1
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Tay MLI, Pek JW. SON protects nascent transcripts from unproductive degradation by counteracting DIP1. PLoS Genet 2019; 15:e1008498. [PMID: 31730657 PMCID: PMC6881055 DOI: 10.1371/journal.pgen.1008498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/27/2019] [Accepted: 10/28/2019] [Indexed: 11/18/2022] Open
Abstract
Gene expression involves the transcription and splicing of nascent transcripts through the removal of introns. In Drosophila, a double-stranded RNA binding protein Disco-interacting protein 1 (DIP1) targets INE-1 stable intronic sequence RNAs (sisRNAs) for degradation after splicing. How nascent transcripts that also contain INE-1 sequences escape degradation remains unknown. Here we observe that these nascent transcripts can also be bound by DIP1 but the Drosophila homolog of SON (Dsn) protects them from unproductive degradation in ovaries. Dsn localizes to the satellite body where active decay of INE-1 sisRNAs by DIP1 occurs. Dsn is a repressor of DIP1 posttranslational modifications (primarily sumoylation) that are assumed to be required for efficient DIP1 activity. Moreover, the pre-mRNA destabilization caused by Dsn depletion is rescued in DIP1 or Sumo heterozygous mutants, suggesting that Dsn is a negative regulator of DIP1. Our results reveal that under normal circumstances nascent transcripts are susceptible to DIP1-mediated degradation, however intronic sequences are protected by Dsn until intron excision has taken place.
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Affiliation(s)
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- * E-mail:
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2
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Babarinde IA, Li Y, Hutchins AP. Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. Comput Struct Biotechnol J 2019; 17:628-637. [PMID: 31193391 PMCID: PMC6526290 DOI: 10.1016/j.csbj.2019.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
The measurement of gene expression has long provided significant insight into biological functions. The development of high-throughput short-read sequencing technology has revealed transcriptional complexity at an unprecedented scale, and informed almost all areas of biology. However, as researchers have sought to gather more insights from the data, these new technologies have also increased the computational analysis burden. In this review, we describe typical computational pipelines for RNA-Seq analysis and discuss their strengths and weaknesses for the assembly, quantification and analysis of coding and non-coding RNAs. We also discuss the assembly of transposable elements into transcripts, and the difficulty these repetitive elements pose. In summary, RNA-Seq is a powerful technology that is likely to remain a key asset in the biologist's toolkit.
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Affiliation(s)
- Isaac A Babarinde
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Lu, Shenzhen, China
| | - Yuhao Li
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Lu, Shenzhen, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Lu, Shenzhen, China
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3
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Stable Intronic Sequence RNAs (sisRNAs): An Expanding Universe. Trends Biochem Sci 2018; 44:258-272. [PMID: 30391089 DOI: 10.1016/j.tibs.2018.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/11/2018] [Accepted: 09/21/2018] [Indexed: 12/26/2022]
Abstract
Intronic sequences are often regarded as 'nonsense' transcripts that are rapidly degraded. We highlight here recent studies on intronic sequences that play regulatory roles as long noncoding RNAs (lncRNAs) which are classified as sisRNAs. Interestingly, sisRNAs come in different forms and are produced via a variety of ways. They regulate genes at the DNA, RNA, and protein levels, and frequently engage in autoregulatory feedback loops to ensure cellular homeostasis under normal and stress conditions. Future directions, evolutionary insights, and potential implications of dysregulated sisRNAs are also discussed, especially in relation to human pathogenesis.
