Epigenetics in male reproduction: A practical introduction to the informatics of next generation sequencing

Abstract

At fertilization, the male germ cell conveys a richly layered genetic landscape consisting of both DNA and its associated epigenetic information. A systems level understanding of these forms of information could reveal some of the origins of idiopathic male infertility. Characterizing the genetic and epigenetic contributions to fertilization could also offer insight into the root causes of aberrant development. Perhaps some of these elements reflect the fetal origins of adult disease. As a host of new tools and techniques emerge, we have the opportunity to reassess our models of gametogenesis in the male. The challenge is no longer to construct biological models from sparse data but to assimilate a wealth of data being generated by high throughput technologies. By aggregating data from multiple high throughput and targeted experiments, bioinformatics offers potential insight into how genetic and epigenetic information are utilized in the sperm-oocyte system. In this chapter, we will review online resources that can aid in conducting an epigenetic investigation as well as describing approaches to managing second and third generation deep sequencing data. © Springer-Verlag Berlin Heidelberg 2011.