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Series GSE55306 Query DataSets for GSE55306
Status Public on Dec 02, 2014
Title ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints
Organisms Drosophila melanogaster; Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP, Drosophila NFkB, Twist and Max—showed that it outperformed existing ChIP protocols in resolution and specificity, pinpointed relevant binding sites within enhancers containing multiple binding motifs, and allowed for the analysis of in vivo binding specificities. Notably, we show that Max frequently interacted with DNA sequences next to its motif, and that this binding pattern correlated with local DNA-sequence features such as DNA shape. ChIP-nexus will be broadly applicable to the study of in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.
Overall design ChIP-nexus was performed against Dorsal (Drosophila melanogaster embryos), Twist (Drosophila melanogaster embryos), Max (Drosophila melanogaster S2 cells), Myc (Drosophila melanogaster S2 cells), and TBP (Human K562 cells)
Contributor(s) He Q, Johnston J, Zeitlinger J
Citation(s) 25751057
Submission date Feb 24, 2014
Last update date May 15, 2019
Contact name Julia Zeitlinger
Organization name Stowers Institute for Medical Research
Lab Zeitlinger Lab
Street address 1000 E 50th St
City Kansas City
State/province MO
ZIP/Postal code 64110
Country USA
Platforms (3)
GPL10942 AB SOLiD System 3.0 (Drosophila melanogaster)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (18)
GSM1333887 Dorsal ChIP-nexus (Drosophila embryos) Rep 1
GSM1333888 Dorsal ChIP-nexus (Drosophila embryos) Rep 2
GSM1333889 Max ChIP-nexus (Drosophila S2 cells) Rep 1
BioProject PRJNA239257
SRA SRP038893

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Supplementary file Size Download File type/resource
GSE55306_RAW.tar 937.6 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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