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Abstract
Long terminal repeat (LTR) retrotransposons constitute significant fractions of many eukaryotic genomes. Two ancient families are Ty1/Copia (Pseudoviridae) and Ty3/Gypsy (Metaviridae). The Ty3/Gypsy family probably gave rise to retroviruses based on the domain order, similarity of sequences, and the envelopes encoded by some members. The Ty3 element of Saccharomyces cerevisiae is one of the most completely characterized elements at the molecular level. Ty3 is induced in mating cells by pheromone stimulation of the mitogen-activated protein kinase pathway as cells accumulate in G1. The two Ty3 open reading frames are translated into Gag3 and Gag3-Pol3 polyprotein precursors. In haploid mating cells Gag3 and Gag3-Pol3 are assembled together with Ty3 genomic RNA into immature virus-like particles in cellular foci containing RNA processing body proteins. Virus-like particle Gag3 is then processed by Ty3 protease into capsid, spacer, and nucleocapsid, and Gag3-Pol3 into those proteins and additionally, protease, reverse transcriptase, and integrase. After haploid cells mate and become diploid, genomic RNA is reverse transcribed into cDNA. Ty3 integration complexes interact with components of the RNA polymerase III transcription complex resulting in Ty3 integration precisely at the transcription start site. Ty3 activation during mating enables proliferation of Ty3 between genomes and has intriguing parallels with metazoan retrotransposon activation in germ cell lineages. Identification of nuclear pore, DNA replication, transcription, and repair host factors that affect retrotransposition has provided insights into how hosts and retrotransposons interact to balance genome stability and plasticity.
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202
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Ghosh S, Sati S, Sengupta S, Scaria V. Distinct patterns of epigenetic marks and transcription factor binding sites across promoters of sense-intronic long noncoding RNAs. J Genet 2016; 94:17-25. [PMID: 25846873 DOI: 10.1007/s12041-015-0484-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a new class of noncoding RNAs that have been extensively studied in the recent past as a regulator of gene expression, including modulation of epigenetic regulation. The lncRNAs class encompasses a number of subclasses, classified based on their genomic loci and relation to protein-coding genes. Functional differences between subclasses have been increasingly studied in the recent years, though the regulation of expression and biogenesis of lncRNAs have been poorly studied. The availability of genome-scale datasets of epigenetic marks has motivated us to understand the patterns and processes of epigenetic regulation of lncRNAs. Here we analysed the occurrence of expressive and repressive histone marks at the transcription start site (TSS) of lncRNAs and their subclasses, and compared these profiles with that of the protein-coding regions. We observe distinct differences in the density of histone marks across the TSS of a few lncRNA subclasses. The sense-intronic lncRNA subclass showed a paucity for mapped histone marks across the TSS which were significantly different than all the lncRNAs and protein-coding genes in most cases. Similar pattern was also observed for the density of transcription factor binding sites (TFBS). These observations were generally consistent across cell and tissue types. The differences in density across the promoter were significantly associated with the expression level of the genes, but the differences between the densities across long noncoding and protein-coding gene promoters were consistent irrespective of the expression levels. Apart from suggesting general differences in epigenetic regulatory marks across long noncoding RNA promoters, our analysis suggests a possible alternative mechanism of regulation and/or biogenesis of sense-intronic lncRNAs.
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Affiliation(s)
- Sourav Ghosh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi 110 007, India.
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203
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Sensing of latent EBV infection through exosomal transfer of 5'pppRNA. Proc Natl Acad Sci U S A 2016; 113:E587-96. [PMID: 26768848 DOI: 10.1073/pnas.1518130113] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Complex interactions between DNA herpesviruses and host factors determine the establishment of a life-long asymptomatic latent infection. The lymphotropic Epstein-Barr virus (EBV) seems to avoid recognition by innate sensors despite massive transcription of immunostimulatory small RNAs (EBV-EBERs). Here we demonstrate that in latently infected B cells, EBER1 transcripts interact with the lupus antigen (La) ribonucleoprotein, avoiding cytoplasmic RNA sensors. However, in coculture experiments we observed that latent-infected cells trigger antiviral immunity in dendritic cells (DCs) through selective release and transfer of RNA via exosomes. In ex vivo tonsillar cultures, we observed that EBER1-loaded exosomes are preferentially captured and internalized by human plasmacytoid DCs (pDCs) that express the TIM1 phosphatidylserine receptor, a known viral- and exosomal target. Using an EBER-deficient EBV strain, enzymatic removal of 5'ppp, in vitro transcripts, and coculture experiments, we established that 5'pppEBER1 transfer via exosomes drives antiviral immunity in nonpermissive DCs. Lupus erythematosus patients suffer from elevated EBV load and activated antiviral immunity, in particular in skin lesions that are infiltrated with pDCs. We detected high levels of EBER1 RNA in such skin lesions, as well as EBV-microRNAs, but no intact EBV-DNA, linking non-cell-autonomous EBER1 presence with skin inflammation in predisposed individuals. Collectively, our studies indicate that virus-modified exosomes have a physiological role in the host-pathogen stand-off and may promote inflammatory disease.
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204
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Wei Y, Xu J, Zhang W, Wen Z, Liu F. RNA polymerase III component Rpc9 regulates hematopoietic stem and progenitor cell maintenance in zebrafish. Development 2016; 143:2103-10. [DOI: 10.1242/dev.126797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 04/25/2016] [Indexed: 12/18/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are capable of self-renewal and replenishing all lineages of blood cells throughout the lifetime and thus critical for tissue homeostasis. However, the mechanism regulating HSPC development is still incompletely understood. Here, we isolate a zebrafish mutant with defective T lymphopoiesis and positional cloning identifies that Rpc9, a component of DNA-directed RNA polymerase III (Pol III) complex, is responsible for the mutant phenotype. Further analysis shows that rpc9-deficiency leads to the impairment of HSPCs and their derivatives in zebrafish embryos. Excessive apoptosis is observed in the caudal hematopoietic tissue (CHT, the equivalent of fetal liver in mammals) of rpc9−/− embryos and the hematopoietic defects in rpc9−/− embryos can be fully rescued by suppression of p53. Thus, our work illustrate that Rpc9, a component of Pol III, plays an important tissue-specific role in HSPC maintenance during zebrafish embryogenesis and that it might be conserved across vertebrates including mammals.
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Affiliation(s)
- Yonglong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Xu
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Wenqing Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, China
| | - Zilong Wen
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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205
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Chen X, Fan S, Song E. Noncoding RNAs: New Players in Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:1-47. [PMID: 27376730 DOI: 10.1007/978-981-10-1498-7_1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The world of noncoding RNAs (ncRNAs) has gained widespread attention in recent years due to their novel and crucial potency of biological regulation. Noncoding RNAs play essential regulatory roles in a broad range of developmental processes and diseases, notably human cancers. Regulatory ncRNAs represent multiple levels of structurally and functionally distinct RNAs, including the best-known microRNAs (miRNAs), the complicated long ncRNAs (lncRNAs), and the newly identified circular RNAs (circRNAs). However, the mechanisms by which they act remain elusive. In this chapter, we will review the current knowledge of the ncRNA field, discussing the genomic context, biological functions, and mechanisms of action of miRNAs, lncRNAs, and circRNAs. We also highlight the implications of the biogenesis and gene expression dysregulation of different ncRNA subtypes in the initiation and development of human malignancies.
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Affiliation(s)
- Xueman Chen
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China
| | - Siting Fan
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China
| | - Erwei Song
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, China.
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206
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Lo PK, Wolfson B, Zhou X, Duru N, Gernapudi R, Zhou Q. Noncoding RNAs in breast cancer. Brief Funct Genomics 2015; 15:200-21. [PMID: 26685283 DOI: 10.1093/bfgp/elv055] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mammalian transcriptome has recently been revealed to encompass a large number of noncoding RNAs (ncRNAs) that play a variety of important regulatory roles in gene expression and other biological processes. MicroRNAs (miRNAs), the best studied of the short noncoding RNAs (sncRNAs), have been extensively characterized with regard to their biogenesis, function and importance in tumorigenesis. Another class of sncRNAs called piwi-interacting RNAs (piRNAs) has also gained attention recently in cancer research owing to their critical role in stem cell regulation. Long noncoding RNAs (lncRNAs) of >200 nucleotides in length have recently emerged as key regulators of developmental processes, including mammary gland development. lncRNA dysregulation has also been implicated in the development of various cancers, including breast cancer. In this review, we describe and discuss the roles of sncRNAs (including miRNAs and piRNAs) and lncRNAs in the initiation and progression of breast tumorigenesis, with a focus on outlining the molecular mechanisms of oncogenic and tumor-suppressor ncRNAs. Moreover, the current and potential future applications of ncRNAs to clinical breast cancer research are also discussed, with an emphasis on ncRNA-based diagnosis, prognosis and future therapeutics.
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207
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Molla-Herman A, Vallés AM, Ganem-Elbaz C, Antoniewski C, Huynh JR. tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription. EMBO J 2015; 34:3009-27. [PMID: 26471728 PMCID: PMC4687792 DOI: 10.15252/embj.201591006] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 09/01/2015] [Accepted: 09/04/2015] [Indexed: 02/01/2023] Open
Abstract
RNase P is a conserved endonuclease that processes the 5' trailer of tRNA precursors. We have isolated mutations in Rpp30, a subunit of RNase P, and find that these induce complete sterility in Drosophila females. Here, we show that sterility is not due to a shortage of mature tRNAs, but that atrophied ovaries result from the activation of several DNA damage checkpoint proteins, including p53, Claspin, and Chk2. Indeed, we find that tRNA processing defects lead to increased replication stress and de-repression of transposable elements in mutant ovaries. We also report that transcription of major piRNA sources collapse in mutant germ cells and that this correlates with a decrease in heterochromatic H3K9me3 marks on the corresponding piRNA-producing loci. Our data thus link tRNA processing, DNA replication, and genome defense by small RNAs. This unexpected connection reveals constraints that could shape genome organization during evolution.
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Affiliation(s)
- Anahi Molla-Herman
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Ana Maria Vallés
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Carine Ganem-Elbaz
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Christophe Antoniewski
- GED, UPMC, CNRS UMR 7622, IBPS, Developmental Biology Laboratory (IBPS-LBD), Paris, France
| | - Jean-René Huynh
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
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208
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Carpenter S. Editorial: Functions of Non-Coding RNA in Innate Immunity. Front Immunol 2015; 6:622. [PMID: 26697016 PMCID: PMC4677271 DOI: 10.3389/fimmu.2015.00622] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/30/2015] [Indexed: 01/18/2023] Open
Affiliation(s)
- Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz , Santa Cruz, CA , USA
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209
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Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S, Kosinski J, Hagen WJH, Sachse C, Müller CW. Molecular structures of unbound and transcribing RNA polymerase III. Nature 2015; 528:231-6. [PMID: 26605533 PMCID: PMC4681132 DOI: 10.1038/nature16143] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022]
Abstract
Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. Here we present the cryo-electron microscopy structures of the Saccharomyces cerevisiae Pol III elongating complex at 3.9 Å resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 Å resolution, respectively, which allow the building of a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82-C34-C31 heterotrimer in close proximity to the stalk. The C53-C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets.
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Affiliation(s)
- Niklas A. Hoffmann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Arjen J. Jakobi
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestr. 85, 22607 Hamburg, Germany
| | - Maria Moreno-Morcillo
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sebastian Glatt
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Wim J. H. Hagen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence and requests for materials should be addressed to C.S. () or C.W.M. ()
| | - Christoph W. Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence and requests for materials should be addressed to C.S. () or C.W.M. ()
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210
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Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics. Cancers (Basel) 2015; 7:2217-35. [PMID: 26569308 PMCID: PMC4695887 DOI: 10.3390/cancers7040887] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 01/08/2023] Open
Abstract
Oncoviruses cause tremendous global cancer burden. For several DNA tumor viruses, human genome integration is consistently associated with cancer development. However, genomic features associated with tumor viral integration are poorly understood. We sought to define genomic determinants for 1897 loci prone to hosting human papillomavirus (HPV), hepatitis B virus (HBV) or Merkel cell polyomavirus (MCPyV). These were compared to HIV, whose enzyme-mediated integration is well understood. A comprehensive catalog of integration sites was constructed from the literature and experimentally-determined HPV integration sites. Features were scored in eight categories (genes, expression, open chromatin, histone modifications, methylation, protein binding, chromatin segmentation and repeats) and compared to random loci. Random forest models determined loci classification and feature selection. HPV and HBV integrants were not fragile site associated. MCPyV preferred integration near sensory perception genes. Unique signatures of integration-associated predictive genomic features were detected. Importantly, repeats, actively-transcribed regions and histone modifications were common tumor viral integration signatures.
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211
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Dumay-Odelot H, Durrieu-Gaillard S, El Ayoubi L, Parrot C, Teichmann M. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription. Transcription 2015; 5:e27526. [PMID: 25764111 DOI: 10.4161/trns.27526] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcription factors and to the definition of minimal promoter sequences for human RNA polymerase III transcription.
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Affiliation(s)
- Hélène Dumay-Odelot
- a INSERM U869; University of Bordeaux; Institut Européen de Chimie et Biologie (IECB); 33607 Pessac, France
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212
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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213
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Kinnersley B, Labussière M, Holroyd A, Di Stefano AL, Broderick P, Vijayakrishnan J, Mokhtari K, Delattre JY, Gousias K, Schramm J, Schoemaker MJ, Fleming SJ, Herms S, Heilmann S, Schreiber S, Wichmann HE, Nöthen MM, Swerdlow A, Lathrop M, Simon M, Bondy M, Sanson M, Houlston RS. Genome-wide association study identifies multiple susceptibility loci for glioma. Nat Commun 2015; 6:8559. [PMID: 26424050 PMCID: PMC4600760 DOI: 10.1038/ncomms9559] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/04/2015] [Indexed: 12/25/2022] Open
Abstract
Previous genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of glioma. To identify new glioma susceptibility loci, we conducted a meta-analysis of four GWAS (totalling 4,147 cases and 7,435 controls), with imputation using 1000 Genomes and UK10K Project data as reference. After genotyping an additional 1,490 cases and 1,723 controls we identify new risk loci for glioblastoma (GBM) at 12q23.33 (rs3851634, near POLR3B, P=3.02 × 10(-9)) and non-GBM at 10q25.2 (rs11196067, near VTI1A, P=4.32 × 10(-8)), 11q23.2 (rs648044, near ZBTB16, P=6.26 × 10(-11)), 12q21.2 (rs12230172, P=7.53 × 10(-11)) and 15q24.2 (rs1801591, near ETFA, P=5.71 × 10(-9)). Our findings provide further insights into the genetic basis of the different glioma subtypes.
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Affiliation(s)
- Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Marianne Labussière
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Anna-Luisa Di Stefano
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Service de Neurologie 2, F-75013 Paris, France
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Jayaram Vijayakrishnan
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Karima Mokhtari
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Laboratoire de neuropathologie R Escourolle, F-75013 Paris, France
| | - Jean-Yves Delattre
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Service de Neurologie 2, F-75013 Paris, France
| | - Konstantinos Gousias
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Straße 25, 53105 Bonn, Germany
| | - Johannes Schramm
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Straße 25, 53105 Bonn, Germany
| | - Minouk J. Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Sarah J. Fleming
- Centre for Epidemiology and Biostatistics, Faculty of Medicine and Health, University of Leeds, Leeds LS2 9JT, UK
| | - Stefan Herms
- Department of Biomedicine, Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
| | - Stefanie Heilmann
- Department of Biomedicine, Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Stefan Schreiber
- 1st Medical Department, University Clinic Schleswig-Holstein, Campus Kiel, House 6, Arnold-Heller-Straße 3, Kiel 24105, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Arnold-Heller-Straße 3, Kiel 24105, Germany
| | - Heinz-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Markus M. Nöthen
- Department of Biomedicine, Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Mark Lathrop
- AP-HP, GH Pitié-Salpêtrière, Laboratoire de neuropathologie R Escourolle, F-75013 Paris, France
- Foundation Jean Dausset-CEPH, 27 Rue Juliette Dodu, 75010 Paris, France
- Génome Québec, Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 0G1
| | - Matthias Simon
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Straße 25, 53105 Bonn, Germany
| | - Melissa Bondy
- Division of Hematology-Oncology, Department of Pediatrics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marc Sanson
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, F-75013 Paris, France
- Onconeurotek, F-75013 Paris, France
- AP-HP, GH Pitié-Salpêtrière, Service de Neurologie 2, F-75013 Paris, France
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
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214
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Ibeagha-Awemu EM, Zhao X. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet 2015; 6:302. [PMID: 26442116 PMCID: PMC4585011 DOI: 10.3389/fgene.2015.00302] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/11/2015] [Indexed: 12/30/2022] Open
Abstract
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.
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Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food CanadaSherbrooke, QC, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-BellevueQC, Canada
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215
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Boissier F, Dumay-Odelot H, Teichmann M, Fribourg S. Structural analysis of human RPC32β-RPC62 complex. J Struct Biol 2015; 192:313-319. [PMID: 26394183 DOI: 10.1016/j.jsb.2015.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 01/22/2023]
Abstract
Transcription initiation by eukaryotic RNA polymerase (Pol) III relies on the subcomplex RPC62/RPC39/RPC32. Two distinct isoforms of RPC32 are encoded in the human genome. RPC32α expression is highly regulated and found only in stem cells and transformed cells, whereas RPC32β is ubiquitously expressed in tissues. Here we identify a core-interacting domain of RPC32 sufficient for the interaction with RPC62. We present the crystal structure of a complex of RPC62 and the RPC32β core domain. RPC32β associates with the extended winged helix 1 and 2 and the coiled coil domain of RPC62 qualifying RPC32 as a molecular bridge in between RPC62 domains. The RPC62-RPC32 complex fit into EM data suggests a bi-functional role for RPC32 through interactions with the largest Pol III subunit and through solvent exposed residues. RPC32 positioning into Pol III suggests that subunit-specific contacts at the surface of the Pol III holoenzyme are critical for its function.
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Affiliation(s)
- Fanny Boissier
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; Institut National de la Santé Et de la Recherche Médicale, INSERM - U869, ARNA Laboratory, F-33000 Bordeaux, France
| | - Hélène Dumay-Odelot
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; INSERM, U869, ARNA Laboratory, Equipe Labellisée Contre le Cancer, F-33076 Bordeaux, France
| | - Martin Teichmann
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; INSERM, U869, ARNA Laboratory, Equipe Labellisée Contre le Cancer, F-33076 Bordeaux, France
| | - Sébastien Fribourg
- Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA Laboratory, F-33607 Pessac, France; Institut National de la Santé Et de la Recherche Médicale, INSERM - U869, ARNA Laboratory, F-33000 Bordeaux, France.
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216
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BRF1, a subunit of RNA polymerase III transcription factor TFIIIB, is essential for cell growth of Trypanosoma brucei. Parasitology 2015; 142:1563-73. [PMID: 26337955 DOI: 10.1017/s0031182015001122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RNA polymerase III (Pol III) synthesizes small RNA molecules that are essential for cell viability. Accurate initiation of transcription by Pol III requires general transcription factor TFIIIB, which is composed of three subunits: TFIIB-related factor BRF1, TATA-binding protein and BDP1. Here we report the molecular characterization of BRF1 in Trypanosoma brucei (TbBRF1), a parasitic protozoa that shows distinctive transcription characteristics. In silico analysis allowed the detection in TbBRF1 of the three conserved domains located in the N-terminal region of all BRF1 orthologues, namely a zinc ribbon motif and two cyclin repeats. Homology modelling suggested that, similarly to other BRF1 and TFIIB proteins, the TbBRF1 cyclin repeats show the characteristic structure of five α-helices per repeat, connected by a short random-coiled linker. As expected for a transcription factor, TbBRF1 was localized in the nucleus. Knock-down of TbBRF1 by RNA interference (RNAi) showed that this protein is essential for the viability of procyclic forms of T. brucei, since ablation of TbBRF1 led to growth arrest of the parasites. Nuclear run-on and quantitative real-time PCR analyses demonstrated that transcription of all the Pol III-dependent genes analysed was reduced, at different levels, after RNAi induction.
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217
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Srivastava R, Ahn SH. Modifications of RNA polymerase II CTD: Connections to the histone code and cellular function. Biotechnol Adv 2015; 33:856-72. [PMID: 26241863 DOI: 10.1016/j.biotechadv.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/08/2015] [Accepted: 07/28/2015] [Indexed: 12/24/2022]
Abstract
At the onset of transcription, many protein machineries interpret the cellular signals that regulate gene expression. These complex signals are mostly transmitted to the indispensable primary proteins involved in transcription, RNA polymerase II (RNAPII) and histones. RNAPII and histones are so well coordinated in this cellular function that each cellular signal is precisely allocated to specific machinery depending on the stage of transcription. The carboxy-terminal domain (CTD) of RNAPII in eukaryotes undergoes extensive posttranslational modification, called the 'CTD code', that is indispensable for coupling transcription with many cellular processes, including mRNA processing. The posttranslational modification of histones, known as the 'histone code', is also critical for gene transcription through the reversible and dynamic remodeling of chromatin structure. Notably, the histone code is closely linked with the CTD code, and their combinatorial effects enable the delicate regulation of gene transcription. This review elucidates recent findings regarding the CTD modifications of RNAPII and their coordination with the histone code, providing integrative pathways for the fine-tuned regulation of gene expression and cellular function.
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Affiliation(s)
- Rakesh Srivastava
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Seong Hoon Ahn
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea.
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218
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Burke JM, Kuny CV, Kincaid RP, Sullivan CS. Identification, validation, and characterization of noncanonical miRNAs. Methods 2015. [PMID: 26210399 DOI: 10.1016/j.ymeth.2015.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Many eukaryotes and some viruses encode microRNAs (miRNAs), small RNAs that post-transcriptionally regulate gene expression. While most miRNAs are generated through the activity of RNA Polymerase II (RNAP II) and subsequent processing by Drosha and Dicer, some viral miRNAs utilize alternative pathways of biogenesis. Some members of the herpesvirus and retrovirus families can direct synthesis of miRNAs through RNAP III transcription rather than RNAP II and can utilize atypical enzymes to generate miRNAs. Though the advantages of alternative miRNA biogenesis remain unclear for herpesviruses, the retroviral miRNA biogenesis routes allow the RNAP II transcribed retroviral genome to escape Drosha cleavage while still expressing abundant, biologically-active miRNAs. These RNAP III-derived miRNAs have unique characteristics that allow for their identification and characterization. In this article, we describe procedures to predict, validate, and characterize RNAP III-transcribed miRNAs and other small RNAs, while providing resources that are also useful for canonical miRNAs.
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Affiliation(s)
- James M Burke
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States
| | - Chad V Kuny
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States
| | - Rodney P Kincaid
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States
| | - Christopher S Sullivan
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Dept. Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, United States.
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219
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A Region of Bdp1 Necessary for Transcription Initiation That Is Located within the RNA Polymerase III Active Site Cleft. Mol Cell Biol 2015; 35:2831-40. [PMID: 26055328 DOI: 10.1128/mcb.00263-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/01/2015] [Indexed: 02/02/2023] Open
Abstract
The RNA polymerase III (Pol III)-specific transcription factor Bdp1 is crucial to Pol III recruitment and promoter opening in transcription initiation, yet structural information is sparse. To examine its protein-binding targets within the preinitiation complex at the residue level, photoreactive amino acids were introduced into Saccharomyces cerevisiae Bdp1. Mutations within the highly conserved SANT domain cross-linked to the transcription factor IIB (TFIIB)-related transcription factor Brf1, consistent with the findings of previous studies. In addition, we identified an essential N-terminal region that cross-linked with the Pol III catalytic subunit C128 as well as Brf1. Closer examination revealed that this region interacted with the C128 N-terminal region, the N-terminal half of Brf1, and the C-terminal domain of the C37 subunit, together positioning this region within the active site cleft of the preinitiation complex. With our functional data, our analyses identified an essential region of Bdp1 that is positioned within the active site cleft of Pol III and necessary for transcription initiation.
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220
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Endocrine Aspects of 4H Leukodystrophy: A Case Report and Review of the Literature. Case Rep Endocrinol 2015; 2015:314594. [PMID: 26113998 PMCID: PMC4465690 DOI: 10.1155/2015/314594] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/18/2015] [Indexed: 11/22/2022] Open
Abstract
Introduction. 4H leukodystrophy is an autosomal recessive RNA polymerase III-related leukodystrophy, characterized by hypomyelination, with or without hypodontia (or other dental abnormalities) and hypogonadotropic hypogonadism. Case Presentation. We describe a 28-year-old female who presented with primary amenorrhea at the age of 19. She had a history of very mild neurological and dental abnormalities. She was found to have hypogonadotropic hypogonadism, and magnetic resonance imaging of the brain showed hypomyelination. The diagnosis of 4H leukodystrophy was made. She was subsequently found to have mutations in the POLR3B gene, which encodes the second largest subunit of RNA polymerase III. She wished to become pregnant and failed to respond to pulsatile GnRH but achieved normal follicular growth and ovulation with subcutaneous gonadotropin therapy. Discussion. Patients with 4H leukodystrophy may initially present with hypogonadotropic hypogonadism, particularly if neurological and dental manifestations are subtle. Making the diagnosis has important implications for prognosis and management. Progressive neurologic deterioration is expected, and progressive endocrine dysfunction may occur. Patients with 4H leukodystrophy should be counseled about disease progression and about this disease's autosomal recessive inheritance pattern. In those who wish to conceive, ovulation induction may be achieved with subcutaneous gonadotropin therapy, but pulsatile GnRH does not appear to be effective.
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221
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Gaiti F, Fernandez-Valverde SL, Nakanishi N, Calcino AD, Yanai I, Tanurdzic M, Degnan BM. Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity. Mol Biol Evol 2015; 32:2367-82. [PMID: 25976353 PMCID: PMC4540969 DOI: 10.1093/molbev/msv117] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire expansion and morphological complexity in vertebrate evolution. However, this claim has not been tested by examining morphologically simple animals. Here, we undertake a systematic investigation of lncRNAs in the demosponge Amphimedon queenslandica, a morphologically simple, early-branching metazoan. We combine RNA-Seq data across multiple developmental stages of Amphimedon with a filtering pipeline to conservatively predict 2,935 lncRNAs. These include intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, long intergenic nonprotein coding RNAs, and precursors for small RNAs. Sponge lncRNAs are remarkably similar to their bilaterian counterparts in being relatively short with few exons and having low primary sequence conservation relative to protein-coding genes. As in bilaterians, a majority of sponge lncRNAs exhibit typical hallmarks of regulatory molecules, including high temporal specificity and dynamic developmental expression. Specific lncRNA expression profiles correlate tightly with conserved protein-coding genes likely involved in a range of developmental and physiological processes, such as the Wnt signaling pathway. Although the majority of Amphimedon lncRNAs appears to be taxonomically restricted with no identifiable orthologs, we find a few cases of conservation between demosponges in lncRNAs that are antisense to coding sequences. Based on the high similarity in the structure, organization, and dynamic expression of sponge lncRNAs to their bilaterian counterparts, we propose that these noncoding RNAs are an ancient feature of the metazoan genome. These results are consistent with lncRNAs regulating the development of animals, regardless of their level of morphological complexity.
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Affiliation(s)
- Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | | | - Nagayasu Nakanishi
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Andrew D Calcino
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Itai Yanai
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Milos Tanurdzic
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
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222
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Ream TS, Haag JR, Pontvianne F, Nicora CD, Norbeck AD, Paša-Tolić L, Pikaard CS. Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit. Nucleic Acids Res 2015; 43:4163-78. [PMID: 25813043 PMCID: PMC4417161 DOI: 10.1093/nar/gkv247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 03/10/2015] [Indexed: 12/17/2022] Open
Abstract
Using affinity purification and mass spectrometry, we identified the subunits of Arabidopsis thaliana multisubunit RNA polymerases I and III (abbreviated as Pol I and Pol III), the first analysis of their physical compositions in plants. In all eukaryotes examined to date, AC40 and AC19 subunits are common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes. Surprisingly, A. thaliana and related species express two distinct AC40 paralogs, one of which assembles into Pol I and the other of which assembles into Pol III. Changes at eight amino acid positions correlate with the functional divergence of Pol I- and Pol III-specific AC40 paralogs. Two genes encode homologs of the yeast C53 subunit and either protein can assemble into Pol III. By contrast, only one of two potential C17 variants, and one of two potential C31 variants were detected in Pol III. We introduce a new nomenclature system for plant Pol I and Pol III subunits in which the 12 subunits that are structurally and functionally homologous among Pols I through V are assigned equivalent numbers.
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Affiliation(s)
- Thomas S Ream
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA
| | - Jeremy R Haag
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63130, USA Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Frederic Pontvianne
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Carrie D Nicora
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Angela D Norbeck
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Craig S Pikaard
- Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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223
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Xie K, Minkenberg B, Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Natl Acad Sci U S A 2015; 112:3570-5. [PMID: 25733849 PMCID: PMC4371917 DOI: 10.1073/pnas.1420294112] [Citation(s) in RCA: 866] [Impact Index Per Article: 96.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 nuclease (Cas9) system is being harnessed as a powerful tool for genome engineering in basic research, molecular therapy, and crop improvement. This system uses a small guide RNA (gRNA) to direct Cas9 endonuclease to a specific DNA site; thus, its targeting capability is largely constrained by the gRNA-expressing device. In this study, we developed a general strategy to produce numerous gRNAs from a single polycistronic gene. The endogenous tRNA-processing system, which precisely cleaves both ends of the tRNA precursor, was engineered as a simple and robust platform to boost the targeting and multiplex editing capability of the CRISPR/Cas9 system. We demonstrated that synthetic genes with tandemly arrayed tRNA-gRNA architecture were efficiently and precisely processed into gRNAs with desired 5' targeting sequences in vivo, which directed Cas9 to edit multiple chromosomal targets. Using this strategy, multiplex genome editing and chromosomal-fragment deletion were readily achieved in stable transgenic rice plants with a high efficiency (up to 100%). Because tRNA and its processing system are virtually conserved in all living organisms, this method could be broadly used to boost the targeting capability and editing efficiency of CRISPR/Cas9 toolkits.
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Affiliation(s)
- Kabin Xie
- Department of Plant Pathology and Environmental Microbiology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Bastian Minkenberg
- Department of Plant Pathology and Environmental Microbiology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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224
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Jalali S, Kapoor S, Sivadas A, Bhartiya D, Scaria V. Computational approaches towards understanding human long non-coding RNA biology. Bioinformatics 2015; 31:2241-51. [DOI: 10.1093/bioinformatics/btv148] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 03/10/2015] [Indexed: 12/18/2022] Open
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225
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Kadakkuzha BM, Liu XA, McCrate J, Shankar G, Rizzo V, Afinogenova A, Young B, Fallahi M, Carvalloza AC, Raveendra B, Puthanveettil SV. Transcriptome analyses of adult mouse brain reveal enrichment of lncRNAs in specific brain regions and neuronal populations. Front Cell Neurosci 2015; 9:63. [PMID: 25798087 PMCID: PMC4351618 DOI: 10.3389/fncel.2015.00063] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/10/2015] [Indexed: 11/13/2022] Open
Abstract
Despite the importance of the long non-coding RNAs (lncRNAs) in regulating biological functions, the expression profiles of lncRNAs in the sub-regions of the mammalian brain and neuronal populations remain largely uncharacterized. By analyzing RNASeq datasets, we demonstrate region specific enrichment of populations of lncRNAs and mRNAs in the mouse hippocampus and pre-frontal cortex (PFC), the two major regions of the brain involved in memory storage and neuropsychiatric disorders. We identified 2759 lncRNAs and 17,859 mRNAs in the hippocampus and 2561 lncRNAs and 17,464 mRNAs expressed in the PFC. The lncRNAs identified correspond to ~14% of the transcriptome of the hippocampus and PFC and ~70% of the lncRNAs annotated in the mouse genome (NCBIM37) and are localized along the chromosomes as varying numbers of clusters. Importantly, we also found that a few of the tested lncRNA-mRNA pairs that share a genomic locus display specific co-expression in a region-specific manner. Furthermore, we find that sub-regions of the brain and specific neuronal populations have characteristic lncRNA expression signatures. These results reveal an unexpected complexity of the lncRNA expression in the mouse brain.
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Affiliation(s)
- Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Xin-An Liu
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Jennifer McCrate
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Gautam Shankar
- Informatics Core, The Scripps Research Institute Jupiter, FL, USA
| | - Valerio Rizzo
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Alina Afinogenova
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Brandon Young
- Genomics Core, The Scripps Research Institute Jupiter, FL, USA
| | - Mohammad Fallahi
- Informatics Core, The Scripps Research Institute Jupiter, FL, USA
| | | | - Bindu Raveendra
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
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226
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Roy AL, Singer DS. Core promoters in transcription: old problem, new insights. Trends Biochem Sci 2015; 40:165-71. [PMID: 25680757 DOI: 10.1016/j.tibs.2015.01.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 12/11/2022]
Abstract
Early studies established that transcription initiates within an approximately 50 bp DNA segment capable of nucleating the assembly of RNA polymerase II (Pol II) and associated general transcription factors (GTFs) necessary for transcriptional initiation; this region is called a core promoter. Subsequent analyses identified a series of conserved DNA sequence elements, present in various combinations or not at all, in core promoters. Recent genome-wide analyses have provided further insights into the complexity of core promoter architecture and function. Here we review recent studies that delineate the active role of core promoters in the transcriptional regulation of diverse physiological systems.
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Affiliation(s)
- Ananda L Roy
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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227
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Zhong Q, Shi G, Zhang Y, Lu L, Levy D, Zhong S. Alteration of BRCA1 expression affects alcohol-induced transcription of RNA Pol III-dependent genes. Gene 2015; 556:74-9. [PMID: 25447904 PMCID: PMC4272617 DOI: 10.1016/j.gene.2014.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 02/05/2023]
Abstract
Emerging evidence has indicated that alcohol consumption is an established risk factor for breast cancer. Deregulation of RNA polymerase III (Pol III) transcription enhances cellular Pol III gene production, leading to an increase in translational capacity to promote cell transformation and tumor formation. We have reported that alcohol intake increases Pol III gene transcription to promote cell transformation and tumor formation in vitro and in vivo. Studies revealed that tumor suppressors, pRb, p53, PTEN and Maf1 repress the transcription of Pol III genes. BRCA1 is a tumor suppressor and its mutation is tightly related to breast cancer development. However, it is not clear whether BRCA1 expression affects alcohol-induced transcription of Pol III genes. At the present studies, we report that restoring BRCA1 in HCC 1937 cells, which is a BRCA1 deficient cell line, represses Pol III gene transcription. Expressing mutant or truncated BRCA1 in these cells does not affect the ability of repression on Pol III genes. Our analysis has demonstrated that alcohol induces Pol III gene transcription. More importantly, overexpression of BRCA1 in estrogen receptor positive (ER+) breast cancer cells (MCF-7) decreases the induction of tRNA(Leu) and 5S rRNA genes by alcohol, whereas reduction of BRCA1 by its siRNA slightly increases the transcription of the class of genes. This suggests that BRCA1 is associated with alcohol-induced deregulation of Pol III genes. These studies for the first time demonstrate the role of BRCA1 in induction of Pol III genes by alcohol and uncover a novel mechanism of alcohol-associated breast cancer.
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Affiliation(s)
- Qian Zhong
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, China
| | - Ganggang Shi
- Shantou University Medical College, Shantou, Guangdong, China
| | - Yanmei Zhang
- Shantou University Medical College, Shantou, Guangdong, China
| | - Lei Lu
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel Levy
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shuping Zhong
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Shantou University Medical College, Shantou, Guangdong, China.
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228
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Longo MS, Brown JD, Zhang C, O'Neill MJ, O'Neill RJ. Identification of a recently active mammalian SINE derived from ribosomal RNA. Genome Biol Evol 2015; 7:775-88. [PMID: 25637222 PMCID: PMC4994717 DOI: 10.1093/gbe/evv015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Complex eukaryotic genomes are riddled with repeated sequences whose derivation does not coincide with phylogenetic history and thus is often unknown. Among such sequences, the capacity for transcriptional activity coupled with the adaptive use of reverse transcription can lead to a diverse group of genomic elements across taxa, otherwise known as selfish elements or mobile elements. Short interspersed nuclear elements (SINEs) are nonautonomous mobile elements found in eukaryotic genomes, typically derived from cellular RNAs such as tRNAs, 7SL or 5S rRNA. Here, we identify and characterize a previously unknown SINE derived from the 3'-end of the large ribosomal subunit (LSU or 28S rDNA) and transcribed via RNA polymerase III. This new element, SINE28, is represented in low-copy numbers in the human reference genome assembly, wherein we have identified 27 discrete loci. Phylogenetic analysis indicates these elements have been transpositionally active within primate lineages as recently as 6 MYA while modern humans still carry transcriptionally active copies. Moreover, we have identified SINE28s in all currently available assembled mammalian genome sequences. Phylogenetic comparisons indicate that these elements are frequently rederived from the highly conserved LSU rRNA sequences in a lineage-specific manner. We propose that this element has not been previously recognized as a SINE given its high identity to the canonical LSU, and that SINE28 likely represents one of possibly many unidentified, active transposable elements within mammalian genomes.
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Affiliation(s)
- Mark S Longo
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
| | - Judy D Brown
- Department of Allied Health Sciences and Institute for Systems Genomics, University of Connecticut
| | - Chu Zhang
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
| | - Michael J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
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Koo CX, Kobiyama K, Shen YJ, LeBert N, Ahmad S, Khatoo M, Aoshi T, Gasser S, Ishii KJ. RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression. J Biol Chem 2015; 290:7463-73. [PMID: 25623070 PMCID: PMC4367256 DOI: 10.1074/jbc.m115.636365] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RNA:DNA hybrids form in the nuclei and mitochondria of cells as transcription-induced R-loops or G-quadruplexes, but exist only in the cytosol of virus-infected cells. Little is known about the existence of RNA:DNA hybrids in the cytosol of virus-free cells, in particular cancer or transformed cells. Here, we show that cytosolic RNA:DNA hybrids are present in various human cell lines, including transformed cells. Inhibition of RNA polymerase III (Pol III), but not DNA polymerase, abrogated cytosolic RNA:DNA hybrids. Cytosolic RNA:DNA hybrids bind to several components of the microRNA (miRNA) machinery-related proteins, including AGO2 and DDX17. Furthermore, we identified miRNAs that are specifically regulated by Pol III, providing a potential link between RNA:DNA hybrids and the miRNA machinery. One of the target genes, exportin-1, is shown to regulate cytosolic RNA:DNA hybrids. Taken together, we reveal previously unknown mechanism by which Pol III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells.
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Affiliation(s)
- Christine Xing'er Koo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, the Laboratory of Adjuvant Innovation and
| | - Kouji Kobiyama
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yu J Shen
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Nina LeBert
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Shandar Ahmad
- the Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), Ibaraki, Osaka 567-0085, Japan, and
| | - Muznah Khatoo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Taiki Aoshi
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Stephan Gasser
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456,
| | - Ken J Ishii
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
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230
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Sohi G, Dilworth FJ. Noncoding RNAs as epigenetic mediators of skeletal muscle regeneration. FEBS J 2015; 282:1630-46. [PMID: 25483175 DOI: 10.1111/febs.13170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 12/16/2022]
Abstract
Skeletal muscle regeneration is a well-characterized biological process in which resident adult stem cells must undertake a series of cell-fate decisions to ensure efficient repair of the damaged muscle fibers while also maintaining the stem cell niche. Satellite cells, the main stem cell contributing to the repaired muscle fiber, are maintained in a quiescent state in healthy muscle. Upon injury, the satellite cells become activated, and proliferate to expand the muscle progenitor cell population before returning to the quiescent state or differentiating to become myofibers. Importantly, the determination of cell fate is controlled at the epigenetic level in response to environmental cues. In this review, we discuss our current understanding of the role played by noncoding RNAs (both miRNAs and long-noncoding RNAs) in the epigenetic control of muscle regeneration.
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Affiliation(s)
- Gurjeev Sohi
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Canada
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231
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Basak J, Nithin C. Targeting Non-Coding RNAs in Plants with the CRISPR-Cas Technology is a Challenge yet Worth Accepting. FRONTIERS IN PLANT SCIENCE 2015; 6:1001. [PMID: 26635829 PMCID: PMC4652605 DOI: 10.3389/fpls.2015.01001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/30/2015] [Indexed: 05/02/2023]
Abstract
Non-coding RNAs (ncRNAs) have emerged as versatile master regulator of biological functions in recent years. MicroRNAs (miRNAs) are small endogenous ncRNAs of 18-24 nucleotides in length that originates from long self-complementary precursors. Besides their direct involvement in developmental processes, plant miRNAs play key roles in gene regulatory networks and varied biological processes. Alternatively, long ncRNAs (lncRNAs) are a large and diverse class of transcribed ncRNAs whose length exceed that of 200 nucleotides. Plant lncRNAs are transcribed by different RNA polymerases, showing diverse structural features. Plant lncRNAs also are important regulators of gene expression in diverse biological processes. There has been a breakthrough in the technology of genome editing, the CRISPR-Cas9 (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9) technology, in the last decade. CRISPR loci are transcribed into ncRNA and eventually form a functional complex with Cas9 and further guide the complex to cleave complementary invading DNA. The CRISPR-Cas technology has been successfully applied in model plants such as Arabidopsis and tobacco and important crops like wheat, maize, and rice. However, all these studies are focused on protein coding genes. Information about targeting non-coding genes is scarce. Hitherto, the CRISPR-Cas technology has been exclusively used in vertebrate systems to engineer miRNA/lncRNAs, but it is still relatively unexplored in plants. While briefing miRNAs, lncRNAs and applications of the CRISPR-Cas technology in human and animals, this review essentially elaborates several strategies to overcome the challenges of applying the CRISPR-Cas technology in editing ncRNAs in plants and the future perspective of this field.
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Affiliation(s)
- Jolly Basak
- Department of Biotechnology, Visva-Bharati UniversitySantiniketan, India
- *Correspondence: Jolly Basak,
| | - Chandran Nithin
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology KharagpurKharagpur, India
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232
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Burke JM, Bass CR, Kincaid RP, Sullivan CS. Identification of tri-phosphatase activity in the biogenesis of retroviral microRNAs and RNAP III-generated shRNAs. Nucleic Acids Res 2014; 42:13949-62. [PMID: 25428356 PMCID: PMC4267658 DOI: 10.1093/nar/gku1247] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Transcripts possessing a 5'-triphosphate are a hallmark of viral transcription and can trigger the host antiviral response. 5'-triphosphates are also found on common host transcripts transcribed by RNA polymerase III (RNAP III), yet how these transcripts remain non-immunostimulatory is incompletely understood. Most microRNAs (miRNAs) are 5'-monophosphorylated as a result of sequential endonucleolytic processing by Drosha and Dicer from longer RNA polymerase II (RNAP II)-transcribed primary transcripts. In contrast, bovine leukemia virus (BLV) expresses subgenomic RNAP III transcripts that give rise to miRNAs independent of Drosha processing. Here, we demonstrate that each BLV pre-miRNA is directly transcribed by RNAP III from individual, compact RNAP III type II genes. Thus, similar to manmade RNAP III-generated short hairpin RNAs (shRNAs), the BLV pre-miRNAs are initially 5'-triphosphorylated. Nonetheless, the derivative 5p miRNAs and shRNA-generated 5p small RNAs (sRNAs) possess a 5'-monophosphate. Our enzymatic characterization and small RNA sequencing data demonstrate that BLV 5p miRNAs are co-terminal with 5'-triphosphorylated miRNA precursors (pre-miRNAs). Thus, these results identify a 5'-tri-phosphatase activity that is involved in the biogenesis of BLV miRNAs and shRNA-generated sRNAs. This work advances our understanding of retroviral miRNA and shRNA biogenesis and may have implications regarding the immunostimulatory capacity of RNAP III transcripts.
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Affiliation(s)
- James M Burke
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department of Molecular Biosciences, 1 University Station A5000, Austin TX 78712-0162, USA
| | - Clovis R Bass
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department of Molecular Biosciences, 1 University Station A5000, Austin TX 78712-0162, USA
| | - Rodney P Kincaid
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department of Molecular Biosciences, 1 University Station A5000, Austin TX 78712-0162, USA
| | - Christopher S Sullivan
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department of Molecular Biosciences, 1 University Station A5000, Austin TX 78712-0162, USA
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233
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Fritah S, Niclou SP, Azuaje F. Databases for lncRNAs: a comparative evaluation of emerging tools. RNA (NEW YORK, N.Y.) 2014; 20:1655-65. [PMID: 25323317 PMCID: PMC4201818 DOI: 10.1261/rna.044040.113] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 07/28/2014] [Indexed: 05/26/2023]
Abstract
The vast majority of the human transcriptome does not code for proteins. Advances in transcriptome arrays and deep sequencing are giving rise to a fast accumulation of large data sets, particularly of long noncoding RNAs (lncRNAs). Although it is clear that individual lncRNAs may play important and diverse biological roles, there is a large gap between the number of existing lncRNAs and their known relation to molecular/cellular function. This and related information have recently been gathered in several databases dedicated to lncRNA research. Here, we review the content of general and more specialized databases on lncRNAs. We evaluate these resources in terms of the quality of annotations, the reporting of validated or predicted molecular associations, and their integration with other resources and computational analysis tools. We illustrate our findings using known and novel cancer-related lncRNAs. Finally, we discuss limitations and highlight potential future directions for these databases to help delineating functions associated with lncRNAs.
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Affiliation(s)
- Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public de la Santé (CRP-Santé), Luxembourg L-1526, Luxembourg
| | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public de la Santé (CRP-Santé), Luxembourg L-1526, Luxembourg
| | - Francisco Azuaje
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public de la Santé (CRP-Santé), Luxembourg L-1526, Luxembourg
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234
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Wang Q, Nowak CM, Korde A, Oh DH, Dassanayake M, Donze D. Compromised RNA polymerase III complex assembly leads to local alterations of intergenic RNA polymerase II transcription in Saccharomyces cerevisiae. BMC Biol 2014; 12:89. [PMID: 25348158 PMCID: PMC4228148 DOI: 10.1186/s12915-014-0089-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/17/2014] [Indexed: 12/26/2022] Open
Abstract
Background Assembled RNA polymerase III (Pol III) complexes exert local effects on chromatin processes, including influencing transcription of neighboring RNA polymerase II (Pol II) transcribed genes. These properties have been designated as ‘extra-transcriptional’ effects of the Pol III complex. Previous coding sequence microarray studies using Pol III factor mutants to determine global effects of Pol III complex assembly on Pol II promoter activity revealed only modest effects that did not correlate with the proximity of Pol III complex binding sites. Results Given our recent results demonstrating that tDNAs block progression of intergenic Pol II transcription, we hypothesized that extra-transcriptional effects within intergenic regions were not identified in the microarray study. To reconsider global impacts of Pol III complex binding, we used RNA sequencing to compare transcriptomes of wild type versus Pol III transcription factor TFIIIC depleted mutants. The results reveal altered intergenic Pol II transcription near TFIIIC binding sites in the mutant strains, where we observe readthrough of upstream transcripts that normally terminate near these sites, 5′- and 3′-extended transcripts, and de-repression of adjacent genes and intergenic regions. Conclusions The results suggest that effects of assembled Pol III complexes on transcription of neighboring Pol II promoters are of greater magnitude than previously appreciated, that such effects influence expression of adjacent genes at transcriptional start site and translational levels, and may explain a function of the conserved ETC sites in yeast. The results may also be relevant to synthetic biology efforts to design a minimal yeast genome. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0089-x) contains supplementary material, which is available to authorized users.
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235
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Blackwell BJ, Lopez MF, Wang J, Krastins B, Sarracino D, Tollervey JR, Dobke M, Jordan IK, Lunyak VV. Protein interactions with piALU RNA indicates putative participation of retroRNA in the cell cycle, DNA repair and chromatin assembly. Mob Genet Elements 2014; 2:26-35. [PMID: 22754750 PMCID: PMC3383447 DOI: 10.4161/mge.19032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Recent analyses suggest that transposable element-derived transcripts are processed to yield a variety of small RNA species that play critical functional roles in gene regulation and chromatin organization as well as genome stability and maintenance. Here we report a mass spectrometry analysis of an RNA-affinity complex isolation using a piRNA homologous sequence derived from Alu retrotransposal RNA. Our data point to potential roles for piALU RNAs in DNA repair, cell cycle and chromatin regulations.
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236
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Novel RNA markers in prostate cancer: functional considerations and clinical translation. BIOMED RESEARCH INTERNATIONAL 2014; 2014:765207. [PMID: 25250334 PMCID: PMC4163430 DOI: 10.1155/2014/765207] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 08/01/2014] [Accepted: 08/05/2014] [Indexed: 12/31/2022]
Abstract
The availability of ultra-high throughput DNA and RNA sequencing technologies in recent years has led to the identification of numerous novel transcripts, whose functions are unknown as yet. Evidence is accumulating that many of these molecules are deregulated in diseases, including prostate cancer, and potentially represent novel targets for diagnosis and therapy. In particular, functional genomic analysis of microRNA (miRNA) and long noncoding RNA (lncRNA) in cancer is likely to contribute insights into tumor development. Here, we compile recent efforts to catalog differential expression of miRNA and lncRNA in prostate cancer and to understand RNA function in tumor progression. We further highlight technologies for molecular characterization of noncoding RNAs and provide an overview of current activities to exploit them for the diagnosis and therapy of this complex tumor.
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237
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Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K. Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PLoS Genet 2014; 10:e1004496. [PMID: 25121733 PMCID: PMC4133162 DOI: 10.1371/journal.pgen.1004496] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/24/2014] [Indexed: 01/12/2023] Open
Abstract
Lichtheimia species are the second most important cause of mucormycosis in Europe. To provide broader insights into the molecular basis of the pathogenicity-associated traits of the basal Mucorales, we report the full genome sequence of L. corymbifera and compared it to the genome of Rhizopus oryzae, the most common cause of mucormycosis worldwide. The genome assembly encompasses 33.6 MB and 12,379 protein-coding genes. This study reveals four major differences of the L. corymbifera genome to R. oryzae: (i) the presence of an highly elevated number of gene duplications which are unlike R. oryzae not due to whole genome duplication (WGD), (ii) despite the relatively high incidence of introns, alternative splicing (AS) is not frequently observed for the generation of paralogs and in response to stress, (iii) the content of repetitive elements is strikingly low (<5%), (iv) L. corymbifera is typically haploid. Novel virulence factors were identified which may be involved in the regulation of the adaptation to iron-limitation, e.g. LCor01340.1 encoding a putative siderophore transporter and LCor00410.1 involved in the siderophore metabolism. Genes encoding the transcription factors LCor08192.1 and LCor01236.1, which are similar to GATA type regulators and to calcineurin regulated CRZ1, respectively, indicating an involvement of the calcineurin pathway in the adaption to iron limitation. Genes encoding MADS-box transcription factors are elevated up to 11 copies compared to the 1-4 copies usually found in other fungi. More findings are: (i) lower content of tRNAs, but unique codons in L. corymbifera, (ii) Over 25% of the proteins are apparently specific for L. corymbifera. (iii) L. corymbifera contains only 2/3 of the proteases (known to be essential virulence factors) in comparison to R. oryzae. On the other hand, the number of secreted proteases, however, is roughly twice as high as in R. oryzae.
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Affiliation(s)
- Volker U. Schwartze
- University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany
| | - Sascha Winter
- University of Jena, Department of Bioinformatics, Jena, Germany
| | - Ekaterina Shelest
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Systems Biology/Bioinformatics, Jena, Germany
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Fabian Horn
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Systems Biology/Bioinformatics, Jena, Germany
| | - Stefanie Wehner
- University of Jena, Department of Bioinformatics, Jena, Germany
| | - Jörg Linde
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Systems Biology/Bioinformatics, Jena, Germany
| | - Vito Valiante
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany
| | - Michael Sammeth
- Centre Nacional d'Anàlisi Genòmica (CNAG), Functional Bioinformatics, Barcelona, Spain
- Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | | | - Minou Nowrousian
- Ruhr University Bochum, Department of General and Molecular Botany, Bochum, Germany
| | - Kerstin Kaerger
- University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany
| | - Ilse D. Jacobsen
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Department of Microbial Immunology, Jena, Germany
| | - Manja Marz
- University of Jena, Department of Bioinformatics, Jena, Germany
| | - Axel A. Brakhage
- University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Kerstin Voigt
- University of Jena, Institute of Microbiology, Department of Microbiology and Molecular Biology, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Hans Knöll Institute, Jena, Germany
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238
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Abstract
The study of long noncoding RNAs (lncRNAs) is still in its infancy with more putative RNAs identified than those with ascribed functions. Defined as transcripts that are longer than 200 nucleotides without a coding sequence, their numbers are on the rise and may well challenge protein coding transcripts in number and diversity. lncRNAs are often expressed at low levels and their sequences are frequently poorly conserved, making it unclear if they are transcriptional noise or bonafide effectors. Despite these limitations, inroads into their functions are being made and it is clear they make a contribution in regulating all aspects of biology. The early verdict on their activity, however, suggests the majority function as chromatin modifiers. A good proportion show a connection to disease highlighting their importance and the need to determine their function. The focus of this review is on lncRNAs which influence developmental processes which in itself covers a large range of known activities.
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Affiliation(s)
- Jamila I Horabin
- Department of Biomedical Sciences, College of Medicine, Florida State University, Rm 3300-G, 1115 W. Call St., Tallahassee, FL, 32306-4300, USA,
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239
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Córdoba M, González Morón D, Rodríguez-Quiroga SA, Kauffman MA. Neurología genómica personalizada: el futuro es ahora. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.neuarg.2014.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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240
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Diebel KW, Claypool DJ, van Dyk LF. A conserved RNA polymerase III promoter required for gammaherpesvirus TMER transcription and microRNA processing. Gene 2014; 544:8-18. [PMID: 24747015 PMCID: PMC4544698 DOI: 10.1016/j.gene.2014.04.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 03/21/2014] [Accepted: 04/14/2014] [Indexed: 12/21/2022]
Abstract
Canonical RNA polymerase III (pol III) type 2 promoters contain a single A and B box and are well documented for their role in tRNA and SINE transcription in eukaryotic cells. The genome of Murid herpesvirus 4 (MuHV-4) contains eight polycistronic tRNA-microRNA encoded RNA (TMER) genes that are transcribed from a RNA pol III type 2-like promoter containing triplicated A box elements. Here, we demonstrate that the triplicated A box sequences are required in their entirety to produce functional MuHV-4 miRNAs. We also identify that these RNA pol III type 2-like promoters are conserved in eukaryotic genomes. Human and mouse predicted tRNA genes containing these promoters also show enrichment of alternative RNA pol III transcription termination sequences and are predicted to give rise to longer tRNA primary transcripts.
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MESH Headings
- 3T3 Cells
- Animals
- Base Sequence
- Blotting, Northern
- Fibroblasts/metabolism
- Fibroblasts/virology
- Gene Expression Regulation, Viral
- Genome, Viral/genetics
- Host-Pathogen Interactions
- Humans
- Mice
- MicroRNAs/genetics
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Polyproteins/genetics
- Promoter Regions, Genetic/genetics
- RNA Folding
- RNA Polymerase III/genetics
- RNA Processing, Post-Transcriptional
- RNA, Transfer/genetics
- RNA, Viral/chemistry
- RNA, Viral/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Rhadinovirus/genetics
- Transcription, Genetic
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Affiliation(s)
- Kevin W Diebel
- Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - David J Claypool
- Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Linda F van Dyk
- Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Immunology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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241
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Wang X, Gupta P, Fairbanks J, Hansen D. Protein kinase CK2 both promotes robust proliferation and inhibits the proliferative fate in the C. elegans germ line. Dev Biol 2014; 392:26-41. [PMID: 24824786 DOI: 10.1016/j.ydbio.2014.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/02/2014] [Accepted: 05/02/2014] [Indexed: 11/18/2022]
Abstract
Stem cells are capable of both self-renewal (proliferation) and differentiation. Determining the regulatory mechanisms controlling the balance between stem cell proliferation and differentiation is not only an important biological question, but also holds the key for using stem cells as therapeutic agents. The Caenorhabditis elegans germ line has emerged as a valuable model to study the molecular mechanisms controlling stem cell behavior. In this study, we describe a large-scale RNAi screen that identified kin-10, which encodes the β subunit of protein kinase CK2, as a novel factor regulating stem cell proliferation in the C. elegans germ line. While a loss of kin-10 in an otherwise wild-type background results in a decrease in the number of proliferative cells, loss of kin-10 in sensitized genetic backgrounds results in a germline tumor. Therefore, kin-10 is not only necessary for robust proliferation, it also inhibits the proliferative fate. We found that kin-10's regulatory role in inhibiting the proliferative fate is carried out through the CK2 holoenzyme, rather than through a holoenzyme-independent function, and that it functions downstream of GLP-1/Notch signaling. We propose that a loss of kin-10 leads to a defect in CK2 phosphorylation of its downstream targets, resulting in abnormal activity of target protein(s) that are involved in the proliferative fate vs. differentiation decision. This eventually causes a shift towards the proliferative fate in the stem cell fate decision.
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Affiliation(s)
- Xin Wang
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Pratyush Gupta
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Jared Fairbanks
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4
| | - Dave Hansen
- Department of Biological Sciences, University of Calgary, 2500 University Drive, Calgary, Alberta, Canada T2N 1N4.
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242
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Towheed A, Markantone DM, Crain AT, Celotto AM, Palladino MJ. Small mitochondrial-targeted RNAs modulate endogenous mitochondrial protein expression in vivo. Neurobiol Dis 2014; 69:15-22. [PMID: 24807207 DOI: 10.1016/j.nbd.2014.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/04/2014] [Accepted: 04/27/2014] [Indexed: 11/26/2022] Open
Abstract
Endogenous mitochondrial genes encode critical oxidative phosphorylation components and their mutation results in a set of disorders known collectively as mitochondrial encephalomyopathies. There is intensive interest in modulating mitochondrial function as organelle dysfunction has been associated with numerous disease states. Proteins encoded by the mitochondrial genome cannot be genetically manipulated by current techniques. Here we report the development of a mitochondrial-targeted RNA expression system (mtTRES) utilizing distinct non-coding leader sequences (NCLs) and enabling in vivo expression of small mitochondrial-targeted RNAs. mtTRES expressing small chimeric antisense RNAs was used as translational inhibitors (TLIs) to target endogenous mitochondrial protein expression in vivo. By utilizing chimeric antisense RNA we successfully modulate expression of two mitochondrially-encoded proteins, ATP6 and COXII, and demonstrate the utility of this system in vivo and in human cells. This technique has important and obvious research and clinical implications.
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Affiliation(s)
- Atif Towheed
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Desiree M Markantone
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Aaron T Crain
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Alicia M Celotto
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Michael J Palladino
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases (PIND), University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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243
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Gruber AR. RNA Polymerase III promoter screen uncovers a novel noncoding RNA family conserved in Caenorhabditis and other clade V nematodes. Gene 2014; 544:236-40. [PMID: 24792899 DOI: 10.1016/j.gene.2014.04.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 10/25/2022]
Abstract
RNA Polymerase III is a highly specialized enzyme complex responsible for the transcription of a very distinct set of housekeeping noncoding RNAs including tRNAs, 7SK snRNA, Y RNAs, U6 snRNA, and the RNA components of RNaseP and RNaseMRP. In this work we have utilized the conserved promoter structure of known RNA Polymerase III transcripts consisting of characteristic sequence elements termed proximal sequence elements (PSE) A and B and a TATA-box to uncover a novel RNA Polymerase III-transcribed, noncoding RNA family found to be conserved in Caenorhabditis as well as other clade V nematode species. Homology search in combination with detailed sequence and secondary structure analysis revealed that members of this novel ncRNA family evolve rapidly, and only maintain a potentially functional small stem structure that links the 5' end to the very 3' end of the transcript and a small hairpin structure at the 3' end. This is most likely required for efficient transcription termination. In addition, our study revealed evidence that canonical C/D box snoRNAs are also transcribed from a PSE A-PSE B-TATA-box promoter in Caenorhabditis elegans.
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Affiliation(s)
- Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
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244
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Tamura A, Niwa A, Ii Y, Sasaki R, Tomimoto H, Saitsu H. [A case of hypomyelinating leukodystrophy with new homozygous mutation in POLR3A]. Rinsho Shinkeigaku 2014; 53:624-9. [PMID: 23965854 DOI: 10.5692/clinicalneurol.53.624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We describe a 34-year-old man with hypomyelination, hypogonadotropic hypogonadism, ataxia, and myopia without hypodontia. He was born to non-consanguineous parents, and had an elder brother who showed a similar phenotype. Laboratory studies demonstrated low level of LH, FSH and testosterone. MRI showed hypomyelination, atrophy of the cerebellum and the hypoplastic corpus callosum. Homozygous missensze mutation c.2350G>A (p.Gly784Ser) was found in POLR3A,which codes for the largest subunit of RNA polymerase III. Since PolIII-related leukodystrophies shows various combination of neurologic and non-neurologic features, additional reports will help to confirm the mechanism of this disease.
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Affiliation(s)
- Asako Tamura
- Department of Neurology, Mie University Graduate School of Medicine, Japan
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245
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Neguembor MV, Jothi M, Gabellini D. Long noncoding RNAs, emerging players in muscle differentiation and disease. Skelet Muscle 2014; 4:8. [PMID: 24685002 PMCID: PMC3973619 DOI: 10.1186/2044-5040-4-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/11/2014] [Indexed: 12/18/2022] Open
Abstract
The vast majority of the mammalian genome is transcribed giving rise to many different types of noncoding RNAs. Among them, long noncoding RNAs are the most numerous and functionally versatile class. Indeed, the lncRNA repertoire might be as rich as the proteome. LncRNAs have emerged as key regulators of gene expression at multiple levels. They play important roles in the regulation of development, differentiation and maintenance of cell identity and they also contribute to disease. In this review, we present recent advances in the biology of lncRNAs in muscle development and differentiation. We will also discuss the contribution of lncRNAs to muscle disease with a particular focus on Duchenne and facioscapulohumeral muscular dystrophies.
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Affiliation(s)
| | | | - Davide Gabellini
- Dulbecco Telethon Institute at San Raffaele Scientific Institute, Division of Regenerative Medicine, Stem cells, and Gene therapy, DIBIT2, 5A3, Via Olgettina 58, 20132 Milano, Italy.
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246
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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247
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Takanashi JI, Osaka H, Saitsu H, Sasaki M, Mori H, Shibayama H, Tanaka M, Nomura Y, Terao Y, Inoue K, Matsumoto N, Barkovich AJ. Different patterns of cerebellar abnormality and hypomyelination between POLR3A and POLR3B mutations. Brain Dev 2014; 36:259-63. [PMID: 23643445 DOI: 10.1016/j.braindev.2013.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/16/2013] [Accepted: 03/27/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Mutations of POLR3A and POLR3B have been reported to cause several allelic hypomyelinating disorders, including hypomyelination with hypogonadotropic hypogonadism and hypodontia (4H syndrome). PATIENTS AND METHODS To clarify the difference in MRI between the two genotypes, we reviewed MRI in three patients with POLR3B mutations, and three with POLR3A mutations. RESULTS Though small cerebellar hemispheres and vermis are common MRI findings with both types of mutations, MRI in patients with POLR3B mutations revealed smaller cerebellar structures, especially vermis, than those in POLR3A mutations. MRI also showed milder hypomyelination in patients with POLR3B mutations than those with POLR3A mutations, which might explain milder clinical manifestations. CONCLUSIONS MRI findings are distinct between patients with POLR3A and 3B mutations, and can provide important clues for the diagnosis, as these patients sometimes have no clinical symptoms suggesting 4H syndrome.
