Journal Article

Divergent transcription is associated with promoters of transcriptional regulators

Bergon, Aurélie, Maqbool, Muhammad Ahmad, Garibal, Marc-Antoine, Belhocine, Mohamed, Zacarias-Cabeza, Joaquin, Spicuglia, Salvatore, Fenouil, Romain, Griffon, Aurélien, Vanhille, Laurent, Loriod, Beatrice, Andrau, Jean-Christophe, Gut, Ivo, Gut, Marta, Koch, Frederic, Lepoivre, Cyrille, Yammine, Miriam, Imbert, Jean, Holota, Hélène, Puthier, Denis

2013

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Animal Genetics and Genomics / Animals / Antisense / Antisense Elements (Genetics) / Base Composition / Biochemistry, Molecular Biology / Biomedical and Life Sciences / Chromatin - genetics / CpG Islands / Epigenesis, Genetic / Epigenetic inheritance / Exons / Gene expression / Gene Expression Regulation / Genetic transcription / Genomics / Human and rodent genomics / Life Sciences / Mammals / Messenger RNA / Methods / Mice / Mice, Inbred C57BL / Microarrays / Microbial Genetics and Genomics / Ontology / Plant Genetics and Genomics / Promoter Regions, Genetic / Promoters (Genetics) / Proteins / Proteomics / Research Article / RNA polymerase / RNA sequencing / RNA, Long Noncoding - genetics / RNA, Messenger - genetics / Sequence Analysis, RNA / Studies / Thymocytes / Transcription factors / Transcription, Genetic