Deep SequencingMaps theMaize Epigenomic Landscape

The age of omics is in full swing. Full genome sequences and the use of DNA microarrays to monitor gene expression on a genome-wide scale arrived on the scene a little over a dozen years ago, and today major developments in DNA sequencing technology have ushered in a new era in the study of gene regulation. Around the turn of the century, the introduction of massively parallel next-generation DNA sequencing technology allowed the development of new assays for analyzing complex nucleic acid samples based on highly parallelized sequencing of vast numbers of DNA molecules in a complex sample, combined with matching to a reference genome (reviewed in Morozova and Marra, 2008; Wold and Myers, 2008). Massively parallel signature sequencing (MPSS), the first of the next-generation sequencing technologies, involved cloning cDNA fragments onto microbeads and a fluorescence-based sequencing method that generated a unique 17-base signature sequence for each mRNA at a specific site upstream from its poly(A) tail (Brenner et al., 2000; Reinartz et al., 2002). The original MPSS platform (from the former Lynx Therapeutics, which became Solexa and now Illumina) has since been replaced by an improved sequencing by synthesis (SBS) method, based on detecting the identity of a nucleotide immediately after its incorporation into a growing strand of newly synthesized cDNA. Other next-generation approaches include 454 Life Sciences' SBS pyrosequencing method, Applied Biosystems' SOLiD sequencing by ligation system, Helicos Biosciences' single-molecule synthesis platform, and several other single-molecule synthesis platforms that will be available soon (Schuster, 2008; Gupta, 2009). These se-quencing technologies are often referred to as ''deep sequencing'' because of their ability to generate huge numbers of sequencing reads per experiment or instrument run. For example, as early as 2005, it was shown that a small-sized bacterial genome could be sequenced with nearly complete coverage and accuracy in a single instrument run using the pyrosequencing technology of the 454 Life Sciences platform (Margulies et al., 2005). These sequencing-based approaches have some distinct advantages over microarray-based approaches for genome-wide transcriptomics (the study of gene expression) and epigenomics (the study of chromatin organization and dynamics), such as avoiding complex intermediate cloning and microarray construction steps and the ability to generate a massive amount of sequence quickly. Using these approaches, gene expression is assayed by directly sequencing cDNA molecules obtained from an mRNA sample and simply counting the number of molecules corresponding to each gene to assess transcript abundance. The power of …