Predicting Differentially Methylated Cytosines in TET and DNMT3 Knockout Mutants via a Large Language Model.

ABSTRACT: DNA cytosine methylation is an epigenetic marker which regulates many cellular processes. Mammalian genomes typically maintain consistent methylation patterns over time, except in specific regulatory regions like promoters and certain types of enhancers. The dynamics of DNA methylation is controlled by a complex cellular machinery, in which the enzymes DNMT3 and TET play a major role. This study explores the identification of differentially methylated cytosines (DMCs) in TET and DNMT3 knockout mutants in mice and human embryonic stem cells. We investigate (i) whether a large language model can be trained to recognize DMCs in human and mouse from the sequence surrounding the cytosine of interest, (ii) whether a classifier trained on human knockout data can predict DMCs in the mouse genome (

SUBMITTER: Sereshki S 

PROVIDER: S-EPMC11398415 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature