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Kassouf M, Ford S, Blayney J, Higgs D. Understanding fundamental principles of enhancer biology at a model locus: Analysing the structure and function of an enhancer cluster at the α-globin locus. Bioessays 2023; 45:e2300047. [PMID: 37404089 DOI: 10.1002/bies.202300047] [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: 03/08/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 07/06/2023]
Abstract
Despite ever-increasing accumulation of genomic data, the fundamental question of how individual genes are switched on during development, lineage-specification and differentiation is not fully answered. It is widely accepted that this involves the interaction between at least three fundamental regulatory elements: enhancers, promoters and insulators. Enhancers contain transcription factor binding sites which are bound by transcription factors (TFs) and co-factors expressed during cell fate decisions and maintain imposed patterns of activation, at least in part, via their epigenetic modification. This information is transferred from enhancers to their cognate promoters often by coming into close physical proximity to form a 'transcriptional hub' containing a high concentration of TFs and co-factors. The mechanisms underlying these stages of transcriptional activation are not fully explained. This review focuses on how enhancers and promoters are activated during differentiation and how multiple enhancers work together to regulate gene expression. We illustrate the currently understood principles of how mammalian enhancers work and how they may be perturbed in enhanceropathies using expression of the α-globin gene cluster during erythropoiesis, as a model.
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Affiliation(s)
- Mira Kassouf
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Seren Ford
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joseph Blayney
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Doug Higgs
- Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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2
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Li Q, Liu X, Wen J, Chen X, Xie B, Zhao Y. Enhancer RNAs: mechanisms in transcriptional regulation and functions in diseases. Cell Commun Signal 2023; 21:191. [PMID: 37537618 PMCID: PMC10398997 DOI: 10.1186/s12964-023-01206-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/23/2023] [Indexed: 08/05/2023] Open
Abstract
In recent years, increasingly more non-coding RNAs have been detected with the development of high-throughput sequencing technology, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), small nucleolar RNAs (snoRNAs), and piwi-interacting RNA (piRNAs). The discovery of enhancer RNAs (eRNAs) in 2010 has further broadened the range of non-coding RNAs revealed. eRNAs are non-coding RNA molecules produced by the transcription of DNA cis-acting elements, enhancer fragments. Recent studies revealed that the transcription of eRNAs may be a biological marker responding to enhancer activity that can participate in the regulation of coding gene transcription. In this review, we discussed the biological characteristics of eRNAs, their functions in transcriptional regulation, the regulation factors of eRNAs production, and the research progress of eRNAs in different diseases. Video Abstract.
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Affiliation(s)
- Qianhui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Xin Liu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Jingtao Wen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Bumin Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangdong Province, Guangzhou City, 510150, People's Republic of China.
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3
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Zhao Y, Bai L, Yao X, Hang R, Xiao Y. Understanding LncRNAs in Biomaterials Development for Osteointegration. Regen Med 2023. [DOI: 10.1007/978-981-19-6008-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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4
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Talbot CD, Walsh MD, Cutty SJ, Elsayed R, Vlachaki E, Bruce AEE, Wardle FC, Nelson AC. Eomes function is conserved between zebrafish and mouse and controls left-right organiser progenitor gene expression via interlocking feedforward loops. Front Cell Dev Biol 2022; 10:982477. [PMID: 36133924 PMCID: PMC9483813 DOI: 10.3389/fcell.2022.982477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
The T-box family transcription factor Eomesodermin (Eomes) is present in all vertebrates, with many key roles in the developing mammalian embryo and immune system. Homozygous Eomes mutant mouse embryos exhibit early lethality due to defects in both the embryonic mesendoderm and the extraembryonic trophoblast cell lineage. In contrast, zebrafish lacking the predominant Eomes homologue A (Eomesa) do not suffer complete lethality and can be maintained. This suggests fundamental differences in either the molecular function of Eomes orthologues or the molecular configuration of processes in which they participate. To explore these hypotheses we initially analysed the expression of distinct Eomes isoforms in various mouse cell types. Next we compared the functional capabilities of these murine isoforms to zebrafish Eomesa. These experiments provided no evidence for functional divergence. Next we examined the functions of zebrafish Eomesa and other T-box family members expressed in early development, as well as its paralogue Eomesb. Though Eomes is a member of the Tbr1 subfamily we found evidence for functional redundancy with the Tbx6 subfamily member Tbx16, known to be absent from eutherians. However, Tbx16 does not appear to synergise with Eomesa cofactors Mixl1 and Gata5. Finally, we analysed the ability of Eomesa and other T-box factors to induce zebrafish left-right organiser progenitors (known as dorsal forerunner cells) known to be positively regulated by vgll4l, a gene we had previously shown to be repressed by Eomesa. Here we demonstrate that Eomesa indirectly upregulates vgll4l expression via interlocking feedforward loops, suggesting a role in establishment of left-right asymmetry. Conversely, other T-box factors could not similarly induce left-right organiser progenitors. Overall these findings demonstrate conservation of Eomes molecular function and participation in similar processes, but differential requirements across evolution due to additional co-expressed T-box factors in teleosts, albeit with markedly different molecular capabilities. Our analyses also provide insights into the role of Eomesa in left-right organiser formation in zebrafish.
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Affiliation(s)
- Conor D. Talbot
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Mark D. Walsh
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Stephen J. Cutty
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, King’s College London, London, United Kingdom
| | - Randa Elsayed
- Warwick Medical School, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Eirini Vlachaki
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Ashley E. E. Bruce
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Fiona C. Wardle
- Randall Centre for Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, King’s College London, London, United Kingdom
| | - Andrew C. Nelson
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
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5
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Gibbons MD, Fang Y, Spicola AP, Linzer N, Jones SM, Johnson BR, Li L, Xie M, Bungert J. Enhancer-Mediated Formation of Nuclear Transcription Initiation Domains. Int J Mol Sci 2022; 23:ijms23169290. [PMID: 36012554 PMCID: PMC9409229 DOI: 10.3390/ijms23169290] [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: 07/19/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Enhancers in higher eukaryotes and upstream activating sequences (UASs) in yeast have been shown to recruit components of the RNA polymerase II (Pol II) transcription machinery. At least a fraction of Pol II recruited to enhancers in higher eukaryotes initiates transcription and generates enhancer RNA (eRNA). In contrast, UASs in yeast do not recruit transcription factor TFIIH, which is required for transcription initiation. For both yeast and mammalian systems, it was shown that Pol II is transferred from enhancers/UASs to promoters. We propose that there are two modes of Pol II recruitment to enhancers in higher eukaryotes. Pol II complexes that generate eRNAs are recruited via TFIID, similar to mechanisms operating at promoters. This may involve the binding of TFIID to acetylated nucleosomes flanking the enhancer. The resulting eRNA, together with enhancer-bound transcription factors and co-regulators, contributes to the second mode of Pol II recruitment through the formation of a transcription initiation domain. Transient contacts with target genes, governed by proteins and RNA, lead to the transfer of Pol II from enhancers to TFIID-bound promoters.
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6
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Wang K, Escobar M, Li J, Mahata B, Goell J, Shah S, Cluck M, Hilton IB. Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions. Nucleic Acids Res 2022; 50:7842-7855. [PMID: 35849129 PMCID: PMC9371918 DOI: 10.1093/nar/gkac582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/19/2022] [Accepted: 06/24/2022] [Indexed: 12/29/2022] Open
Abstract
Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer-promoter pairs. Here, we systematically compared the most widely adopted dCas9-based transcriptional activators, as well as an activator consisting of dCas9 fused to the catalytic core of the human CBP protein, at human enhancer-promoter pairs. We find that these platforms display variable relative expression levels in different human cell types and that their transactivation efficacies vary based upon the effector domain, effector recruitment architecture, targeted locus and cell type. We also show that each dCas9-based activator can induce the production of enhancer RNAs (eRNAs) and that this eRNA induction is positively correlated with downstream mRNA expression from a cognate promoter. Additionally, we use dCas9-based activators to demonstrate that an intrinsic transcriptional and epigenetic reciprocity can exist between human enhancers and promoters and that enhancer-mediated tracking and engagement of a downstream promoter can be synthetically driven by targeting dCas9-based transcriptional activators to an enhancer. Collectively, our study provides new insights into the enhancer-mediated control of human gene expression and the use of dCas9-based activators.
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Affiliation(s)
- Kaiyuan Wang
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Mario Escobar
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Jing Li
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jacob Goell
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Spencer Shah
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Madeleine Cluck
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.,Department of BioSciences, Rice University, Houston, TX 77005, USA
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7
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Kovina AP, Petrova NV, Komkov DS, Dashinimaev EB, Razin SV. Regulatory systems of chicken alpha-globin gene domain suppress bidirectional transcription. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194850. [PMID: 35940436 DOI: 10.1016/j.bbagrm.2022.194850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Affiliation(s)
- A P Kovina
- Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - N V Petrova
- Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - D S Komkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - E B Dashinimaev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - S V Razin
- Institute of Gene Biology RAS, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
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8
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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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9
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Higashi M, Ikehara T, Nakagawa T, Yoneda M, Hattori N, Ikeda M, Ito T. Long noncoding RNAs transcribed downstream of the human β-globin locus regulate β-globin gene expression. J Biochem 2021; 171:287-294. [PMID: 34878533 DOI: 10.1093/jb/mvab130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/07/2021] [Indexed: 01/29/2023] Open
Abstract
The five β-like globin genes (ε, Gγ, Aγ, δ, and β) at the human β-globin gene locus are known to be expressed at specific developmental stages, although details of the underlying mechanism remain to be uncovered. Here we used an in vitro transcription assay to clarify the mechanisms that control this gene expression. We first tested nuclear RNA from HeLa cells using RT-qPCR and discovered a long noncoding RNAs (lncRNAs) within a 5.2-kb region beginning 4.4 kb downstream of the β-globin gene coding region. We investigated nuclear RNA from K562 cells using a primer-extension assay and determined the transcription start sites (TSSs) of these lncRNAs. To clarify their functional role, we performed knockdown (KD) of these lncRNAs in K562 cells. Hydroxyurea, which induces differentiation of K562 cells, increased hemoglobin peptide production, and the effect was enhanced by KD of these lncRNAs, which also enhanced upregulation of the γ-globin expression induced by hydroxyurea. To confirm these results, we performed an in vitro transcription assay. Noncoding single-stranded RNAs inhibited β-globin expression, which was upregulated by GATA1. Furthermore, lncRNAs interacted with GATA1 without sequence specificity and inhibited its binding to its target DNA response element in vitro. Our results suggest that lncRNAs downstream of the β-globin gene locus are key factors regulating globin gene ex pression.
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Affiliation(s)
- Miki Higashi
- Department of Biochemistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Physiology, Saitama Medical University, Saitama, Japan
| | - Tsuyoshi Ikehara
- Department of Biochemistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Food Science and Technology, National Fisheries University, Yamaguchi, Japan
| | - Takeya Nakagawa
- Department of Biochemistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Mitsuhiro Yoneda
- Department of Biochemistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naoko Hattori
- Department of Biochemistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masaaki Ikeda
- Department of Physiology, Saitama Medical University, Saitama, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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10
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Zhou Y, Xu S, Zhang M, Wu Q. Systematic functional characterization of antisense eRNA of protocadherin α composite enhancer. Genes Dev 2021; 35:1383-1394. [PMID: 34531317 DOI: 10.1101/gad.348621.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022]
Abstract
Enhancers generate bidirectional noncoding enhancer RNAs (eRNAs) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5' capped antisense eRNA PEARL (Pcdh eRNA associated with R-loop formation) that is transcribed from the protocadherin (Pcdh) α HS5-1 enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA fragment editing, CRISPRi, and CRISPRa, as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we found that PEARL regulates Pcdhα gene expression by forming local RNA-DNA duplexes (R-loops) in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancers and target promoters. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 lead to strengthened local three-dimensional chromatin organization within the Pcdh superTAD. These findings have important implications regarding molecular mechanisms by which the HS5-1 enhancer regulates stochastic Pcdhα promoter choice in single cells in the brain.
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Affiliation(s)
- Yuxiao Zhou
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.,WLA Laboratories, Shanghai 201203, China
| | - Siyuan Xu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.,WLA Laboratories, Shanghai 201203, China
| | - Mo Zhang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.,WLA Laboratories, Shanghai 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.,WLA Laboratories, Shanghai 201203, China
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11
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Enhancer RNA: biogenesis, function, and regulation. Essays Biochem 2021; 64:883-894. [PMID: 33034351 DOI: 10.1042/ebc20200014] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
Enhancers are noncoding DNA elements that are present upstream or downstream of a gene to control its spatial and temporal expression. Specific histone modifications, such as monomethylation on histone H3 lysine 4 (H3K4me1) and H3K27ac, have been widely used to assign enhancer regions in mammalian genomes. In recent years, emerging evidence suggests that active enhancers are bidirectionally transcribed to produce enhancer RNAs (eRNAs). This finding not only adds a new reliable feature to define enhancers but also raises a fundamental question of how eRNAs function to activate transcription. Although some believe that eRNAs are merely transcriptional byproducts, many studies have demonstrated that eRNAs execute crucial tasks in regulating chromatin conformation and transcription activation. In this review, we summarize the current understanding of eRNAs from their biogenesis, functions, and regulation to their pathological significance. Additionally, we discuss the challenges and possible mechanisms of eRNAs in regulated transcription.
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12
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Roberts BS, Partridge EC, Moyers BA, Agarwal V, Newberry KM, Martin BK, Shendure J, Myers RM, Cooper GM. Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands. Genome Res 2021; 31:866-876. [PMID: 33879525 PMCID: PMC8092006 DOI: 10.1101/gr.270751.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/18/2021] [Indexed: 11/24/2022]
Abstract
Massively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human genomes. An aspect of MPRAs that is not typically the focus of analysis is their intrinsic ability to differentiate activity levels for a given sequence element when placed in both of its possible orientations relative to the reporter construct. Here, we describe pervasive strand asymmetry of MPRA signals in data sets from multiple reporter configurations in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that function related to endogenous transcription is driving the phenomenon. Similarly, we find that within Alu mobile element insertions, strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes and is more pronounced in less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and show its prediction from sequence alone. We see some evidence for RNA stabilization and transcriptional activation mechanisms and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry is a pervasive and reproducible feature in MPRA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.
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Affiliation(s)
- Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
| | | | - Bryan A Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Vikram Agarwal
- Calico Life Sciences LLC, South San Francisco, California 94080, USA
| | | | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, Seattle, Washington 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
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13
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Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021; 22:108. [PMID: 33858480 PMCID: PMC8051032 DOI: 10.1186/s13059-021-02322-1] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.
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Affiliation(s)
- Anil Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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14
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Gurumurthy A, Yu DT, Stees JR, Chamales P, Gavrilova E, Wassel P, Li L, Stribling D, Chen J, Brackett M, Ishov AM, Xie M, Bungert J. Super-enhancer mediated regulation of adult β-globin gene expression: the role of eRNA and Integrator. Nucleic Acids Res 2021; 49:1383-1396. [PMID: 33476375 PMCID: PMC7897481 DOI: 10.1093/nar/gkab002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 01/05/2023] Open
Abstract
Super-enhancers (SEs) mediate high transcription levels of target genes. Previous studies have shown that SEs recruit transcription complexes and generate enhancer RNAs (eRNAs). We characterized transcription at the human and murine β-globin locus control region (LCR) SE. We found that the human LCR is capable of recruiting transcription complexes independently from linked globin genes in transgenic mice. Furthermore, LCR hypersensitive site 2 (HS2) initiates the formation of bidirectional transcripts in transgenic mice and in the endogenous β-globin gene locus in murine erythroleukemia (MEL) cells. HS2 3′eRNA is relatively unstable and remains in close proximity to the globin gene locus. Reducing the abundance of HS2 3′eRNA leads to a reduction in β-globin gene transcription and compromises RNA polymerase II (Pol II) recruitment at the promoter. The Integrator complex has been shown to terminate eRNA transcription. We demonstrate that Integrator interacts downstream of LCR HS2. Inducible ablation of Integrator function in MEL or differentiating primary human CD34+ cells causes a decrease in expression of the adult β-globin gene and accumulation of Pol II and eRNA at the LCR. The data suggest that transcription complexes are assembled at the LCR and transferred to the globin genes by mechanisms that involve Integrator mediated release of Pol II and eRNA from the LCR.
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Affiliation(s)
- Aishwarya Gurumurthy
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - David T Yu
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Jared R Stees
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Pamela Chamales
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Ekaterina Gavrilova
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Paul Wassel
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Daniel Stribling
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, Gainesville, FL 32610, USA
| | - Jinyang Chen
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Marissa Brackett
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, Center for Epigenetics, Genetics Institute, UF Health Cancer Center, Powell-Gene Therapy Center, Gainesville, FL 32610, USA
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15
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Lidschreiber K, Jung LA, von der Emde H, Dave K, Taipale J, Cramer P, Lidschreiber M. Transcriptionally active enhancers in human cancer cells. Mol Syst Biol 2021; 17:e9873. [PMID: 33502116 PMCID: PMC7838827 DOI: 10.15252/msb.20209873] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/30/2022] Open
Abstract
The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. Here, we use transient transcriptome sequencing (TT-seq) to map thousands of transcriptionally active putative enhancers in fourteen human cancer cell lines covering seven types of cancer. These enhancers were associated with cell type-specific gene expression, enriched for genetic variants that predispose to cancer, and included functionally verified enhancers. Enhancer-promoter (E-P) pairing by correlation of transcription activity revealed ~ 40,000 putative E-P pairs, which were depleted for housekeeping genes and enriched for transcription factors, cancer-associated genes, and 3D conformational proximity. The cell type specificity and transcription activity of target genes increased with the number of paired putative enhancers. Our results represent a rich resource for future studies of gene regulation by enhancers and their role in driving cancerous cell growth.
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Affiliation(s)
- Katja Lidschreiber
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
| | - Lisa A Jung
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
- Department of Cell and Molecular BiologyKarolinska InstitutetBiomedicumSolnaSweden
| | - Henrik von der Emde
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Kashyap Dave
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetBiomedicumSolnaSweden
| | - Jussi Taipale
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetBiomedicumSolnaSweden
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Genome‐Scale Biology ProgramUniversity of HelsinkiHelsinkiFinland
| | - Patrick Cramer
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
| | - Michael Lidschreiber
- Department of Molecular BiologyMax Planck Institute for Biophysical ChemistryGöttingenGermany
- Department of Biosciences and NutritionKarolinska InstitutetNEOHuddingeSweden
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16
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Hou TY, Kraus WL. Spirits in the Material World: Enhancer RNAs in Transcriptional Regulation. Trends Biochem Sci 2020; 46:138-153. [PMID: 32888773 DOI: 10.1016/j.tibs.2020.08.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
Responses to developmental and environmental cues depend on precise spatiotemporal control of gene transcription. Enhancers, which comprise DNA elements bound by regulatory proteins, can activate target genes in response to these external signals. Recent studies have shown that enhancers are transcribed to produce enhancer RNAs (eRNAs). Do eRNAs play a functional role in activating gene expression or are they non-functional byproducts of nearby transcription machinery? The unstable nature of eRNAs and over-reliance on knockdown approaches have made elucidating the possible functions of eRNAs challenging. We focus here on studies using cloned eRNAs to study their function as transcripts, revealing roles for eRNAs in enhancer-promoter looping, recruiting transcriptional machinery, and facilitating RNA polymerase pause-release to regulate gene expression.
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Affiliation(s)
- Tim Y Hou
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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17
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Ibragimov AN, Bylino OV, Shidlovskii YV. Molecular Basis of the Function of Transcriptional Enhancers. Cells 2020; 9:E1620. [PMID: 32635644 PMCID: PMC7407508 DOI: 10.3390/cells9071620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription.
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Affiliation(s)
- Airat N. Ibragimov
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Oleg V. Bylino
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; (A.N.I.); (O.V.B.)
- I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia
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18
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Abstract
Cell-type- and condition-specific profiles of gene expression require coordination between protein-coding gene promoters and cis-regulatory sequences called enhancers. Enhancers can stimulate gene activity at great genomic distances from their targets, raising questions about how enhancers communicate with specific gene promoters and what molecular mechanisms underlie enhancer function. Characterization of enhancer loci has identified the molecular features of active enhancers that accompany the binding of transcription factors and local opening of chromatin. These characteristics include coactivator recruitment, histone modifications, and noncoding RNA transcription. However, it remains unclear which of these features functionally contribute to enhancer activity. Here, we discuss what is known about how enhancers regulate their target genes and how enhancers and promoters communicate. Further, we describe recent data demonstrating many similarities between enhancers and the gene promoters they control, and we highlight unanswered questions in the field, such as the potential roles of transcription at enhancers.
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Affiliation(s)
- Andrew Field
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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19
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Zhang F, Ma Y, Xu L, Xu H, Xu Y, Yan N. Long non‑coding RNA profile revealed by microarray indicates that lncCUEDC1 serves a negative regulatory role in breast cancer stem cells. Int J Oncol 2020; 56:807-820. [PMID: 32124947 DOI: 10.3892/ijo.2020.4960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/29/2019] [Indexed: 11/05/2022] Open
Abstract
Previous studies have demonstrated that long non‑coding RNAs (lncRNAs) are involved in breast cancer development, progression and metastasis. However, the association between lncRNAs and breast cancer stem cells (BCSCs) has been poorly explored. To address this issue, microarray analyses were performed to detect the lncRNA profile of BCSCs. In addition, bioinformatics analyses, including Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses, were performed to explore the functional roles of lncRNAs in BCSCs. Lastly, loss of function assays were used to explore the potential function of lncRNA CUE domain containing 1 (lncCUEDC1). A total of 142 differentially expressed lncRNAs were identified. Among these, 25 were downregulated and 117 were upregulated in BCSCs compared with in non‑BCSCs. In addition, the present study revealed that the lncRNAs were largely associated with stemness‑related signaling pathways. Furthermore, it was demonstrated that lncCUEDC1 negatively regulated the phenotype and biological functions of BCSCs in vitro. Mechanistically, lncCUEDC1 could bind NANOG to inhibit the stemness. To the best of our knowledge, the present study was the first to established the lncRNA profile of BCSCs. These findings provided evidence for exploring the functions of lncRNAs in BCSCs and indicated that lncCUEDC1 is a prospective target in BCSCs.
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Affiliation(s)
- Fengchun Zhang
- Department of Oncology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, Jiangsu 215021, P.R. China
| | - Yue Ma
- Department of Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Liang Xu
- The First Department of Prevention and Cure Centre of Breast Disease, The Third Hospital of Nanchang City, Nanchang, Jiangxi 330009, P.R. China
| | - Haiyan Xu
- Department of Oncology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, Jiangsu 215021, P.R. China
| | - Yingchun Xu
- Department of Oncology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200127, P.R. China
| | - Ningning Yan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450002, P.R. China
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20
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Wissink EM, Vihervaara A, Tippens ND, Lis JT. Nascent RNA analyses: tracking transcription and its regulation. Nat Rev Genet 2019; 20:705-723. [PMID: 31399713 PMCID: PMC6858503 DOI: 10.1038/s41576-019-0159-6] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
Abstract
The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.
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Affiliation(s)
- Erin M Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Anniina Vihervaara
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Nathaniel D Tippens
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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21
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Dai X, Kaushik AC, Zhang J. The Emerging Role of Major Regulatory RNAs in Cancer Control. Front Oncol 2019; 9:920. [PMID: 31608229 PMCID: PMC6771296 DOI: 10.3389/fonc.2019.00920] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Alterations and personal variations of RNA interactions have been mechanistically coupled with disease etiology and phenotypical variations. RNA biomarkers, RNA mimics, and RNA antagonists have been developed for diagnostic, prognostic, and therapeutic uses. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are two major types of RNA molecules with regulatory roles, deregulation of which has been implicated in the initiation and progression of many human malignancies. Accumulating evidence indicated the clinical roles of regulatory RNAs in cancer control, stimulating a surge in exploring the functionalities of regulatory RNAs for improved understanding on disease pathogenesis and management. In this review, we highlight the critical roles of lncRNAs and miRNAs played in tumorigenesis, scrutinize their potential functionalities as diagnostic/prognostic biomarkers and/or therapeutic targets in clinics, outline opportunities that ncRNAs may bring to complement current clinical practice for improved cancer management and identify challenges faced by translating frontier knowledge on non-coding RNAs (ncRNAs) to bedside clinics as well as possible solutions.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Aman Chandra Kaushik
- Wuxi School of Medicine, Jiangnan University, Wuxi, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianying Zhang
- Henan Key Laboratory of Tumor Epidemiology, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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22
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Debrand E, Chakalova L, Miles J, Dai YF, Goyenechea B, Dye S, Osborne CS, Horton A, Harju-Baker S, Pink RC, Caley D, Carter DRF, Peterson KR, Fraser P. An intergenic non-coding RNA promoter required for histone modifications in the human β-globin chromatin domain. PLoS One 2019; 14:e0217532. [PMID: 31412036 PMCID: PMC6693763 DOI: 10.1371/journal.pone.0217532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/22/2019] [Indexed: 12/05/2022] Open
Abstract
Transcriptome analyses show a surprisingly large proportion of the mammalian genome is transcribed; much more than can be accounted for by genes and introns alone. Most of this transcription is non-coding in nature and arises from intergenic regions, often overlapping known protein-coding genes in sense or antisense orientation. The functional relevance of this widespread transcription is unknown. Here we characterize a promoter responsible for initiation of an intergenic transcript located approximately 3.3 kb and 10.7 kb upstream of the adult-specific human β-globin genes. Mutational analyses in β-YAC transgenic mice show that alteration of intergenic promoter activity results in ablation of H3K4 di- and tri-methylation and H3 hyperacetylation extending over a 30 kb region immediately downstream of the initiation site, containing the adult δ- and β-globin genes. This results in dramatically decreased expression of the adult genes through position effect variegation in which the vast majority of definitive erythroid cells harbor inactive adult globin genes. In contrast, expression of the neighboring ε- and γ-globin genes is completely normal in embryonic erythroid cells, indicating a developmentally specific variegation of the adult domain. Our results demonstrate a role for intergenic non-coding RNA transcription in the propagation of histone modifications over chromatin domains and epigenetic control of β-like globin gene transcription during development.
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Affiliation(s)
- Emmanuel Debrand
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Lyubomira Chakalova
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Joanne Miles
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Yan-Feng Dai
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Beatriz Goyenechea
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Sandra Dye
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Cameron S. Osborne
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Alice Horton
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Susanna Harju-Baker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Ryan C. Pink
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Daniel Caley
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - David R. F. Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Kenneth R. Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Peter Fraser
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
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23
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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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24
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Perenthaler E, Yousefi S, Niggl E, Barakat TS. Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development. Front Cell Neurosci 2019; 13:352. [PMID: 31417368 PMCID: PMC6685065 DOI: 10.3389/fncel.2019.00352] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/16/2019] [Indexed: 12/22/2022] Open
Abstract
The development of the human cerebral cortex is a complex and dynamic process, in which neural stem cell proliferation, neuronal migration, and post-migratory neuronal organization need to occur in a well-organized fashion. Alterations at any of these crucial stages can result in malformations of cortical development (MCDs), a group of genetically heterogeneous neurodevelopmental disorders that present with developmental delay, intellectual disability and epilepsy. Recent progress in genetic technologies, such as next generation sequencing, most often focusing on all protein-coding exons (e.g., whole exome sequencing), allowed the discovery of more than a 100 genes associated with various types of MCDs. Although this has considerably increased the diagnostic yield, most MCD cases remain unexplained. As Whole Exome Sequencing investigates only a minor part of the human genome (1–2%), it is likely that patients, in which no disease-causing mutation has been identified, could harbor mutations in genomic regions beyond the exome. Even though functional annotation of non-coding regions is still lagging behind that of protein-coding genes, tremendous progress has been made in the field of gene regulation. One group of non-coding regulatory regions are enhancers, which can be distantly located upstream or downstream of genes and which can mediate temporal and tissue-specific transcriptional control via long-distance interactions with promoter regions. Although some examples exist in literature that link alterations of enhancers to genetic disorders, a widespread appreciation of the putative roles of these sequences in MCDs is still lacking. Here, we summarize the current state of knowledge on cis-regulatory regions and discuss novel technologies such as massively-parallel reporter assay systems, CRISPR-Cas9-based screens and computational approaches that help to further elucidate the emerging role of the non-coding genome in disease. Moreover, we discuss existing literature on mutations or copy number alterations of regulatory regions involved in brain development. We foresee that the future implementation of the knowledge obtained through ongoing gene regulation studies will benefit patients and will provide an explanation to part of the missing heritability of MCDs and other genetic disorders.
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Affiliation(s)
- Elena Perenthaler
- Department of Clinical Genetics, Erasmus MC - University Medical Center, Rotterdam, Netherlands
| | - Soheil Yousefi
- Department of Clinical Genetics, Erasmus MC - University Medical Center, Rotterdam, Netherlands
| | - Eva Niggl
- Department of Clinical Genetics, Erasmus MC - University Medical Center, Rotterdam, Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC - University Medical Center, Rotterdam, Netherlands
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25
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Line-1: Implications in the etiology of cancer, clinical applications, and pharmacologic targets. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 778:51-60. [DOI: 10.1016/j.mrrev.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/21/2022]
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26
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Ji K, Zhang J, Fan R, Yang S, Dong C. Differential expression of lncRNAs and predicted target genes in normal mouse melanocytes and B16 cells. Exp Dermatol 2018; 27:1230-1236. [DOI: 10.1111/exd.13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/26/2018] [Accepted: 08/08/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Kaiyuan Ji
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Junzhen Zhang
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Ruiwen Fan
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Shanshan Yang
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
| | - Changsheng Dong
- College of Animal Science and Veterinary Medicine; Shanxi Agricultural University; Taigu China
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27
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Yu H, Rong L. Emerging role of long non-coding RNA in the development of gastric cancer. World J Gastrointest Oncol 2018; 10:260-270. [PMID: 30254721 PMCID: PMC6147769 DOI: 10.4251/wjgo.v10.i9.260] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/14/2018] [Accepted: 06/27/2018] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer is a common, worldwide malignancy and has a poor prognosis due to late diagnosis. Long non-coding RNAs (lncRNAs) are a significant subtype of RNA molecules with a length longer than 200 nucleotides (nt) that rarely encode proteins. In recent decades, deregulation of lncRNAs has been shown to be involved in tumorigenesis and tumor progression in various human carcinomas, including gastric cancer. Accumulating evidence has shown that some lncRNAs may function as diagnostic biomarkers or therapeutic targets for gastric cancer. Thus, exploring the specific functions of lncRNAs will help both gain a better understanding of the pathogenesis and develop novel treatments for gastric cancer. In this review, we highlight the expression and functional roles of lncRNAs in gastric cancer, and analyze the potential applications of lncRNAs as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Hang Yu
- Department of Endoscopic Center, Peking University First Hospital, Beijing 100034, China
| | - Long Rong
- Department of Endoscopic Center, Peking University First Hospital, Beijing 100034, China
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28
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Sun Z, Chadwick BP. Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene. Epigenetics Chromatin 2018; 11:45. [PMID: 30103804 PMCID: PMC6088404 DOI: 10.1186/s13072-018-0218-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/10/2018] [Indexed: 01/04/2023] Open
Abstract
Background The product of dosage compensation in female mammals is the inactive X chromosome (Xi). Xi facultative heterochromatin is organized into two different types, one of which is defined by histone H3 trimethylated at lysine 9 (H3K9me3). The rationale for this study was to assess SET domain bifurcated 1 (SETDB1) as a candidate for maintaining this repressive modification at the human Xi. Results Here, we show that loss of SETDB1 does not result in large-scale H3K9me3 changes at the Xi, but unexpectedly we observed striking decompaction of the Xi territory. Close examination revealed a 0.5 Mb region of the Xi that transitioned from H3K9me3 heterochromatin to euchromatin within the 3′ end of the IL1RAPL1 gene that is part of a common chromosome fragile site that is frequently deleted or rearranged in patients afflicted with intellectual disability and other neurological ailments. Centrally located within this interval is a powerful enhancer adjacent to an ERVL-MaLR element. In the absence of SETDB1, the enhancer is reactivated on the Xi coupled with bidirectional transcription from the ERVL-MaLR element. Xa deletion of the enhancer/ERVL-MaLR resulted in loss of full-length IL1RAPL1 transcript in cis, coupled with trans decompaction of the Xi chromosome territory, whereas Xi deletion increased detection of full-length IL1RAPL1 transcript in trans, but did not impact Xi compaction. Conclusions These data support a critical role for SETDB1 in maintaining the ERVL-MaLR element and adjacent enhancer in the 3′ end of the IL1RAPL1 gene in a silent state to facilitate Xi compaction. Electronic supplementary material The online version of this article (10.1186/s13072-018-0218-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhuo Sun
- Department of Biological Science, Florida State University, 319 Stadium Drive, King 3076, Tallahassee, FL, 32306-4295, USA
| | - Brian P Chadwick
- Department of Biological Science, Florida State University, 319 Stadium Drive, King 3076, Tallahassee, FL, 32306-4295, USA.
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29
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Iarovaia OV, Kovina AP, Petrova NV, Razin SV, Ioudinkova ES, Vassetzky YS, Ulianov SV. Genetic and Epigenetic Mechanisms of β-Globin Gene Switching. BIOCHEMISTRY (MOSCOW) 2018; 83:381-392. [PMID: 29626925 DOI: 10.1134/s0006297918040090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Vertebrates have multiple forms of hemoglobin that differ in the composition of their polypeptide chains. During ontogenesis, the composition of these subunits changes. Genes encoding different α- and β-polypeptide chains are located in two multigene clusters on different chromosomes. Each cluster contains several genes that are expressed at different stages of ontogenesis. The phenomenon of stage-specific transcription of globin genes is referred to as globin gene switching. Mechanisms of expression switching, stage-specific activation, and repression of transcription of α- and β-globin genes are of interest from both theoretical and practical points of view. Alteration of balanced expression of globin genes, which usually occurs due to damage to adult β-globin genes, leads to development of severe diseases - hemoglobinopathies. In most cases, reactivation of the fetal hemoglobin gene in patients with β-thalassemia and sickle cell disease can reduce negative consequences of irreversible alterations of expression of the β-globin genes. This review focuses on the current state of research on genetic and epigenetic mechanisms underlying stage-specific switching of β-globin genes.
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Affiliation(s)
- O V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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30
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Alvarez-Dominguez JR, Knoll M, Gromatzky AA, Lodish HF. The Super-Enhancer-Derived alncRNA-EC7/Bloodlinc Potentiates Red Blood Cell Development in trans. Cell Rep 2018. [PMID: 28636939 DOI: 10.1016/j.celrep.2017.05.082] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Enhancer-derived RNAs are thought to act locally by contributing to their parent enhancer function. Whether large domains of clustered enhancers (super-enhancers) also produce cis-acting RNAs, however, remains unclear. Unlike typical enhancers, super-enhancers form large spans of robustly transcribed chromatin, amassing capped and polyadenylated RNAs that are sufficiently abundant to sustain trans functions. Here, we show that one such RNA, alncRNA-EC7/Bloodlinc, is transcribed from a super-enhancer of the erythroid membrane transporter SLC4A1/BAND3 but diffuses beyond this site. Bloodlinc localizes to trans-chromosomal loci encoding critical regulators and effectors of terminal erythropoiesis and directly binds chromatin-organizing and transcription factors, including the chromatin attachment factor HNRNPU. Inhibiting Bloodlinc or Hnrnpu compromises the terminal erythropoiesis gene program, blocking red cell production, whereas expressing Bloodlinc ectopically stimulates this program and can promote erythroblast proliferation and enucleation in the absence of differentiation stimuli. Thus, Bloodlinc is a trans-acting super-enhancer RNA that potentiates red blood cell development.
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Affiliation(s)
- Juan R Alvarez-Dominguez
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Marko Knoll
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Austin A Gromatzky
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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31
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Yavropoulou MP, Yovos JG. The "dark matter" of DNA and the regulation of bone metabolism: The role of non-coding RNAs. JOURNAL OF MUSCULOSKELETAL & NEURONAL INTERACTIONS 2018; 18:18-31. [PMID: 29504575 PMCID: PMC5881125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Epigenetics, present a new discipline that attempts to explain significant differences in phenotypes among patients with the same disease. In contrast to the other epigenetic mechanisms that modulate gene transcription, non-coding RNAs act at the post-transcriptional level. They directly modulate the gene expression of mRNA genes leading to mRNA target cleavage and degradation and translation repression. Bioinformatic predictions indicate that non coding RNAs may be involved in the regulation of 60% of the coding genes and each non-coding RNA can have multiple target genes, and each gene may be regulated by more than one non-coding RNAs. In the last decade several studies have shown a significant role of non-coding RNAs in the regulation of bone metabolism and function of bone cells opening a new era in the understanding of bone biology in health and disease.
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Affiliation(s)
- Maria P. Yavropoulou
- Laboratory of Clinical and Molecular Endocrinology, 1st Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece,Corresponding author: Maria P. Yavropoulou, MD, MSc, PhD, Endocrinologist Consultant, 1st Department of Internal Medicine, AHEPA Univ. Hospital, 1 S. Kyriakidi street 54636, Thessaloniki, Greece E-mail:
| | - John G. Yovos
- Laboratory of Clinical and Molecular Endocrinology, 1st Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Aberrant expression of lncRNAs and mRNAs in patients with intracranial aneurysm. Oncotarget 2018; 8:2477-2484. [PMID: 27965470 PMCID: PMC5356817 DOI: 10.18632/oncotarget.13908] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/01/2016] [Indexed: 01/14/2023] Open
Abstract
Intracranial aneurysm (IA) is pathological dilatations of the cerebral artery and rupture of IAs can cause subarachnoid hemorrhage, which has a high ratio of fatality and morbidity. However, the pathogenesis of IAs remains unknown. We performed long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in IA tissues and superficial temporal arteries (STAs). A total of 4129 differentially expressed lncRNAs and 2926 differentially expressed mRNAs were obtained from the microarrays (P < 0.05). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that up-regulated mRNAs were enriched in immune response, inflammatory response, regulation of immune response and lysosome, et al; while the down-regulated mRNAs were enriched in muscle contraction, smooth muscle contraction, cGMP-PKG signaling pathway and vascular smooth muscle contraction, et al. The lncRNA-mRNA co-expression networks were represented in immune response, inflammatory response, muscle contraction and vascular smooth muscle contraction. These findings may gain insight in the pathogenesis of IAs and provide clues to find key roles for IA patients.
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33
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Meng H, Bartholomew B. Emerging roles of transcriptional enhancers in chromatin looping and promoter-proximal pausing of RNA polymerase II. J Biol Chem 2017; 293:13786-13794. [PMID: 29187597 DOI: 10.1074/jbc.r117.813485] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Initiation and regulation of transcription by RNA polymerase II (RNAPII) in eukaryotes rely on the transcriptional regulatory elements. Promoters and enhancers share similar architectures and functions, and the prevailing view is that they can initiate bidirectional transcription. We summarize functional roles of enhancer transcription and possible mechanisms in enhancer-promoter communication. We discuss the potential roles of enhancer RNAs (eRNAs) in early elongation and highlight that transcriptional enhancers might modulate the release of paused RNAPII via 3D chromatin looping. Emerging evidence suggests that transcriptional enhancers regulate the promoter-proximal pausing of RNAPII, a key rate-limiting step required for productive elongation.
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Affiliation(s)
- Huan Meng
- From the Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Blaine Bartholomew
- From the Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
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34
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Schneider HW, Raiol T, Brigido MM, Walter MEMT, Stadler PF. A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts. BMC Genomics 2017; 18:804. [PMID: 29047334 PMCID: PMC5648457 DOI: 10.1186/s12864-017-4178-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/05/2017] [Indexed: 12/31/2022] Open
Abstract
Background In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts. Methods The proposed method is based on SVM and uses the first ORF relative length and frequencies of nucleotide patterns selected by PCA as features. FASTA files were used as input to calculate all possible features. These features were divided in two sets: (i) 336 frequencies of nucleotide patterns; and (ii) 4 features derived from ORFs. PCA were applied to the first set to identify 6 groups of frequencies that could most contribute to the distinction. Twenty-four experiments using the 6 groups from the first set and the features from the second set where built to create the best model to distinguish lncRNAs from PCTs. Results This method was trained and tested with human (Homo sapiens), mouse (Mus musculus) and zebrafish (Danio rerio) data, achieving 98.21%, 98.03% and 96.09%, accuracy, respectively. Our method was compared to other tools available in the literature (CPAT, CPC, iSeeRNA, lncRNApred, lncRScan-SVM and FEELnc), and showed an improvement in accuracy by ≈3.00%. In addition, to validate our model, the mouse data was classified with the human model, and vice-versa, achieving ≈97.80% accuracy in both cases, showing that the model is not overfit. The SVM models were validated with data from rat (Rattus norvegicus), pig (Sus scrofa) and fruit fly (Drosophila melanogaster), and obtained more than 84.00% accuracy in all these organisms. Our results also showed that 81.2% of human pseudogenes and 91.7% of mouse pseudogenes were classified as non-coding. Moreover, our method was capable of re-annotating two uncharacterized sequences of Swiss-Prot database with high probability of being lncRNAs. Finally, in order to use the method to annotate transcripts derived from RNA-seq, previously identified lncRNAs of human, gorilla (Gorilla gorilla) and rhesus macaque (Macaca mulatta) were analyzed, having successfully classified 98.62%, 80.8% and 91.9%, respectively. Conclusions The SVM method proposed in this work presents high performance to distinguish lncRNAs from PCTs, as shown in the results. To build the model, besides using features known in the literature regarding ORFs, we used PCA to identify features among nucleotide pattern frequencies that contribute the most in distinguishing lncRNAs from PCTs, in reference data sets. Interestingly, models created with two evolutionary distant species could distinguish lncRNAs of even more distant species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4178-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hugo W Schneider
- Department of Computer Science, University of Brasilia, ICC Central, Instituto de Ciências Exatas, Campus Universitario Darcy Ribeiro, Asa Norte, CEP: 70910-900, Brasilia, Brazil.
| | - Taina Raiol
- Gerência Regional de Brasilia (GEREB), Oswaldo Cruz Foundation (Fiocruz), Av. L3 Norte, Campus Universitário Darcy Ribeiro, Gleba A, Asa Norte, CEP: 70910-900, Brasília, Brazil
| | - Marcelo M Brigido
- Laboratory of Molecular Biology, University of Brasilia, Instituto de Ciencias Biologicas, Campus Universitario Darcy Ribeiro, Asa Norte, CEP: 70910-900, Brasilia, Brazil
| | - Maria Emilia M T Walter
- Department of Computer Science, University of Brasilia, ICC Central, Instituto de Ciências Exatas, Campus Universitario Darcy Ribeiro, Asa Norte, CEP: 70910-900, Brasilia, Brazil
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Hartelstrasse 16-18, Leipzig, D-04107, Germany
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35
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Deveson IW, Hardwick SA, Mercer TR, Mattick JS. The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome. Trends Genet 2017; 33:464-478. [PMID: 28535931 DOI: 10.1016/j.tig.2017.04.004] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 01/02/2023]
Abstract
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing. These features are consistent with their role as modular epigenetic regulators. We describe here the key studies and technological advances that have shaped our understanding of the dimensions, dynamics, and biological relevance of the mammalian noncoding transcriptome.
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Affiliation(s)
- Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Simon A Hardwick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - John S Mattick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
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36
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How does chromatin package DNA within nucleus and regulate gene expression? Int J Biol Macromol 2017; 101:862-881. [PMID: 28366861 DOI: 10.1016/j.ijbiomac.2017.03.165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 03/28/2017] [Indexed: 01/26/2023]
Abstract
The human body is made up of 60 trillion cells, each cell containing 2 millions of genomic DNA in its nucleus. How is this genomic deoxyribonucleic acid [DNA] organised into nuclei? Around 1880, W. Flemming discovered a nuclear substance that was clearly visible on staining under primitive light microscopes and named it 'chromatin'; this is now thought to be the basic unit of genomic DNA organization. Since long before DNA was known to carry genetic information, chromatin has fascinated biologists. DNA has a negatively charged phosphate backbone that produces electrostatic repulsion between adjacent DNA regions, making it difficult for DNA to fold upon itself. In this article, we will try to shed light on how does chromatin package DNA within nucleus and regulate gene expression?
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37
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Liu Y, Han X, Yuan J, Geng T, Chen S, Hu X, Cui IH, Cui H. Biallelic insertion of a transcriptional terminator via the CRISPR/Cas9 system efficiently silences expression of protein-coding and non-coding RNA genes. J Biol Chem 2017; 292:5624-5633. [PMID: 28196870 DOI: 10.1074/jbc.m116.769034] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/09/2017] [Indexed: 11/06/2022] Open
Abstract
The type II bacterial CRISPR/Cas9 system is a simple, convenient, and powerful tool for targeted gene editing. Here, we describe a CRISPR/Cas9-based approach for inserting a poly(A) transcriptional terminator into both alleles of a targeted gene to silence protein-coding and non-protein-coding genes, which often play key roles in gene regulation but are difficult to silence via insertion or deletion of short DNA fragments. The integration of 225 bp of bovine growth hormone poly(A) signals into either the first intron or the first exon or behind the promoter of target genes caused efficient termination of expression of PPP1R12C, NSUN2 (protein-coding genes), and MALAT1 (non-protein-coding gene). Both NeoR and PuroR were used as markers in the selection of clonal cell lines with biallelic integration of a poly(A) signal. Genotyping analysis indicated that the cell lines displayed the desired biallelic silencing after a brief selection period. These combined results indicate that this CRISPR/Cas9-based approach offers an easy, convenient, and efficient novel technique for gene silencing in cell lines, especially for those in which gene integration is difficult because of a low efficiency of homology-directed repair.
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Affiliation(s)
- Yangyang Liu
- From the Institute of Epigenetics and Epigenomics.,College of Animal Science and Technology
| | - Xiao Han
- From the Institute of Epigenetics and Epigenomics.,College of Animal Science and Technology
| | - Junting Yuan
- From the Institute of Epigenetics and Epigenomics.,College of Bioscience and Biotechnology
| | - Tuoyu Geng
- From the Institute of Epigenetics and Epigenomics.,College of Animal Science and Technology
| | - Shihao Chen
- From the Institute of Epigenetics and Epigenomics.,College of Animal Science and Technology
| | - Xuming Hu
- From the Institute of Epigenetics and Epigenomics.,College of Animal Science and Technology
| | - Isabelle H Cui
- the Department of Pathology and Laboratory Medicine, New York Presbyterian-Weill Cornell Medicine, New York, New York 10065
| | - Hengmi Cui
- From the Institute of Epigenetics and Epigenomics, .,College of Animal Science and Technology.,Institute of Comparative Medicine.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, China and
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38
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Long Noncoding RNA: Genome Organization and Mechanism of Action. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:47-74. [PMID: 28815536 DOI: 10.1007/978-981-10-5203-3_2] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For the last four decades, we have known that noncoding RNAs maintain critical housekeeping functions such as transcription, RNA processing, and translation. However, in the late 1990s and early 2000s, the advent of high-throughput sequencing technologies and computational tools to analyze these large sequencing datasets facilitated the discovery of thousands of small and long noncoding RNAs (lncRNAs) and their functional role in diverse biological functions. For example, lncRNAs have been shown to regulate dosage compensation, genomic imprinting, pluripotency, cell differentiation and development, immune response, etc. Here we review how lncRNAs bring about such copious functions by employing diverse mechanisms such as translational inhibition, mRNA degradation, RNA decoys, facilitating recruitment of chromatin modifiers, regulation of protein activity, regulating the availability of miRNAs by sponging mechanism, etc. In addition, we provide a detailed account of different mechanisms as well as general principles by which lncRNAs organize functionally different nuclear sub-compartments and their impact on nuclear architecture.
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van Arensbergen J, FitzPatrick VD, de Haas M, Pagie L, Sluimer J, Bussemaker HJ, van Steensel B. Genome-wide mapping of autonomous promoter activity in human cells. Nat Biotechnol 2016; 35:145-153. [PMID: 28024146 DOI: 10.1038/nbt.3754] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 12/01/2016] [Indexed: 12/20/2022]
Abstract
Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of the sequences that could be tested. Here we present 'survey of regulatory elements' (SuRE), a method that assays more than 108 DNA fragments, each 0.2-2 kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library of random genomic fragments upstream of a 20-bp barcode is constructed, and decoded by paired-end sequencing. This library is used to transfect cells, and barcodes in transcribed RNA are quantified by high-throughput sequencing. When applied to the human genome, we achieve 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide in K562 cells. By computational modeling we delineate subregions within promoters that are relevant for their activity. We show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites.
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Affiliation(s)
- Joris van Arensbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Vincent D FitzPatrick
- Department of Biological Sciences, Columbia University, New York, New York, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - Marcel de Haas
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jasper Sluimer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, New York, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
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40
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Long non-coding RNAs: Mechanism of action and functional utility. Noncoding RNA Res 2016; 1:43-50. [PMID: 30159410 PMCID: PMC6096411 DOI: 10.1016/j.ncrna.2016.11.002] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022] Open
Abstract
Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs.
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41
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Tomita S, Abdalla MOA, Fujiwara S, Yamamoto T, Iwase H, Nakao M, Saitoh N. Roles of long noncoding RNAs in chromosome domains. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [DOI: 10.1002/wrna.1384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Saori Tomita
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences; Kumamoto University; Kumamoto Japan
| | - Mohamed Osama Ali Abdalla
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Department of Clinical Pathology, Faculty of Medicine; Suez Canal University; Ismailia Egypt
| | - Saori Fujiwara
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences; Kumamoto University; Kumamoto Japan
| | - Tatsuro Yamamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
| | - Hirotaka Iwase
- Department of Breast and Endocrine Surgery, Graduate School of Medical Sciences; Kumamoto University; Kumamoto Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development; Tokyo Japan
| | - Noriko Saitoh
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics; Kumamoto University; Kumamoto Japan
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42
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Schmitz SU, Grote P, Herrmann BG. Mechanisms of long noncoding RNA function in development and disease. Cell Mol Life Sci 2016; 73:2491-509. [PMID: 27007508 PMCID: PMC4894931 DOI: 10.1007/s00018-016-2174-5] [Citation(s) in RCA: 749] [Impact Index Per Article: 93.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Since decades it has been known that non-protein-coding RNAs have important cellular functions. Deep sequencing recently facilitated the discovery of thousands of novel transcripts, now classified as long noncoding RNAs (lncRNAs), in many vertebrate and invertebrate species. LncRNAs are involved in a wide range of cellular mechanisms, from almost all aspects of gene expression to protein translation and stability. Recent findings implicate lncRNAs as key players of cellular differentiation, cell lineage choice, organogenesis and tissue homeostasis. Moreover, lncRNAs are involved in pathological conditions such as cancer and cardiovascular disease, and therefore provide novel biomarkers and pharmaceutical targets. Here we discuss examples illustrating the versatility of lncRNAs in gene control, development and differentiation, as well as in human disease.
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Affiliation(s)
- Sandra U Schmitz
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
- Institute for Medical Genetics, Campus Benjamin Franklin, Charite-University Medicine Berlin, Hindenburgdamm 30, 12203, Berlin, Germany.
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43
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Long noncoding RNAs in cell differentiation and pluripotency. Cell Tissue Res 2016; 366:509-521. [PMID: 27365087 DOI: 10.1007/s00441-016-2451-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) were once regarded as nonfunctional by-products of transcription but their effects are now gradually being elucidated. Evidence suggests that lncRNAs play crucial roles in cell biology, especially in regulating gene expression. However, because of the diversity and complexity of their regulatory mechanisms, our knowledge of the function of lncRNAs represents only the tip of the iceberg. Recent studies have shown that lncRNAs are capable of regulating cell differentiation and pluripotency. Thus, we consider it to be an appropriate time to review the progress in understanding the role of lncRNAs in these two biological processes. In this review, the biological characteristics and regulatory mechanisms of lncRNAs at the chromatin remodeling level, transcriptional level and post-transcriptional level are described and recent advances in our comprehension of the role of lncRNAs in cell differentiation and pluripotency are discussed.
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Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016; 57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research.
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Affiliation(s)
- Krysta L Engel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States.
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45
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Li W, Notani D, Rosenfeld MG. Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat Rev Genet 2016; 17:207-23. [PMID: 26948815 DOI: 10.1038/nrg.2016.4] [Citation(s) in RCA: 487] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Networks of regulatory enhancers dictate distinct cell identities and cellular responses to diverse signals by instructing precise spatiotemporal patterns of gene expression. However, 35 years after their discovery, enhancer functions and mechanisms remain incompletely understood. Intriguingly, recent evidence suggests that many, if not all, functional enhancers are themselves transcription units, generating non-coding enhancer RNAs. This observation provides a fundamental insight into the inter-regulation between enhancers and promoters, which can both act as transcription units; it also raises crucial questions regarding the potential biological roles of the enhancer transcription process and non-coding enhancer RNAs. Here, we review research progress in this field and discuss several important, unresolved questions regarding the roles and mechanisms of enhancers in gene regulation.
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Affiliation(s)
- Wenbo Li
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
| | - Dimple Notani
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
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46
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Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS. J Neurosci 2016; 35:13819-26. [PMID: 26468181 DOI: 10.1523/jneurosci.2622-15.2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Sprinkled throughout the genome are a million regulatory sequences called transcriptional enhancers that activate gene promoters in the right cells, at the right time. Enhancers endow the brain with its incredible diversity of cell types and also translate neural activity into gene induction. Thanks to rapid advances in genomic technologies, it is now possible to identify thousands of enhancers rapidly, test their transcriptional function en masse, and address their neurobiological functions via genome editing. Enhancers also promise to be a great technological opportunity for neuroscience, offering the potential for cell-type-specific genetic labeling and manipulation without the need for transgenesis. The objective of this review and the accompanying 2015 SfN mini-symposium is to highlight the use of new and emerging genomic technologies to probe enhancer function in the nervous system. SIGNIFICANCE STATEMENT Transcriptional enhancers turn on genes in the right cells, at the right time. Enhancers are also the genomic sequences that encode the incredible diversity of cell types in the brain and enable the brain to turn genes on in response to new experiences. New technology enables enhancers to be found and manipulated. The study of enhancers promises to inform our understanding of brain development and function. The application of enhancer technology holds promise in accelerating basic neuroscience research and enabling gene therapies to be targeted to specific cell types in the brain.
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De Kumar B, Krumlauf R. HOXs and lincRNAs: Two sides of the same coin. SCIENCE ADVANCES 2016; 2:e1501402. [PMID: 27034976 PMCID: PMC4805430 DOI: 10.1126/sciadv.1501402] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/28/2015] [Indexed: 05/13/2023]
Abstract
The clustered Hox genes play fundamental roles in regulation of axial patterning and elaboration of the basic body plan in animal development. There are common features in the organization and regulatory landscape of Hox clusters associated with their highly conserved functional roles. The presence of transcribed noncoding sequences embedded within the vertebrate Hox clusters is providing insight into a new layer of regulatory information associated with Hox genes.
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Affiliation(s)
- Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
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48
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Kim TK, Shiekhattar R. Architectural and Functional Commonalities between Enhancers and Promoters. Cell 2015; 162:948-59. [PMID: 26317464 DOI: 10.1016/j.cell.2015.08.008] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/23/2023]
Abstract
With the explosion of genome-wide studies of regulated transcription, it has become clear that traditional definitions of enhancers and promoters need to be revisited. These control elements can now be characterized in terms of their local and regional architecture, their regulatory components, including histone modifications and associated binding factors, and their functional contribution to transcription. This Review discusses unifying themes between promoters and enhancers in transcriptional regulatory mechanisms.
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Affiliation(s)
- Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA.
| | - Ramin Shiekhattar
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Room 719, 1501 NW 10(th) Avenue, Miami, FL 33136, USA.
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49
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Karijolich J, Abernathy E, Glaunsinger BA. Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway. PLoS Pathog 2015; 11:e1005260. [PMID: 26584434 PMCID: PMC4652899 DOI: 10.1371/journal.ppat.1005260] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023] Open
Abstract
Short interspersed nuclear elements (SINEs) are highly abundant, RNA polymerase III-transcribed noncoding retrotransposons that are silenced in somatic cells but activated during certain stresses including viral infection. How these induced SINE RNAs impact the host-pathogen interaction is unknown. Here we reveal that during murine gammaherpesvirus 68 (MHV68) infection, rapidly induced SINE RNAs activate the antiviral NF-κB signaling pathway through both mitochondrial antiviral-signaling protein (MAVS)-dependent and independent mechanisms. However, SINE RNA-based signaling is hijacked by the virus to enhance viral gene expression and replication. B2 RNA expression stimulates IKKβ-dependent phosphorylation of the major viral lytic cycle transactivator protein RTA, thereby enhancing its activity and increasing progeny virion production. Collectively, these findings suggest that SINE RNAs participate in the innate pathogen response mechanism, but that herpesviruses have evolved to co-opt retrotransposon activation for viral benefit. Short interspersed nuclear elements (SINEs) are noncoding mobile genetic elements that are present at ~106 copies per mammalian genome, roughly comprising 10% of mammalian genomic real estate. SINEs are typically transcriptionally silenced, though in some cases viral infection can promote their expression, yet to an unknown functional outcome. Thus, SINE elements represent the largest class of infection-inducible noncoding RNAs that are functionally uncharacterized. Here, we reveal that SINE RNAs play a critical role in the host-pathogen interaction in that they are required for efficient murine gammaherpesvirus 68 (MHV68) replication and gene expression. We demonstrate that SINE RNAs, both exogenously expressed and infection-induced, are robust activators of the IKKβ kinase, a key signaling molecule in the innate immune response. Activation of the IKKβ kinase by SINE RNA is mediated through both MAVS-dependent and independent mechanisms. Moreover, we demonstrate the activation of the IKKβ via SINE RNA is required to drive the phosphorylation of MHV68 RTA, the main viral transcriptional activator, which enhances its transcriptional activating property. Collectively, we reveal the first example of a role for SINE RNAs in the host-pathogen interaction and identify them as a key immune signaling molecule early during infection. Though SINE RNAs activate the innate immune response, MHV68 has co-opted SINE-mediate innate immune activation to enhance the viral lifecycle.
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Affiliation(s)
- John Karijolich
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Emma Abernathy
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Britt A. Glaunsinger
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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50
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Onorati MC, Arancio W, Cavalieri V, Ingrassia AMR, Pavesi G, Corona DFV. Trans-Reactivation: A New Epigenetic Phenomenon Underlying Transcriptional Reactivation of Silenced Genes. PLoS Genet 2015; 11:e1005444. [PMID: 26292210 PMCID: PMC4546373 DOI: 10.1371/journal.pgen.1005444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/15/2015] [Indexed: 12/04/2022] Open
Abstract
In order to study the role played by cellular RNA pools produced by homologous genomic loci in defining the transcriptional state of a silenced gene, we tested the effect of non-functional alleles of the white gene in the presence of a functional copy of white, silenced by heterochromatin. We found that non-functional alleles of white, unable to produce a coding transcript, could reactivate in trans the expression of a wild type copy of the same gene silenced by heterochromatin. This new epigenetic phenomenon of transcriptional trans-reactivation is heritable, relies on the presence of homologous RNA’s and is affected by mutations in genes involved in post-transcriptional gene silencing. Our data suggest a general new unexpected level of gene expression control mediated by homologous RNA molecules in the context of heterochromatic genes. We discovered a new epigenetic phenomenon we called trans-reactivation. We found that genes, unable to produce a functional coding transcript, but with the potential of transcribing other RNA’s within their gene body, strongly reactivate the transcription of a wildtype copy of the same gene silenced by heterochomatin. This new epigenetic phenomenon is heritable, relies on the presence of diffusible RNAs able to carry and transfer epigenetic information and is affected by mutations in genes involved in Post-Transcriptional Gene Silencing. Our data strongly suggest that homologous non-coding RNA can reactivate the expression of genes silenced by heterochromatin, thus defining a new unpredicted level of gene expression control in the context of heterochromatic genes.
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Affiliation(s)
| | | | - Vincenzo Cavalieri
- Università degli Studi di Palermo, Dipartimento STEBICEF–Sezione Biologia Cellulare, Palermo, Italy
| | | | - Giulio Pavesi
- Department of Biosciences, University of Milano, Milano, Italy
| | - Davide F. V. Corona
- Dulbecco Telethon Institute, Palermo, Italy
- Università degli Studi di Palermo, Dipartimento STEBICEF–Sezione Biologia Cellulare, Palermo, Italy
- * E-mail:
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