metaRE R package for meta-analysis of transcriptome data to identify the cis-regulatory code behind the transcriptional reprogramming

Daria D. Novikova, Pavel A. Cherenkov, Yana G. Sizentsova, Victoria V. Mironova*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. A significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism’s response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here, we showed metaRE performance for the identification of low-temperature-responsive cis-regulatory code in Arabidopsis thaliana and Danio rerio. MetaRE identified potential binding sites for known as well as unknown cold response regulators. A notable part of cis-elements was found in both searches discovering great conservation in low-temperature responses between plants and animals.

Original languageEnglish
Article number634
Pages (from-to)1-14
Number of pages14
JournalGenes
Volume11
Issue number6
DOIs
Publication statusPublished - Jun 2020

Keywords

  • Binding sites
  • CAMTA1
  • CBF
  • Chilling stress
  • DREB
  • Genomics
  • Meta-analysis
  • Transcription factor
  • Transcriptomics

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