A synergistic DNA logic predicts genome-wide chromatin accessibility

Tatsunori Hashimoto, Richard I. Sherwood, Daniel D. Kang, Nisha Rajagopal, Amira A. Barkal, Haoyang Zeng, Bart J.M. Emons, Sharanya Srinivasan, Tommi Jaakkola, David K. Gifford

Research output: Contribution to journalArticlepeer-review


Enhancers and promoters commonly occur in accessible chromatin characterized by depleted nucleosome contact; however, it is unclear how chromatin accessibility is governed. We show that log-additive cis-acting DNA sequence features can predict chromatin accessibility at high spatial resolution.We develop a new type of high-dimensional machine learning model, the Synergistic Chromatin Model (SCM), which when trained with DNase-seq data for a cell type is capable of predicting expected read counts of genome-wide chromatin accessibility at every base from DNA sequence alone, with the highest accuracy at hypersensitive sites shared across cell types. We confirm that a SCM accurately predicts chromatin accessibility for thousands of synthetic DNA sequences using a novel CRISPR-based method of highly efficient site-specific DNA library integration. SCMs are directly interpretable and reveal that a logic based on local, nonspecific synergistic effects, largely among pioneer TFs, is sufficient to predict a large fraction of cellular chromatin accessibility in a wide variety of cell types.

Original languageEnglish (US)
Pages (from-to)1430-1440
Number of pages11
JournalGenome Research
Issue number10
StatePublished - Oct 2016
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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