the methods that are utilized to elucidate their functions. In this review, we survey a collection of different methods used to modulate lncRNA expression levels for the assessment of biological function. From RNA-targeted strategies, genetic deletions, to engineered gene regulatory systems, the advantages and caveats of each method will be discussed. Ultimately, the selection of tools will be guided by which potential lncRNA mechanisms are being investigated, and no single method alone will likely be sufficient to reveal the function of any particular lncRNA.
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Affiliation(s)
- S John Liu
- Department of Neurological Surgery, University of California, San Francisco, CA, USA .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, CA, USA .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA.,San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
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68
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Elling R, Robinson EK, Shapleigh B, Liapis SC, Covarrubias S, Katzman S, Groff AF, Jiang Z, Agarwal S, Motwani M, Chan J, Sharma S, Hennessy EJ, FitzGerald GA, McManus MT, Rinn JL, Fitzgerald KA, Carpenter S. Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell Rep 2018; 25:1511-1524.e6. [PMID: 30404006 PMCID: PMC6291222 DOI: 10.1016/j.celrep.2018.10.027] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 09/04/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
An inducible gene expression program is a hallmark of the host inflammatory response. Recently, long intergenic non-coding RNAs (lincRNAs) have been shown to regulate the magnitude, duration, and resolution of these responses. Among these is lincRNA-Cox2, a dynamically regulated gene that broadly controls immune gene expression. To evaluate the in vivo functions of this lincRNA, we characterized multiple models of lincRNA-Cox2-deficient mice. LincRNA-Cox2-deficient macrophages and murine tissues had altered expression of inflammatory genes. Transcriptomic studies from various tissues revealed that deletion of the lincRNA-Cox2 locus also strongly impaired the basal and inducible expression of the neighboring gene prostaglandin-endoperoxide synthase (Ptgs2), encoding cyclooxygenase-2, a key enzyme in the prostaglandin biosynthesis pathway. By utilizing different genetic manipulations in vitro and in vivo, we found that lincRNA-Cox2 functions through an enhancer RNA mechanism to regulate Ptgs2. More importantly, lincRNA-Cox2 also functions in trans, independently of Ptgs2, to regulate critical innate immune genes in vivo.
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Affiliation(s)
- Roland Elling
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA; Center for Pediatrics, Department of General Pediatrics, University of Freiburg, Freiburg, Germany
| | - Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Stephen C Liapis
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sol Katzman
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Abigail F Groff
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Zhaozhao Jiang
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shiuli Agarwal
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mona Motwani
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jennie Chan
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shruti Sharma
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Elizabeth J Hennessy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
| | - Garret A FitzGerald
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - John L Rinn
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Department of Biochemistry, BioFrontiers, University of Colorado Boulder, Boulder, CO 80301, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
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69
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Font-Cunill B, Arnes L, Ferrer J, Sussel L, Beucher A. Long Non-coding RNAs as Local Regulators of Pancreatic Islet Transcription Factor Genes. Front Genet 2018; 9:524. [PMID: 30459811 PMCID: PMC6232259 DOI: 10.3389/fgene.2018.00524] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022] Open
Abstract
The transcriptional programs of differentiated cells are tightly regulated by interactions between cell type-specific transcription factors and cis-regulatory elements. Long non-coding RNAs (lncRNAs) have emerged as additional regulators of gene transcription. Current evidence indicates that lncRNAs are a very heterogeneous group of molecules. For example, selected lncRNAs have been shown to regulate gene expression in cis or trans, although in most cases the precise underlying molecular mechanisms is unknown. Recent studies have uncovered a large number of lncRNAs that are selectively expressed in pancreatic islet cells, some of which were shown to regulate β cell transcriptional programs. A subset of such islet lncRNAs appears to control the expression of β cell-specific transcription factor (TF) genes by local cis-regulation. In this review, we discuss current knowledge of molecular mechanisms underlying cis-regulatory lncRNAs and discuss challenges involved in using genetic perturbations to define their function. We then discuss known examples of pancreatic islet lncRNAs that appear to exert cis-regulation of TF genes. We propose that cis-regulatory lncRNAs could represent a molecular target for modulation of diabetes-relevant genes.
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Affiliation(s)
- Berta Font-Cunill
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Luis Arnes
- Department of Systems Biology, Columbia University Medical Center, New York, NY, United States.,Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, United States
| | - Jorge Ferrer
- Department of Medicine, Imperial College London, London, United Kingdom.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain
| | - Lori Sussel
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, United States.,Barbara Davis Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Anthony Beucher
- Department of Medicine, Imperial College London, London, United Kingdom
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70
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Zhang X, Li DY, Reilly MP. Long intergenic noncoding RNAs in cardiovascular diseases: Challenges and strategies for physiological studies and translation. Atherosclerosis 2018; 281:180-188. [PMID: 30316538 DOI: 10.1016/j.atherosclerosis.2018.09.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/05/2018] [Accepted: 09/27/2018] [Indexed: 12/25/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as important mediators of many biological processes relevant to human pathophysiologies, including cardiovascular diseases. In vitro studies have provided important knowledge of cellular functions and mechanisms for an increasing number of lincRNAs. Dysregulated lncRNAs have been associated with cell fate programming and development, vascular diseases, atherosclerosis, dyslipidemia and metabolic syndrome, and cardiac pathological hypertrophy. However, functional interrogation of individual lincRNAs in physiological and disease states is largely limited. The complex nature of lincRNA actions and poor species conservation of human lincRNAs pose substantial challenges to physiological studies in animal model systems and in clinical translation. This review summarizes recent findings of specific lincRNA physiological studies, including MALAT1, MeXis, Lnc-DC and others, in the context of cardiovascular diseases, examines complex mechanisms of lincRNA actions, reviews in vivo research strategies to delineate lincRNA functions and highlights challenges and approaches for physiological studies of primate-specific lincRNAs.
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Affiliation(s)
- Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Daniel Y Li
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, 10032, USA.
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71
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72
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Balas MM, Johnson AM. Exploring the mechanisms behind long noncoding RNAs and cancer. Noncoding RNA Res 2018; 3:108-117. [PMID: 30175284 PMCID: PMC6114262 DOI: 10.1016/j.ncrna.2018.03.001] [Citation(s) in RCA: 200] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/23/2018] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, long noncoding RNAs (lncRNAs) have been identified as significant players in gene regulation. They are often differentially expressed and widely-associated with a majority of cancer types. The aberrant expression of these transcripts has been linked to tumorigenesis, metastasis, cancer stage progression and patient survival. Despite their apparent link to cancer, it has been challenging to gain a mechanistic understanding of how they contribute to cancer, partially due the difficulty in discriminating functional RNAs from other noncoding transcription events. However, there are several well-studied lncRNAs where specific mechanisms have been more clearly defined, leading to new discoveries into how these RNAs function. One major observation that has come to light is the context-dependence of lncRNA mechanisms, where they often have unique function in specific cell types and environment. Here, we review the molecular mechanisms of lncRNAs with a focus on cancer pathways, illustrating a few informative examples. Together, this type of detailed insight will lead to a greater understanding of the potential for the application of lncRNAs as targets of cancer therapies and diagnostics.
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Affiliation(s)
- Maggie M. Balas
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- RNA Bioscience Initiative, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
| | - Aaron M. Johnson
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- RNA Bioscience Initiative, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
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73
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Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell 2018; 173:1398-1412.e22. [PMID: 29731168 PMCID: PMC5984165 DOI: 10.1016/j.cell.2018.03.068] [Citation(s) in RCA: 318] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/08/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Abstract
Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers suggest alternative mechanisms. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.
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MESH Headings
- Animals
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- CRISPR-Cas Systems
- Carcinogenesis/genetics
- Cell Line, Tumor
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromatin
- DNA, Neoplasm/genetics
- Enhancer Elements, Genetic
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, myc
- Humans
- Mice
- Mice, Inbred NOD
- Mutation
- Neoplasm Transplantation
- Promoter Regions, Genetic
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Transcription, Genetic
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Affiliation(s)
- Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Y Grace Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jeewon Kim
- Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Jing He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Stephanie A Nevins
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Breast Cancer Program, CRUK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 2QQ, UK
| | - S John Liu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA 94121, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
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74
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Goyal A, Myacheva K, Groß M, Klingenberg M, Duran Arqué B, Diederichs S. Challenges of CRISPR/Cas9 applications for long non-coding RNA genes. Nucleic Acids Res 2017; 45:e12. [PMID: 28180319 PMCID: PMC5388423 DOI: 10.1093/nar/gkw883] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/01/2016] [Accepted: 09/23/2016] [Indexed: 12/14/2022] Open
Abstract
The CRISPR/Cas9 system provides a revolutionary genome editing tool for all areas of molecular biology. In long non-coding RNA (lncRNA) research, the Cas9 nuclease can delete lncRNA genes or introduce RNA-destabilizing elements into their locus. The nuclease-deficient dCas9 mutant retains its RNA-dependent DNA-binding activity and can modulate gene expression when fused to transcriptional repressor or activator domains. Here, we systematically analyze whether CRISPR approaches are suitable to target lncRNAs. Many lncRNAs are derived from bidirectional promoters or overlap with promoters or bodies of sense or antisense genes. In a genome-wide analysis, we find only 38% of 15929 lncRNA loci are safely amenable to CRISPR applications while almost two-thirds of lncRNA loci are at risk to inadvertently deregulate neighboring genes. CRISPR- but not siPOOL or Antisense Oligo (ASO)-mediated targeting of lncRNAs NOP14-AS1, LOC389641, MNX1-AS1 or HOTAIR also affects their respective neighboring genes. Frequently overlooked, the same restrictions may apply to mRNAs. For example, the tumor suppressor TP53 and its head-to-head neighbor WRAP53 are jointly affected by the same sgRNAs but not siPOOLs. Hence, despite the advantages of CRISPR/Cas9 to modulate expression bidirectionally and in cis, approaches based on ASOs or siPOOLs may be the better choice to target specifically the transcript from complex loci.
