Abundant Bidirectional Transcription around Transcription Start Sites in Mammals

Experiment ID:DRP000894
Technology:RNA-Seq
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.
Source:DRP000894 SRA
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Bulk RNA-Seq processed expression values in Pan troglodytes

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Library ID
Identifier of the RNA-Seq library
Anat. entity ID
ID of the anatomical localization of the sample
Anat. entity name
Name of the anatomical localization of the sample
Anat. entity author annotation
Free text annotation of anatomical localization of the sample as provided by authors
Stage ID
ID of the developmental and life stage of the sample
Stage name
Name of the developmental and life stage of the sample
Stage author annotation
Free text annotation of the developmental and life stage of the sample as provided by authors
Sex
Annotation of the sex of the sample
Strain
Annotation of the strain of the sample
Time
Free text annotation of the time of sampling as provided by authors
Time unit
Unit for the time of sampling as provided by authors
Species
Physiological status
Physiological status of the organism at time of sampling
Technology
Sequencing platform
Sequenced transcript part
Possible values are: full length, all parts of the transcript are sequenced; 3': only the 3' end of the transcript is sequenced; 5': only the 5' end of the transcript is sequenced.
Fragmentation
Size of the RNA fragmentation
Run sequencing type
Paired-end or single-read run
Total read count
Total number of reads for the library.
Mapped read count
Number of reads that could be mapped to the transcriptome.
Total UMI count
Total number of individual RNA molecules (UMI) for the annotated sample. Only applicable for libraries producing UMIs.
Mapped UMI count
Number of UMIs that could be mapped to the transcriptome. Only applicable for libraries producing UMIs.
Distinct rank count
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, number of distinct ranks observed, to have a value of the power for distinguishing expression levels. Used as a weight to compute a weighted mean rank accross samples for each gene and compute expression scores in Bgee.
Max rank
When performing a fractional ranking of the genes in the annotated sample, based on their expression level, maximum rank attained in the sample. Used to normalize ranks accross samples and compute expression scores in Bgee.
Link to processed expression values
See the processed expression value results for this assay
DRX002691UBERON:0013541 Brodmann (1909) area 10BA10 areaPtroDv:0000033 28-year-old stage (chimpanzee)28 year-oldfemaleNANANAPan troglodytesNAIlluminaIllumina HiSeq 2000FULL_LENGTH100single7501264149411818002025422373.5Browse results
DRX002692UBERON:0013541 Brodmann (1909) area 10BA10 areaPtroDv:0000033 28-year-old stage (chimpanzee)28 year-oldfemaleNANANAPan troglodytesNAIlluminaIllumina HiSeq 2000FULL_LENGTH100single7714198450627890002031222437Browse results
DRX002693UBERON:0002037 cerebellumcerebellumPtroDv:0000033 28-year-old stage (chimpanzee)28 year-oldfemaleNANANAPan troglodytesNAIlluminaIllumina HiSeq 2000FULL_LENGTH100single7634219145849504002006822280.5Browse results
DRX002694UBERON:0002037 cerebellumcerebellumPtroDv:0000033 28-year-old stage (chimpanzee)28 year-oldfemaleNANANAPan troglodytesNAIlluminaIllumina HiSeq 2000FULL_LENGTH100single7608103345426398002002022240.5Browse results

Showing 1 to 4 of 4 entries

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