Genetic information is stored in DNA, which is a string of four nucleotides (i.e. adenine, thymine, guanine and cytosine). DNA is not a linear molecule; it is wrapped around a nucleosome which is composed of histone proteins. Conventionally, the information stored in DNA is expressed through a process known as transcription when the transcriptional factor binds to the promoter of a gene or sequence. Besides transcription factor binding, the transcriptional regulation is also modulated by other processes including DNA methylation and histone modification. These mechanisms are known as epigenetics. Aberrations of these epigenetic mechanisms are associated with various diseases, including cancer. DNA methylation and histone modification can be studied at the entire genome level (i.e. epigenomics) using microarray and sequencing methods. However, sequencing methods provide a more comprehensive and thorough investigation and as a result, sequencing methods have replaced microarrays in epigenomic studies. Over the past few years, significant progress has been achieved in epigenomics attributed to the developments of high-throughput sequencing technologies that can generate ten to hundred gigabases of sequencing data per instrument run. These advances in epigenomics are summarized and discussed in our review paper. (By Chee Seng Ku, http://jmg.bmj.com/content/early/2011/08/08/jmedgenet-2011-100242.abstract?papetoc )