Identification of lineage-specific cis-trans regulatory networks related to kiwifruit ripening initiation.

ABSTRACT: Previous research on the ripening process of many fruit crop varieties typically involved analyses of the conserved genetic factors among species. However, even for seemingly identical ripening processes, the associated gene expression networks often evolved independently, as reflected by the diversity in the interactions between transcription factors (TFs) and the targeted cis-regulatory elements (CREs). In this study, explainable deep learning (DL) frameworks were used to predict expression patterns on the basis of CREs in promoter sequences. We initially screened potential lineage-specific CRE-TF interactions influencing the kiwifruit ripening process, which is triggered by ethylene, similar to the corresponding processes in other climacteric fruit crops. Some novel regulatory relations

SUBMITTER: Kuwada E 

PROVIDER: S-EPMC11629749 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature