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Epigenetics in Male Reproduction: A Practical Introduction to the Informatics of Next Generation Sequencing

  • Adrian E. Platts
  • Claudia Lalancette
  • Stephen A. Krawetz
Chapter
Part of the Epigenetics and Human Health book series (EHH)

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.

Keywords

Bioinformatics Epigenetics Imprinting Male gamete Micro RNA NGS-Next generation sequencing RNA 

Abbreviations

CDC

Centers for Disease Control and Prevention

CpG

CG dinucleotides (linked by a phosphor diester bond hence CpG)

DGE

Differential gene expression

DoE

Department of Energy

gDNA

Genomic DNA

HAT

Histone acetyltransferase

HDAC

Histone deacetylase

HMT

Histone methyltransferase

ICR

Imprinting control region

JGI

Joint genome initiative

miRNA

Micro RNA

NGS

Next generation sequencing, also referred to as second generation sequencing or “now generation” sequencing (Illumina)

piRNA

Piwi-interacting RNA

rasiRNA

Repeat associated small interacting RNAs

sncRNA

Small non coding RNA

snoRNA

Small nucleolar RNA

SNP

Single nucleotide polymorphism

TByte

Tera Byte, 1012 bytes, 1,000 gigabytes or 1,000,000 megabytes

WGS

Whole genome sequencing

Notes

Acknowledgments

This work is supported in part by the NIH grant HD36512, the Presidential Research Enhancement Program in Computational Biology and the Charlotte B. Failing Professorship to SAK. We gratefully acknowledge the use of the UCSC genome browser (http://genome.ucsc.edu/) and the Ensembl genome browser (http://www.ensembl.org) that were used in the creation of some of the illustrations.

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Copyright information

© Springer Berlin Heidelberg 2011

Authors and Affiliations

  • Adrian E. Platts
    • 1
    • 2
  • Claudia Lalancette
    • 1
    • 2
  • Stephen A. Krawetz
    • 1
    • 2
    • 3
  1. 1.Center for Molecular Medicine and GeneticsWayne State University School of MedicineDetroitUSA
  2. 2.Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitUSA
  3. 3.Institute for Scientific ComputingWayne State UniversityDetroitUSA

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