SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks.

ABSTRACT: Silencers are repressive cis-regulatory elements that play crucial roles in transcriptional regulation. Experimental methods for identifying silencers are always costly and time-consuming. Computational methods, which relies on genomic sequence features, have been introduced as alternative approaches. However, silencers do not have significant epigenomic signature. Therefore, we explore a new way to computationally identify silencers, by incorporating chromatin structural information. We propose the SilenceREIN method, which focuses on finding silencers on anchors of chromatin loops. By using graph neural networks, we extracted chromatin structural information from a regulatory element interaction network. SilenceREIN integrated the chromatin structural information with linear genomic sign

SUBMITTER: Pan JH 

PROVIDER: S-EPMC10782921 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature