Identification of RNA 3´ ends and termination sites in

3' Untranslated Regions Algorithms Cluster Analysis Computational Biology / methods Gene Expression Regulation, Archaeal Genome, Archaeal Genomics / methods Haloferax volcanii / genetics Molecular Sequence Annotation Nucleotide Motifs Open Reading Frames Operon RNA, Archaeal / genetics Transcription Termination, Genetic
3´ UTR Haloarchaea Haloferax volcanii RNA 3´ ends RNAseq Transcription termination archaea

Journal

RNA biology
ISSN: 1555-8584
Titre abrégé: RNA Biol
Pays: United States
ID NLM: 101235328

Informations de publication

Date de publication:
05 2020
Historique:
pubmed: 12 2 2020
medline: 13 5 2021
entrez: 12 2 2020
Statut: ppublish

Résumé

Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3´ termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea,

Identifiants

DOI: 10.1080/15476286.2020.1723328 PMID: 32041469 PMC: PMC7237163
pubmed: 32041469
doi: 10.1080/15476286.2020.1723328
pmc: PMC7237163
doi:

Substances chimiques

3' Untranslated Regions 0
RNA, Archaeal 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

663-676

Références

Mol Syst Biol. 2009;5:285
pubmed: 19536208
BMC Genomics. 2016 Aug 12;17(1):629
pubmed: 27519343
Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):E6767-E6773
pubmed: 28760969
Trends Microbiol. 2005 Jun;13(6):262-5
pubmed: 15936657
Arch Microbiol. 2008 Sep;190(3):281-99
pubmed: 18592220
RNA Biol. 2018;15(7):967-975
pubmed: 29683387
Mol Microbiol. 2016 Feb;99(4):719-28
pubmed: 26514343
OMICS. 2005 Spring;9(1):91-105
pubmed: 15805780
Crit Rev Microbiol. 1989;16(4):287-338
pubmed: 2467783
BMC Bioinformatics. 2008 Nov 11;9:474
pubmed: 19014431
J Bacteriol. 2008 Mar;190(6):2244-8
pubmed: 18192385
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Bioinformatics. 2017 Jul 15;33(14):2089-2096
pubmed: 28334186
Microbiol Mol Biol Rev. 2011 Jun;75(2):286-300
pubmed: 21646430
Algorithms Mol Biol. 2011 Nov 24;6:26
pubmed: 22115189
Bioinformatics. 2014 Jul 1;30(13):1837-43
pubmed: 24626854
Emerg Top Life Sci. 2018 Dec 14;2(4):517-533
pubmed: 33525828
Trends Genet. 2016 Aug;32(8):508-522
pubmed: 27371117
Mol Microbiol. 2008 Mar;67(5):958-70
pubmed: 18182021
Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):306-17
pubmed: 23092677
Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):318-30
pubmed: 23099421
Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544
pubmed: 29790989
FEMS Microbiol Rev. 2011 Jul;35(4):577-608
pubmed: 21265868
Crit Rev Biochem Mol Biol. 2019 Jun;54(3):242-300
pubmed: 31464530
Annu Rev Biochem. 2016 Jun 2;85:319-47
pubmed: 27023849
Nat Rev Mol Cell Biol. 2011 May;12(5):283-94
pubmed: 21487437
J Mol Biol. 2006 Jan 13;355(2):196-210
pubmed: 16305799
J Bacteriol. 2009 Nov;191(22):7102-8
pubmed: 19749050
J Mol Biol. 2011 Oct 7;412(5):793-813
pubmed: 21439297
Mol Microbiol. 2007 Dec;66(5):1092-106
pubmed: 17973910
Elife. 2012 Dec 13;1:e00078
pubmed: 23240084
Nat Rev Microbiol. 2011 Feb;9(2):85-98
pubmed: 21233849
Appl Environ Microbiol. 2010 Mar;76(6):1759-69
pubmed: 20097827
Trends Microbiol. 2019 Jan;27(1):86-87
pubmed: 30459094
Appl Environ Microbiol. 2004 Feb;70(2):943-53
pubmed: 14766575
Annu Rev Microbiol. 2017 Sep 8;71:331-348
pubmed: 28657884
Annu Rev Genet. 2010;44:167-88
pubmed: 20707673
Nat Microbiol. 2016 Aug 22;1(10):16143
pubmed: 27670118
Bioinformatics. 2012 Oct 1;28(19):2530-1
pubmed: 22829626
Nucleic Acids Res. 2016 Jul 8;44(W1):W46-53
pubmed: 27154273
J Bacteriol. 2003 Feb;185(3):772-8
pubmed: 12533452
Mol Microbiol. 2000 Apr;36(1):114-22
pubmed: 10760168
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
PLoS Comput Biol. 2009 Sep;5(9):e1000502
pubmed: 19750212
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419
Nucleic Acids Res. 2010 Jul;38(12):4040-51
pubmed: 20197319
Science. 2016 Apr 8;352(6282):aad9822
pubmed: 27120414
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
Biochimie. 2015 Oct;117:129-37
pubmed: 25754521
PLoS Genet. 2009 Jul;5(7):e1000552
pubmed: 19593371

Auteurs

Sarah J Berkemer (SJ)

Bioinformatics Group, Department of Computer Science - and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
ORCID: 0000-0003-2028-7670

Lisa-Katharina Maier (LK)

Biology II, Ulm University, Ulm, Germany.
ORCID: 0000-0001-5834-9035

Fabian Amman (F)

Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
Division of Cell and Developmental Biology, Medical University Vienna, Vienna, Austria.
ORCID: 0000-0002-8646-859X

Stephan H Bernhart (SH)

Bioinformatics Group, Department of Computer Science - and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
Transcriptome Bioinformatics, Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany.
ORCID: 0000-0002-5928-9449

Julia Wörtz (J)

Biology II, Ulm University, Ulm, Germany.

Pascal Märkle (P)

Biology II, Ulm University, Ulm, Germany.

Friedhelm Pfeiffer (F)

Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany.
ORCID: 0000-0003-4691-3246

Peter F Stadler (PF)

Bioinformatics Group, Department of Computer Science - and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.
Center for RNA in Technology and Health, University Copenhagen, Frederiksberg C, Denmark.
Santa Fe Institute, Santa Fe, NM, USA.
German Centre for Integrative Biodiversity Research (iDiv), Halle, Jena and Leipzig, Germany.
Competence Center for Scalable Data Services and Solutions, and Leipzig, Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany.
ORCID: 0000-0002-5016-5191

Anita Marchfelder (A)

Biology II, Ulm University, Ulm, Germany.
ORCID: 0000-0002-1382-1794

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Régions non traduites › Régions 3' non traduites › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Statistiques comme sujet › Analyse de regroupements › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes archéens › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome d'archéobactérie › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Archéobactéries › Euryarchaeota › Halobacteriales › Halobacteriaceae › Haloferax › Haloferax volcanii › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Motifs nucléotidiques › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Cadres ouverts de lecture › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Opéron › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN des archées › Identification of RNA 3´ ends and termination sites in
questionsmedicales.fr › Phénomènes génétiques › Expression des gènes › Transcription génétique › Terminaison de la transcription › Identification of RNA 3´ ends and termination sites in