Divergent transcription is associated with promoters of transcriptional regulators

Autor: Hélène Holota, Romain Fenouil, Frederic Koch, Jean Imbert, Muhammad Ahmad Maqbool, Salvatore Spicuglia, Marta Gut, Aurélien Griffon, Jean-Christophe Andrau, Cyrille Lepoivre, Aurélie Bergon, Laurent Vanhille, Denis Puthier, Mohamed Belhocine, Miriam Yammine, Ivo Gut, Béatrice Loriod, Joaquin Zacarias-Cabeza, Marc-Antoine Garibal
Přispěvatelé: Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Centre Nacional D'Anàlisi Genómica, Parc Cientific de Barcelona, ARC (project n° SFI20111203756), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), European Project: 282510,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,BLUEPRINT(2011), European Project: 262055,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,ESGI(2011), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Research in SS laboratory was supported by recurrent funding from the Inserm and Aix-Marseille University, the ARC (project n° SFI20111203756) and the A*MIDEX project (n° ANR-11-IDEX-0001-02) funded by the ' Investissements d'Avenir ' French Government program., BMC, Ed., INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, A BLUEPRINT of Haematopoietic Epigenomes - BLUEPRINT - - EC:FP7:HEALTH2011-10-01 - 2016-09-30 - 282510 - VALID, European Sequencing and Genotyping Infrastructure - ESGI - - EC:FP7:INFRA2011-02-01 - 2015-07-31 - 262055 - VALID, Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Technologies avancées pour le génôme et la clinique ( TAGC ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre d'Immunologie de Marseille - Luminy ( CIML ), Centro Nacional de Análisi Genómico ( CNAG ), Centro Nacional de Análisis Genómico, ARC - project n°SFI20111203756, ANR-11-IDEX-0001-02/11-IDEX-0001,Amidex,Amidex ( 2011 ), European Project : 282510,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,BLUEPRINT ( 2011 ), European Project : 262055,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,ESGI ( 2011 )
Jazyk: angličtina
Rok vydání: 2013
Předmět:
Transcription
Genetic
RNA polymerase II
Divergent transcription
Epigenesis
Genetic
Mice
Exon
0302 clinical medicine
lncRNA
Transcription (biology)
Transcriptional regulation
Promoter Regions
Genetic
[ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Regulation of gene expression
Genetics
Base Composition
0303 health sciences
Thymocytes
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Exons
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Chromatin
[ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
RNA
Long Noncoding
Research Article
Biotechnology
Biology
Developmental transcription factor
03 medical and health sciences
[ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM]
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
Animals
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
RNA
Messenger
Epigenetics
Gene
030304 developmental biology
GC skew
Sequence Analysis
RNA
Promoter
Mice
Inbred C57BL
Antisense Elements (Genetics)
Gene Expression Regulation
Bidirectional promoter
biology.protein
CpG Islands
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
030217 neurology & neurosurgery
Zdroj: BMC Genomics
BMC Genomics, 2013, 14, pp.914. ⟨10.1186/1471-2164-14-914⟩
BMC Genomics, BioMed Central, 2013, 14, pp.914. ⟨10.1186/1471-2164-14-914⟩
BMC Genomics, 2013, 14 (1), pp.914. ⟨10.1186/1471-2164-14-914⟩
BMC Genomics; Vol 14
BMC Genomics, BioMed Central, 2013, 14 (1), pp.914. ⟨10.1186/1471-2164-14-914⟩
BMC Genomics, BioMed Central, 2013, 14 (1), pp.914. 〈10.1186/1471-2164-14-914〉
ISSN: 1471-2164
DOI: 10.1186/1471-2164-14-914⟩
Popis: International audience; BACKGROUND: Divergent transcription is a wide-spread phenomenon in mammals. For instance, short bidirectional transcripts are a hallmark of active promoters, while longer transcripts can be detected antisense from active genes in conditions where the RNA degradation machinery is inhibited. Moreover, many described long non-coding RNAs (lncRNAs) are transcribed antisense from coding gene promoters. However, the general significance of divergent lncRNA/mRNA gene pair transcription is still poorly understood. Here, we used strand-specific RNA-seq with high sequencing depth to thoroughly identify antisense transcripts from coding gene promoters in primary mouse tissues. RESULTS: We found that a substantial fraction of coding-gene promoters sustain divergent transcription of long non-coding RNA (lncRNA)/mRNA gene pairs. Strikingly, upstream antisense transcription is significantly associated with genes related to transcriptional regulation and development. Their promoters share several characteristics with those of transcriptional developmental genes, including very large CpG islands, high degree of conservation and epigenetic regulation in ES cells. In-depth analysis revealed a unique GC skew profile at these promoter regions, while the associated coding genes were found to have large first exons, two genomic features that might enforce bidirectional transcription. Finally, genes associated with antisense transcription harbor specific H3K79me2 epigenetic marking and RNA polymerase II enrichment profiles linked to an intensified rate of early transcriptional elongation. CONCLUSIONS: We concluded that promoters of a class of transcription regulators are characterized by a specialized transcriptional control mechanism, which is directly coupled to relaxed bidirectional transcription.
Databáze: OpenAIRE
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