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It has long been known that DNA sequence elements known as cis-regulatory elements (CREs) are important keys to understanding when and where a gene is expressed.  CREs reside in the genome in close proximity to each gene's transcription start site (TSS), and while relatively few studies in plants have attempted to decode the combinations of CREs that lead to gene expression, recent progress is underway.  Three papers just published by the Megraw Lab help to address the question of how to precisely identify the TSSs of all genes in a tissue sample (where to look for CREs), how to identify regions of open chromatin where CREs are most likely to be active in recalcitrant plant tissues such as roots, and how to combine biological information about CREs from large-scale datasets into a machine-learning model that "mines" information about which CREs are most likely to be contributing to gene expression at a particular locus in a particular tissue sample.

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites


Jason Cumbie, Maria Ivanchenko, Molly Megraw - BMC Genomics

Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Jason Cumbie, Sergei Filchkin, Molly Megraw - Plant Methods

TIPR: transcription initiation pattern recognition on a genome scale

Taj Morton, Weng-Keen Wong, Molly Megraw - Bioinformatics