title: Visualizing and characterizing in vivo DNA-binding events and direct target genes of plant transcription factors.
abstract: Physical interactions between transcription factors and specific DNA sites are essential for gene regulation. Recent progress in genome-wide in vivo techniques, like chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-SEQ), enables plant researchers to generate genome-wide, high-resolution DNA-binding maps of transcription factors. These new types of data require the use of advanced bioinformatic tools in order to understand the molecular mechanisms of functional specificity and target gene regulation by transcription factors. Here, we will review the use of a genome browser to visualize genome-wide DNA-binding maps of plant transcription factors along with other publicly available data and the program MEME to determine DNA sequence motifs in the bound regions. We also describe a tool for functional classification of target genes using GO annotations. Analysis of transcriptional regulatory networks requires the integration of multiple types of data, and this chapter aims at giving an overview about different bioinformatic approaches for meta-analysis and data integration.
authors: Business Unit Bioscience, Plant Research International, Wageningen, The Netherlands. jose.muino@wur.nl
authors: Jose M
authors: JM
authors: Muiño
authors: Gerco C
authors: GC
authors: Angenent
authors: Kerstin
authors: K
authors: Kaufmann
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods; D018744:DNA, Plant / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D053263:Gene Regulatory Networks / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010940:Plant Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D052156:SELEX Aptamer Technique / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000032:analysis* / Q000235:genetics / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D004268:DNA-Binding Proteins; D010940:Plant Proteins; D014157:Transcription Factors