Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines.

ABSTRACT:

Background

Genome-wide landscape of alternative promoter use remains unknown. We determined expression profiles of promoters in 26 lung adenocarcinoma cell lines using the transcriptional start site-sequencing data and proposed an index 'canonical promoter usage' to quantify the diversity of alternative promoter usage.

Methods

Transcriptional start site-sequencing and other datasets were obtained from the DataBase of Transcriptional Start Sites. Transcriptional start site-sequencing read clusters were mapped onto RefGene to determine the promoters. Commonly used promoters were designated as canonical promoters. The sequence logos, CpG islands, DNA methylation and histone modifications of canonical and non-canonical promoters were examined. Canonical promoter usage was calcul

SUBMITTER: Hamaya Y 

PROVIDER: S-EPMC9885743 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature