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A Comprehensive Atlas of Arabidopsis Regulatory DNA [DAP-seq]

ABSTRACT: We have developed a high throughput, next-generation DNA sequencing assay for rapid transcription factor binding site (TFBS) discovery in a genomic context. DNA affinity purification sequencing (DAP-seq), which uses affinity-purified transcription factors (TFs) to capture genomic DNA fragments, was applied to all 1,725 Arabidopsis thaliana TFs. High confidence TFBS motifs for 529 TFs and genome-wide enrichment maps for 349 factors were identified. In total,~ 2.7 million TFBS were identified which predict thousands of TF target genes enriched for known and novel functions.. Comparison of TF-binding using cytosine-methylated and -unmethylated genomic DNA revealed a 2-50 fold inhibition at methylated motifs for ~82% (264) of factors tested while 4.6% (15) showed stronger binding to methylated motifs. Finally, we describe how binding of Arabidopsis and maize Auxin Response Factors (ARFs) at phased motif repeats is highly enriched at ARF target gene promoters and how this architecture may allow for stabilization of dimers/multimers.

ORGANISM(S): Arabidopsis thaliana Zea mays

PROVIDER: GSE60141 | GEO | 2016/05/25

SECONDARY ACCESSION(S): PRJNA257556

REPOSITORIES: GEO

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The DNA affinity purification DAP-Seq assay [ChIP-seq]

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Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (validation)

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Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (different concentrations)

2013-03-29 | GSE44436 | GEO

Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (validation)

2013-03-29 | GSE44437 | GEO

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