title: Genome-wide mapping of transcription factor binding reveals developmental process integration and a fresh look at evolutionary dynamics.
abstract: How does evolution forge adaptive responses? Are many changes required or few? Just how complex are the transcriptional networks that control development? Diverse questions like these are being newly addressed by next-generation sequencing-based techniques. Facilitating a mechanistic understanding, these approaches reveal the direct in vivo interactions between transcription factors and their physical targets, combined with genome-scale readouts to comprehensively map adaptive gene regulatory networks (GRNs). Here I focus on pioneering work from the last 3 years that has leveraged these data to investigate diverse aspects of GRN circuitry controlling the reproductive transition in plants. These approaches have revealed surprising new functions for long-investigated key players in developmental programs and laid bare the basis for pleiotropy in many others, suggesting widespread process integration at the transcriptional level. Evolutionary questions begged by the recent deluge of GRN mapping data are being assessed anew, both by emerging work outside Arabidopsis thaliana and novel analyses within. These studies have swiftly exposed the distinctive power and adaptability of genome-wide GRN mapping and illustrate that this unique data type holds tremendous promise for plant biology.
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, 22 Oxford Street, Cambridge, Massachusetts 02138, USA. lyant@oeb.harvard.edu
authors.forename: Levi
authors.initials: L
authors.lastname: Yant
mesh_terms: D017360:Arabidopsis / Q000145:classification / Q000235:genetics / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping / Q000379:methods*; D019143:Evolution, Molecular; D035264:Flowers / Q000166:cytology / Q000254:growth & development; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D056426:Genetic Loci; D058685:Genetic Pleiotropy; D018398:Homeodomain Proteins / Q000235:genetics; D026161:MADS Domain Proteins / Q000235:genetics; D010802:Phylogeny; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; C418902:At5g10140 protein, Arabidopsis; D018398:Homeodomain Proteins; D026161:MADS Domain Proteins; C121158:SEP3 protein, Arabidopsis; D014157:Transcription Factors