Abstract:
:The CCCTC-binding zinc-finger protein (CTCF)-mediated network of long-range chromatin interactions is important for genome organization and function. Although this network has been considered largely invariant, we find that it exhibits extensive cell-type-specific interactions that contribute to cell identity. Here, we present Lollipop, a machine-learning framework, which predicts CTCF-mediated long-range interactions using genomic and epigenomic features. Using ChIA-PET data as benchmark, we demonstrate that Lollipop accurately predicts CTCF-mediated chromatin interactions both within and across cell types, and outperforms other methods based only on CTCF motif orientation. Predictions are confirmed computationally and experimentally by Chromatin Conformation Capture (3C). Moreover, our approach identifies other determinants of CTCF-mediated chromatin wiring, such as gene expression within the loops. Our study contributes to a better understanding about the underlying principles of CTCF-mediated chromatin interactions and their impact on gene expression.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Kai Y,Andricovich J,Zeng Z,Zhu J,Tzatsos A,Peng Wdoi
10.1038/s41467-018-06664-6subject
Has Abstractpub_date
2018-10-11 00:00:00pages
4221issue
1issn
2041-1723pii
10.1038/s41467-018-06664-6journal_volume
9pub_type
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