Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops

Deng, Yajing; Tang, Li; Zhou, Xiaolong; Wang, Wenkang; Li, Min

doi:10.1016/j.isci.2022.105687

Cited by 2 publications

(1 citation statement)

References 56 publications

(69 reference statements)

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“…Although many computational models that can predict CTCF-mediated loops with varied sensitivity and specificity (Cao et al, 2021; Deng et al, 2022; Ibn-Salem and Andrade-Navarro, 2019; Kai et al, 2018; Kuang and Wang, 2021; Lv et al, 2021; Matthews and Waxman, 2018; Oti et al, 2016; Wang et al, 2021; Xi and Beer, 2021; Zhang et al, 2018), they usually learn from CTCF ChIA-PET data and barely evaluate the regulatory potential and loop attribute among different types of CBS. Here, we applied cohesin ChIA-PET/ChIP-seq data, ChromHMM-predicted insulator, and strict CTCF binding evidence to specifically analyze CTCF binding patterns at three types of CTCF-mediated CREs.…”

Section: Discussionmentioning

confidence: 99%

Inferring CTCF binding patterns and anchored loops across human tissues and cell types

Wang

et al. 2022

Preprint

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How CTCF recognizes insulators to exert chromosome barrier or enhancer blocking effects remains to be interrogated. Despite many computational tools were developed to predict CTCF-mediated loops qualitatively or quantitatively, few could specially evaluate the insulative potential of DNA sequence at CTCF binding sites (CBSs) and how it affects chromatin loop formation. Here, we developed a deep learning model, DeepAnchor, to precisely predict the insulative potential of CBS. By incorporating base-wise genomic/epigenomic features, we revealed distinct chromatin and sequence features for CTCF-mediated insulation at a high resolution, such as two sequence motifs flanking the core CTCF motif only at positive CTCF insulators. Besides, we leveraged the predicted insulator score to optimize the loop extrusion model and achieved the best performance in predicting CTCF-anchored loops. We established a compendium of context-specific CTCF-anchored loops across 52 human tissue/cell types and found that genomic disruption of CTCF-anchored loops may represent a general causal mechanism of disease pathogenesis. These computational models, together with the established resource, could facilitate the mechanistic research on how the CTCF-mediated insulation shapes context-specific gene regulation in cell development and disease progression.

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Section: Discussionmentioning

confidence: 99%

Inferring CTCF binding patterns and anchored loops across human tissues and cell types

Wang

et al. 2022

Preprint

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Inferring CTCF-binding patterns and anchored loops across human tissues and cell types

Fan

et al. 2023

Patterns

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Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops

Cited by 2 publications

References 56 publications

Inferring CTCF binding patterns and anchored loops across human tissues and cell types

Inferring CTCF binding patterns and anchored loops across human tissues and cell types

Inferring CTCF-binding patterns and anchored loops across human tissues and cell types

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