A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants

Transcription factors (TFs) regulate gene expression by binding cis-regulatory elements, of which the identification remains an on-going challenge owing to the prevalence of large numbers of non-functional TF binding sites. Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved non-coding 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 ten dicot plants, yielding 1,032,291 CNSs associated with 243,187 genes. To annotate CNSs with TFBSs, we made use of binding site information of 642 TFs originating from 35 TF families in Arabidopsis. In three species, the identified CNSs were evaluated using TF chromatin immunoprecipitation sequencing (ChIP-Seq) data resulting in significant overlap for the majority of datasets. To identify ultra-conserved 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 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 dataset in a user-friendly platform enables the exploration of functional non-coding DNA to study gene regulation in a variety of plant species, including crops.

Van de Velde, J., Van Bel, M., Van Eechoutte, D., Vandepoele, K. (2016) A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants. Plant Physiol. pp.00821.2016. [Epub ahead of print].

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