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Patricia J. Pukkila


Professor (Emerita)

Contact Information

Office: 201 Fordham Hall
Email: pukkila[at]unc.edu
Office Phone: 919-967-4476

Affiliations

None- I retired from UNC-Chapel Hill in 2013

Research Description

Synopsis

The source of specificity for accurate chromosome pairing during meiosis is not understood, even though homologous pairing is essential for the production of viable gametes. My laboratory has pioneered the use of the basidiomycete fungus Coprinus cinereus (recently renamed Coprinopsis cinerea) as a model system for the genetic control of chromosome pairing and synapsis because many features of the C. cinereus life cycle facilitate such studies. Meiosis occurs synchronously in this mushroom, which is easily cultivated on defined medium. Certain features of the mating system greatly facilitate the recovery of recessive mutations that completely block meiosis and/or spore formation, which has enabled us and others to undertake extensive genetic analyses of meiosis. The methods we developed for DNA-mediated transformation have been used both to disrupt genes as well as to complement induced mutations.

My lab headed the C. cinereus genome project, and we were able to produce telomere-to-telomere sequence assembly for the majority of the chromosomes.  This analysis together with a high-resolution genetic map and improved sequence annotation revealed sub-telomeric hot spots for meiotic recombination that coincide with regions where meiotic synapsis initiates.  We also observed a striking enrichment for single copy orthologs in regions with low rates of meiotic recombination, and an enrichment for paralogous multicopy genes in regions with high rates of meiotic recombination.

The genome project also revealed two genes encoding DNA methyltransferases of the DNMT1 family, which are responsible for conversion of selected cytosines within the CpG sequence context to 5-methylcytosine.  We have shown that methylated genes lie within regions of “closed chromatin” in the genome.  Recent attention has been focused on an additional modified base, 5-hydroxymethylcycosine, and its role in “poised chromatin” in stem cells.  Remarkably, the C. cinereus genome includes 38 copies of a gene predicted to carry out this conversion, and 5-hydroxymethylcytosine has been detected in the C. cinereus genome.  Currently, we are investigating chromatin dynamics during meiosis, with particular attention on meiosis-specific conversion of closed to open chromatin in hot spots.  We also head a community functional genomics project sponsored by the Joint Genome Institute to explore the regulation of enzymes most relevant to biomass degradation, to inventory genes that are under developmental control to understand “how to build a mushroom”, and to understand changing chromatin dynamics and epigenetic marks during mushroom development.

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