DNA is methylated on cytosine in the context of CpG dinucleotide in mammalian cells. The absence of such methylation in CpG-rich promoter regions known as CpG islands (CGIs) is a hallmark of transcriptional activity. In contrast, CpGs in intergenic and intronic regions are frequently heavily methylated. Such methylation likely serves to maintain transposable elements in these regions in a transcriptionally inert state. Although the mammalian “de novo” DNA methyltransferases Dnmt3A and Dnmt3B were cloned several years ago, very little is known about the mechanism by which specific regions of the genome are targeted for methylation by these enzymes. As CpG islands are typically a kilobase or longer in length, it is likely that some attribute of chromatin structure, rather than transcription factor binding per se, protects these regions from de novo methylation. Whatever the nature of this protective affect, it clearly breaks down in cancer cells, in which CGIs are frequently aberrantly methylated, coincident with hypomethylation of the rest of the genome.
Recently, 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 required for transcription. Intriguingly, histones associated with the promoter regions of actively transcribing genes are marked by a unique combination of covalent modifications, including H3K4 methylation, 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, may 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 in the regulation of genes, retroelements and chimaeric transcripts. These studies are made possible by low-cell input methods for whole genome analysis of chromatin marks (ULI-ChIP-seq), DNA methylation (PBAT) and transcription (RNAseq), and in house pipelines developed to integrate the analyses of these epigenomic datasets at an allele-specific level.
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 Weaver Syndromes; 2) characterizing the “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 and 4) characterizing the role of LTR-initiated transcripts in the establishment of imprinting in oocytes.
Chen CCL. Goyal P, Karimi MM, Abildgaard MH, Kimura H, Lorincz M H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2. Genome Research 28 (1) 37-51 (2018).
Lorincz MC, Schubeler D Evidence for Converging DNA Methylation Pathways in Placenta and Cancer Developmental Cell 43 (3), 257-258 (2017).
Wolf G, Rebollo R, Karimi MM, Ewing A, Kamada R, Wu W, Wu B, Bachu M, Ozato K, Faulkner G, Mager D, Lorincz M, Macfarlan T On the role of H3.3 in retroviral silencing Nature 548 (7665) E1 (2017).
Mager DL, Lorincz MC Epigenetic modifier drugs trigger widespread transcription of endogenous retroviruses. Nature Genetics 49 (7), 974 (2017).
Sharif J, Endo TA, Nakayama M, Karimi MM, Shimada M, Katsuyama K, Goyal P, Brind’Amour J, Sun MA, Sun Z, Ishikura T, Mizutani-Koseki Y, Ohara O, Shinkai Y, Nakanishi M, Xie H, Lorincz MC, Koseki H Activation of Endogenous Retroviruses in Dnmt1(-/-) ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA.. Cell Stem Cell 19 (1), 81-94 (2016).
Peter J. Thompson, Todd S. Macfarlan, and Matthew C. Lorincz. Long terminal repeats: from parasitic elements to building blocks for the transcriptional regulatory repertoire Molecular Cell, 62(5), 666-676 (2016).
Peter J. Thompson, Vered Dulberg, Kyung-Mee Moon, Leonard J. Foster, Carol Chen, Mohammad M. Karimiand Matthew C. Lorincz hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells. In Press, PLoS Genetics (2014)
Brind’Amour J, Liu S, Hudson M, Chen C, Karimi MM, Lorincz MC, An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nature communications, 6, 6033 (2015).