Negative Regulation of Sir-dependent Silencing by a Universally
Conserved Histone Variant.
Marc Meneghini (1), Shivkumar Venkatasubrahmanyam (1), Michelle
Wu (1), William Hwang (1), Amy Tong (2), Charlie Boone (2), Hiten
Madhani (1)
(1) Biochemistry and Biophysics, University of California SF, 513
Parnassus Avenue, San Francisco, CA 94143, USA;
(2) Banting and Best Department of Medical Research, University of
Toronto, 112 College St., Toronto, ON M5G 1L6, Canada
Despite recent progress in identifying the mechanisms by which Sir-dependent gene silencing initiates and spreads, relatively little is
known about how this presumably autocatalytic process is inhibited. We
investigated the function of the poorly understood yet universally
conserved histone variant H2A.Z (encoded by HTZ1 in yeast), which
replaces H2A in 10% of nucleosomes. Microarray analysis revealed that
H2A.Z-dependent genes cluster strikingly near telomeres suggesting that
H2A.Z insulates these genes from telomeric silencing. Consistent with
this model, the expression defect of half of these genes was reversed by
removal of the histone deacetylase Sir2. In addition, the expression
defect in htz1delta of a cluster of genes proximal to the
HMR silent cassette can be reversed by either deletion of
SIR2 or a deletion of HMR that includes the silencers.
These data suggest that, in htz1 cells, silencing spreads from
HMR to the adjacent region. Quantitative chromatin
immunoprecipitation analysis of the disribution of Sir2 and histone
acetylation in the HMR-proximal region and a strongly anti-silenced telomeric region supports this view. A genome-wide screen
identified >20 genes whose deletion produces a synthetic lethal or very
sick phenotype with htz1delta. One of these, SIF2 (Sir4-interacting factor 2), is a known antagonist of silencing. Consistent
with the anti-silencing model, the severe growth defect of htz1
sif2 can be partially suppressed by deletions of SIR2 or
SIR3.
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