Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

Tineke Casneuf,Klaas Vandepoele,Yves Van de Peer

doi:10.1186/gb-2006-7-11-r103

Tineke Casneuf, Klaas Vandepoele

Open Access

https://doi.org/10.1186/gb-2006-7-11-r103

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Abstract

A strategy combining classical motif overrepresentation in co-regulated genes with comparative footprinting is applied to identify 80 transcription factor binding sites and 139 regulatory modules in Arabidopsis thaliana.

Highlights

Transcriptional regulation plays an important role in the control of many biological processes
Whereas the expression data are required for creating sets of co-regulated genes that serve as input for the detection of Transcription factor binding sites (TFBSs) using MotifSampler, the genomic sequences are used to delineate orthologous gene pairs between Arabidopsis and poplar, forming the basis for the evolutionary conservation filter
Inferring functional regulatory modules To get a general overview of the involvement of all 80 TFBSs (34 from co-expressed genes in the first stage plus 46 from two-way clustering in the second stage) and the derived cis-regulatory modules (CRMs) in different biological processes, we identified all modules with two to four motifs and again used overrepresented Gene Ontology (GO) terms for functional annotation

Summary

Introduction

Transcriptional regulation plays an important role in the control of many biological processes. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity and are organized into separable cis-regulatory modules, each defining the cooperation of several transcription factors required for a specific spatio-temporal expression pattern. Transcription factor binding sites (TFBSs; or DNA sequence motifs, or motifs for short) are the functional elements that determine the timing and location of transcriptional activity. As a consequence of this complex organization, understanding the combinatorial nature of transcriptional regulation at a genomic scale is a major challenge, as the number of possible combinations between TFs and targets is enormous. In the absence of already characterized TFBSs or systematic genome-wide location (that is, chromatin immunoprecipitation-chip) data revealing interactions between TFs and target genes, sequence and expression data are the only sources of information that can be combined to identify CRMs [7,8,9]

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