Research

A number of factors have been described that catalyze the post-translational addition or removal of specific moieties, such as acetyl or methyl groups, to/from specific residues on the core nucleosomal histones. A subset of these ‘histone-modifying enzymes’, including histone acetyltransferases and histone H3 lysine 4 (H3K4) methyltransferases are targeted to the promoters and/or enhancers of actively transcribed genes. Indeed, histones associated with promoter regions for example are marked by a unique combination of covalent modifications, including H3K4 trimethylation, which may serve to protect promoters from DNA methylation. Conversely, the presence of repressive histone marks, such as H3K9me3 and H3K36me3, in promoter regions and gene bodies, respectively, are thought to promote methylation of associated DNA.

Research in the lab is directed towards understanding the interplay between transcription, DNA methylation and histone modifications in early development and in the germline, using the mouse as a model system. We employ CRISPR/Cas9 and conventional genetic knockouts of chromatin factors or regulatory regions with genome-wide analyses of chromatin structure and function to dissect the roles of specific epigenetic marks, such as H3K9me3, in the regulation of genes, retroelements and chimaeric transcripts. These studies have been made possible by the development of low-cell input methods for whole genome analysis, including of chromatin marks using ultra-low input (ULI)-ChIP-seq (developed in the Lorincz lab), DNA methylation using PBAT and RNAseq optimized for small cell numbers. In addition, we have developed a bioinformatic pipeline (ALEA) to integrate the analyses of these epigenomic datasets at an allele-specific level, such that the parental contributions of epigenetic marks and transcription can be followed through fertilization using F1 hybrid mice.

Ongoing projects include: 1) dissecting the interplay between the histone modifications H3K36me2 and H3K27me3, deposited by NSD1 and EZH2, respectively, in early embryonic development to define the molecular basis of the related overgrowth disorders Sotos and Weavers Syndromes; 2) characterizing the intergenerational “heritability” of covalent histone modifications and DNA methylation through fertilization using F1 hybrid mice and allele-specific analyses; 3) characterizing the role of H3K9 “writers” (methyltransferases) and “readers” in transcriptional regulation; 4) characterizing the role of LTR-initiated transcripts in the establishment of imprinting in oocytes; 5) characterizing the role of the H3K36 KMTase SETD2 in H3K36 methylation and de novo DNA methylation in growing oocytes and 6) characterization of the distribution and role of interphase H3S10ph in embryonic stem cells and somatic cells.