Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.

ABSTRACT:

Background

Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not to take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult.

Results

Here, we develop methods to identify transcription factor binding sites in modified DNA. Our models expand the standard A/C/G/T DNA alphabet to include cytosine modifications. We develop Cytomod to create modified genomic sequences and we also enhance the MEME Suite, adding the capacity to handle custom alphabets. We

SUBMITTER: Viner C 

PROVIDER: S-EPMC10773111 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature