Cis-regulatory units of grass genomes identified by their DNA methylation.

With the large number of genomes currently being sequenced, detailed annotation of these sequences has now become the bottleneck of genome analysis. Identification of protein-coding genes and transposable elements is easy compared with the difficult task of annotating the regulatory regions upstream of core promoters. These regions are relatively small and do not have obvious features such as open reading frames (ORFs), slowing their discovery. Promoter regulatory regions (termed cis-regulatory units) can be located at a far distance from the core promoters and ORFs they control. For example, an enhancer region of the maize b1 gene was mapped to ∼100 kb upstream of the ORF (1). ATAC-seq (assay for transposase-accessible chromatin using sequencing) is a technique that has been adopted to identify the genome-wide set of cis-regulatory units (2⇓–4). This technique locates the regions of accessible chromatin within and upstream of core promoters. These accessible chromatin regions are important because they are the sites of protein binding (including transcription factors) and chromosome looping associated with promoter activity (including distal enhancers) (5⇓–7). The weakness of ATAC-seq is that the regulatory units identified are tissue specific: they differ between each cell type, developmental stage, and treatment/condition as the genes expressed vary (8). Therefore, identifying … [↵][1]1To whom correspondence may be addressed. Email: kslotkin{at}danforthcenter.org. [1]: #xref-corresp-1-1