Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns

Abstract

BackgroundRegulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods.ResultsHere, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values.ConclusionsUsing unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks.

Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement

“…The availability of genomic and transcriptomic data for many horticultural crops allows the identification of novel CREs using bioinformaticsbased and experimental approaches 11,90,91 . The de novo CRE discovery is based on sequence conservation that exists among groups of genes that are co-expressed as well as gene families within a single genome, and among orthologs of multiple species [91][92][93] .…”

DETECTING PATTERNS IN 5’ UNTRANSLATED REGIONS OF GENES INVOLVED IN THE REGULATION OF BLOOD PRESSURE AND OXIDATIVE STRESS

“…In this work, we found that in vasorelaxing group, the motif length was higher (50 nt) with respect to those detected in the vasocontractile group (18 to 40 nt). Besides, due to vasorelaxing sequences are closer to the transcription starting point (-240 bp on average) than vasocontractile sequences (-590 bp on average), both could have different molecular crowding for the transcription, or distinct interaction modes with cisregulation elements (Gruel et al, 2011).…”