manner to modulate histone transcript levels. Rather
than acting as a direct repressor of gene transcription,
Yta7 could play a role in the post-transcriptional turn-
over of histone mRNA (Hereford et al. 1982). However,
since Yta7 has a putative bromodomain, transcriptional
gene regulatory activity, and associates with chromatin,
we favor a direct mechanism that would involve the
Yta7 protein binding to the histone loci (Tackett et al.
To determine if the Yta7 protein indeed directly
associated with the histone loci, we performed a series
of in vivo and in vitro binding studies. Genomewide
ChIP-chip of Yta7 revealed direct chromatin association
at 177 novel sites (Figure 6). Six of the top 10 binding
sites were the histone loci (Figure 6B). Yta7 binding was
observed across each ORF and intergenic region at the
histone loci. It is possible that such a binding proﬁle
could provide for formation of a chromatin state that
represses transcription. Binding of Yta7 to the histone
loci further strengthens the hypothesis that Yta7 is di-
rectly regulating histone gene transcription. Since Yta7
contains a histone H3 binding bromodomain-like region
(Figure 7A), we investigated whether there was a partic-
ular histone H3 PTM code that promoted Yta7 associa-
tion. Full-length Yta7 and Yta7bd were found to engage
histone H3 at the N terminus with a preferential asso-
ciation in the absence of tested PTMs (Figure 7, B–D).
Puriﬁcation of in vivo associated histone H3, revealed
signiﬁcant levels of H3K56ac, but this PTM did not
stimulate Yta7 protein association nor was H3K56ac
dependent upon Yta7 (Figure 7, C and E; Figure 8).
The in vivo puriﬁcation of H3K56ac with Yta7 would be
predicted because both are associated with the intergenic
regions at histone loci (Figure 6; Xu et al. 2005). Our
chromatin association studies are consistent with the
hypothesis that Yta7 mediated transcriptional repression
occurs through direct association at the histone loci.
The results presented shed light on the cellular pro-
gram needed for transcriptional regulation of the his-
tone genes. There appear to be multiple levels of
regulation that provide for proper histone dosage,
which is not surprising for a key cellular process. We
ﬁnd that Yta7 serves a key role in a previously unchar-
acterized branch of the histone gene transcriptional
regulatory pathway. Our ﬁndings also provide for a
broader understanding of the function of Yta7, which
seems to regulate transcription not only at transition
zones between silent and active chromatin, but also via a
dynamic mechanism at other chromosomal regions.
We thank Lauren Blair and Cagdas Tazearslan for critical reading,
Piotr Zimniak for access to real-time PCR instrumentation, Andrew
Krutchinsky and Markus Kalkum for assistance with mass spectromet-
ric hardware/software development, Cecile Artaud and Anastas
Pashov for ﬂow cytometry analysis, Tim Formosa for the spt16-11
strain, and Judith Recht for the H3K56R strain. The following National
Institutes of Health (NIH) grants supported this work: P20RR015569
(A.J.T., co-investigator), GM63959 (C.D.A.), RR022220 and
GM076547 (J.D.A.). A.J.T. acknowledges support from the Arkansas
Biosciences Institute and recognizes mass spectrometric support from
Sam Mackintosh and Chris Warthen funded through an NIH IDeA
Network of Biomedical Research Excellence grant (P20RR016460).
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