title: A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.
abstract: Understanding the mechanisms underlying gene regulation is paramount to comprehend the translation from genotype to phenotype. The two are connected by gene expression, and it is generally thought that variation in transcription factor (TF) function is an important determinant of phenotypic evolution. We analyzed publicly available genome-wide chromatin immunoprecipitation experiments for 27 TFs in Arabidopsis thaliana and constructed an experimental network containing 46,619 regulatory interactions and 15,188 target genes. We identified hub targets and highly occupied target (HOT) regions, which are enriched for genes involved in development, stimulus responses, signaling, and gene regulatory processes in the currently profiled network. We provide several lines of evidence that TF binding at plant HOT regions is functional, in contrast to that in animals, and not merely the result of accessible chromatin. HOT regions harbor specific DNA motifs, are enriched for differentially expressed genes, and are often conserved across crucifers and dicots, even though they are not under higher levels of purifying selection than non-HOT regions. Distal bound regions are under purifying selection as well and are enriched for a chromatin state showing regulation by the Polycomb repressive complex. Gene expression complexity is positively correlated with the total number of bound TFs, revealing insights in the regulatory code for genes with different expression breadths. The integration of noncanonical and canonical DNA motif information yields new hypotheses on cobinding and tethering between specific TFs involved in flowering and light regulation.
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Ken S
authors.identifier: http://orcid.org/0000-0001-5831-0536
authors.initials: KS
authors.lastname: Heyndrickx
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Jan
authors.identifier: http://orcid.org/0000-0001-7742-1266
authors.initials: J
authors.lastname: Van de Velde
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Congmao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
authors.forename: Detlef
authors.identifier: http://orcid.org/0000-0002-2114-7963
authors.initials: D
authors.lastname: Weigel
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium klaas.vandepoele@psb.vib-ugent.be.
authors.forename: Klaas
authors.identifier: http://orcid.org/0000-0003-4790-2725
authors.initials: K
authors.lastname: Vandepoele
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D059372:Nucleotide Motifs / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D018744:DNA, Plant; D014157:Transcription Factors