Details

Autor(en) / Beteiligte

• Van de Velde, Jan
• Van Bel, Michiel
• Vaneechoutte, Dries
• Vandepoele, Klaas

Titel

A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants1[OPEN]

Ist Teil von

• Plant physiology (Bethesda), 2016-06, Vol.171 (4), p.2586-2598

Ort / Verlag

American Society of Plant Biologists

Erscheinungsjahr

2016

Link zum Volltext

Quelle

Elektronische Zeitschriftenbibliothek (Open access)

Beschreibungen/Notizen

• Comparative sequence analysis delineates conserved noncoding sequences that are functionally relevant, a subset of which are conserved throughout green plants. Transcription factors ( TF s) 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 ( CNS s), 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 CNS s in 10 dicot plants, yielding 1,032,291 CNS s associated with 243,187 genes. To annotate CNS s with TF binding sites, we made use of binding site information for 642 TF s originating from 35 TF families in Arabidopsis ( Arabidopsis thaliana ). In three species, the identified CNS s were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. To identify ultraconserved CNS s, 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 CNS s 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.