Role of epigenetic regulation in human sperm and egg analysis of DNA methylation and POLYA regulation

Our work focused on how germ cell DNA is packaged and if it is poised by distinctive chromatin to infl uence early embryo development. We studied human male and female germ cells and profi led their epigenetic repertoire. Further, we asked the question, is misregulation of that poising a common theme observed in infertility and aging in sperm? We pursued one part of this question in Chapter 2 where we investigated the changes in DNA methylation in sperm during the natural process of aging. We analyzed sperm from aged-matched donors and found that sperm on a global level gained DNA methylation over time, but notably, specifi c regions associated with genes linked to neuropsychiatric disorders signifi cantly lost DNA methylation in sperm from aged donors. This raised the intriguing question if the increase in observed neuropsychiatric disorders in offspring from older fathers could be linked to the loss of DNA methylation in sperm of specifi c genes also implicated in neuropsychiatric disorders. Further, we asked if abnormalities in chromatin are seen in sperm from infertile patients. We tested seven imprinted regions in oligozoospermic and abnormal protamine patients and found a correlation of DNA methylation abnormalities at the promoters of these genes in infertile sperm. Our fi ndings from this study are summarized in a publication detailed in Appendix A. Finally, we asked if changes in polyadenylation of transcripts in human oocytes could give us an insight into oocyte maturation and early human embryo development. We developed a novel bioinformatics tool called PANDA (Chapter 3) that enabled the analysis of relative polyA changes in transcripts between two different conditions. One of the advantages of this method is that it can utilize any iv RNA-seq dataset as long as it has not been biased for PolyA selection. Hence, we applied PANDA to the existing RNA-seq dataset, generated by our lab from human oocytes and early embryos, and investigated PolyA changes (Chapter 4). Strikingly, we were able to identify transcripts in humans that were previously reported to gain polyA in oocytes of drosophila and xenopus. We also identifi ed completely novel transcripts previously unknown to gain polyA during oocyte maturation. Hence, we are the fi rst group to identify these transcripts in human oocytes and embryos. Together we hope that by studying the epigenetic setup of germ cells we have gained more insight into understanding the regulation of programs critical in early embryo development.