The study began when the group, in collaboration with Stowers proteomics experts Michael Washburn, Ph.D., and Laurence Florens, Ph.D., applied mass spectrometry analysis to identify any protein expressed in yeast Saccharomyces cerevisiae that bound to chromatin in regions patrolled by Set2. Those regions were readily apparent by the presence of Set2's red flag methyl group planted in a specific histone protein interacting with DNA.
"We knew that Set2 added this mark in the middle and downstream parts of genes to recruit de-acetylases," says the study's lead author Michaela Smolle, Ph.D., a postdoctoral researcher in the Workman lab. "But the proteomic search allowed us to cast a wide net for other proteins associated with that marka bit like fishing."
Among the fish caught was a component of a yeast chromatin "remodeler" known as Isw1, providing circumstantial evidence that the Set2 red flag attracts Isw1 as well as de-acetylases. Additional genomic experiments evaluating the entire genome of a yeast mutant lacking Set2 supported that idea: not only were the red methyl flags missing but the chromatin landscape was devoid of Isw1 as well.
To assess Isw1's biological function the group exploited yet another yeast mutant, this one lacking the ISW1 gene itself. Microarray analysis of global transcription in ISW1 CHD1 mutants showed widely perturbed gene expression marked by aberrant expression of RNA snippets rather than complete transcripts. Biologists view the presence of such "cryptic transcripts" as indicators of cellular stress.
Analysis of acetylation and methylation patterns in chromatin of ISW1 mutants revealed the probable cause: mutants showed ramped up histone exchange activity marked by excessive levels green-flagged pre-acetylated histones along the length of many genes, a condition likely favoring initiation of truncated RNAs.
"Our work shows that the Set2 methylation mark plays tw
|Contact: Gina Kirchweger|
Stowers Institute for Medical Research