We are interested in understanding how chromatin structure is regulated in vivo.
In eukaryotic cells, DNA is packaged into chromatin. This allows compact storage of the genome, but limits the access of DNA binding proteins to their targets. Therefore, chromatin structure strongly influences all the processes that rely on protein-DNA interactions, such as transcription, DNA replication, repair and recombination. We are therefore elucidating the mechanisms that regulate chromatin structure in vivo to understand how these fundamental processes can be achieved. We are using the budding yeast Saccharomyces cerevisiae as a model organism, because functions of genes can be studied most readily by genetic and biochemical approaches in this system but easily applied to multicellular eukaryotes.
At the current time, our interest is focused in the following areas. One goal is to understand the mechanisms of ATP-dependent chromatin remodeling. To address this issue, we are studying a few ATPases that have potent biochemical activities to change chromatin structure. These enzymes have been known to be required for normal transcriptional regulation and DNA replication, as well as maintenance of chromosome structure. However, how they function at the molecular level is not well understood. For example, it is not understood how they might alter nucleosome structure to allow the transctional machinery access to promoters. We are using molecular genetic, biochemical and genomic approaches to understand what these factors do, and how they function in vivo.
We also study how chromatin structure affects DNA replication. It is a complete mystery how the DNA replication machinery can copy the genome with complete precision in the context of the complex and compact chromatin template that it must duplicate. We are currently focusing on how histone modifications and ATP-dependent chromatin remodeling affect DNA replication.
We are also trying to understand how nucleosome positions are determined in vivo. The nucleosome is the fundamental unit of chromatin, which has 147 base pairs of DNA wrapped around eight copies of core histones. It has been known that many parameters, including the physical property of DNA, DNA binding proteins, ATP-dependent chromatin structure and passage of RNA polymerases, can affect nucleosome positioning. However, how these parameters work together to determine nucleosome position in vivo is not known. We are using genomic approaches to uncover the fundamental rules that determine the positioning of nucleosomes in vivo.
Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi.. Nature structural & molecular biology.. 2016.
Systematic approaches to identify functional lncRNAs.. Current opinion in genetics & development. 37:46-50.. 2016.
Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry.. Molecular cell. 59(5):732-43.. 2015.
The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.. Genomics data. 6:245-8.. 2015.
A Molecular Off Switch for Transcriptional Quiescence.. Cell cycle (Georgetown, Tex.). 14(23):3667-8.. 2015.
Chromatin remodeling factors isw2 and ino80 regulate checkpoint activity and chromatin structure in s phase.. Genetics. 199(4):1077-91.. 2015.
ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape.. Genes & development. 28(21):2348-60.. 2014.
Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM.. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]. 108:21.28.1-21.28.16.. 2014.
Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome.. PloS one. 9(12):e114545.. 2014.
DNA looping-dependent targeting of a chromatin remodeling factor.. Cell cycle (Georgetown, Tex.). 12(12):1809-10.. 2013.
ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies.. PLoS genetics. 9(2):e1003317.. 2013.
DNA looping facilitates targeting of a chromatin remodeling enzyme.. Molecular cell. 50(1):93-103.. 2013.
An efficient purification system for native minichromosome from Saccharomyces cerevisiae.. Methods in molecular biology (Clifton, N.J.). 833:115-23.. 2012.
ATP-dependent chromatin remodeling factors tune S phase checkpoint activity.. Molecular and cellular biology. 31(22):4454-63.. 2011.
SnapShot: Chromatin remodeling: ISWI.. Cell. 144(3):453-453.e1.. 2011.
Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription.. Molecular and cellular biology. 30(21):5110-22.. 2010.
Dynamic changes in histone acetylation regulate origins of DNA replication.. Nature structural & molecular biology. 17(4):430-7.. 2010.
Opening windows to the genome.. Cell. 137(3):400-2.. 2009.
ATP-dependent chromatin remodeling shapes the DNA replication landscape.. Nature structural & molecular biology. 15(5):477-84.. 2008.