Matthew Lorincz

Classic genomic imprinted loci display parent-of-origin transcription in adult cells. Such allele-specific expression is thought to be driven by epigenetic marks, including DNA methylation (DNAme) and histone modifications, established in the gametes. However, the extent of monoallelic transcription in early mammalian development has remained relatively unexplored. As chromatin is highly dynamic before implantation, parent-of- origin directed transcription may be particularly high at this stage.To identify parent-of-origin controlled transcription, including during early embryogenesis, I helped develop MEA, a Methylomic and Epigenomic Allele-specific analysis pipeline designed to integrate whole genome bisulphite (WGBS)-, RNA- and ChIP-sequencing datasets. To demonstrate the utility and sensitivity of MEA, I processed existing mouse and human datasets and uncovered classical as well as novel candidate imprinted genes.Subsequently, I applied MEA to analyze WGBS and ChIP-seq data generated from adult gametes and preimplantation mouse embryos, which yielded female/maternal and male/paternal epigenomic profiles. Surprisingly, despite global DNAme loss following fertilization, I uncovered several dozen CpG island promoters that are de novo methylated on the paternal genome in 2-cell embryos, coincident with H3K4me3 loss on the same allele. A subset of these loci is hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts, confirming the paternal genome is susceptible to post-fertilization DNAme activity. Notably, this zygotic paternal DNAme gain was ablated following genetic depletion of maternal DNMT3A. Parental DNAme levels at these loci are harmonized in the post-implantation embryo and beyond: thus, unlike classic imprinted regions, these novel DMRs are established on the paternal genome by maternal stores of DNMT3A in the zygote and likely only transiently impart allelic transcription in the embryo. Indeed, expression analysis of DNMT3A maternal KO preimplantation embryos revealed that genes normally gaining paternal DNAme following fertilization are prematurely activated from the paternal allele in 4C embryos.Taken together, the results presented in my thesis illustrate the benefits of increasing the range and sensitivity of allele-specific analyses, and uncover zygotic de novo DNAme activity at CpG island promoters on the paternal genome against a backdrop of acute global demethylation.

View record

Phosphorylation of histone H3 at serine 10 (H3S10ph) has been observed in two paradoxical contexts, depending on the stage of the cell cycle – it is a hallmark of condensed mitotic chromatin, but is also found at specific mitogen-inducible genic promoters and distal enhancers. In the work presented in this thesis, I derived a mouse embryonic stem cell (ESC) line harbouring an endogenous fluorescent cell cycle reporter (FUCCI) in combination with next-generation sequencing to comprehensively map H3S10ph at distinct stages of the mammalian cell cycle and examined the crosstalk between this mark and the repressive mark, H3K9me. I found that H3S10ph broadly demarcates gene-rich, early-replicating euchromatic regions in G1, marking up to 30% of the ESC genome. Reminiscent of H3S10ph deposited by JIL-1 kinase in Drosophila, interphase H3S10ph pervasively marks gene-dense regions to prevent the accumulation of H3K9me2 at actively transcribed genes in ESCs. In contrast to H3S10ph at euchromatin, mitotic phosphorylation mediated by Aurora kinase is also detectable in ESCs in G1 at young endogenous retroviruses (ERVs), specifically in combination with H3K9me3. Finally, to identify the kinases responsible for interphase H3S10ph, I generated knockout (KO) ESC lines of serine kinases homologous to JIL-1, including Msk1/2 and Rsk1/2/3/4. Msk2-/- ESCs showed the greatest loss of interphase H3S10ph at active promoter/enhancers. Furthermore, known H3K9me3 repressed targets, including imprinted genes, young ERVs and germline genes, were downregulated in MSK2-deficient cells. Taken together, this work revealed that H3S10ph plays a previously unappreciated role in interphase chromatin architecture and facilitates appropriate genic transcription by countering the repressive effects exerted by H3K9 methyltransferases.

