Overview

Genetic information (in the form of DNA) is ‘packaged’ in different ways and to different degrees into structures called chromosomes. Our lab is interested in what controls genome packaging and the dynamic fluctuations between different states of compaction. The degree of compaction profoundly affects gene expression and other DNA-templated processes such as replication and repair, and packaging mistakes in different regions of the genome have been associated with a range of human diseases.

 

A closer look at packaging

In the nucleus, genetic information is assembled into “chromatin” by wrapping around cores of small histone proteins to make basic repeating units called nucleosomes, which are often depicted as “beads on a string” along the DNA. Interactions between individual nucleosomes result in higher order folding and compaction of DNA. The histone proteins in the nucleosome core are often decorated with small chemical groups (modifications) that differ across regions of genetic information. Particular combinations of modifications make “codes” that direct more extensive packaging of chromatin. Our lab investigates the enzymes that make the codes by answering the following questions: Which enzymes do it?  On what parts of the genome do they act?  How are they specifically targeted to the correct genome region? When in the cell life cycle do they act?  How do they alter the code?  What molecular mechanism do they use, and which other protein partners are necessary?

 

Discoveries

So far, we have focused our efforts primarily on one family of enzymes called histone deacetylases (HDAC), which remove acetyl modifications from histones. For this research we use the ciliated protozoan Tetrahymena as a model system, and we have published the following new discoveries about the function of HDAC enzymes:

1. The class I histone deacetylase Thd1p assists in controlling nuclear DNA content and maintaining the integrity of chromosomes. It also plays a role in maintaining highly phosphorylated histone H1 in growing cells. (Wiley et al., 2005)

2. Thd1p is important for the normal reversible condensation of the genome under conditions of physiological stress, through mechanisms involving the regulation of H1 phosphorylation and core histone acetylation/deacetylation kinetics. (Parker et al., 2007)

3. The class II HDAC Thd2 acts on newly synthesized histones to remove deposition-related acetyl moieties and promotes chromatin maturation after DNA replication, including the proteolytic “clipping” of histone H3. The THD2 transcript is alternatively spliced, and the major form contains a putative inositol polyphosphate kinase (IPK) domain similar to Ipk2, an enzyme that promotes chromatin remodeling by SWI/SNF remodeling complexes. (Smith et al., 2008)

 

Current Questions and Projects

1. How are HDACs targeted to specific genome locations?

We are searching for factors that bind and target HDACs and histone modifications that HDACs bind to.

2. Which HDACs are involved in the formation and maintenance of heterochromatin domains with different biological functions?

We are mutating, or “knocking out” individual HDAC genes and examining the consequence to different bodies of heterochromatin.

3. How do HDACs promote chromatin condensation and heterochromatin formation?

We are investigating the way that HDACs cause chromatin to condense. Along the way, we are discovering important factors in this process. We are testing hypotheses related to altering patterns of modifications on the histone tails, histone modification (on/off) kinetics, histone proteolysis (“clipping”), and binding of non-histone proteins to chromatin.