A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants

Abstract

Transcription factors (TFs) regulate gene expression by binding cis-regulatory elements, of which the identification remains an ongoing challenge owing to the prevalence of large numbers of nonfunctional TF binding sites. Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences (CNSs), which are functionally constrained and can greatly help in reducing the number of false-positive elements. In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in 10 dicot plants, yielding 1,032,291 CNSs associated with 243,187 genes. To annotate CNSs with TF binding sites, we made use of binding site information for 642 TFs originating from 35 TF families in Arabidopsis (Arabidopsis thaliana). In three species, the identified CNSs were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. To identify ultraconserved CNSs, we included genomes of additional plant families and identified 715 binding sites for 501 genes conserved in dicots, monocots, mosses, and green algae. Additionally, we found that genes that are part of conserved mini-regulons have a higher coherence in their expression profile than other divergent gene pairs. All identified CNSs were integrated in the PLAZA 3.0 Dicots comparative genomics platform (http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops.

Evolution of conserved noncoding sequences in Arabidopsis thaliana

“…random occurrence of the shortest CNS (15bp). TFBS colocalize with accessible chromatin in mammalian genomes, as do CNS as demonstrated previously in plants (4,(9)(10)(11)(12)(13)(14) .…”

Genome-wide Identification of PP2C Genes and Their Expression Profiling in Response to Drought and Cold Stresses in Medicago truncatula

“…The InterPro PP2C domain “IPR001932” was used to search the Plaza3.0 database ( http://bioinformatics.psb.ugent.be/plaza/ ) in order to identify PP2C candidate genes in M . truncatula 50 . Amino acid sequences (Supplementary Data 1 ), CDS sequences (Supplementary Data 2 ) and Genomic sequences (Supplementary Data 3 ) of PP2C genes in M .…”

STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species

“…In animals, many CNSs are large (R100 bp) (Stephen et al, 2008), while different analyses in plants have primarily identified smaller (15-50 bp) CNSs (Thomas et al, 2007;Baxter et al, 2012;Haudry et al, 2013;Turco et al, 2013). Various algorithmic approaches are currently employed to identify CNSs in plants including both manual (Thomas et al, 2007) and automated (Turco et al, 2013) curation of BLASTN results, global alignments of sliding windows of promoter regions (Baxter et al, 2012), the use of whole-genome alignment algorithms (Haudry et al, 2013), alignment-independent detection of enriched IUPAC motifs (De Witte et al, 2015), and searches for biologically defined transcription factor binding sites across orthologous genes (Van de Velde et al, 2016). The majority of these approaches are either based on two-at-a-time sequence alignments (Baxter et al, 2012;Haudry et al, 2013;Turco et al, 2013) and/or do not retain information on conserved microsynteny within the promoter (De Witte et al, 2015;Van de Velde et al, 2016).…”