metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming

Genes (Basel). 2020 Jun 9;11(6):634. doi: 10.3390/genes11060634.

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.

Keywords: CAMTA1; CBF; DREB; binding sites; chilling stress; genomics; meta-analysis; transcription factor; transcriptomics.

Publication types

  • Meta-Analysis
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arabidopsis / genetics
  • Arabidopsis / growth & development
  • Cellular Reprogramming / genetics*
  • Gene Expression Regulation, Plant / genetics
  • Humans
  • Plant Proteins / genetics
  • Promoter Regions, Genetic / genetics
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Transcription, Genetic*
  • Transcriptome / genetics*
  • Zebrafish / genetics

Substances

  • Plant Proteins