Genomic and functional analyses of Polycomb group proteins in mouse preimplantation development

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Project Summary Polycomb group (PcG) proteins play critical roles in maintaining epigenetic memory of gene silencing in normal development and human diseases. PcG proteins function in two enzymatic multi-subunit complexes: Polycomb repressive complex 1 and 2 (PRC1 and 2). PRC1 deposits monoubiquitin to lysine 119 on histone H2A (H2Aub) whereas PRC2 methylates all states of lysine 27 on histone H3 (H3K27me1/2/3). How Polycomb domains are reprogrammed during mammalian preimplantation development remains largely unknown. Recent advances on low input epigenomic profiling techniques make it feasible to investigate chromatin dynamics in mammalian preimplantation embryos. The discovery that non-canonical H3K27me3 in oocytes can mediate germline DNA methylation-independent genomic imprinting has raised several important questions on Polycomb domain regulation in early development. For example, whether H2Aub follows a similar reprogramming dynamic as H3K27me3, what’s the role of PRC1/2 in regulating 3D chromatin, and whether PRC1/2 form a positive feedback loop to reinforce each other during preimplantation development. To address these questions, I have generated preliminary data showing that, in contrast to conventional view that H2Aub and H3K27me3 are largely co- localized, H2Aub and H3K27me3 undergo genome-wide distinct reprogramming dynamics after fertilization. In addition, H2Aub deposition by PRC1 is independent of PRC2 in oocytes and preimplantation embryos, suggesting a more critical role of PRC1 than PRC2 during this developmental window. Built on the unexpected observations, I propose to use a combination of low input epigenomics, bioinformatics, and rapid protein degradation approach to understand mechanisms and functions of PRC1/2 as well as the chromatin modifications they respectively deposit in mouse preimplantation development. In Aim 1 (K99 phase), I will identify mechanisms underlying the distinct reprogramming dynamics of H2Aub and H3K27me3 after fertilization. In Aim 2 (K99 phase), I will rapidly degrade PRC1 in zygotes to assess its impact on zygotic genome activation, PRC2 recruitment, and 3D chromatin structures. I will be trained by Drs. Yi Zhang (Boston Children’s Hospital/Harvard Medical School), Peter Park (Harvard Medical School), and Bin Gu (Michigan State University) to establish low input epigenomic profiling tools, biochemical assays, computational pipelines, and the rapid protein degradation technique. In Aim 3 (R00 phase), I will take advantage of the techniques and computational pipelines established during the K99 phase to study the role of variant PRC1 subcomplexes in preimplantation development. The NIH K99/R00 Pathway to Independence Award, together with the outstanding research environment at BCH/HMS will facilitate my completion of the proposed work and transition to an independent investigator. Collectively, completion of these aims will reveal mechanisms underlying PcG recruitment, define the role of PcG-mediated gene silencing in mouse preimplantation development, and uncover new paradigms on chromatin reprogramming during mammalian gamete-to-embryo transition.