Unknown,Transcriptomics,Genomics,Proteomics

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Benchmark study of different chromatin isolation methods using the E2Fa transcription factor


ABSTRACT: Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation (ChIP), this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis thaliana cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional ChIP and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and co-expression network analyses demonstrates the quality of the E2Fa TChAP-seq data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency. Illumina Seq analysis of E2Fa bound DNA elements isolated using different chromatin isolation methods. BioProject PRJNA172013; SRA study ID SRP014713

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Ken Heyndrickx 

PROVIDER: E-GEOD-53422 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification.

Verkest Aurine A   Abeel Thomas T   Heyndrickx Ken S KS   Van Leene Jelle J   Lanz Christa C   Van De Slijke Eveline E   De Winne Nancy N   Eeckhout Dominique D   Persiau Geert G   Van Breusegem Frank F   Inzé Dirk D   Vandepoele Klaas K   De Jaeger Geert G  

Plant physiology 20140122 3


Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation, this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis (Arabidopsis thaliana) cells by tandem ch  ...[more]

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