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Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
- Source :
- Cell. 166:1598
- Publication Year :
- 2016
- Publisher :
- Elsevier BV, 2016.
-
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.
- Subjects :
- 0106 biological sciences
0301 basic medicine
DNA, Plant
genetic processes
Amino Acid Motifs
Cell
Arabidopsis
Computational biology
Biology
Response Elements
01 natural sciences
Genome
Article
General Biochemistry, Genetics and Molecular Biology
Epigenesis, Genetic
03 medical and health sciences
chemistry.chemical_compound
medicine
natural sciences
Binding site
Transcription factor
Plant Proteins
Genetics
Indoleacetic Acids
Sequence Analysis, DNA
biology.organism_classification
DNA binding site
genomic DNA
030104 developmental biology
medicine.anatomical_structure
chemistry
Cistrome
Genome, Plant
DNA
010606 plant biology & botany
Transcription Factors
Subjects
Details
- ISSN :
- 00928674
- Volume :
- 166
- Database :
- OpenAIRE
- Journal :
- Cell
- Accession number :
- edsair.doi.dedup.....b2d279dd9d9d40d17ae167fbbcee8aa9