TY - JOUR

T1 - metaRE R package for meta-analysis of transcriptome data to identify the cis-regulatory code behind the transcriptional reprogramming

AU - Novikova, Daria D.

AU - Cherenkov, Pavel A.

AU - Sizentsova, Yana G.

AU - Mironova, Victoria V.

PY - 2020/6/1

Y1 - 2020/6/1

N2 - 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.

AB - 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.

KW - Binding sites

KW - CAMTA1

KW - CBF

KW - Chilling stress

KW - DREB

KW - Genomics

KW - Meta-analysis

KW - Transcription factor

KW - Transcriptomics

UR - http://www.scopus.com/inward/record.url?scp=85086328663&partnerID=8YFLogxK

U2 - 10.3390/genes11060634

DO - 10.3390/genes11060634

M3 - Article

C2 - 32526881

AN - SCOPUS:85086328663

VL - 11

SP - 1

EP - 14

JO - Genes

JF - Genes

SN - 2073-4425

IS - 6

M1 - 634

ER -