We are interested in discovering and characterizing the general mechanisms that organize DNA in the nucleus. We are especially interested in understanding the fundamental processes that involve interactions between apparently intact segments of homologous DNA. Such processes are remarkably ubiquitous, yet their molecular nature remains one of the most enigmatic unanswered questions in biology.
Using the premeiotic phenomenon of Repeat Induced Point mutation (RIP) in the fungus Neurospora crassa as a model system, we have shown that DNA homology can be recognized using a fundamentally new approach, by which long segments of double-stranded DNA (dsDNA) are compared to one another as arrays of interspersed base-pair triplets. Importantly, this process does not require the RecA-like proteins. The ability of RIP to detect any two identical DNA segments placed at the arbitrary sites in the genome suggests that RIP involves an exhaustive, “genome-by-genome” homology search. Therefore, this search process must be very efficient. Intriguingly, we have found that RIP mutation can be mediated by an epigenetic pathway that includes the SUV39 methyltransferase DIM-5, which catalyzes trimethylation of histone H3 lysine-9 residues. Thus, we have proposed that SUV39 methyltransferases can be recruited to repetitive DNA ab initio in response to homologous dsDNA-dsDNA interactions. In our ongoing work, in collaboration with the laboratory of Tom Hammond, we now find that the same homology-recognition principles that guide RIP are also applicable to Meiotic Silencing by Unpaired DNA (MSUD). These new results (i) reveal the role of a recombination-independent homology-directed process in programming the expression of small interfering RNAs, (ii) suggest that homologous chromosomes can be matched during meiosis by a mechanism that operates on intact DNA double helices, and (iii) raise an intriguing possibility that the revealed recombination-independent process may represent a general, perhaps even fundamental, mode of DNA homology search and recognition.
Current & prospective projects in the lab include (i) discovering molecular factors that recognize repetitive DNA in N. crassa, (ii) elucidating the mechanism of recruitment of DIM-5 to repetitive DNA in N. crassa, (iii) further understanding the DNA homology requirements for RIP and MSUD in N. crassa, (iv) using a range of imaging techniques to characterize the state of chromatin in the premeiotic nuclei of N. crassa, and (v) dissecting the role of heterochromatin during the invasive growth of the human pathogen Aspergillus fumigatus.