Epigenetic Control of Development: Establishment and function of placenta-specific DNA methylation patterns

我的中心研究项目是研究控制胎盘发育的分子过程。我的研究重点是基因是如何通过指导性的信息层进行调控的，这些信息层统称为表观基因组。我的目标是了解表观遗传修饰如何通过建立细胞类型特定的转录网络来驱动和加强细胞命运的决定，这些网络对发育进程至关重要，最终确保繁殖成功。DNA甲基化是一种表观遗传修饰，对胚胎发育是不可或缺的。DNA甲基化在细胞谱系和细胞类型上的基因组分布是加强细胞命运决定从而确保稳定分化的关键。胎盘滋养层细胞系具有独特的DNA甲基化特征，与胚胎细胞的DNA甲基化特征非常不同。这种特殊模式的建立对滋养层细胞分化和正常胎盘形成至关重要。因此，在DNA甲基化机制的各个部分有缺陷或缺乏特定甲基化标记的小鼠突变体在发育过程中过早死亡，并伴有严重的胎盘异常。尽管DNA甲基化对胎盘发育至关重要，但目前尚不清楚这种表观遗传标记是如何针对基因组中的特定位置来建立独特的滋养细胞特有的表观基因组图谱的。这个基本的机械问题是我的NSERC计划的重点。由于DNA甲基化机制本身并不表现出序列特异性，本工作的中心假设是滋养层系特有的一组特定的DNA结合蛋白赋予DNA甲基化机制针对特定序列元件的靶向性。将序列特异的DNA结合亲和力与DNA甲基化成分的吸引力结合在一起的因子称为Kruppel相关框锌指蛋白(KRAB-ZFP)。这项工作计划旨在确定共同建立滋养层甲基组的关键KRAB-ZFP。目标1：鉴定和鉴定滋养细胞富含KRAB-ZFP的基因。目标2：建立滋养细胞KRAB-ZFP的基因组定位图谱。目标3：确定KRAB-ZFP建立滋养细胞特异性DNA甲基化模式的能力。目标4：评估KRAB-ZFP对滋养细胞发育的影响，本研究将为我们从机制上理解胎盘DNA甲基化模式的建立奠定里程碑，这对发育和生殖具有重要意义。我们的HQP将学习尖端干细胞和CRISPR基因编辑技术、生物信息学分析方法和表观基因组图谱技术，这将使他们成为加拿大自然科学领域的领导者。

My central research program examines the molecular processes that govern development of the placenta. My particular research focus is on how genes are regulated through instructive layers of information that are collectively known as the epigenome. I am aiming to understand how epigenetic modifications drive and reinforce cell fate decisions by establishing cell type-specific transcriptional networks that are of critical importance for developmental progression, ultimately ensuring reproductive success. DNA methylation is an epigenetic modification that is indispensable for embryonic development. The genomic distribution of DNA methylation in a cell lineage- and cell type-specific manner is key to reinforcing cell fate decisions, thereby ensuring stable differentiation. The placental trophoblast lineage is characterized by a unique DNA methylation profile that is highly distinct from that of embryonic cells. The establishment of this specific pattern is of crucial importance for trophoblast differentiation and normal placentation. Thus, mouse mutants that are defective in various components of the DNA methylation machinery or that lack specific methylation marks die early during development with severe placental abnormalities. Despite the pivotal importance of DNA methylation for placental development, it remains unknown how this epigenetic mark is targeted to specific sites in the genome to establish the distinct trophoblast-specific epigenomic landscape. This fundamental mechanistic question is the focus of my NSERC program. Since the DNA methylation machinery does not exhibit sequence-specificity by itself, the central hypothesis of this work is that a particular collection of DNA binding proteins unique to the trophoblast lineage confers the targeting of the DNA methylation machinery to particular sequence elements. The factors that combine sequence-specific DNA binding affinity with the attraction of DNA methylation components are called Kruppel-associated box zinc finger proteins (KRAB-ZFPs). This program of work is aimed at identifying critical KRAB-ZFPs that collectively establish the trophoblast methylome. The specific objectives are to: Aim #1: Identify and characterize trophoblast-enriched KRAB-ZFPs Aim #2: Establish the genomic occupancy profile of trophoblast KRAB-ZFPs Aim #3: Determine the capacity of KRAB-ZFPs to establish trophoblast-specific DNA methylation patterns Aim #4: Evaluate the impact of KRAB-ZFP ablation on trophoblast development Overall, this study will set milestones for our mechanistic understanding of how placental DNA methylation patterns are established, which is of fundamental importance for development and reproduction. Our HQP will learn cutting-edge stem cell and CRISPR gene editing techniques, bioinformatics analysis methods and epigenomic profiling technology, which will position them as leaders in Canada's natural sciences sector.