gryderart / aqua-hichip

Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.

AQuA-HiChIP

Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.

DEMO instructions: https://github.com/GryderArt/AQuA-HiChIP/blob/master/README_DEMO.NatureProtocols.txt

Method preprint at Protocol Exchange: https://www.nature.com/protocolexchange/protocols/7121

UPDATE, Feb 2020 Nature Protocols now available! https://www.nature.com/articles/s41596-019-0285-9

for questions or comments, feel free to contact berkley dot gryder at gmail dot com

AQuA-HiChIP uncovers global changes in protein-mediated contact frequency

Induced chromatin interactions anchored with protein contacts will be readily differentiated using AQuA-HiChIP, but with normalizing by total interactive paired-end tags (PETs), differential interaction frequencies may produce false positives or false negatives.

Comparison of HiChIP and AQuA-HiChIP between treated and untreated cells reveals the difference between apparent and absolute contact changes

Direct comparison of AQuA-HiChIP and non-reference normalized samples indicates apparent chromatin interaction changes anchored in H3-acetylation marks after rapid HDAC inhibition. These changes in architecture are focused near super enhancers (SEs) proximal to a TSS on chr11.