1
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Khoshnam SE, Moalemnia A, Anbiyaee O, Farzaneh M, Ghaderi S. LncRNA MALAT1 and Ischemic Stroke: Pathogenesis and Opportunities. Mol Neurobiol 2024; 61:4369-4380. [PMID: 38087169 DOI: 10.1007/s12035-023-03853-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/21/2023] [Indexed: 07/11/2024]
Abstract
Ischemic stroke (IS) stands as a prominent cause of mortality and long-term disability around the world. It arises primarily from a disruption in cerebral blood flow, inflicting severe neural injuries. Hence, there is a pressing need to comprehensively understand the intricate mechanisms underlying IS and identify novel therapeutic targets. Recently, long noncoding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules with the potential to attenuate pathogenic mechanisms following IS. Among these lncRNAs, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) has been extensively studied due to its involvement in the pathophysiological processes of IS. In this review, we provide an in-depth analysis of the essential role of MALAT1 in the development and progression of both pathogenic and protective mechanisms following IS. These mechanisms include oxidative stress, neuroinflammation, cell death signaling, blood brain barrier dysfunction, and angiogenesis. Furthermore, we summarize the impact of MALAT1 on the susceptibility and severity of IS. This review highlights the potential risks associated with the therapeutic use of MALAT1 for IS, which are attributable to the stimulatory action of MALAT1 on ischemia/reperfusion injury. Ultimately, this review sheds light on the potential molecular mechanisms and associated signaling pathways underlying MALAT1 expression post-IS, with the aim of uncovering potential therapeutic targets.
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Affiliation(s)
- Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Arash Moalemnia
- Faculty of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Omid Anbiyaee
- School of Medicine, Cardiovascular Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Shahab Ghaderi
- Department of Neuroscience, School of Science and Advanced Technologies in Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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2
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Huuki-Myers LA, Montgomery KD, Kwon SH, Page SC, Hicks SC, Maynard KR, Collado-Torres L. Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue. Genome Biol 2023; 24:233. [PMID: 37845779 PMCID: PMC10578035 DOI: 10.1186/s13059-023-03066-w] [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: 04/28/2022] [Accepted: 09/20/2023] [Indexed: 10/18/2023] Open
Abstract
We define and identify a new class of control genes for next-generation sequencing called total RNA expression genes (TREGs), which correlate with total RNA abundance in cell types of different sizes and transcriptional activity. We provide a data-driven method to identify TREGs from single-cell RNA sequencing data, allowing the estimation of total amount of RNA when restricted to quantifying a limited number of genes. We demonstrate our method in postmortem human brain using multiplex single-molecule fluorescent in situ hybridization and compare candidate TREGs against classic housekeeping genes. We identify AKT3 as a top TREG across five brain regions.
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Affiliation(s)
- Louise A Huuki-Myers
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Kelsey D Montgomery
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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3
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Corral A, Alcala M, Carmen Duran-Ruiz M, Arroba AI, Ponce-Gonzalez JG, Todorčević M, Serra D, Calderon-Dominguez M, Herrero L. Role of long non-coding RNAs in adipose tissue metabolism and associated pathologies. Biochem Pharmacol 2022; 206:115305. [DOI: 10.1016/j.bcp.2022.115305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
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4
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Nadhan R, Isidoro C, Song YS, Dhanasekaran DN. Signaling by LncRNAs: Structure, Cellular Homeostasis, and Disease Pathology. Cells 2022; 11:2517. [PMID: 36010595 PMCID: PMC9406440 DOI: 10.3390/cells11162517] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 12/11/2022] Open
Abstract
The cellular signaling network involves co-ordinated regulation of numerous signaling molecules that aid the maintenance of cellular as well as organismal homeostasis. Aberrant signaling plays a major role in the pathophysiology of many diseases. Recent studies have unraveled the superfamily of long non-coding RNAs (lncRNAs) as critical signaling nodes in diverse signaling networks. Defective signaling by lncRNAs is emerging as a causative factor underlying the pathophysiology of many diseases. LncRNAs have been shown to be involved in the multiplexed regulation of diverse pathways through both genetic and epigenetic mechanisms. They can serve as decoys, guides, scaffolds, and effector molecules to regulate cell signaling. In comparison with the other classes of RNAs, lncRNAs possess unique structural modifications that contribute to their diversity in modes of action within the nucleus and cytoplasm. In this review, we summarize the structure and function of lncRNAs as well as their vivid mechanisms of action. Further, we provide insights into the role of lncRNAs in the pathogenesis of four major disease paradigms, namely cardiovascular diseases, neurological disorders, cancers, and the metabolic disease, diabetes mellitus. This review serves as a succinct treatise that could open windows to investigate the role of lncRNAs as novel therapeutic targets.
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Affiliation(s)
- Revathy Nadhan
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ciro Isidoro
- Laboratory of Molecular Pathology and NanoBioImaging, Department of Health Sciences, Università del Piemonte Orientale, Via Solaroli 17, 28100 Novara, Italy
| | - Yong Sang Song
- Department of Obstetrics and Gynecology, Cancer Research Institute, College of Medicine, Seoul National University, Seoul 151-921, Korea
| | - Danny N. Dhanasekaran
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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5
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MALAT1-related signaling pathways in colorectal cancer. Cancer Cell Int 2022; 22:126. [PMID: 35305641 PMCID: PMC8933897 DOI: 10.1186/s12935-022-02540-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 03/05/2022] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal and prevalent solid malignancies worldwide. There is a great need of accelerating the development and diagnosis of CRC. Long noncoding RNAs (lncRNA) as transcribed RNA molecules play an important role in every level of gene expression. Metastasis‐associated lung adenocarcinoma transcript‐1 (MALAT1) is a highly conserved nucleus-restricted lncRNA that regulates genes at the transcriptional and post-transcriptional levels. High expression of MALAT1 is closely related to numerous human cancers. It is generally believed that MALAT1 expression is associated with CRC cell proliferation, tumorigenicity, and metastasis. MALAT1 by targeting multiple signaling pathways and microRNAs (miRNAs) plays a pivotal role in CRC pathogenesis. Therefore, MALAT1 can be a potent gene for cancer prediction and diagnosis. In this review, we will demonstrate signaling pathways associated with MALAT1 in CRC.
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Wei L, Lai EC. Regulation of the Alternative Neural Transcriptome by ELAV/Hu RNA Binding Proteins. Front Genet 2022; 13:848626. [PMID: 35281806 PMCID: PMC8904962 DOI: 10.3389/fgene.2022.848626] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
The process of alternative polyadenylation (APA) generates multiple 3' UTR isoforms for a given locus, which can alter regulatory capacity and on occasion change coding potential. APA was initially characterized for a few genes, but in the past decade, has been found to be the rule for metazoan genes. While numerous differences in APA profiles have been catalogued across genetic conditions, perturbations, and diseases, our knowledge of APA mechanisms and biology is far from complete. In this review, we highlight recent findings regarding the role of the conserved ELAV/Hu family of RNA binding proteins (RBPs) in generating the broad landscape of lengthened 3' UTRs that is characteristic of neurons. We relate this to their established roles in alternative splicing, and summarize ongoing directions that will further elucidate the molecular strategies for neural APA, the in vivo functions of ELAV/Hu RBPs, and the phenotypic consequences of these regulatory paradigms in neurons.
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Affiliation(s)
- Lu Wei
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, United States
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7
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Pfleiderer MM, Galej WP. Emerging insights into the function and structure of the Integrator complex. Transcription 2021; 12:251-265. [PMID: 35311473 PMCID: PMC9006982 DOI: 10.1080/21541264.2022.2047583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
The Integrator was originally discovered as a specialized 3'-end processing endonuclease complex required for maturation of RNA polymerase II (RNAPII)-dependent small nuclear RNAs (snRNAs). Since its discovery, Integrator's spectrum of substrates was significantly expanded to include non-polyadenylated long noncoding RNAs (lncRNA), enhancer RNAs (eRNAs), telomerase RNA (tertRNA), several Herpesvirus transcripts, and messenger RNAs (mRNAs). Recently emerging transcriptome-wide studies reveled an important role of the Integrator in protein-coding genes, where it contributes to gene expression regulation through promoter-proximal transcription attenuation. These new functional data are complemented by several structures of Integrator modules and higher-order complexes, providing mechanistic insights into Integrator-mediated processing events. In this work, we summarize recent progress in our understanding of the structure and function of the Integrator complex.
