Chromatin mediation of a transcriptional memory effect in yeast

G3 : Genes - Genomes - Genetics
Emily PaulRandall H Morse

Abstract

Previous studies have described a transcriptional "memory effect," whereby transcript levels of many Abf1-regulated genes in the budding yeast Saccharomyces cerevisiae are undiminished even after Abf1 has dissociated from its regulatory sites. Here we provide additional support for this effect and investigate its molecular basis. We show that the effect is observed in a distinct abf1 ts mutant from that used in earlier studies, demonstrating that it is robust, and use chromatin immunoprecipitation to show that Abf1 association is decreased similarly from memory effect and transcriptionally responsive genes at the restrictive temperature. We also demonstrate that the association of TATA-binding protein and Pol II decreases after the loss of Abf1 binding for transcriptionally responsive genes but not for memory effect genes. Examination of genome-wide nucleosome occupancy data reveals that although transcriptionally responsive genes exhibit increased nucleosome occupancy in abf1 ts yeast, the promoter regions of memory effect targets show no change in abf1 ts mutants, maintaining an open chromatin conformation even after Abf1 eviction. This contrasting behavior reflects different inherent propensity for nucleosome formation betwe...Continue Reading

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Citations

Jun 6, 2016·Current Genetics·Beatrice FermiGiorgio Dieci
Dec 7, 2020·Molecular Systems Biology·Wim J de JongeFrank Cp Holstege
Apr 10, 2018·Biophysical Journal·Răzvan V Chereji, David J Clark

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Datasets Mentioned

BETA
E-MTAB-3208

Methods Mentioned

BETA
footprinting
immunoprecipitation
ChIP
ChIP-seq
PCR
ChIP-chip

Software Mentioned

ArchTEx
Integrative Genomics Viewer
MEME
CERES

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