DNA Sequence Changes Resulting from Codon Optimization Affect Gene Expression in <i>Pichia pastoris</i> by Altering Chromatin Accessibility.

ABSTRACT: Codon optimization is a widely employed strategy to enhance protein expression. However, it occasionally leads to unexpected transcriptional repression despite preserving amino acid sequences. This study investigates the mechanistic basis of such transcriptional attenuation by analyzing two gene candidates (0432 and Fluc) in the common expression chassis P. pastoris. Both genes experienced severe mRNA reduction following codon optimization. Evidenced by histone H3 chromatin immunoprecipitation (ChIP) and a DNase I hypersensitivity assay, gene sequences with transcriptional repression displayed elevated nucleosome occupancy and reduced chromatin accessibility. The above change was caused by an ORF sequence change independent of the promoter, since transcriptional attenu

SUBMITTER: Lu C 

PROVIDER: S-EPMC12029099 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature