A Collection of Conserved Noncoding 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 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.
Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.).
Jan
0000-0001-7742-1266
J
Van de Velde
Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.).
Michiel
0000-0002-1873-2563
M
Van Bel
Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.).
Dries
0000-0002-8975-2801
D
Vaneechoutte
Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.) klaas.vandepoele@psb.vib-ugent.be.
Klaas
0000-0003-4790-2725
K
Vandepoele
D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D017124:Conserved Sequence / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics*; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D019684:Magnoliopsida / Q000235:genetics*; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
D021901:DNA, Intergenic; D014157:Transcription Factors