Research in my laboratory is aimed at deciphering mechanisms of gene regulation as governed by chromatin structure. Chromatin boundary elements function to delimit the domains of active and inactive chromatin. A major question in eukaryotic gene regulation is how heterochromatin and euchromatin are physically and functionally separated by chromatin boundaries.
Boundary elements are divided into two classes: insulators are DNA sequences that block enhancer activation of a promoter, preventing inappropriate gene activation. Barriers are sequences that block the propagation of heterochromatin, thereby separating domains of active and inactive chromatin. In both cases, the function is to prevent regulatory regions from a given chromatin domain from inappropriately affecting another region.
Using the yeast Saccharomyces cerevisiae as a model system, we have
identified several DNA elements that are heterochromatin barriers. One is a
unique tRNA gene (tDNA) located downstream from the silenced HMR locus.
Current genetic and biochemical studies center on analyzing mechanisms of barrier
function, and we have found that bromodomain proteins, which bind to acetyllysine
moieties on histones and other proteins, are important for barrier integrity.
We are currently focusing on the molecular characterization of the yeast YTA7
gene, which codes for one such bromodomain containing protein.
We are also assessing the potential global role of RNA polymerase III promoters
as chromatin boundaries. We have found that other tDNAs in the yeast genome
can act as boundary elements, suggesting a more general extra-transcriptional
role for RNA polymerase III transcribed genes in sculpting genome architecture
and function.
RNA Polymerase III and Polymerase II Promoter Complexes are Heterochromatin
Barriers in Saccharomyces cerevisiae.
David Donze and Rohinton T. Kamakaka
EMBO Journal, Vol. 20 No. 3, 520-531 (2001)
Sir2p Exists in Two Nucleosome-binding Complexes with Distinct Deacetylase Activities. Sonja Ghidelli, David Donze, Namrita Dhillon, and Rohinton T. Kamakaka EMBO Journal, Vol. 20, No. 16, 4522-4535 (2001)
Braking the Silence: How Heterochromatic Gene Repression is Stopped in its
Tracks. David Donze and Rohinton T. Kamakaka
Bioessays, Vol. 24, No. 4, 344-349 (2002)
Breaking the Histone Code of Silence: The Propagation and Blocking of Heterochromatin.
David Donze
Current Organic Chemistry, Vol. 8, 211-221 (2004)
The S. cerevisiae TRT2 tRNAThrgene upstream of STE6 is a barrier
to repression in MATα cells and exerts a potential tRNA position effect
in MATa cells. Tiffany A. Simms, Elsy C. Miller, Nicolas P.
Buisson, Nithya Jambunathan, and David Donze
Nucleic Acids Research, Vol. 32, 5206-5213 (2004)
Modulation of yeast genome expression in response to defective RNA polymerase
III-dependent transcription.
Christine Conesa, Roberta Ruotolo, Pascal Soularue, Tiffany A. Simms, David
Donze, André Sentenac, and Giorgio Dieci
Mol. Cell. Biol. Vol. 25, 8631-8642 (2005)
Multiple bromodomain genes are involved in restricting the spread of heterochromatic
silencing at the S. cerevisiae HMR-tRNA boundary.
Nithya Jambunathan, Adam W. Martinez, Elizabeth C. Robert, Nneamaka B. Agochukwu,
Megan E. Ibos, Sandra L. Dugas, and David Donze.
Genetics, Vol. 171, 913-922 (2005)
Nhp6 participates in tRNA gene transcription and heterochromatin barrier function in S. cerevisiae.
Priscilla Braglia, David Donze, and Giorgio Dieci
Submitted to Mol. Cell. Biol., May 2006