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8
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Song Z, Lin J, Li Z, Huang C. The nuclear functions of long noncoding RNAs come into focus. Noncoding RNA Res 2021; 6:70-79. [PMID: 33898883 PMCID: PMC8053782 DOI: 10.1016/j.ncrna.2021.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Corresponding author. School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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9
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Vo TV, Dhakshnamoorthy J, Larkin M, Zofall M, Thillainadesan G, Balachandran V, Holla S, Wheeler D, Grewal SIS. CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing. Cell Rep 2020; 28:267-281.e5. [PMID: 31269446 DOI: 10.1016/j.celrep.2019.05.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/16/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic genomes, heterochromatin is targeted by RNAi machinery and/or by pathways requiring RNA elimination and transcription termination factors. However, a direct connection between termination machinery and RNA polymerase II (RNAPII) transcriptional activity at heterochromatic loci has remained elusive. Here, we show that, in fission yeast, the conserved cleavage and polyadenylation factor (CPF) is a key component involved in RNAi-independent assembly of constitutive and facultative heterochromatin domains and that CPF is broadly required to silence genes regulated by Clr4SUV39H. Remarkably, CPF is recruited to non-canonical termination sites within the body of genes by the YTH family RNA-binding protein Mmi1 and is required for RNAPII transcription termination and facultative heterochromatin assembly. CPF loading by Mmi1 also promotes the selective termination of long non-coding RNAs that regulate gene expression in cis. These analyses delineate a mechanism in which CPF loaded onto non-canonical termination sites specifies targets of heterochromatin assembly and gene silencing.
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Affiliation(s)
- Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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10
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Tatomer DC, Wilusz JE. Attenuation of Eukaryotic Protein-Coding Gene Expression via Premature Transcription Termination. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:83-93. [PMID: 32086332 DOI: 10.1101/sqb.2019.84.039644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A complex network of RNA transcripts is generated from eukaryotic genomes, many of which are processed in unexpected ways. Here, we highlight how premature transcription termination events at protein-coding gene loci can simultaneously lead to the generation of short RNAs and attenuate production of full-length mRNA transcripts. We recently showed that the Integrator (Int) complex can be selectively recruited to protein-coding gene loci, including Drosophila metallothionein A (MtnA), where the IntS11 RNA endonuclease cleaves nascent transcripts near their 5' ends. Such premature termination events catalyzed by Integrator can repress the expression of some full-length mRNAs by more than 100-fold. Transcription at small nuclear RNA (snRNA) loci is likewise terminated by Integrator cleavage, but protein-coding and snRNA gene loci have notably distinct dependencies on Integrator subunits. Additional mechanisms that attenuate eukaryotic gene outputs via premature termination have been discovered, including by the cleavage and polyadenylation machinery in a manner controlled by U1 snRNP. These mechanisms appear to function broadly across the transcriptome. This suggests that synthesis of full-length transcripts is not always the default option and that premature termination events can lead to a variety of transcripts, some of which may have important and unexpected biological functions.
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Affiliation(s)
- Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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11
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Kakegawa J, Sakane N, Suzuki K, Yoshida T. JTE-607, a multiple cytokine production inhibitor, targets CPSF3 and inhibits pre-mRNA processing. Biochem Biophys Res Commun 2019; 518:32-37. [PMID: 31399191 DOI: 10.1016/j.bbrc.2019.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
JTE-607 is a small molecule that was developed as an inflammatory cytokine inhibitor and also as an anti-leukemia reagent for monocytic leukemia. However, the mode of action of JTE-607 remains unknown. In this study, we identified JTE-607 to be a prodrug compound that is converted to an active form by ester hydrolysis. Furthermore, we determined that the active form of JTE-607 bound cleavage and polyadenylation specificity factor subunit 3 (CPSF3), using compound-immobilized affinity chromatography. CPSF3 is a 73-kDa subunit of the cleavage and polyadenylation specificity factor complex, which functions as an RNA endonuclease. The protein is involved in the 3'-end processing of messenger RNA precursors (pre-mRNAs) at the cleavage site located downstream of the poly(A) addition signal. We found that treatment with JTE-607 caused accumulation of pre-mRNAs. Furthermore, knockdown experiments showed that CPSF3 deficiency also caused accumulation of pre-mRNAs and suppressed the expression of inflammatory cytokines, like JTE-607. These findings indicated that CPSF3 is a direct target of JTE-607 and a new potential target for the treatment of disease-related abnormal cytokine production.
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Affiliation(s)
- Junya Kakegawa
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan
| | - Naoki Sakane
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan
| | - Kensuke Suzuki
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan
| | - Takayuki Yoshida
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa 236-0004, Japan.
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12
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Sun Q, Hao Q, Prasanth KV. Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. Trends Genet 2018; 34:142-157. [PMID: 29249332 PMCID: PMC6002860 DOI: 10.1016/j.tig.2017.11.005] [Citation(s) in RCA: 388] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells. In addition, we update current knowledge about the involvement of the most-abundant and conserved lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), in gene expression control.
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Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
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13
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Norman KL, Chen TC, Zeiner G, Sarnow P. Precursor microRNA-122 inhibits synthesis of Insig1 isoform mRNA by modulating polyadenylation site usage. RNA (NEW YORK, N.Y.) 2017; 23:1886-1893. [PMID: 28928276 PMCID: PMC5689008 DOI: 10.1261/rna.063099.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/09/2017] [Indexed: 06/07/2023]
Abstract
The insulin-induced gene 1 protein (Insig1) inhibits the cholesterol biosynthesis pathway by retaining transcription factor SREBP in the endoplasmic reticulum, and by causing the degradation of HMGCR, the rate-limiting enzyme in cholesterol biosynthesis. Liver-specific microRNA miR-122, on the other hand, enhances cholesterol biosynthesis by an unknown mechanism. We have found that Insig1 mRNAs are generated by alternative cleavage and polyadenylation, resulting in specific isoform mRNA species. During high cholesterol abundance, the short 1.4-kb Insig1 mRNA was found to be preferentially translated to yield Insig1 protein. Precursor molecules of miR-122 down-regulated the translation of the 1.4-kb Insig1 isoform mRNA by interfering with the usage of the promoter-proximal cleavage-polyadenylation site that gives rise to the 1.4-kb Insig1 mRNA. These findings argue that precursor miR-122 molecules modulate polyadenylation site usage in Insig1 mRNAs, resulting in down-regulation of Insig1 protein abundance. Thus, precursor microRNAs may have hitherto undetected novel functions in nuclear gene expression.
