GenomicLinks: deep learning predictions of 3D chromatin interactions in the maize genome.

ABSTRACT: Gene regulation in eukaryotes is partly shaped by the 3D organization of chromatin within the cell nucleus. Distal interactions between cis-regulatory elements and their target genes are widespread, and many causal loci underlying heritable agricultural traits have been mapped to distal non-coding elements. The biology underlying chromatin loop formation in plants is poorly understood. Dissecting the sequence features that mediate distal interactions is an important step toward identifying putative molecular mechanisms. Here, we trained GenomicLinks, a deep learning model, to identify DNA sequence features predictive of 3D chromatin interactions in maize. We found that the presence of binding motifs of specific transcription factor classes, especially bHLH, is predictive of chromati

SUBMITTER: Schlegel L 

PROVIDER: S-EPMC11420838 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature