Predicting gene expression state and prioritizing putative enhancers using 5hmC signal.

ABSTRACT:

Background

Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC, generated through the action of TET dioxygenases at gene bodies of actively-transcribed genes and at active or lineage-specific enhancers. Although such enrichments are reported for 5hmC, to date, predictive models of gene expression state or putative regulatory regions for genes using 5hmC have not been developed.

Results

Here, by using only 5hmC enrichment in genic regions and their vicinity, we develop neural network models that predict gene expression state across 49 cell types. We show that our deep neural network models distinguish high vs low expressi

SUBMITTER: Gonzalez-Avalos E 

PROVIDER: S-EPMC11145787 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature