home > bioproject > PRJDB1766
identifier PRJDB1766
type bioproject
sra-study  DRP000894
organism Mus musculus
title Abundant Bidirectional Transcription around Transcription Start Sites in Mammals
description In mammals, more than 60% of the genome is use for transcription for mRNAs and noncoding RNAs (ncRNAs). A fraction of ncRNAs have been believed to downregulate the corresponding mRNA expression level in a pre- or post- transcriptional manner by forming RNA-RNA duplex structures.To examine the directional properties of transcription at the whole genome level, we performed directional RNA-seq analysis of mouse brain and heart samples. Our analysis revealed that there is only a small fraction of the genome where both the top and bottom strands are utilized for transcription.A significant fraction of transcription start sites (TSSs) of protein-coding genes contain borders that separate antisense- and sense-biased transcription, suggesting that head-to-head transcription at the TSS is more prevalent than previously thought.The expression of the resultant promoter-associated ncRNAs (pancRNAs) tends to occur together with that of the corresponding mRNA in a coordinated manner. A fraction of genes with tissue-specific pancRNAs show a positive correlation between their pancRNA and mRNA expression, which is in accord with the proposed role for pancRNA in facultative gene activation, whereas genes with constitutive expression lack an association with pancRNA. More than 90% of head-to-head type promoters contain CpG islands. Moreover, CCG and CGG repeats are significantly enriched in the upstream regions and downstream regions, respectively, of TSSs located in head-to-head type promoters. Here, we propose that head-to-head transcription from GC-rich sequences regulates gene expression.
data type DDBJ SRA Study
external link
sra-run  DRR003367DRR003368DRR003369DRR003370DRR003371DRR003372DRR003373DRR003374DRR003375DRR003376
sra-submission  DRA000860
biosample  SAMD00000595SAMD00000596SAMD00000593SAMD00000597SAMD00000594
sra-study  DRP000894
sra-sample  DRS002784DRS002785DRS002786DRS002787DRS002788
sra-experiment  DRX002691DRX002692DRX002693DRX002694DRX002695DRX002696DRX002697DRX002698DRX002699DRX002700
distribution JSONJSON-LD
status public
visibility unrestricted-access
dateCreated 2014-05-12T00:46:27+0000
dateModified 2014-05-12T00:46:27+0000
datePublished 2014-05-12T00:46:27+0000