The placenta is a specialized and essential structure that regulates gas exchange and the transport of nutrients and waste between the mother and the fetus in eutherian mammals. Gene expression in the placenta is tightly controlled, and this finely-tuned gene regulation is a pre-requisite for proper placental development and function. A specialized form of gene regulation known as genomic imprinting is critical for placental function. Genomic imprinting results in the preferential expression of either the maternally- or paternally-inherited allele of a gene. Imprinted genes are hypothesized to regulate the growth rate of fetal tissues, and dysregulation of genomically imprinted loci has been linked to abnormal placental growth and changes in vascularization of the placental tissues. Genomic imprinting in the placenta parallels another intriguing epigenetic process, imprinted X-chromosome inactivation. Imprinted X-inactivation results in the preferential epigenetic silencing of the paternally-inherited inherited X-chromosome in all cells of the early embryo in XX females to equalize the dosage of X-linked genes to that of XY males. While many genomically imprinted loci have been described, how the preferential expression of one allele in a parent-of-origin-specific manner occurs remains poorly understood. Both imprinted X-inactivation and imprinted autosomal gene expression have been linked to long non-coding RNAs (lncRNAs). LncRNAs are non protein-coding transcripts that are hypothesized to recruit chromatin modifying complexes to defined genomic regions, either facilitating transcription or leading to gene silencing during development. Imprinted gene expression relies on differential epigenetic marking in the parental germlines, which is then manifested in expression of one or the other parental allele in the offspring. LncRNA expression can act as an instrument of this differential epigenetic germline marking to establish parent-of-origin-specific gene expression patterns in the embryo. My working hypothesis is that undiscovered lncRNAs trigger regional, parent-of-origin specific epigenetic silencing in the placenta during embryogenesis. Here, I propose to utilize a novel strand- and allele-specific RNA-sequencing approach and a computational pipeline that I have devised in order to identify novel parent-of-origin-specific lncRNAs. I will ue trophoblast stem cells as a source of the RNA. These cells undergo imprinted X- inactivation and also display robust imprinted gene expression on autosomes, and represent an in vitro model of the stem cell population that gives rise to the placenta. Through these experiments, we hope to identify initiators of genomic imprinting in the placenta, and pave the way for further understanding of the molecular mechanisms underlying parent-of-origin specific gene regulation.
Genomic imprinting is a form of gene regulation that results in the mitotically stable, parent-of- origin-specific gene silencing. Genomic imprinting is common in the placenta and is critical to the growth and function of this specialized organ that supports fetl development. However, the mechanisms underlying the initiation of imprinted gene silencing in the placenta are poorly understood. Here, we propose to identify and characterize novel candidate regulators of imprinted gene silencing in trophoblast stem cells, which contribute to the placenta, in order to provide insight into how this essential form of gene regulation is established in the placental lineage.