title: Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.
abstract: The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TF-specific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
authors.forename: Ronan C
authors.initials: RC
authors.lastname: O'Malley
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
authors.forename: Shao-Shan Carol
authors.initials: SC
authors.lastname: Huang
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
authors.forename: Liang
authors.initials: L
authors.lastname: Song
authors.affiliation: Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
authors.forename: Mathew G
authors.initials: MG
authors.lastname: Lewsey
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Bartlett
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Galli
authors.affiliation: Waksman Institute, Rutgers University, Piscataway, NJ 08854-8020, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Gallavotti
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Rd., La Jolla, CA 92037, USA. Electronic address: ecker@salk.edu.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
mesh_terms: D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D018745:Genome, Plant; D007210:Indoleacetic Acids / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics; D020218:Response Elements; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D018744:DNA, Plant; D007210:Indoleacetic Acids; D010940:Plant Proteins; D014157:Transcription Factors