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Affiliation(s)
- Ashish Goyal
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ksenia Myacheva
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Matthias Groß
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Klingenberg
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
| | - Berta Duran Arqué
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
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75
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Andersen RE, Lim DA. Forging our understanding of lncRNAs in the brain. Cell Tissue Res 2017; 371:55-71. [PMID: 29079882 DOI: 10.1007/s00441-017-2711-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
During both development and adulthood, the human brain expresses many thousands of long noncoding RNAs (lncRNAs), and aberrant lncRNA expression has been associated with a wide range of neurological diseases. Although the biological significance of most lncRNAs remains to be discovered, it is now clear that certain lncRNAs carry out important functions in neurodevelopment, neural cell function, and perhaps even diseases of the human brain. Given the relatively inclusive definition of lncRNAs-transcripts longer than 200 nucleotides with essentially no protein coding potential-this class of noncoding transcript is both large and very diverse. Furthermore, emerging data indicate that lncRNA genes can act via multiple, non-mutually exclusive molecular mechanisms, and specific functions are difficult to predict from lncRNA expression or sequence alone. Thus, the different experimental approaches used to explore the role of a lncRNA might each shed light upon distinct facets of its overall molecular mechanism, and combining multiple approaches may be necessary to fully illuminate the function of any particular lncRNA. To understand how lncRNAs affect brain development and neurological disease, in vivo studies of lncRNA function are required. Thus, in this review, we focus our discussion upon a small set of neural lncRNAs that have been experimentally manipulated in mice. Together, these examples illustrate how studies of individual lncRNAs using multiple experimental approaches can help reveal the richness and complexity of lncRNA function in both neurodevelopment and diseases of the brain.
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Affiliation(s)
- Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA.,Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA. .,San Francisco Veterans Affairs Medical Center, San Francisco, CA, 94121, USA.
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76
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Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis. Blood 2017; 130:1965-1975. [PMID: 28928124 DOI: 10.1182/blood-2017-06-788695] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as vital components of gene programs controlling cell differentiation and function. Central to their functions is an ability to act as scaffolds or as decoys that recruit or sequester effector proteins from their DNA, RNA, or protein targets. lncRNA-modulated effectors include regulators of transcription, chromatin organization, RNA processing, and translation, such that lncRNAs can influence gene expression at multiple levels. Here we review the current understanding of how lncRNAs help coordinate gene expression to modulate cell fate in the hematopoietic system. We focus on a growing number of mechanistic studies to synthesize emerging principles of lncRNA function, emphasizing how they facilitate diversification of gene programming during development. We also survey how disrupted lncRNA function can contribute to malignant transformation, highlighting opportunities for therapeutic intervention in specific myeloid and lymphoid cancers. Finally, we discuss challenges and prospects for further elucidation of lncRNA mechanisms.
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77
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Yan P, Luo S, Lu JY, Shen X. Cis- and trans-acting lncRNAs in pluripotency and reprogramming. Curr Opin Genet Dev 2017; 46:170-178. [PMID: 28843809 DOI: 10.1016/j.gde.2017.07.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022]
Abstract
Pervasive transcription in mammalian genomes produces thousands of long noncoding RNA (lncRNA) transcripts. Although they have been implicated in diverse biological processes, the functional relevance of most lncRNAs remains unknown. Recent studies reveal the prevalence of lncRNA-mediated cis regulation on nearby transcription. In this review, we summarize cis- and trans-acting lncRNAs involved in stem cell pluripotency and reprogramming, highlighting the role of regulatory lncRNAs in providing an additional layer of complexity to the regulation of genes that govern cell fate during development.