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Affiliation(s)
- Kara L Norman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tzu-Chun Chen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gusti Zeiner
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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14
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Masuda I, Igarashi T, Sakaguchi R, Nitharwal RG, Takase R, Han KY, Leslie BJ, Liu C, Gamper H, Ha T, Sanyal S, Hou YM. A genetically encoded fluorescent tRNA is active in live-cell protein synthesis. Nucleic Acids Res 2017; 45:4081-4093. [PMID: 27956502 PMCID: PMC5397188 DOI: 10.1093/nar/gkw1229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/06/2016] [Indexed: 11/14/2022] Open
Abstract
Transfer RNAs (tRNAs) perform essential tasks for all living cells. They are major components of the ribosomal machinery for protein synthesis and they also serve in non-ribosomal pathways for regulation and signaling metabolism. We describe the development of a genetically encoded fluorescent tRNA fusion with the potential for imaging in live Escherichia coli cells. This tRNA fusion carries a Spinach aptamer that becomes fluorescent upon binding of a cell-permeable and non-toxic fluorophore. We show that, despite having a structural framework significantly larger than any natural tRNA species, this fusion is a viable probe for monitoring tRNA stability in a cellular quality control mechanism that degrades structurally damaged tRNA. Importantly, this fusion is active in E. coli live-cell protein synthesis allowing peptidyl transfer at a rate sufficient to support cell growth, indicating that it is accommodated by translating ribosomes. Imaging analysis shows that this fusion and ribosomes are both excluded from the nucleoid, indicating that the fusion and ribosomes are in the cytosol together possibly engaged in protein synthesis. This fusion methodology has the potential for developing new tools for live-cell imaging of tRNA with the unique advantage of both stoichiometric labeling and broader application to all cells amenable to genetic engineering.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Takao Igarashi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Reiko Sakaguchi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Ram G Nitharwal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC 75124, Uppsala, Sweden
| | - Ryuichi Takase
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Kyu Young Han
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,CREOL, College of Optics & Photonics, University of Central Florida, 4304 Scorpius St., Orlando, FL 32816, USA
| | - Benjamin J Leslie
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Cuiping Liu
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Baltimore, MD 21205, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC 75124, Uppsala, Sweden
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
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15
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İnce İA, Pijlman GP, Vlak JM, van Oers MM. Hairpin structures with conserved sequence motifs determine the 3' ends of non-polyadenylated invertebrate iridovirus transcripts. Virology 2017; 511:344-353. [PMID: 28709684 DOI: 10.1016/j.virol.2017.06.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
Previously, we observed that the transcripts of Invertebrate iridescent virus 6 (IIV6) are not polyadenylated, in line with the absence of canonical poly(A) motifs (AATAAA) downstream of the open reading frames (ORFs) in the genome. Here, we determined the 3' ends of the transcripts of fifty-four IIV6 virion protein genes in infected Drosophila Schneider 2 (S2) cells. By using ligation-based amplification of cDNA ends (LACE) it was shown that the IIV6 mRNAs often ended with a CAUUA motif. In silico analysis showed that the 3'-untranslated regions of IIV6 genes have the ability to form hairpin structures (22-56 nt in length) and that for about half of all IIV6 genes these 3' sequences contained complementary TAATG and CATTA motifs. We also show that a hairpin in the 3' flanking region with conserved sequence motifs is a conserved feature in invertebrate-infecting iridoviruses (genus Iridovirus and Chloriridovirus).
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Affiliation(s)
- İkbal Agah İnce
- Department of Medical Microbiology, Acıbadem University Medical School, Atasehir, 34752 Istanbul, Turkey.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Just M Vlak
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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16
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Cantara WA, Olson ED, Musier-Forsyth K. Analysis of RNA structure using small-angle X-ray scattering. Methods 2017; 113:46-55. [PMID: 27777026 PMCID: PMC5253320 DOI: 10.1016/j.ymeth.2016.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/10/2016] [Accepted: 10/20/2016] [Indexed: 11/22/2022] Open
Abstract
In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist. Recently, small-angle X-ray scattering (SAXS) has been increasingly employed to characterize the 3D structures of RNAs and RNA-protein complexes. SAXS is capable of providing low-resolution tertiary structure information under physiological conditions and with less intensive sample preparation and data analysis requirements than XRC, NMR and cryo-EM. In this article, we describe best practices involved in the process of RNA and RNA-protein sample preparation, SAXS data collection, data analysis, and structural model building.
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Affiliation(s)
- William A Cantara
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
| | - Erik D Olson
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States.
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17
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Li SC, Vu LT, Luo JJ, Zhong JF, Li Z, Dethlefs BA, Loudon WG, Kabeer MH. Tissue Elasticity Bridges Cancer Stem Cells to the Tumor Microenvironment Through microRNAs: Implications for a "Watch-and-Wait" Approach to Cancer. Curr Stem Cell Res Ther 2017; 12:455-470. [PMID: 28270089 PMCID: PMC5587377 DOI: 10.2174/1574888x12666170307105941] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/01/2017] [Accepted: 03/01/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Targeting the tumor microenvironment (TME) through which cancer stem cells (CSCs) crosstalk for cancer initiation and progression, may open new treatments different from those centered on the original hallmarks of cancer genetics thereby implying a new approach for suppression of TME driven activation of CSCs. Cancer is dynamic, heterogeneous, evolving with the TME and can be influenced by tissue-specific elasticity. One of the mediators and modulators of the crosstalk between CSCs and mechanical forces is miRNA, which can be developmentally regulated, in a tissue- and cellspecific manner. OBJECTIVE Here, based on our previous data, we provide a framework through which such gene expression changes in response to external mechanical forces can be understood during cancer progression. Recognizing the ways mechanical forces regulate and affect intracellular signals with applications in cancer stem cell biology. Such TME-targeted pathways shed new light on strategies for attacking cancer stem cells with fewer side effects than traditional gene-based treatments for cancer, requiring a "watchand- wait" approach. We attempt to address both normal brain microenvironment and tumor microenvironment as both works together, intertwining in pathology and physiology - a balance that needs to be maintained for the "watch-and-wait" approach to cancer. CONCLUSION This review connected the subjects of tissue elasticity, tumor microenvironment, epigenetic of miRNAs, and stem-cell biology that are very relevant in cancer research and therapy. It attempts to unify apparently separate entities in a complex biological web, network, and system in a realistic and practical manner, i.e., to bridge basic research with clinical application.
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Affiliation(s)
- Shengwen Calvin Li
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children’s Hospital Research Institute, 1201 West La Veta Ave., Orange, CA 92868, USA
- Department of Neurology, University of California-Irvine School of Medicine, Orange, CA 92697-4292, USA
- Department of Biological Science, California State University, Fullerton, CA 92834, USA
| | - Long T. Vu
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children’s Hospital Research Institute, 1201 West La Veta Ave., Orange, CA 92868, USA
- Department of Biological Science, California State University, Fullerton, CA 92834, USA
| | | | - Jiang F. Zhong
- Division of Periodontology, Diagnostic Sciences & Dental Hygiene and Biomedical Sciences, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhongjun Li
- Division of Periodontology, Diagnostic Sciences & Dental Hygiene and Biomedical Sciences, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA
- Division of Radiation Biology, Department of Blood Transfusion, The Second Affiliated Hospital, Third Military Medical University, Xinqiao Road, Shapingba, Chongqing 400037, China
| | - Brent A Dethlefs
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children’s Hospital Research Institute, 1201 West La Veta Ave., Orange, CA 92868, USA
| | - William G. Loudon
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children’s Hospital Research Institute, 1201 West La Veta Ave., Orange, CA 92868, USA
- Department of Biological Science, California State University, Fullerton, CA 92834, USA
- Division of Radiation Biology, Department of Blood Transfusion, The Second Affiliated Hospital, Third Military Medical University, Xinqiao Road, Shapingba, Chongqing 400037, China
- Department of Neurological Surgery, Saint Joseph Hospital, Orange, CA 92868, USA
- Department of Neurological Surgery, University of California-Irvine School of Medicine, Orange, CA 92862, USA
| | - Mustafa H. Kabeer
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children’s Hospital Research Institute, 1201 West La Veta Ave., Orange, CA 92868, USA
- Department of Pediatric Surgery, CHOC Children’s Hospital, 1201 West La Veta Ave., Orange, CA 92868, USA
- Department of Surgery, University of California-Irvine School of Medicine, 333 City Blvd. West, Suite 700, Orange, CA 92868, USA
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18
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Wang H, Li R, Zhou X, Xue L, Xu X, Liu B. Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data. Sci Rep 2016; 6:36388. [PMID: 27812017 PMCID: PMC5095665 DOI: 10.1038/srep36388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 10/14/2016] [Indexed: 12/05/2022] Open
Abstract
Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3′ end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3′UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.
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Affiliation(s)
- Hongyang Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Rui Li
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Xiang Zhou
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Liyao Xue
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education &Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture; Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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19
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Nitsche A, Stadler PF. Evolutionary clues in lncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27436689 DOI: 10.1002/wrna.1376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 12/13/2022]
Abstract
The diversity of long non-coding RNAs (lncRNAs) in the human transcriptome is in stark contrast to the sparse exploration of their functions concomitant with their conservation and evolution. The pervasive transcription of the largely non-coding human genome makes the evolutionary age and conservation patterns of lncRNAs to a topic of interest. Yet it is a fairly unexplored field and not that easy to determine as for protein-coding genes. Although there are a few experimentally studied cases, which are conserved at the sequence level, most lncRNAs exhibit weak or untraceable primary sequence conservation. Recent studies shed light on the interspecies conservation of secondary structures among lncRNA homologs by using diverse computational methods. This highlights the importance of structure on functionality of lncRNAs as opposed to the poor impact of primary sequence changes. Further clues in the evolution of lncRNAs are given by selective constraints on non-coding gene structures (e.g., promoters or splice sites) as well as the conservation of prevalent spatio-temporal expression patterns. However, a rapid evolutionary turnover is observable throughout the heterogeneous group of lncRNAs. This still gives rise to questions about its functional meaning. WIREs RNA 2017, 8:e1376. doi: 10.1002/wrna.1376 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Anne Nitsche
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Institute de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Cedex, France
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany.,Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Santa Fe Institute, Santa Fe, NM, USA
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20
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Ogorodnikov A, Kargapolova Y, Danckwardt S. Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end. Pflugers Arch 2016; 468:993-1012. [PMID: 27220521 PMCID: PMC4893057 DOI: 10.1007/s00424-016-1828-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023]
Abstract
The human transcriptome is highly dynamic, with each cell type, tissue, and organ system expressing an ensemble of transcript isoforms that give rise to considerable diversity. Apart from alternative splicing affecting the "body" of the transcripts, extensive transcriptome diversification occurs at the 3' end. Transcripts differing at the 3' end can have profound physiological effects by encoding proteins with distinct functions or regulatory properties or by affecting the mRNA fate via the inclusion or exclusion of regulatory elements (such as miRNA or protein binding sites). Importantly, the dynamic regulation at the 3' end is associated with various (patho)physiological processes, including the immune regulation but also tumorigenesis. Here, we recapitulate the mechanisms of constitutive mRNA 3' end processing and review the current understanding of the dynamically regulated diversity at the transcriptome 3' end. We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.
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Affiliation(s)
- Anton Ogorodnikov
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Yulia Kargapolova
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Langenbeckstr 1, 55131, Mainz, Germany.
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21
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Zong X, Nakagawa S, Freier SM, Fei J, Ha T, Prasanth SG, Prasanth KV. Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. Nucleic Acids Res 2016; 44:2898-908. [PMID: 26826711 PMCID: PMC4824109 DOI: 10.1093/nar/gkw047] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/17/2016] [Indexed: 01/09/2023] Open
Abstract
The RNase P-mediated endonucleolytic cleavage plays a crucial role in the 3′ end processing and cellular accumulation of MALAT1, a nuclear-retained long noncoding RNA that promotes malignancy. The regulation of this cleavage event is largely undetermined. Here we characterize a broadly expressed natural antisense transcript at the MALAT1 locus, designated as TALAM1, that positively regulates MALAT1 levels by promoting the 3′ end cleavage and maturation of MALAT1 RNA. TALAM1 RNA preferentially localizes at the site of transcription, and also interacts with MALAT1 RNA. Depletion of TALAM1 leads to defects in the 3′ end cleavage reaction and compromises cellular accumulation of MALAT1. Conversely, overexpression of TALAM1 facilitates the cleavage reaction in trans. Interestingly, TALAM1 is also positively regulated by MALAT1 at the level of both transcription and RNA stability. Together, our data demonstrate a novel feed-forward positive regulatory loop that is established to maintain the high cellular levels of MALAT1, and also unravel the existence of sense-antisense mediated regulatory mechanism for cellular lncRNAs that display RNase P-mediated 3′ end processing.
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Affiliation(s)
- Xinying Zong
- Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan
| | | | - Jingyi Fei
- Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA
| | - Taekjip Ha
- Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA
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22
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Fong N, Brannan K, Erickson B, Kim H, Cortazar MA, Sheridan RM, Nguyen T, Karp S, Bentley DL. Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition. Mol Cell 2016; 60:256-67. [PMID: 26474067 DOI: 10.1016/j.molcel.2015.09.026] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/06/2015] [Accepted: 09/17/2015] [Indexed: 01/13/2023]
Abstract
The torpedo model of transcription termination asserts that the exonuclease Xrn2 attacks the 5'PO4-end exposed by nascent RNA cleavage and chases down the RNA polymerase. We tested this mechanism using a dominant-negative human Xrn2 mutant and found that it delayed termination genome-wide. Xrn2 nuclease inactivation caused strong termination defects downstream of most poly(A) sites and modest delays at some histone and U snRNA genes, suggesting that the torpedo mechanism is not limited to poly(A) site-dependent termination. A central untested feature of the torpedo model is that there is kinetic competition between the exonuclease and the pol II elongation complex. Using pol II rate mutants, we found that slow transcription robustly shifts termination upstream, and fast elongation extends the zone of termination further downstream. These results suggest that kinetic competition between elongating pol II and the Xrn2 exonuclease is integral to termination of transcription on most human genes.
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Affiliation(s)
- Nova Fong
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Kristopher Brannan
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Benjamin Erickson
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Hyunmin Kim
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Michael A Cortazar
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Ryan M Sheridan
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Tram Nguyen
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Shai Karp
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Deptartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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23
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Wilusz JE. Long noncoding RNAs: Re-writing dogmas of RNA processing and stability. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:128-38. [PMID: 26073320 PMCID: PMC4676738 DOI: 10.1016/j.bbagrm.2015.06.003] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/16/2015] [Accepted: 06/04/2015] [Indexed: 12/14/2022]
Abstract
Most of the human genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs. Many of these transcripts have a 5' cap and a poly(A) tail, yet some of the most abundant long noncoding RNAs are processed in unexpected ways and lack these canonical structures. Here, I highlight the mechanisms by which several of these well-characterized noncoding RNAs are generated, stabilized, and function. The MALAT1 and MEN β (NEAT1_2) long noncoding RNAs each accumulate to high levels in the nucleus, where they play critical roles in cancer progression and the formation of nuclear paraspeckles, respectively. Nevertheless, MALAT1 and MEN β are not polyadenylated as the tRNA biogenesis machinery generates their mature 3' ends. In place of a poly(A) tail, these transcripts are stabilized by highly conserved triple helical structures. Sno-lncRNAs likewise lack poly(A) tails and instead have snoRNA structures at their 5' and 3' ends. Recent work has additionally identified a number of abundant circular RNAs generated by the pre-mRNA splicing machinery that are resistant to degradation by exonucleases. As these various transcripts use non-canonical strategies to ensure their stability, it is becoming increasingly clear that long noncoding RNAs may often be regulated by unique post-transcriptional control mechanisms. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States.
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24
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Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Investigations exploring the dynamic interactions between lncRNAs and MYC, referred to as the lncRNA-MYC network, have proven to be especially complex. Genome-wide studies have shown that MYC transcriptionally regulates many lncRNA genes. Conversely, recent reports identified lncRNAs that regulate MYC expression both at the transcriptional and post-transcriptional levels. These findings are of particular interest because they suggest roles of lncRNAs as regulators of MYC oncogenic functions and the possibility that targeting lncRNAs could represent a novel avenue to cancer treatment. Here, we briefly review the current understanding of how lncRNAs regulate chromatin structure and gene transcription, and then focus on the new developments in the emerging field exploring the lncRNA-MYC network in cancer.
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Affiliation(s)
- Michael J. Hamilton
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Matthew D. Young
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Silvia Sauer
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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25
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Yu NYL, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y, Uhlén M, Daub CO. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res 2015; 43:6787-98. [PMID: 26117540 PMCID: PMC4538815 DOI: 10.1093/nar/gkv608] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/20/2022] Open
Abstract
Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5'-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes.
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Affiliation(s)
- Nancy Yiu-Lin Yu
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, 751 85, Sweden
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
| | - Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, Solna, 17121, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan
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26
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Betat H, Mörl M. The CCA-adding enzyme: A central scrutinizer in tRNA quality control. Bioessays 2015; 37:975-82. [DOI: 10.1002/bies.201500043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Heike Betat
- Institute for Biochemistry; University of Leipzig; Leipzig Germany
| | - Mario Mörl
- Institute for Biochemistry; University of Leipzig; Leipzig Germany
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27
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Guo X, Gao L, Wang Y, Chiu DKY, Wang T, Deng Y. Advances in long noncoding RNAs: identification, structure prediction and function annotation. Brief Funct Genomics 2015; 15:38-46. [PMID: 26072035 PMCID: PMC5863772 DOI: 10.1093/bfgp/elv022] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Long noncoding RNAs (lncRNAs), generally longer than 200 nucleotides and with poor protein coding potential, are usually considered collectively as a heterogeneous class of RNAs. Recently, an increasing number of studies have shown that lncRNAs can involve in various critical biological processes and a number of complex human diseases. Not only the primary sequences of many lncRNAs are directly interrelated to a specific functional role, strong evidence suggests that their secondary structures are even more interrelated to their known functions. As functional molecules, lncRNAs have become more and more relevant to many researchers. Here, we review recent, state-of-the-art advances in the three levels (the primary sequence, the secondary structure and the function annotation) of the lncRNA research, as well as computational methods for lncRNA data analysis.
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Rodríguez-Romero J, Franceschetti M, Bueno E, Sesma A. Multilayer regulatory mechanisms control cleavage factor I proteins in filamentous fungi. Nucleic Acids Res 2014; 43:179-95. [PMID: 25514925 PMCID: PMC4288187 DOI: 10.1093/nar/gku1297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cleavage factor I (CFI) proteins are core components of the polyadenylation machinery that can regulate several steps of mRNA life cycle, including alternative polyadenylation, splicing, export and decay. Here, we describe the regulatory mechanisms that control two fungal CFI protein classes in Magnaporthe oryzae: Rbp35/CfI25 complex and Hrp1. Using mutational, genetic and biochemical studies we demonstrate that cellular concentration of CFI mRNAs is a limited indicator of their protein abundance. Our results suggest that several post-transcriptional mechanisms regulate Rbp35/CfI25 complex and Hrp1 in the rice blast fungus, some of which are also conserved in other ascomycetes. With respect to Rbp35, these include C-terminal processing, RGG-dependent localization and cleavage, C-terminal autoregulatory domain and regulation by an upstream open reading frame of Rbp35-dependent TOR signalling pathway. Our proteomic analyses suggest that Rbp35 regulates the levels of proteins involved in melanin and phenylpropanoids synthesis, among others. The drastic reduction of fungal CFI proteins in carbon-starved cells suggests that the pre-mRNA processing pathway is altered. Our findings uncover broad and multilayer regulatory mechanisms controlling fungal polyadenylation factors, which have profound implications in pre-mRNA maturation. This area of research offers new avenues for fungicide design by targeting fungal-specific proteins that globally affect thousands of mRNAs.
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Affiliation(s)
- J Rodríguez-Romero
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - M Franceschetti
- Disease & Stress Biology Department, John Innes Centre, Colney lane, Norwich NR4 7UH, UK
| | - E Bueno
- Disease & Stress Biology Department, John Innes Centre, Colney lane, Norwich NR4 7UH, UK
| | - A Sesma
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
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29
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The putative Leishmania telomerase RNA (LeishTER) undergoes trans-splicing and contains a conserved template sequence. PLoS One 2014; 9:e112061. [PMID: 25391020 PMCID: PMC4229120 DOI: 10.1371/journal.pone.0112061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/11/2014] [Indexed: 02/07/2023] Open
Abstract
Telomerase RNAs (TERs) are highly divergent between species, varying in size and sequence composition. Here, we identify a candidate for the telomerase RNA component of Leishmania genus, which includes species that cause leishmaniasis, a neglected tropical disease. Merging a thorough computational screening combined with RNA-seq evidence, we mapped a non-coding RNA gene localized in a syntenic locus on chromosome 25 of five Leishmania species that shares partial synteny with both Trypanosoma brucei TER locus and a putative TER candidate-containing locus of Crithidia fasciculata. Using target-driven molecular biology approaches, we detected a ∼2,100 nt transcript (LeishTER) that contains a 5′ spliced leader (SL) cap, a putative 3′ polyA tail and a predicted C/D box snoRNA domain. LeishTER is expressed at similar levels in the logarithmic and stationary growth phases of promastigote forms. A 5′SL capped LeishTER co-immunoprecipitated and co-localized with the telomerase protein component (TERT) in a cell cycle-dependent manner. Prediction of its secondary structure strongly suggests the existence of a bona fide single-stranded template sequence and a conserved C[U/C]GUCA motif-containing helix II, representing the template boundary element. This study paves the way for further investigations on the biogenesis of parasite TERT ribonucleoproteins (RNPs) and its role in parasite telomere biology.
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30
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Saldi TK, Ash PE, Wilson G, Gonzales P, Garrido-Lecca A, Roberts CM, Dostal V, Gendron TF, Stein LD, Blumenthal T, Petrucelli L, Link CD. TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA. EMBO J 2014; 33:2947-66. [PMID: 25391662 PMCID: PMC4282642 DOI: 10.15252/embj.201488740] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Caenorhabditis elegans mutants deleted for TDP-1, an ortholog of the neurodegeneration-associated RNA-binding protein TDP-43, display only mild phenotypes. Nevertheless, transcriptome sequencing revealed that many RNAs were altered in accumulation and/or processing in the mutant. Analysis of these transcriptional abnormalities demonstrates that a primary function of TDP-1 is to limit formation or stability of double-stranded RNA. Specifically, we found that deletion of tdp-1: (1) preferentially alters the accumulation of RNAs with inherent double-stranded structure (dsRNA); (2) increases the accumulation of nuclear dsRNA foci; (3) enhances the frequency of adenosine-to-inosine RNA editing; and (4) dramatically increases the amount of transcripts immunoprecipitable with a dsRNA-specific antibody, including intronic sequences, RNAs with antisense overlap to another transcript, and transposons. We also show that TDP-43 knockdown in human cells results in accumulation of dsRNA, indicating that suppression of dsRNA is a conserved function of TDP-43 in mammals. Altered accumulation of structured RNA may account for some of the previously described molecular phenotypes (e.g., altered splicing) resulting from reduction of TDP-43 function.
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Affiliation(s)
- Tassa K Saldi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Peter Ea Ash
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Gavin Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Patrick Gonzales
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA
| | - Alfonso Garrido-Lecca
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | | | - Vishantie Dostal
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Lincoln D Stein
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Thomas Blumenthal
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | | | - Christopher D Link
- Institute for Behavioral Genetics University of Colorado, Boulder, CO, USA Integrative Physiology, University of Colorado, Boulder, CO, USA
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31
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Novikova IV, Hennelly SP, Sanbonmatsu KY. Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure? BIOARCHITECTURE 2014; 2:189-99. [PMID: 23267412 PMCID: PMC3527312 DOI: 10.4161/bioa.22592] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) play a key role in many important areas of epigenetics, stem cell biology, cancer, signaling and brain function. This emerging class of RNAs constitutes a large fraction of the transcriptome, with thousands of new lncRNAs reported each year. The molecular mechanisms of these RNAs are not well understood. Currently, very little structural data exist. We review the available lncRNA sequence and secondary structure data. Since almost no tertiary information is available for lncRNAs, we review crystallographic structures for other RNA systems and discuss the possibilities for lncRNAs in the context of existing constraints.
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32
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Abstract
Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.
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Affiliation(s)
- Sean R Eddy
- Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia 20147;
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33
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Schlackow M, Marguerat S, Proudfoot NJ, Bähler J, Erban R, Gullerova M. Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. RNA (NEW YORK, N.Y.) 2013; 19:1617-1631. [PMID: 24152550 PMCID: PMC3884648 DOI: 10.1261/rna.040675.113] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/17/2013] [Indexed: 05/31/2023]
Abstract
Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).
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MESH Headings
- 3' Untranslated Regions
- Base Sequence
- Chromosome Mapping
- Chromosomes, Fungal/genetics
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Genome, Fungal
- Molecular Sequence Annotation
- Molecular Sequence Data
- Polyadenylation
- RNA Cleavage
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Schizosaccharomyces/genetics
- Schizosaccharomyces/metabolism
- Sequence Analysis, RNA
- Transcription Termination, Genetic
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Affiliation(s)
- Margarita Schlackow
- Mathematical Institute, University of Oxford, Oxford, Oxfordshire OX1 3LB, United Kingdom
| | - Samuel Marguerat
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Nicholas J. Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire OX1 3RE, United Kingdom
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Radek Erban
- Mathematical Institute, University of Oxford, Oxford, Oxfordshire OX1 3LB, United Kingdom
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire OX1 3RE, United Kingdom
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34
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Conrad NK. The emerging role of triple helices in RNA biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:15-29. [PMID: 24115594 DOI: 10.1002/wrna.1194] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/31/2013] [Accepted: 08/06/2013] [Indexed: 12/19/2022]
Abstract
The ability of RNA to form sophisticated secondary and tertiary structures enables it to perform a wide variety of cellular functions. One tertiary structure, the RNA triple helix, was first observed in vitro over 50 years ago, but biological activities for triple helices are only beginning to be appreciated. The recent determination of several RNA structures has implicated triple helices in distinct biological functions. For example, the SAM-II riboswitch forms a triple helix that creates a highly specific binding pocket for S-adenosylmethionine. In addition, a triple helix in the conserved pseudoknot domain of the telomerase-associated RNA TER is essential for telomerase activity. A viral RNA cis-acting RNA element called the ENE contributes to the nuclear stability of a viral noncoding RNA by forming a triple helix with the poly(A) tail. Finally, a cellular noncoding RNA, MALAT1, includes a triple helix at its 3'-end that contributes to RNA stability, but surprisingly also supports translation. These examples highlight the diverse roles that RNA triple helices play in biology. Moreover, the dissection of triple helix mechanisms has the potential to uncover fundamental pathways in cell biology.
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Affiliation(s)
- Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX, USA
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35
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Kramps T, Probst J. Messenger RNA-based vaccines: progress, challenges, applications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:737-49. [PMID: 23893949 DOI: 10.1002/wrna.1189] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/27/2013] [Accepted: 06/27/2013] [Indexed: 12/21/2022]
Abstract
Twenty years after the demonstration that messenger RNA (mRNA) was expressed and immunogenic upon direct injection in mice, the first successful proof-of-concept of specific protection against viral infection in small and large animals was reported. These data indicate wider applicability to infectious disease and should encourage continued translation of mRNA-based prophylactic vaccines into human clinical trials. At the conceptual level, mRNA-based vaccines-more than other genetic vectors-combine the simplicity, safety, and focused immunogenicity of subunit vaccines with favorable immunological properties of live viral vaccines: (1) mRNA vaccines are molecularly defined and carry no excess information. In the environment and upon physical contact, RNA is rapidly degraded by ubiquitous RNases and cannot persist. These characteristics also guarantee tight control over their immunogenic profile (including avoidance of vector-specific immune responses that could interfere with repeated administration), pharmacokinetics, and dosing. (2) mRNA vaccines are synthetically produced by an enzymatic process, just requiring information about the nucleic acid sequence of the desired antigen. This greatly reduces general complications associated with biological vaccine production, such as handling of infectious agents, genetic variability, environmental risks, or restrictions to vaccine distribution. (3) RNA can be tailored to provide potent adjuvant stimuli to the innate immune system by direct activation of RNA-specific receptors; this may reduce the need for additional adjuvants. The formation of native antigen in situ affords great versatility, including intracellular localization, membrane association, posttranslational modification, supra-molecular assembly, or targeted structural optimization of delivered antigen. Messenger RNA vaccines induce balanced immune responses including B cells, helper T cells, and cytotoxic T lymphocytes, rendering them an extremely adaptable platform. This article surveys the design, mode of action, and capabilities of state-of-the-art mRNA vaccines, focusing on the paradigm of influenza prophylaxis.
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36
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Smekalova EM, Shubernetskaya OS, Zvereva MI, Gromenko EV, Rubtsova MP, Dontsova OA. Telomerase RNA biosynthesis and processing. BIOCHEMISTRY (MOSCOW) 2013; 77:1120-8. [PMID: 23157292 DOI: 10.1134/s0006297912100045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Telomerase synthesizes repetitive G-rich sequences (telomeric repeats) at the ends of eukaryotic chromosomes. This mechanism maintains the integrity of the genome, as telomere shortening leads to degradation and fusion of chromosomes. The core components of telomerase are the telomerase catalytic subunit and telomerase RNA, which possesses a small template region serving for the synthesis of a telomeric repeat. Mutations in the telomerase RNA are associated with some cases of aplastic anemia and also cause dyskeratosis congenita, myelodysplasia, and pulmonary fibrosis. Telomerase is active in 85% of cancers, and telomerase activation is one of the first steps in cell transformation. The study of telomerase and pathways where this enzyme is involved will help to understand the mechanism of the mentioned diseases and to develop new approaches for their treatment. In this review we describe the modern conception of telomerase RNA biosynthesis, processing, and functioning in the three most studied systems - yeast, vertebrates, and ciliates.
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Affiliation(s)
- E M Smekalova
- Chemical Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
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37
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Gutschner T, Hämmerle M, Diederichs S. MALAT1 — a paradigm for long noncoding RNA function in cancer. J Mol Med (Berl) 2013; 91:791-801. [DOI: 10.1007/s00109-013-1028-y] [Citation(s) in RCA: 560] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 12/31/2022]
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38
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Novikova IV, Hennelly SP, Tung CS, Sanbonmatsu KY. Rise of the RNA machines: exploring the structure of long non-coding RNAs. J Mol Biol 2013; 425:3731-46. [PMID: 23467124 DOI: 10.1016/j.jmb.2013.02.030] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 01/19/2023]
Abstract
Novel, profound and unexpected roles of long non-coding RNAs (lncRNAs) are emerging in critical aspects of gene regulation. Thousands of lncRNAs have been recently discovered in a wide range of mammalian systems, related to development, epigenetics, cancer, brain function and hereditary disease. The structural biology of these lncRNAs presents a brave new RNA world, which may contain a diverse zoo of new architectures and mechanisms. While structural studies of lncRNAs are in their infancy, we describe existing structural data for lncRNAs, as well as crystallographic studies of other RNA machines and their implications for lncRNAs. We also discuss the importance of dynamics in RNA machine mechanism. Determining commonalities between lncRNA systems will help elucidate the evolution and mechanistic role of lncRNAs in disease, creating a structural framework necessary to pursue lncRNA-based therapeutics.
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39
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Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA. A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 2012; 26:2392-407. [PMID: 23073843 DOI: 10.1101/gad.204438.112] [Citation(s) in RCA: 347] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) locus is misregulated in many human cancers and produces an abundant long nuclear-retained noncoding RNA. Despite being transcribed by RNA polymerase II, the 3' end of MALAT1 is produced not by canonical cleavage/polyadenylation but instead by recognition and cleavage of a tRNA-like structure by RNase P. Mature MALAT1 thus lacks a poly(A) tail yet is expressed at a level higher than many protein-coding genes in vivo. Here we show that the 3' ends of MALAT1 and the MEN β long noncoding RNAs are protected from 3'-5' exonucleases by highly conserved triple helical structures. Surprisingly, when these structures are placed downstream from an ORF, the transcript is efficiently translated in vivo despite the lack of a poly(A) tail. The triple helix therefore also functions as a translational enhancer, and mutations in this region separate this translation activity from simple effects on RNA stability or transport. We further found that a transcript ending in a triple helix is efficiently repressed by microRNAs in vivo, arguing against a major role for the poly(A) tail in microRNA-mediated silencing. These results provide new insights into how transcripts that lack poly(A) tails are stabilized and regulated and suggest that RNA triple-helical structures likely have key regulatory functions in vivo.
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Affiliation(s)
- Jeremy E Wilusz
- Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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40
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Li J, Akagi K, Hu Y, Trivett AL, Hlynialuk CJ, Swing DA, Volfovsky N, Morgan TC, Golubeva Y, Stephens RM, Smith DE, Symer DE. Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance. Genome Res 2012; 22:870-84. [PMID: 22367191 PMCID: PMC3337433 DOI: 10.1101/gr.130740.111] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 02/09/2012] [Indexed: 01/15/2023]
Abstract
Endogenous retrotransposons have caused extensive genomic variation within mammalian species, but the functional implications of such mobilization are mostly unknown. We mapped thousands of endogenous retrovirus (ERV) germline integrants in highly divergent, previously unsequenced mouse lineages, facilitating a comparison of gene expression in the presence or absence of local insertions. Polymorphic ERVs occur relatively infrequently in gene introns and are particularly depleted from genes involved in embryogenesis or that are highly expressed in embryonic stem cells. Their genomic distribution implies ongoing negative selection due to deleterious effects on gene expression and function. A polymorphic, intronic ERV at Slc15a2 triggers up to 49-fold increases in premature transcriptional termination and up to 39-fold reductions in full-length transcripts in adult mouse tissues, thereby disrupting protein expression and functional activity. Prematurely truncated transcripts also occur at Polr1a, Spon1, and up to ∼5% of other genes when intronic ERV polymorphisms are present. Analysis of expression quantitative trait loci (eQTLs) in recombinant BxD mouse strains demonstrated very strong genetic associations between the polymorphic ERV in cis and disrupted transcript levels. Premature polyadenylation is triggered at genomic distances up to >12.5 kb upstream of the ERV, both in cis and between alleles. The parent of origin of the ERV is associated with variable expression of nonterminated transcripts and differential DNA methylation at its 5'-long terminal repeat. This study defines an unexpectedly strong functional impact of ERVs in disrupting gene transcription at a distance and demonstrates that ongoing retrotransposition can contribute significantly to natural phenotypic diversity.
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Affiliation(s)
- Jingfeng Li
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Keiko Akagi
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Yongjun Hu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Christopher J.W. Hlynialuk
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Deborah A. Swing
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Natalia Volfovsky
- Advanced Biomedical Computing Center, Information Systems Program and
| | - Tamara C. Morgan
- Histotechnology Laboratory, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Maryland 21702, USA
| | - Yelena Golubeva
- Histotechnology Laboratory, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Maryland 21702, USA
| | | | - David E. Smith
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - David E. Symer
- Human Cancer Genetics Program and Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
- Department of Internal Medicine and Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
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41
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Wilusz JE, Whipple JM, Phizicky EM, Sharp PA. tRNAs marked with CCACCA are targeted for degradation. Science 2011; 334:817-21. [PMID: 22076379 DOI: 10.1126/science.1213671] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase] adds CCA to the 3' ends of transfer RNAs (tRNAs), a critical step in tRNA biogenesis that generates the amino acid attachment site. We found that the CCA-adding enzyme plays a key role in tRNA quality control by selectively marking structurally unstable tRNAs and tRNA-like small RNAs for degradation. Instead of adding CCA to the 3' ends of these transcripts, CCA-adding enzymes from all three kingdoms of life add CCACCA. In addition, hypomodified mature tRNAs are subjected to CCACCA addition as part of a rapid tRNA decay pathway in vivo. We conjecture that CCACCA addition is a universal mechanism for controlling tRNA levels and preventing errors in translation.
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Affiliation(s)
- Jeremy E Wilusz
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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42
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Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:385-96. [PMID: 22012871 DOI: 10.1002/wrna.116] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pre-mRNA cleavage and polyadenylation is an essential step for 3' end formation of almost all protein-coding transcripts in eukaryotes. The reaction, involving cleavage of nascent mRNA followed by addition of a polyadenylate or poly(A) tail, is controlled by cis-acting elements in the pre-mRNA surrounding the cleavage site. Experimental and bioinformatic studies in the past three decades have elucidated conserved and divergent elements across eukaryotes, from yeast to human. Here we review histories and current models of these elements in a broad range of species.
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Affiliation(s)
- Bin Tian
- UMDNJ-New Jersey Medical School, Newark, NJ, USA.
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43
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Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res 2011; 21:1929-43. [PMID: 21994249 DOI: 10.1101/gr.112516.110] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. We have developed a comparative method, EvoFam, for genome-wide identification of families of regulatory RNA structures, based on primary sequence and secondary structure similarity. We apply EvoFam to a 41-way genomic vertebrate alignment. Genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural RNA elements. Known families identified include both noncoding RNAs, e.g., miRNAs and the recently identified MALAT1/MEN β lincRNA family; and cis-regulatory structures, e.g., iron-responsive elements. We also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as GO term enrichments. For some of these, detailed analysis has led to the formulation of specific functional hypotheses. Examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3'-UTR of MAT2A, a key metabolic gene that produces the primary human methyl donor S-adenosylmethionine; the other involving a tRNA-like structure in the intron of the tRNA maturation gene POP1. We experimentally validate the predicted MAT2A structures. Finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF, FOS, and CTLA4, which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding RNAs.
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Affiliation(s)
- Brian J Parker
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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44
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Rose D, Stadler PF. Molecular evolution of the non-coding eosinophil granule ontogeny transcript. Front Genet 2011; 2:69. [PMID: 22303364 PMCID: PMC3268622 DOI: 10.3389/fgene.2011.00069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 09/16/2011] [Indexed: 01/22/2023] Open
Abstract
Eukaryotic genomes are pervasively transcribed. A large fraction of the transcriptional output consists of long, mRNA-like, non-protein-coding transcripts (mlncRNAs). The evolutionary history of mlncRNAs is still largely uncharted territory. In this contribution, we explore in detail the evolutionary traces of the eosinophil granule ontogeny transcript (EGOT), an experimentally confirmed representative of an abundant class of totally intronic non-coding transcripts (TINs). EGOT is located antisense to an intron of the ITPR1 gene. We computationally identify putative EGOT orthologs in the genomes of 32 different amniotes, including orthologs from primates, rodents, ungulates, carnivores, afrotherians, and xenarthrans, as well as putative candidates from basal amniotes, such as opossum or platypus. We investigate the EGOT gene phylogeny, analyze patterns of sequence conservation, and the evolutionary conservation of the EGOT gene structure. We show that EGO-B, the spliced isoform, may be present throughout the placental mammals, but most likely dates back even further. We demonstrate here for the first time that the whole EGOT locus is highly structured, containing several evolutionary conserved, and thermodynamic stable secondary structures. Our analyses allow us to postulate novel functional roles of a hitherto poorly understood region at the intron of EGO-B which is highly conserved at the sequence level. The region contains a novel ITPR1 exon and also conserved RNA secondary structures together with a conserved TATA-like element, which putatively acts as a promoter of an independent regulatory element.
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Affiliation(s)
- Dominic Rose
- Bioinformatics Group, Department of Computer Science, University of FreiburgFreiburg, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of LeipzigLeipzig, Germany
- Max Planck Institute for Mathematics in the SciencesLeipzig, Germany
- Fraunhofer Institut für Zelltherapie und ImmunologieLeipzig, Germany
- Department of Theoretical Chemistry, University of ViennaWien, Austria
- Center for non-coding RNA in Technology and Health, University of CopenhagenFrederiksberg, Denmark
- Santa Fe InstituteSanta Fe, NM, USA
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Martin J, Jenkins RH, Bennagi R, Krupa A, Phillips AO, Bowen T, Fraser DJ. Post-transcriptional regulation of Transforming Growth Factor Beta-1 by microRNA-744. PLoS One 2011; 6:e25044. [PMID: 21991303 PMCID: PMC3186795 DOI: 10.1371/journal.pone.0025044] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 08/23/2011] [Indexed: 11/18/2022] Open
Abstract
Transforming Growth Factor Beta-1 (TGF-β1) is a pleiotropic cytokine that is of central importance in wound healing, inflammation, and in key pathological processes including cancer and progressive tissue fibrosis. TGF-β1 is post-transcriptionally regulated, but the underlying mechanisms remain incompletely defined. Previously, we have extensively delineated post-transcriptional regulation of TGF-β1 synthesis in the kidney, with evidence for relief of translational repression in proximal tubular cells in the context of diabetic nephropathy. In this study, we have investigated the role of the TGF-β1 3'Untranslated Region (3'UTR). Two different 3'UTR lengths have been reported for TGF-β1, of 543 and 137 nucleotides. Absolute quantification showed that, while both UTR lengths were detectable in various human cell types and in a broad range of tissues, the short form predominated in the kidney and elsewhere. Expression of both forms was up-regulated following auto-induction by TGF-β1, but the short:long UTR ratio remained constant. Incorporation of the short UTR into a luciferase reporter vector significantly reduced reporter protein synthesis without major effect on RNA amount, suggesting post-transcriptional inhibition. In silico approaches identified multiple binding sites for miR-744 located in the proximal TGF-β1 3'UTR. A screen in RNA from human tissues showed widespread miR-744 expression. miR-744 transfection inhibited endogenous TGF-β1 synthesis, while direct targeting of TGF-β1 was shown in separate experiments, in which miR-744 decreased TGF-β1 3'UTR reporter activity. This work identifies miR-744-directed post-transcriptional regulation of TGF-β1 which, given the pleiotropic nature of cellular responses to TGF-β1, is potentially widely significant.
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Affiliation(s)
- John Martin
- School of Medicine, Institute of Nephrology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Robert H. Jenkins
- School of Medicine, Institute of Nephrology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Rasha Bennagi
- School of Medicine, Institute of Nephrology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Aleksandra Krupa
- School of Medicine, Institute of Nephrology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Aled O. Phillips
- School of Medicine, Institute of Nephrology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Timothy Bowen
- School of Medicine, Institute of Nephrology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Donald J. Fraser
- School of Medicine, Institute of Nephrology, Cardiff University, Cardiff, Wales, United Kingdom
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Yeast pheromone receptor genes STE2 and STE3 are differently regulated at the transcription and polyadenylation level. Proc Natl Acad Sci U S A 2011; 108:17082-6. [PMID: 21969566 DOI: 10.1073/pnas.1114648108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The orderly expression of specific genes is the basis for cell differentiation. Saccharomyces cerevisiae has two haploid mating types, a and α cells, in which the mating-specific genes are differentially expressed. When a and α cells are committed to mate, their growth is arrested. Here we show that a cryptic polyadenylation site is present inside the coding region of the a-specific STE2 gene, encoding the receptor for the α-factor. The two cell types produce an incomplete STE2 transcript, but only a cells generate full-length STE2 mRNA. We eliminated the cryptic poly(A) signal, thereby allowing the production of a complete STE2 mRNA in α cells. We mutagenized α cells and isolated a mutant producing full-length STE2 mRNA. The mutation occurred in the ITC1 gene, whose product, together with the product of ISW2, is known to repress STE2 transcriptional initiation. We propose that the regulation of the yeast mating genes is achieved through a concerted mechanism involving transcriptional and posttranscriptional events. In particular, the early poly(A) site in STE2 could contribute to a complete shutoff of its expression in α cells, avoiding autocrine activation and growth arrest. Remarkably, no cryptic poly(A) sites are present in the a-factor receptor STE3 gene, indicating that S. cerevisiae has devised different strategies to regulate the two receptor genes. It is predictable that a correlation between the repression of a gene and the presence of a cryptic poly(A) site could also be found in other organisms, especially when expression of that gene may be harmful.
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Dominissini D, Moshitch-Moshkovitz S, Amariglio N, Rechavi G. Adenosine-to-inosine RNA editing meets cancer. Carcinogenesis 2011; 32:1569-77. [PMID: 21715563 DOI: 10.1093/carcin/bgr124] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The role of epigenetics in tumor onset and progression has been extensively addressed. Discoveries in the last decade completely changed our view on RNA. We now realize that its diversity lies at the base of biological complexity. Adenosine-to-inosine (A-to-I) RNA editing emerges a central generator of transcriptome diversity and regulation in higher eukaryotes. It is the posttranscriptional deamination of adenosine to inosine in double-stranded RNA catalyzed by enzymes of the adenosine deaminase acting on RNA (ADAR) family. Thought at first to be restricted to coding regions of only a few genes, recent bioinformatic analyses fueled by high-throughput sequencing revealed that it is a widespread modification affecting mostly non-coding repetitive elements in thousands of genes. The rise in scope is accompanied by discovery of a growing repertoire of functions based on differential decoding of inosine by the various cellular machineries: when recognized as guanosine, it can lead to protein recoding, alternative splicing or altered microRNA specificity; when recognized by inosine-binding proteins, it can result in nuclear retention of the transcript or its degradation. An imbalance in expression of ADAR enzymes with consequent editing dysregulation is a characteristic of human cancers. These alterations may be responsible for activating proto-oncogenes or inactivating tumor suppressors. While unlikely to be an early initiating 'hit', editing dysregulation seems to contribute to tumor progression and thus should be considered a 'driver mutation'. In this review, we examine the contribution of A-to-I RNA editing to carcinogenesis.
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Affiliation(s)
- Dan Dominissini
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel
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Jia H, Wang X, Liu F, Guenther UP, Srinivasan S, Anderson JT, Jankowsky E. The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex. Cell 2011; 145:890-901. [PMID: 21663793 PMCID: PMC3115544 DOI: 10.1016/j.cell.2011.05.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 03/03/2011] [Accepted: 05/06/2011] [Indexed: 11/24/2022]
Abstract
Many steps in nuclear RNA processing, surveillance, and degradation require TRAMP, a complex containing the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for decay or trimming by the nuclear exosome. It has been unclear how polyadenylation by TRAMP differs from polyadenylation by conventional poly(A) polymerase, which produces poly(A) tails that stabilize RNAs. Using reconstituted S. cerevisiae TRAMP, we show that TRAMP inherently suppresses poly(A) addition after only 3-4 adenosines. This poly(A) tail length restriction is controlled by Mtr4p. The helicase detects the number of 3'-terminal adenosines and, over several adenylation steps, elicits precisely tuned adjustments of ATP affinities and rate constants for adenylation and TRAMP dissociation. Our data establish Mtr4p as a critical regulator of polyadenylation by TRAMP and reveal that an RNA helicase can control the activity of another enzyme in a highly complex fashion and in response to features in RNA.
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Affiliation(s)
- Huijue Jia
- Center for RNA Molecular Biology & Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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Jackowiak P, Nowacka M, Strozycki PM, Figlerowicz M. RNA degradome--its biogenesis and functions. Nucleic Acids Res 2011; 39:7361-70. [PMID: 21653558 PMCID: PMC3177198 DOI: 10.1093/nar/gkr450] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
RNA degradation is among the most fundamental processes that occur in living cells. The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control. The efficiency of RNA decay is ensured by a broad spectrum of both specific and non-specific ribonucleases. Some of these ribonucleases participate mainly in processing primary transcripts and in RNA quality control. Others preferentially digest mature, functional RNAs to yield a variety of molecules that together constitute the RNA degradome. Recently, it has become increasingly clear that the composition of the cellular RNA degradome can be modulated by numerous endogenous and exogenous factors (e.g. by stress). In addition, instead of being hydrolyzed to single nucleotides, some intermediates of RNA degradation can accumulate and function as signalling molecules or participate in mechanisms that control gene expression. Thus, RNA degradation appears to be not only a process that contributes to the maintenance of cellular homeostasis but also an underestimated source of regulatory molecules.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Martyna Nowacka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Pawel M. Strozycki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań and Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
- *To whom correspondence should be addressed. Tel: 48 61 8528503; Fax: 48 61 8520532;
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Hurto RL. Unexpected functions of tRNA and tRNA processing enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 722:137-55. [PMID: 21915787 DOI: 10.1007/978-1-4614-0332-6_9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
tRNA and tRNA processing enzymes impact more than protein production. Studies have uncovered roles for tRNA in the regulation of transcription, translation and protein turnover. Induced by stress or as a programmed part of development, nonrandom tRNA fragments can guide mRNA cleavage, inhibit translation and promote morphological changes. Similarly, tRNA processing enzymes, such as RNaseP and tRNA aminoacyl-synthetases participate in tasks affecting more than tRNA function (i.e., mRNA function and cellular signaling). Unraveling the complexities of their functions will increase our understanding of how mutations associated with disease impact these functions and the downstream consequences. This chapter focuses on how tRNA and tRNA processing enzymes influence cellular function and RNA-infrastructure via pathways beyond the decoding activities that tRNA are known for.
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Affiliation(s)
- Rebecca L Hurto
- Department of Molecular Genetics, The Ohio State University, Columbus, USA.
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