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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
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A Rapid In Vivo Bioassay for Developmentally Active Enhancers
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Tissue-specific RNA expression marks distant-acting developmental enhancers.

Han Wu1, Alex S Nord1, Jennifer A Akiyama1

  • 1Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

Plos Genetics
|September 5, 2014
PubMed
Summary
This summary is machine-generated.

Tissue-specific enhancer RNAs (eRNAs) are common, with ~80% of enhancers showing expression linked to tissue activity. This study identifies thousands of new enhancer regions and demonstrates eRNA expression can predict enhancer function.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Developmental Biology

Background:

  • Short non-coding transcripts, enhancer RNAs (eRNAs), originate from transcriptional enhancers.
  • The prevalence and functional significance of eRNAs in tissue-specific gene regulation are not well understood.

Purpose of the Study:

  • To investigate the expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues.
  • To determine the association between eRNA expression and enhancer activity in vivo.
  • To identify novel enhancer regions based on transcription patterns.

Main Methods:

  • Deep RNA sequencing of embryonic mouse tissues.
  • Validation of enhancer activity using transgenic mouse reporter assays.
  • Genomic analysis of identified non-coding regions.

Main Results:

  • Approximately 80% of validated in vivo enhancers exhibit tissue-specific RNA expression correlating with enhancer activity.
  • Thousands of tissue-specifically transcribed non-coding regions (TSTRs) with enhancer hallmarks were identified.
  • Over 50% of tested TSTRs demonstrated enhancer function in vivo, confirming their regulatory role.

Conclusions:

  • Tissue-specific eRNA expression is a widespread feature of active enhancers.
  • eRNAs contribute significantly to extragenic transcription.
  • eRNA expression signatures can predict tissue-specific enhancers, offering an alternative to epigenomic marks.