Identifying improved sites for heterologous gene integration using ATAC-seq

We analyzed the chromatin accessibility and nucleosome positioning by ATAC-seq of both null and transgene-expressing strains of Komagataella phaffii (Pichia pastoris) under different growth conditions. These data enabled identification of the features that determine performance of various integration sites for transgene expression. Understanding chromatin accessibility and nucleosome positioning can provide further clarity into gene regulation and expression broadly in this organism. Overall design: ATAC-seq was performed on Komagataella phaffii NRRL Y-11430 after 24h growth on glycerol-containing medium as well as after an additional 24h growth on methanol-containing medium. Four strains were analyzed: 1 null (wild-type) strain and 3 transgene-expressing strains with modified pPICZA (Invitrogen) vectors integrated upstream of the AOX1, DAS2, or OLE1 genes. For all samples, accessibility peaks and nucleosome positioning were determined.