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4
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Osman I, Pek JW. A sisRNA/miRNA Axis Prevents Loss of Germline Stem Cells during Starvation in Drosophila. Stem Cell Reports 2018; 11:4-12. [PMID: 30008327 PMCID: PMC6067505 DOI: 10.1016/j.stemcr.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
Animal reproduction responds to nutritional status. During starvation, Drosophila and Caenorhabditis elegans enter a period of reproductive diapause with increase apoptosis, while maintaining a stable pool of germline stem cells (GSCs). How GSCs are protected is not understood. Here, we show that a sisRNA/miRNA axis maintains ovarian GSCs during starvation in Drosophila. Starvation induces the expression of an ovary-enriched sisRNA sisR-2, which negatively regulates GSC maintenance via a fatty acid metabolism gene dFAR1. sisR-2 promotes the expression of bantam, which in turn inhibits the activity of sisR-2, forming a negative feedback loop. Therefore, bantam acts as a buffer to counteract sisR-2 activity to prevent GSC loss during starvation. We propose that the sisR-2/bantam axis confers robustness to GSCs in Drosophila. sisR-2 regulates the number of GSCs sisR-2 regulates GSC maintenance by repressing dFAR1 bantam regulates GSC maintenance by repressing sisR-2 activity sisR-2/bantam axis protects GSCs from starvation
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Affiliation(s)
- Ismail Osman
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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5
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Ng AYE, Peralta KRG, Pek JW. Germline Stem Cell Heterogeneity Supports Homeostasis in Drosophila. Stem Cell Reports 2018; 11:13-21. [PMID: 29887366 PMCID: PMC6066994 DOI: 10.1016/j.stemcr.2018.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023] Open
Abstract
Adult and embryonic stem cells exhibit fluctuating gene expression; however, the biological significance of stem cell heterogeneity is not well understood. We show that, in Drosophila, female germline stem cells (GSCs) exhibit heterogeneous expression of a GSC differentiation-promoting factor Regena (Rga). The Drosophila homolog of human SON, dsn, is required to maintain GSC heterogeneity by suppressing sustained high levels of Rga. Reducing the expression of Rga in dsn mutants restores GSC heterogeneity and self-renewal. Thus, GSC heterogeneity is linked to GSC homeostasis. Female germline stem cells have heterogeneous Rga expression dsn suppresses rga transcription and maintains heterogeneity dsn maintains germline stem cells Lowering rga restores heterogeneity and suppresses dsn phenotypes
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | | | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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6
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Jia Ng SS, Zheng RT, Osman I, Pek JW. Generation of Drosophila sisRNAs by Independent Transcription from Cognate Introns. iScience 2018; 4:68-75. [PMID: 30240754 PMCID: PMC6146417 DOI: 10.1016/j.isci.2018.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/25/2018] [Accepted: 05/14/2018] [Indexed: 01/26/2023] Open
Abstract
Although stable intronic sequence RNAs (sisRNAs) are conserved in plants and animals, their functional significance is still unclear. We identify a pool of polyadenylated maternally deposited sisRNAs in Drosophila melanogaster. These sisRNAs can be generated by independent transcription from the cognate introns. The ovary-specific poly(A) polymerase Wispy mediates the polyadenylation of maternal sisRNAs and confers their stability as maternal transcripts. A developmentally regulated sisRNA sisR-3 represses the expression of a long noncoding RNA CR44148 and is required during development. Our results expand the pool of sisRNAs and suggest that sisRNAs perform regulatory functions during development in Drosophila. Identification of polyadenylated sisRNAs sisRNAs can be produced from independent transcription sisR-3 regulates a long noncoding RNA sisR-3 is required during development
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Affiliation(s)
- Sharon Si Jia Ng
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore 529757, Singapore
| | - Ruther Teo Zheng
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore 599489, Singapore
| | - Ismail Osman
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore 117543, Singapore, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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7
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Pek JW. Stable Intronic Sequence RNAs Engage in Feedback Loops. Trends Genet 2018; 34:330-332. [DOI: 10.1016/j.tig.2018.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/10/2018] [Indexed: 01/27/2023]
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8
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Li Y, Aggarwal MB, Ke K, Nguyen K, Spitale RC. Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA-Protein Complexes. Biochemistry 2018; 57:1577-1581. [PMID: 29474061 PMCID: PMC6234203 DOI: 10.1021/acs.biochem.8b00053] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent analysis of transcriptomes has revealed that RNAs perform a myriad of functions beyond encoding proteins. Critical to RNA function is its transport to unique subcellular locations. Despite the importance of RNA localization, it is still very challenging to study in an unbiased manner. We recently described the ability to tag RNA molecules within subcellular locations through spatially restricted nucleobase oxidation. Herein, we describe a dramatic improvement of this protocol through the localized oxidation and tagging of proteins. Isolation of RNA-protein complexes enabled the enrichment of challenging RNA targets on chromatin and presented a considerably optimized protocol for the analysis of RNA subcellular localization within living cells.
