ABSTRACT
At its inception massively parallel sequencing was ill suited for the task of sequencing the human genome. Perhaps then it is not surprising that some of the first publications that utilized next-generation sequencing were directed at chromatin immuno-precipitation enriched fractions of the genome [1-3]. Since their introduction, short read massively parallel sequencing platforms have continued to improve at an exponential rate, generating longer sequences of better quality in ever increasing numbers [4]. The research community has leveraged these improvements to develop a diverse collection of sequence-based methodologies to probe the functional genome [4-6]. These methodologies can be broadly divided into protocols that profile transcribed regions of the genome and those that profile the processes regulating transcription. Transcriptional regulation is maintained through complex interactions between sequence specific transcription factors which act in short time frame, generally in response to specific cellular stimuli, and those which act on longer time scales in response to more generalized environmental and developmental signals. The study of the mechanistic features that control this latter category is called epigenetics and the study of how these marks are patterned across the genome is called epigenomics.
