title: A resource for characterizing genome-wide binding and putative target genes of transcription factors expressed during secondary growth and wood formation in Populus.
abstract: Identifying transcription factor target genes is essential for modeling the transcriptional networks underlying developmental processes. Here we report a chromatin immunoprecipitation sequencing (ChIP-seq) resource consisting of genome-wide binding regions and associated putative target genes for four Populus homeodomain transcription factors expressed during secondary growth and wood formation. Software code (programs and scripts) for processing the Populus ChIP-seq data are provided within a publically available iPlant image, including tools for ChIP-seq data quality control and evaluation adapted from the human Encyclopedia of DNA Elements (ENCODE) project. Basic information for each transcription factor (including members of Class I KNOX, Class III HD ZIP, BEL1-like families) binding are summarized, including the number and location of binding regions, distribution of binding regions relative to gene features, associated putative target genes, and enriched functional categories of putative target genes. These ChIP-seq data have been integrated within the Populus Genome Integrative Explorer (PopGenIE) where they can be analyzed using a variety of web-based tools. We present an example analysis that shows preferential binding of transcription factor ARBORKNOX1 to the nearest neighbor genes in a pre-calculated co-expression network module, and enrichment for meristem-related genes within this module including multiple orthologs of Arabidopsis KNOTTED-like Arabidopsis 2/6.
authors.affiliation: USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.
authors.forename: Lijun
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Computer Science, University of California Davis, Davis, CA, 95618, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Ramsay
authors.affiliation: USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Zinkgraf
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, University of Umeå, SE-901-87, Umeå, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: Sundell
authors.affiliation: Umeå Plant Science Centre, Department of Plant Physiology, University of Umeå, SE-901-87, Umeå, Sweden.
authors.forename: Nathaniel Robert
authors.initials: NR
authors.lastname: Street
authors.affiliation: Department of Computer Science, University of California Davis, Davis, CA, 95618, USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Filkov
authors.affiliation: USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.|Department of Plant Biology, University of California Davis, Davis, CA, 95618, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Groover
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D007091:Image Processing, Computer-Assisted; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D032107:Populus / Q000235:genetics* / Q000254:growth & development; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014934:Wood / Q000235:genetics / Q000254:growth & development*; D057188:Workflow
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors
keywords: Populus trichocarpa; cambium; chromatin immunoprecipitation sequencing; secondary growth; transcription factor; wood formation