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9
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Discovery of new RNA classes and global RNA-binding proteins. Curr Opin Microbiol 2017; 39:152-160. [PMID: 29179042 DOI: 10.1016/j.mib.2017.11.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022]
Abstract
The identification of new RNA functions and the functional annotation of transcripts in genomes represent exciting yet challenging endeavours of modern biology. Crucial insights into the biological roles of RNA molecules can be gained from the identification of the proteins with which they form specific complexes. Modern interactome techniques permit to profile RNA-protein interactions in a genome-wide manner and identify new RNA classes associated with globally acting RNA-binding proteins. Applied to a variety of organisms, these methods are already revolutionising our understanding of RNA-mediated biological processes. Here, we focus on one such approach-Gradient sequencing or Grad-seq-which has recently guided the discovery of protein ProQ and its associated small RNAs as a new domain of post-transcriptional control in bacteria.
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Li Y, Aggarwal MB, Nguyen K, Ke K, Spitale RC. Assaying RNA Localization in Situ with Spatially Restricted Nucleobase Oxidation. ACS Chem Biol 2017; 12:2709-2714. [PMID: 28952711 DOI: 10.1021/acschembio.7b00519] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report herein a novel chemical-genetic method for assaying RNA localization within living cells. RNA localization is critical for normal physiology as well as the onset of cancer and neurodegenerative disorders. Despite its importance, there is a real lack of chemical methods to directly assay RNA localization with high resolution in living cells. Our novel approach relies on in situ nucleobase oxidation by singlet oxygen generated from spatially confined fluorophores. We demonstrate that our novel method can identify RNA molecules localized within specific cellular compartments. We anticipate that this platform will provide the community with a much-needed methodology for tracking RNA localization within living cells, and set the stage for systematic large scale analysis of RNA localization in living systems.
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Affiliation(s)
- Ying Li
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Mahima B. Aggarwal
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Kim Nguyen
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Ke Ke
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
| | - Robert C. Spitale
- Department
of Pharmaceutical Sciences and ‡Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States
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11
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Wong JT, Akhbar F, Ng AYE, Tay MLI, Loi GJE, Pek JW. DIP1 modulates stem cell homeostasis in Drosophila through regulation of sisR-1. Nat Commun 2017; 8:759. [PMID: 28970471 PMCID: PMC5624886 DOI: 10.1038/s41467-017-00684-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/19/2017] [Indexed: 01/09/2023] Open
Abstract
Stable intronic sequence RNAs (sisRNAs) are by-products of splicing and regulate gene expression. How sisRNAs are regulated is unclear. Here we report that a double-stranded RNA binding protein, Disco-interacting protein 1 (DIP1) regulates sisRNAs in Drosophila. DIP1 negatively regulates the abundance of sisR-1 and INE-1 sisRNAs. Fine-tuning of sisR-1 by DIP1 is important to maintain female germline stem cell homeostasis by modulating germline stem cell differentiation and niche adhesion. Drosophila DIP1 localizes to a nuclear body (satellite body) and associates with the fourth chromosome, which contains a very high density of INE-1 transposable element sequences that are processed into sisRNAs. DIP1 presumably acts outside the satellite bodies to regulate sisR-1, which is not on the fourth chromosome. Thus, our study identifies DIP1 as a sisRNA regulatory protein that controls germline stem cell self-renewal in Drosophila. Stable intronic sequence RNAs (sisRNAs) are by-products of splicing from introns with roles in embryonic development in Drosophila. Here, the authors show that the RNA binding protein DIP1 regulates sisRNAs in Drosophila, which is necessary for germline stem cell homeostasis.
