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Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
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Cryptic sequence features in the active postmortem transcriptome.

Peter A Noble1, Alexander E Pozhitkov2

  • 1Department of Periodontics, University of Washington, Box 357444, Seattle, WA, 98195, USA. panoble2017@gmail.com.

BMC Genomics
|September 16, 2018
PubMed
Summary
This summary is machine-generated.

Postmortem transcripts possess unique sequence features that regulate gene expression. These features act as binding sites, influencing transcript stability and fate during stress, with implications for disease.

Keywords:
3’UTR5’UTRChaos game representationMolecular spongeMotifsMouseORFsPost-transcriptional regulationPostmortem gene expressionSequence featuresStress responseZebrafish

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Area of Science:

  • Molecular Biology
  • Genomics
  • Post-transcriptional Regulation

Background:

  • Previous studies identified over 500 transcripts with increased abundance postmortem in zebrafish and mice.
  • Existing literature indicates mRNA post-transcriptional regulation is common under stress.
  • Hypothesized that unique sequence features (3- to 9-mers) in postmortem transcripts mediate this regulation.

Purpose of the Study:

  • To identify unique sequence features in postmortem transcripts.
  • To investigate the role of these features in post-transcriptional regulation.
  • To understand the implications for stress response and disease.

Main Methods:

  • Bioinformatic analysis of transcriptomes from postmortem zebrafish and mice.
  • Identification and quantification of over-represented sequence features (mers).
  • Analysis of feature distribution within transcripts and correlation with known regulatory proteins.

Main Results:

  • Identified 5117 (mouse) and 2245 (zebrafish) over-represented sequence features.
  • Observed disproportionate distribution of features, particularly in 3' UTRs (zebrafish) and ORFs (mouse).
  • Discovered high-density features in specific mouse transcripts, suggesting 'molecular sponge' activity for RNA-binding proteins and microRNAs.

Conclusions:

  • Postmortem transcripts exhibit distinct sequence features, supporting their role in stress response.
  • These features act as binding sites for regulatory molecules, controlling transcript stability and fate.
  • High-density features may sequester regulatory factors, impacting gene expression networks with relevance to disease states.