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Affiliation(s)
- Jun-ichi Takanashi
- Department of Pediatrics, Kameda Medical Center, Kamogawa, Japan; Department of Radiology, Toho University Sakura Medical Center, Sakura, Japan.
| | - Hitoshi Osaka
- Division of Neurology, Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Harushi Mori
- Department of Radiology, The University of Tokyo, Tokyo, Japan
| | | | - Manabu Tanaka
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | | | - Yasuo Terao
- Department of Neurology, The University of Tokyo, Tokyo, Japan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - A James Barkovich
- Department of Radiology and Biomedical Imaging, University of California San Francisco, CA, USA
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248
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Irizar H, Muñoz-Culla M, Sepúlveda L, Sáenz-Cuesta M, Prada Á, Castillo-Triviño T, Zamora-López G, de Munain AL, Olascoaga J, Otaegui D. Transcriptomic profile reveals gender-specific molecular mechanisms driving multiple sclerosis progression. PLoS One 2014; 9:e90482. [PMID: 24587374 PMCID: PMC3938749 DOI: 10.1371/journal.pone.0090482] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 01/31/2014] [Indexed: 12/21/2022] Open
Abstract
Background Although the most common clinical presentation of multiple sclerosis (MS) is the so called Relapsing-Remitting MS (RRMS), the molecular mechanisms responsible for its progression are currently unknown. To tackle this problem, a whole-genome gene expression analysis has been performed on RRMS patients. Results The comparative analysis of the Affymetrix Human Gene 1.0 ST microarray data from peripheral blood leucocytes obtained from 25 patients in remission and relapse and 25 healthy subjects has revealed 174 genes altered in both remission and relapse, a high proportion of them showing what we have called “mirror pattern”: they are upregulated in remission and downregulated in relapse or vice versa. The coexpression analysis of these genes has shown that they are organized in three female-specific and one male-specific modules. Conclusions The interpretation of the modules of the coexpression network suggests that Epstein-Barr virus (EBV) reactivation of B cells happens in MS relapses; however, qPCR expression data of the viral genes supports that hypothesis only in female patients, reinforcing the notion that different molecular processes drive disease progression in females and males. Besides, we propose that the “primed” state showed by neutrophils in women is an endogenous control mechanism triggered to keep EBV reactivation under control through vitamin B12 physiology. Finally, our results also point towards an important sex-specific role of non-coding RNA in MS.
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Affiliation(s)
- Haritz Irizar
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Maider Muñoz-Culla
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Lucia Sepúlveda
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
| | - Matías Sáenz-Cuesta
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Álvaro Prada
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
- Hospital Universitario Donostia, Immunology Department, Donostia-San Sebastian, Spain
| | - Tamara Castillo-Triviño
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
| | - Gorka Zamora-López
- Bernstein Center for Computational Neuroscience, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Brain and Cognition, Universistat Pompeu Fabra, Barcelona, Spain
| | - Adolfo López de Munain
- Hospital Universitario Donostia, Neurology Department, Donostia-San Sebastian, Spain
- Centro de Investigaciones Biomédicas en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, Ministerio de Ciencia e Innovación, Madrid, Spain
| | - Javier Olascoaga
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
- Hospital Universitario Donostia, Neurology Department, Donostia-San Sebastian, Spain
| | - David Otaegui
- Multiple Sclerosis Unit, Neuroscience Area, Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- Spanish Multiple Sclerosis Net (REEM), Barcelona, Spain
- * E-mail:
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249
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Wang HW, Huang TS, Lo HH, Huang PH, Lin CC, Chang SJ, Liao KH, Tsai CH, Chan CH, Tsai CF, Cheng YC, Chiu YL, Tsai TN, Cheng CC, Cheng SM. Deficiency of the microRNA-31-microRNA-720 pathway in the plasma and endothelial progenitor cells from patients with coronary artery disease. Arterioscler Thromb Vasc Biol 2014; 34:857-69. [PMID: 24558106 DOI: 10.1161/atvbaha.113.303001] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Defects in angiogenesis/vasculogenesis or vessel repair are major complications of coronary artery disease (CAD). Endothelial progenitor cells (EPCs) play a fundamental role in postnatal vascular repair and CAD. The role of microRNAs in CAD pathogenesis and their potential as biomarkers remain to be elucidated. APPROACH AND RESULTS MicroRNA-31 (miR-31) level in both the plasma and EPCs of patients with CAD is found lower. miR-31 regulates EPC activities by targeting FAT atypical cadherin 4 and thromboxane A2 receptor, which show increased expression in CAD EPCs. Overexpressing miR-31 in CAD EPCs rescued their angiogenic and vasculogenic abilities both in vitro and in vivo. When exploring approaches to restore endogenous miR-31, we found that far-infrared treatment enhanced the expression of not only miR-31, but also miR-720 in CAD EPCs. miR-720, which was also decreased in EPCs and the plasma of patients with CAD, stimulated EPC activity by targeting vasohibin 1. The miR720-vasohibin 1 pair was shown to be downstream of FAT atypical cadherin 4, but not of thromboxane A2 receptor. FAT atypical cadherin 4 inhibited miR-720 expression via repression of the planar cell polarity signaling gene four-jointed box 1 (FJX1), which was required for miR-720 expression through a hypoxia-inducible factor 1, α subunit-dependent mechanism. Restoring miR-720 level strengthened activity of CAD EPCs. The miR-31-miR-720 pathway is shown critical to EPC activation and that downregulation of this pathway contributes to CAD pathogenesis. Circulating levels of miR-31, miR-720, and vasohibin 1 have the potential to allow early diagnosis of CAD and to act as prognosis biomarkers for CAD and other EPC-related diseases. CONCLUSIONS Manipulating the expression of the miR-31-miR-720 pathway in malfunction EPCs should help develop novel therapeutic modalities.
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Affiliation(s)
- Hsei-Wei Wang
- From the Institute of Microbiology and Immunology, School of Life Science (H.-W.W., T.-S.H., H.-H.L., K.-H.L., C.-F.T., Y.-C.C., Y.-L.C.), Cancer Research Center & Genome Research Center (H.-W.W.), School of Medicine (P.-H.H., C.-C.L.), and Cardiovascular Research Center (P.-H.H.), National Yang-Ming University, Taipei, Taiwan; Division of Cardiology, Department of Medicine (P.-H.H.) and Division of Nephrology, Department of Medicine (C.-C.L.), Taipei Veterans General Hospital, Taipei, Taiwan ; Department of Education and Research, Taipei City Hospital, Taipei, Taiwan (H.-W.W.); Department of Obstetrics and Gynecology, Hsin-Chu Mackay Memorial Hospital, Hsin Chu, Taiwan (S.-J.C., C.-H.T., C.-H.C.); and Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan (T.-N.T., C.-C.C., S.-M.C.)
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250
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Alla RK, Cairns BR. RNA polymerase III transcriptomes in human embryonic stem cells and induced pluripotent stem cells, and relationships with pluripotency transcription factors. PLoS One 2014; 9:e85648. [PMID: 24465633 PMCID: PMC3896398 DOI: 10.1371/journal.pone.0085648] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/29/2013] [Indexed: 01/03/2023] Open
Abstract
Recent genomic approaches have revealed that the repertoire of RNA Pol III-transcribed genes varies in different human cell types, and that this variation is likely determined by a combination of the chromatin landscape, cell-specific DNA-binding transcription factors, and collaboration with RNA Pol II. Although much is known about this regulation in differentiated human cells, there is presently little understanding of this aspect of the Pol III system in human ES cells. Here, we determine the occupancy profiles of Pol III components in human H1 ES cells, and also induced pluripotent cells, and compare to known profiles of chromatin, transcription factors, and RNA expression. We find a relatively large fraction of the Pol III repertoire occupied in human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs). In ES cells we find clear correlations between Pol III occupancy and active chromatin. Interestingly, we find a highly significant fraction of Pol III-occupied genes with adjacent binding events by pluripotency factors in ES cells, especially NANOG. Notably, in human ES cells we find H3K27me3 adjacent to but not overlapping many active Pol III loci. We observe in all such cases, a peak of H3K4me3 and/or RNA Pol II, between the H3K27me3 and Pol III binding peaks, suggesting that H3K4me3 and Pol II activity may "insulate" Pol III from neighboring repressive H3K27me3. Further, we find iPSCs have a larger Pol III repertoire than their precursors. Finally, the active Pol III genome in iPSCs is not completely reprogrammed to a hESC like state and partially retains the transcriptional repertoire of the precursor. Together, our correlative results are consistent with Pol III binding and activity in human ES cells being enabled by active/permissive chromatin that is shaped in part by the pluripotency network of transcription factors and RNA Pol II activity.
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Affiliation(s)
- Ravi K. Alla
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Bradley R. Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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