View record

Schimke immuno-osseous dysplasia (SIOD) is a rare autosomal recessive multisystemic disorder characterized by disproportionate short stature due to skeletal dysplasia, renal disease due to focal segmental glomerulosclerosis (FSGS), T-cell immunodeficiency, and vascular disease. SIOD is caused by mutations in the SWI/SNF-related matrix-associated actin-dependent regulator of chromatin, subfamily A-like 1 (SMARCAL1) gene, which encodes for a DNA annealing helicase with roles in DNA replication, DNA repair, and gene expression. Although SMARCAL1 functions to maintain genomic integrity, it is not known how SMARCAL1 deficiency leads to the various clinical features of SIOD. My aim was therefore to characterize the molecular pathogenesis of the dental, vascular, renal, and immune features. Given that SMARCAL1 has a role in modulating gene expression and that phenotypic changes are typically preceded by changes in gene expression, I hypothesized that SMARCAL1 deficiency pathologically alters the expression of key genes that lead to the clinical features of SIOD. To test this, SIOD patient tissues were studied using molecular biological analyses. With respect to vascular disease, an SIOD aorta had decreased expression of elastin, and both transcriptional and post-transcriptional mechanisms contributed to the elastin deficiency. Elastin is critical for the structural integrity of the arteries and its deficiency is a known cause of vascular disease. With respect to renal disease, SIOD glomeruli have increased expression and activation of the Wnt and Notch signaling pathways. Wnt and Notch signaling are required for kidney development and the postnatal reactivation of these pathways is an established cause of FSGS. With respect to immune disease, SIOD T cells have decreased mRNA and protein expression of interleukin 7 receptor alpha chain (IL7R). IL7R is critical for T-cell development and its deficiency is a known cause of T-cell immunodeficiency. In conclusion, the gene expression alterations detected are known causes of disease and differ among the tissues studied. These findings suggest that SMARCAL1 deficiency may cause each disease feature by tissue-specific gene expression changes. Further studies are required to define the mechanism of how SMARCAL1 deficiency alters the expression of these genes.

View record

Transcription of endogenous retroviruses (ERVs) is inhibited by de novo DNA methylation during gametogenesis, a process initiated after birth in oocytes and at approximately embryonic day 15.5 (E15.5) in prospermatogonia. However earlier in germline development, the genome, including most retrotransposons, is progressively demethylated. As DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes, raising the question whether repressive histone methylations play a role in silencing of retrotransposons at this stage of development. To answer this question, I first focused on developing low input assays for profiling histone modifications, DNA methylation and transcription from rare cell populations. In close collaboration with Dr. Julie Brind’Amour, I was able to develop the “SmallCell” protocol package, which enables chromatin immunoprecipitation, bisulfite conversion of DNA, RNA isolation-reverse transcription using ~1000 cells per assay, but also construction of sequencing library from pictograms of DNA. This allows profiling of epigenetic information at both locus-specific and genome-wide scales. I then developed the “InterSeq” software (R package) to intersect and explore different types of epigenomic data. This package allows converting sequencing data into genomic interval measures in spreadsheet (SeqData), interfacing this spreadsheet into flowcytometry data (SeqFrame), and an intuitive graphical interface to gate and explore the inter-relationship between different types of epigenomic sequencing data similar to flowcytometry (SeqViz). With these tools we first determined whether retrotransposons are marked by H3K9me3 and H3K27me3. Although these repressive histone modifications are found predominantly on distinct genomic regions in E13.5 PGCs, they concurrently mark partially methylated long terminal repeats and LINE1 elements. Germline-specific conditional knockout of the H3K9 methyltransferase SETDB1 yields a decrease of both marks and DNA methylation at H3K9me3-enriched retrotransposon families. Strikingly, Setdb1 knockout E13.5 PGCs show concomitant derepression of many marked ERVs, including IAP, ETn, and ERVK10C elements, and ERV-proximal genes, a subset in a sex-dependent manner. Furthermore, Setdb1 deficiency is associated with a reduced number of male E13.5 PGCs and postnatal hypogonadism in both sexes. Taken together, these observations reveal that SETDB1 is an essential guardian against proviral expression prior to the onset of de novo DNA methylation in the germline.

View record

Histone lysine methylation is essential for mammalian development and maintenance of somatic cell identity, as evidenced by a group of Mendelian diseases and cancers linked with mutations in lysine methyltransferases (KMTs). The transcriptional silencing of a class of retrotransposons known as endogenous retroviruses (ERVs) in murine embryonic stem cells (mESCs) provides a unique model system in which to investigate epigenetic regulation by the H3K9 family of KMTs and characterize novel molecular mechanisms of relevance to human biology and disease. In mESCs, class I and II ERVs are silenced by the SETDB1/KAP1 complex, which deposits histone H3K9 trimethylation (H3K9me3). In contrast, class III MERVL ERVs are silenced by the G9a/ GLP complex, which deposits H3K9me2. The molecular mechanisms governing the recruitment of these KMTs to their genomic ERV targets remain poorly understood. The goal of this work was to identify and characterize novel factors that regulate the functions of these KMTs in ERV silencing. In the first part of my thesis work, I identified the RNA-binding protein and transcription factor hnRNP K as a novel co-repressor for the SETDB1/KAP1 complex. HnRNP K coordinates recruitment of the KMT SETDB1 by KAP1 to its ERV targets. This function of hnRNP K involves a previously uncharacterized influence on the levels of chromatin protein SUMOylation. In the second part of my thesis work, I demonstrated that MERVL elements are also repressed by hnRNP K and can remain inactive in the absence of H3K9me2, likely due to the lack of transcriptional activators. HnRNP K forms a novel RNA-dependent complex with G9a/GLP, is required for global H3K9me2 and provides a repressive barrier to MERVL expression in the presence and absence of H3K9me2. Taken together my work has provided significant insights into the epigenetic repression of ERV transcription by KMTs and demonstrates that hnRNP K is a novel co-repressor for two different KMT complexes. As recent studies have linked mutations in HNRNPK to the novel Mendelian disorder Au-Kline syndrome and cancer, these insights should also guide future studies on the role of hnRNP K in regulation of KMT-mediated signaling pathways in human disease.

View record

Endogenous retroviruses (ERVs) are found in genomes of all higher eukaryotes. As retrotransposition is deleterious, pathways have evolved to repress these retroelements. While DNA methylation transcriptionally represses ERVs in differentiated cells, this epigenetic mark is dispensable for maintaining proviral silencing during early stages of mouse embryogenesis and in embryonic stem cells (mESCs). Studies in diverse species have found histone H3K9 methylation and DNA methylation to function together to repress retrotransposons. However, until recently, little was known about the role of this histone modification in proviral silencing in mESCs. Interestingly, our analysis of mESCs lacking G9a, an H3K9-specific lysine methyltransferase (KMTase) revealed that although ERVs lost H3K9 di-methylation (me2) and DNA methylation, they remained silent. Strikingly, the levels of H3K9 tri-methylation (me3) remained unaltered, suggesting that this mark may instead be responsible for maintaining these parasitic elements transcriptionally inactive. The first stage of my research focused on identifying the enzyme depositing H3K9me3 at ERVs and on determining its role in proviral silencing. I discovered that Setdb1, another H3K9-specific KMTase, was indeed depositing H3K9me3 at a subset of ERVs and was required for maintaining transcriptional repression. Interestingly, this silencing pathway operated independently of DNA methylation. Through collaboration, we also discovered that this pathway played a diminished role in differentiated cells. Taken together, these findings indicate the existence of a DNA methylation-independent proviral silencing pathway in mESCs. The second stage of my research focused on the establishment of transcriptional repression of newly integrated proviruses. By employing an exogenous retroviral construct, I discovered a dramatic silencing defect in mESCs lacking G9a, which phenocopied cells depleted of the de novo DNA methyltransferases. Furthermore, efficient DNA methylation of proviruses required G9a-mediated H3K9me2. These findings reveal that histone modifications and DNA methylation function in concert to defend the genome against invading retroviral elements in mESCs. Taken together with discoveries regarding the mechanism of DNA demethylation in early embryos, I propose that cells undergoing DNA methylation reprogramming predominantly employ histone modification-based pathways to maintain these parasitic elements in a silent state; however, the establishment of transcriptional repression for newly integrated elements also requires de novo DNA methylation.

View record