Research papers that give you an idea of what the lab does:
1. Graham-Paquin A., Saini D., Sirois J., Hossain I., Katz M.S., Zhuang Q.K., Kwon S.Y., Yamanaka Y., Bourque G., Bouchard M., Pastor W.A. (2022) ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development. BioRxiv
https://www.biorxiv.org/content/10.1101/2022.09.13.507699v2
During early mammalian development, DNA methylation is globally lost and then reestablished across the genome. In collaboration with the lab of Maxime Bouchard, we demonstrated that mice deficient for the transcriptional corepressor Zmym2 fail to methylate germ cell genes and young LINE transposons during this reprogramming event, with concomitant overexpression of these targets and embryonic lethality. By a combination of experiments and analysis in mESCs, we demonstrated that ZMYM2 homes to genes and transposons by recognition of the heterochromatic PRC1.6 and TRIM28 complexes respectively. Loss of ZMYM2 results in excessive H3K4 methylation at its target loci, antagonizing 5mC establishment. We thus establish ZMYM2 as a key player in epigenetic regulation during development.
2. Chen H., Hu B., Horth C., Bareke E., Rosenbaum P., Kwon S.Y., Sirois J., Weinberg D.N., Robison F.M., Garcia B.A., Lu C., Pastor W.A., Majewski J. (2022). H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells. Genome Research. 32(5):825-837
https://genome.cshlp.org/content/32/5/825.long
Histone 36 dimethylation (H3K36me2) is a critical and understudied epigenetic mark. In this paper, we assisted the Majewski lab in demonstrating that DNA and H3K27 methylation patterns are dramatically influenced by the underlying H3K36 methylation landscape. Loss of the H3K36 methyltransferase NSD1 results in global loss of 5mC and spread of H3K27me3. By contrast loss of DNA methyltranserases or PRC2 results in loss of DNA methylation and H3K27me3 respectively, but has a much more limited effect on the distribution of other epigenetic marks. H3K36me2 is a king among epigenetic marks.
3. Azevedo Portilho N., Saini D., Hossain I., Sirois J., Moraes C., Pastor W.A. (2021) The DNMT1 inhibitor GSK-3484862 mediates global demethylation in murine embryonic stem cells. Epigenetics & Chromatin 14(1):56
https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s1307...
In order to figure out what genes are regulated by DNA methylation in a given cell or biological process, it would be helpful to have a small molecule that removes DNA methylation altogether. Unfortunately, the best established chemicals for this purpose, 5-azanucleosides, are highly toxic to cells. We tested a new chemical developed by GlaxoSmithKline (GSK-3484862) in murine embryonic stem cells. We demonstrated low toxicity, reactivation of transcripts with methylated promoters, and dramatic demethylation. The manuscript is intended as a resource for other researchers who might have use for such a compound.
4. Cinkornpumin J.K., Kwon S.Y., Guo Y., Hossain I., Sirois J., Russett C.S., Tseng H., Okae H., Arima T., Duchaine T.F., Liu W., Pastor W.A. (2020) Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome. Stem Cell Reports. 15(1):198-213.
https://www.sciencedirect.com/science/article/pii/S2213671120302241?via%...
The first developmental decision that arises in mammalian embryogenesis is specification of the trophoblast (future placenta). For practical and ethical reasons, this period of development is very difficult to study, so we sought to model trophoblast specification using stem cells. In this paper, we demonstrate the we can convert specially cultured "naive" human embryonic stem cells (hESCs) into cells very similar to human trophoblast stem cells (hTSCs). We show how to purify such "transdifferentiated" hTSCs and demonstrate that they can grow and differentiate similar to real hTSCs purified from placenta. They also acquire a pattern of DNA methylation similar to what normally arises in placental development. We thus have a system to model the specification and the epigenetic patterning of placenta.
Review articles and book chapters:
1. Pastor W.A., Kwon S.Y. (2022) Distinctive aspects of the placental epigenome and theories as to how they arise. Cell and Molecular Life Sciences. 79(11):569
https://link.springer.com/article/10.1007/s00018-022-04568-9
The pattern of DNA methylation in placenta is strongly dissimilar to that present in somatic cells. In this review, we discuss the unique aspects of the placental methylome. We also discuss recent mechanistic advances in the cancer field which may explain aspects of how the placental epigenome arises and is maintained. This review is written with the goal of introducing placental researchers to epigenetics and epigenetics researchers to placenta.
2. Cinkornpumin J.K., Hossain I., Pastor W.A. Mapping Chromatin Accessibility in Human Naïve Pluripotent Stem Cells Using ATAC-Seq. (2022). Methods in Molecular Biology. 2416:201-211
https://link.springer.com/protocol/10.1007/978-1-0716-1908-7_13
ATAC-seq is one of the lab's favourite techniques. This publication includes a description of the history and value of ATAC-seq as well as a step by step description of how to conduct ATAC-seq in embryonic stem cells.
Collaboration outside our core research program
1. Rahbani J.F., Scholtes C., Lagarde D.M., Hussain M.F., Roesler A., Dykstra C.B., Bunk J., Samborska B., O'Brien S.L., Tripp E., Pacis A., Angueira A.R., Johansen O.S., Cinkornpumin J., Hossain I., Lynes M.D., Zhang Y., White A.P., Pastor W.A., Chondronikola M., Sidossis L., Klein S., Kralli A., Cypess A.M., Pedersen S.B., Jessen N., Tseng Y.H., Gerhart-Hines Z., Seale P., Calebiro D., Giguère V., Kazak L. ADRA1A-Gαq signalling potentiates adipocyte thermogenesis through CKB and TNAP. Nature Metabolism. 4(11):1459-1473
https://www.nature.com/articles/s42255-022-00667-w
A collaboration with the lab of Lawrence Kazak (McGill University), this critical work showed that α-adrenergic receptor signalling is important for thermogenesis in brown fat. Our lab helped generate ATAC-seq data from adipocytes in order to determine which transcription factors act downstream of α-adrenergic signalling.
2. Cai T., Cinkornpumin J.K., Yu Z., Villareal O.D., Pastor W.A., Richard S. (2021) Deletion of RBMX RGG/RG motif in Shashi-XLID syndrome leads to aberrant p53 activation and neuronal differentiation defects. Cell Reports. 36(2):109337.
https://www.sciencedirect.com/science/article/pii/S2211124721007130?via%...
A collaboration with the lab of Stéphane Richard (McGill University). This paper demonstrates that the protein RBMX regulates the splicing of MDM4 and by extension the apoptosis master-regulator p53. This activity depends on RBMX's RGG/RG motif, an RNA-binding region which is deleted in patients with a neurological disorder called Shashi syndrome. Our contribution to this paper was to help the Richard lab make a CRISPR deletion in iPSCs similar to that observed in Shashi syndrome patients. These iPSCs show increased p53 activity and impaired neuronal differentiation, potentially explaining the mechanism behind this genetic disorder. We're happy to collaborate with other labs interested in implementing CRISPR and/or working with stem cells.
3. Xue Y., Meehan B., Fu Z., Wang X.Q.D., Fiset P., Rieker R., Levins C., Kong T., Zhu X., Morin G., Skerritt L., Esther H., Venneti S., Martinez D., Jung S., Gonzalez A.V., Guiot M.C., Lockwood W., Spicer J., Agaimy A., Pastor W.A., Dostie J., Rak J., Foulkes W.D., Huang S. (2019) SMARCA4 loss is synthetic lethal with CDK4/6 inhibition in non-small cell lung cancer. Nature Communications. 10(1): 557.
https://www.nature.com/articles/s41467-019-08380-1
A collaboration with the lab of Sidong Huang (McGill University). The Huang lab had discovered that ovarian and lung cancers with null mutations of the chromatin remodeller SMARCA4 show down regulation of Cyclin D1, making these cancers vulnerable to cyclin dependent kinase inhibitors. We performed bioinformatic analysis of ATAC and ChIP-seq data to demonstrate an indirect mechanism whereby SMARCA4 upregulates the transcription factor JUN, which in turn regulates Cyclin D1, potentially by opening adjacent enhancers. This paper is a good illustration of the bioinformatic techniques our lab uses.
(For a list of Dr. Pastor's papers throughout his career, see Google Scholar Citations)