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Affiliation(s)
- Jing Ting Wong
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore, 599489, Singapore
| | - Farzanah Akhbar
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore, 529757, Singapore
| | - Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Mandy Li-Ian Tay
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Gladys Jing En Loi
- National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore.
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12
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Gao YE, Wang Y, Chen FQ, Feng JY, Yang G, Feng GX, Yang Z, Ye LH, Zhang XD. Post-transcriptional modulation of protein phosphatase PPP2CA and tumor suppressor PTEN by endogenous siRNA cleaved from hairpin within PTEN mRNA 3'UTR in human liver cells. Acta Pharmacol Sin 2016; 37:898-907. [PMID: 27133296 PMCID: PMC4933753 DOI: 10.1038/aps.2016.18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/03/2016] [Indexed: 01/08/2023] Open
Abstract
Aim: Increasing evidence shows that mRNAs exert regulatory function along with coding proteins. Recently we report that a hairpin within YAP mRNA 3′UTR can modulate the Hippo signaling pathway. PTEN is a tumor suppressor, and is mutated in human cancers. In this study we examined whether PTEN mRNA 3′UTR contained a hairpin structure that could regulate gene regulation at the post-transcriptional level. Methods: The secondary structure of PTEN mRNA 3′UTR was analyzed using RNAdraw and RNAstructure. Function of hairpin structure derived from the PTEN mRNA 3′UTR was examined using luciferase reporter assay, RT-PCR and Western blotting. RNA-immunoprecipitation (RIP) assay was used to analyze the interaction between PTEN mRNA and microprocessor Drosha and DGCR8. Endogenous siRNA (esiRNA) derived from PTEN mRNA 3′UTR was identified by RT-PCR and rt-PCR, and its target genes were predicted using RNAhybrid. Results: A bioinformatics analysis revealed that PTEN mRNA contained a hairpin structure (termed PTEN-sh) within 3′UTR, which markedly increased the reporter activities of AP-1 and NF-κB in 293T cells. Moreover, treatment with PTEN-sh (1 and 2 μg) dose-dependently inhibited the expression of PTEN in human liver L-O2 cells. RIP assay demonstrated that the microprocessor Drosha and DGCR8 was bound to PTEN-sh in L-O2 cells, leading to the cleavage of PTEN-sh from PTEN mRNA 3′UTR. In addition, microprocessor Dicer was involved in the processing of PTEN-sh. Interestingly, esiRNA (termed PTEN-sh-3p21) cleaved from PTEN-sh was identified in 293T cells and human liver tissues, which was found to target the mRNA 3′UTRs of protein phosphatase PPP2CA and PTEN in L-O2 cells. Treatment of L-O2 or Chang liver cells with PTEN-sh-3p21 (50, 100 nmol/L) promoted the cell proliferation in dose- and time-dependent manners. Conclusion: The endogenous siRNA (PTEN-sh-3p21) cleaved from PTEN-sh within PTEN mRNA 3′UTR modulates PPP2CA and PTEN at the post-transcriptional level in liver cells.
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13
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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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14
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Montes M, Lund AH. Emerging roles of lncRNAs in senescence. FEBS J 2016; 283:2414-26. [PMID: 26866709 DOI: 10.1111/febs.13679] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 01/16/2016] [Accepted: 02/09/2016] [Indexed: 12/13/2022]
Abstract
Cellular senescence is a complex stress response that leads to an irreversible state of cell growth arrest. Senescence may be induced by various stimuli such as telomere shortening, DNA damage or oncogenic insult, among others. Senescent cells are metabolically highly active, producing a wealth of cytokines and chemokines that, depending on the context, may have a beneficial or deleterious effect on the organism. Senescence is considered a tightly regulated stress response that is largely governed by the p53/p21 and p16/Rb pathways. Many molecules have been identified as regulators of these two networks, such as transcription factors, chromatin modifiers and non-coding RNAs. The expression level of several long non-coding RNAs is affected during different types of senescence; however, which of these are important for the biological function remains poorly understood. Here we review our current knowledge of the mechanistic roles of lncRNAs affecting the main senescence pathways, and discuss the importance of identifying new regulators.
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Affiliation(s)
- Marta Montes
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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