We are analyzing https://link.springer.com/article/10.1186/s13059-017-1379-8.

Title:
Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers | Genome Biology
Description:
Background Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhancers and as such has been utilized to experimentally identify active enhancers de novo. Results Here, we show that bidirectional transcription initiation is a pervasive feature of accessible chromatin, including at enhancers, promoters, and other DNase hypersensitive regions not marked with canonical histone modification profiles. Transcription is less predictive for enhancer activity than epigenetic modifications such as H3K4me1 or the accessibility of DNA when measured both in enhancer assays and at endogenous loci. The stability of enhancer initiated transcripts does not influence measures of enhancer activity and we cannot detect evidence of purifying selection on the resulting enhancer RNAs within the human population. Conclusions Our results indicate that bidirectional transcription initiation from accessible chromatin is not sufficient for, nor specific to, enhancer activity. Transcription initiating at enhancers may be a frequent by-product of promiscuous RNA polymerase initiation at accessible chromatin and is unlikely to generally play a functional role in enhancer activity.
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Keywords {🔍}

transcription, chromatin, initiation, pubmed, enhancers, enhancer, article, bidirectional, activity, google, scholar, state, gene, cell, cas, additional, central, promoters, regions, dhss, fig, file, measured, annotated, regulatory, transcripts, expression, cells, cage, human, data, genome, active, figure, loci, evidence, sites, dhs, accessible, promoter, analysis, elements, reporter, defined, transcribed, stable, dnase, dna, ernas, hypersensitivity,

Topics {✒️}

genome-scale high-resolution mapping tissue-specific chromatin domain embryonic stem cells /goldenpath/hg19/encodedcc/wgencodeuwdnase/ /goldenpath/hg19/encodedcc/wgencoderikencage/ /goldenpath/hg19/encodedcc/wgencodecshllongrnaseq/ methylation-induced repression--belts oestrogen-dependent transcriptional activation long-range gene activation article download pdf high-throughput functional testing long-range regulatory elements lagging-strand replication shapes promoter-proximal regulatory elements inhibiting enhancer-directed transcription mapped rna-seq reads related subjects neuronal activity-regulated enhancers bidirectionally transcribed-defined enhancers chromatin marks characteristic bidirectionally transcribed-defined enhancer rna polymerase ii medical research foundation measured 48 hours post-transfection chromatin mark-defined enhancer chromatin-defined enhancers relative long-range enhancer function repressive chromatin marks privacy choices/manage cookies cross-cell correlation analysis full access chromatin modifications assimilated hoffman mm core lj de procé sm characteristic chromatin profile proximal gene transcription open chromatin regions long noncoding rnas creative commons license candidate regulatory elements rna-independent linkage nascent rna identifies regulated transcriptional programs de hoon mj nearest annotated gene article young error bars represent predicts enhancer activity multi-exonic transcripts built

Questions {❓}

002 copies per cell for the CAGE libraries used in this study [40, 41]), but are all of those products really consequential for the biology of the organism?
Promoter or enhancer, what’s the difference?

Schema {🗺️}

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         description:Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhancers and as such has been utilized to experimentally identify active enhancers de novo. Here, we show that bidirectional transcription initiation is a pervasive feature of accessible chromatin, including at enhancers, promoters, and other DNase hypersensitive regions not marked with canonical histone modification profiles. Transcription is less predictive for enhancer activity than epigenetic modifications such as H3K4me1 or the accessibility of DNA when measured both in enhancer assays and at endogenous loci. The stability of enhancer initiated transcripts does not influence measures of enhancer activity and we cannot detect evidence of purifying selection on the resulting enhancer RNAs within the human population. Our results indicate that bidirectional transcription initiation from accessible chromatin is not sufficient for, nor specific to, enhancer activity. Transcription initiating at enhancers may be a frequent by-product of promiscuous RNA polymerase initiation at accessible chromatin and is unlikely to generally play a functional role in enhancer activity.
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      description:Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhancers and as such has been utilized to experimentally identify active enhancers de novo. Here, we show that bidirectional transcription initiation is a pervasive feature of accessible chromatin, including at enhancers, promoters, and other DNase hypersensitive regions not marked with canonical histone modification profiles. Transcription is less predictive for enhancer activity than epigenetic modifications such as H3K4me1 or the accessibility of DNA when measured both in enhancer assays and at endogenous loci. The stability of enhancer initiated transcripts does not influence measures of enhancer activity and we cannot detect evidence of purifying selection on the resulting enhancer RNAs within the human population. Our results indicate that bidirectional transcription initiation from accessible chromatin is not sufficient for, nor specific to, enhancer activity. Transcription initiating at enhancers may be a frequent by-product of promiscuous RNA polymerase initiation at accessible chromatin and is unlikely to generally play a functional role in enhancer activity.
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         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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