Next-Generation Sequencing Applied to Flower Development: ChIP-Seq

Abstract

Over the past 20 years, classic genetic approaches have shown that the developmental program underlying flower formation involves a large number of transcriptional regulators. However, the target genes of these transcription factors, as well as the gene regulatory networks they control, remain largely unknown. Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-Seq), which allows the identification of transcription factor binding sites on a genome-wide scale, has been successfully applied to a number of transcription factors in Arabidopsis. The ChIP-Seq procedure involves chemical cross-linking of proteins to DNA, followed by chromatin fragmentation and immunoprecipitation of specific protein-DNA complexes. The regions of the genome bound by a specific transcription factor can then be identified after next-generation sequencing.

Gene network analysis of Arabidopsis thaliana flower development through dynamic gene perturbations

“…However, as both FACS and LCM require expensive instrumentation and involve time‐consuming procedures, their general applicability is limited (Wang et al ., ). Furthermore, use of these techniques for genome‐wide localization studies through chromatin immunoprecipitation, as well as for proteomic or metabolomic approaches, is limited as large quantities of tissue are required for these types of analyses (Smaczniak et al ., ; Graciet et al ., ). To facilitate the isolation of homogenous stage‐specific floral tissue, a flower induction system may be used that allows collection of hundreds of synchronized floral buds from a single plant (Wellmer et al ., ).…”