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Affiliation(s)
- Pixi Yan
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sai Luo
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - J Yuyang Lu
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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78
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Espinosa JM. On the Origin of lncRNAs: Missing Link Found. Trends Genet 2017; 33:660-662. [PMID: 28778681 DOI: 10.1016/j.tig.2017.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Non-coding (nc)RNAs known as enhancer-derived RNAs (eRNAs) and as long ncRNAs (lncRNAs) have received much attention, but their true functional specialization and evolutionary origins remain obscure. The recent characterization of Bloodlinc, an eRNA derived from a super-enhancer that also functions as a lncRNA, suggests that lncRNAs can evolve from eRNAs.
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Affiliation(s)
- Joaquín M Espinosa
- Linda Crnic Institute for Down Syndrome and Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80203, USA.
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79
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Pradeepa MM, McKenna F, Taylor GCA, Bengani H, Grimes GR, Wood AJ, Bhatia S, Bickmore WA. Psip1/p52 regulates posterior Hoxa genes through activation of lncRNA Hottip. PLoS Genet 2017; 13:e1006677. [PMID: 28384324 PMCID: PMC5383017 DOI: 10.1371/journal.pgen.1006677] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 03/09/2017] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in various biological functions including the regulation of gene expression, however, the functionality of lncRNAs is not clearly understood and conflicting conclusions have often been reached when comparing different methods to investigate them. Moreover, little is known about the upstream regulation of lncRNAs. Here we show that the short isoform (p52) of a transcriptional co-activator-PC4 and SF2 interacting protein (Psip1), which is known to be involved in linking transcription to RNA processing, specifically regulates the expression of the lncRNA Hottip-located at the 5' end of the Hoxa locus. Using both knockdown and knockout approaches we show that Hottip expression is required for activation of the 5' Hoxa genes (Hoxa13 and Hoxa10/11) and for retaining Mll1 at the 5' end of Hoxa. Moreover, we demonstrate that artificially inducing Hottip expression is sufficient to activate the 5' Hoxa genes and that Hottip RNA binds to the 5' end of Hoxa. By engineering premature transcription termination, we show that it is the Hottip lncRNA molecule itself, not just Hottip transcription that is required to maintains active expression of posterior Hox genes. Our data show a direct role for a lncRNA molecule in regulating the expression of developmentally-regulated mRNA genes in cis.
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Affiliation(s)
- Madapura M. Pradeepa
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at University of Edinburgh, Edinburgh, United Kingdom
- School of biological sciences, University of Essex, Colchester, United Kingdom
| | - Fionnuala McKenna
- School of biological sciences, University of Essex, Colchester, United Kingdom
| | - Gillian C. A. Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at University of Edinburgh, Edinburgh, United Kingdom
| | - Hemant Bengani
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at University of Edinburgh, Edinburgh, United Kingdom
| | - Graeme R. Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew J. Wood
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at University of Edinburgh, Edinburgh, United Kingdom
| | - Shipra Bhatia
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at University of Edinburgh, Edinburgh, United Kingdom
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80
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Chaudhary R, Lal A. Long noncoding RNAs in the p53 network. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27990773 DOI: 10.1002/wrna.1410] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 12/14/2022]
Abstract
The tumor-suppressor protein p53 is activated in response to numerous cellular stresses including DNA damage. p53 functions primarily as a sequence-specific transcription factor that controls the expression of hundreds of protein-coding genes and noncoding RNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). While the role of protein-coding genes and miRNAs in mediating the effects of p53 has been extensively studied, the physiological function and molecular mechanisms by which p53-regulated lncRNAs act is beginning to be understood. In this review, we discuss recent studies on lncRNAs that are directly or indirectly regulated by p53 and how they contribute to the biological outcomes of p53 activation. WIREs RNA 2017, 8:e1410. doi: 10.1002/wrna.1410 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ritu Chaudhary
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
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81
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Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 2016; 355:science.aah7111. [PMID: 27980086 DOI: 10.1126/science.aah7111] [Citation(s) in RCA: 492] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/30/2016] [Indexed: 12/29/2022]
Abstract
The human genome produces thousands of long noncoding RNAs (lncRNAs)-transcripts >200 nucleotides long that do not encode proteins. Although critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. We developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in seven diverse cell lines, including six transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth-modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type specificity of many lncRNAs.
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Affiliation(s)
- S John Liu
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Harjus S Birk
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Martina Malatesta
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Daniel He
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Frank J Attenello
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Min Y Cho
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Yuwen Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Mohammad A Mandegar
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
| | - Michael P Olvera
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Bruce R Conklin
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.,Deparment of Medicine, University of California, San Francisco, CA 94143, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA. .,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143, USA.,Center for RNA Systems Biology, University of California, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA.,San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
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