RSAT 2015: Regulatory Sequence Analysis Tools

Abstract

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.

Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds

“…Moreover, unlike wild-type plants, the hb21 hb40 hb53-2 triple mutant had a similar number of secondary cauline (CII) branches Peak height is proportional to the similarity between sequence and consensus. Numbers indicate the peaks with the highest Rsat score (12). (G) Relative enrichment of GFP:BRC1 binding to sites 1-6.…”

Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis

“…The RSA-tool matrix scan (Medina-Rivera et al, 2015) was used to search for the occurrences of PSSMs from all clusters in the promoters (3 kb upstream of ATG) of all 49 core HRGs (Supplemental Data Set 3). Hypergeometric tests for enrichment were made by comparison with their occurrences in the full genome of A. thaliana (Supplemental Table 2).…”

“…PSSMs of each cluster were converted to tab-formatted matrices and used as a query in the RSA-tool matrix scan (Medina-Rivera et al, 2015). Upstream 3000-bp promoter sequences from the 49 core HRGs and from all 27,206 protein-coding genes of Arabidopsis were obtained from TAIR and screened for the number of occurrences and positions of the respective motif, using a statistical significance cutoff value of >4.5.…”

From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress

“…With RSAT, a tool specifically designed to detect regulatory signals in non‐coding sequences, we could retrieve the exact positions of experimentally determined motifs (known for most TFs but unavailable for ERF9, WRKY6, WRKY28, ZAT6, and MYB51) in the different promoters (Weirauch et al , 2014; Medina‐Rivera et al , 2015; Source Data for Appendix Fig S25). We could observe that the overall effect of the co‐regulation of two TFs depended on three factors.…”

“…For five genes, ERF9 , WRKY6 , WRKY28 , ZAT6, and MYB51 , the binding motif was not yet experimentally determined and was left out of the analysis. The PSSMs were converted from cis‐bp format to transfac format with the convert matrix tool on RSAT (http://floresta.eead.csic.es/rsat/; Medina‐Rivera et al , 2015). To retrieve the exact positions and significance of motifs in the different promoters, the pattern‐matching tool in RSAT was used (Source Data for Appendix Fig S25).…”