Enhanced TF binding site maps improve regulatory networks learned from accessible chromatin data

摘要: ABSTRACT Determining where transcription factors (TF) bind in genomes provides insights into which transcriptional programs are active across organs, tissue types, and environmental conditions. Recent advances high-throughput profiling of regulatory DNA have yielded large amounts information about chromatin accessibility. Interpreting the functional significance these datasets requires knowledge regulators likely to regions. This can be achieved by using TF binding preferences, or motifs, identify events that functional. Although different approaches exist map motifs sequences, a systematic evaluation tools plants is missing. Here we compare four motif mapping widely used Arabidopsis research community evaluate their performance immunoprecipitation for 40 TFs. Downstream gene network (GRN) reconstruction was found sensitive mapper used. We further show low recall FIMO, one most frequently tools, overcome an Ensemble approach, combines results from tools. Several examples provided demonstrating how approach extends our view on control TFs biological processes. Finally, new protocol presented effectively derive more complete cell type-specific GRNs through integrative analysis open regions, known site information, expression datasets.