The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model.

ABSTRACT: Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species ev

SUBMITTER: Ouyang Z 

PROVIDER: S-EPMC11260490 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature