Motif2Site: a Bioconductor package to detect accurate transcription factor binding sites from ChIP-seq

Abstract: Transcription factors (TFs) binding are in the core of the Regulatory networks studies. ChIP-seq experiments are available for many TFs in various species. As TFs co-bind in cis-regulatory elements regions to control gene expression, studying the existing relation among co binding TFs such as distance of binding sites or co occupancy are highly important to understand the regulatory mechanisms. Currently, to detect binding sites of each TF in cis-regulatory elements, first binding regions of each TF are detected by standard peak calling methods, and at the second step the best candidate binding sites are prioritized by motif detection methods in binding regions. However, it is well-known that the best prioritized candidate motifs are not necessarily the actual binding sites of TFs. Furthermore, motif prioritizing methods that consider more genomic features complexities of TFs bindings are usually computationally expensive methods. Here, we tend to improve the TF binding sites accuracy detection by using the original ChIP-seq signal. The motifs which are located closer to the summits of binding region peaks are more likely to be the actual binding sites. Therefore, We developed a novel post-processing Bioconductor package called Motif2Site to detect TFs binding sites from user provided motif sets and recenter them across experiments. We applied Motif2Site method to detect TF binding sites for major mouse embryonic stem cell (mESC) as well as mouse fetal and birth time (P0) heart TFs. Motif2Site could detect binding regions with comparable accuracy to the existing state-of-the-art while it substantially increased the accuracy of the detected binding sites. Motif2Site could future improve the accuracy of binding sites prediction by recentering binding sites across developmental conditions (fetal/P0 heart) and across homologous TFs (ex. GATA4/GATA6 and MEF2A/MEF2C). Purifying high-confidence binding sites in mouse fetal heart, enabled us to study the co-binding properties of TFs in cis-regulatory elements. We could also traced TFs footprints in selected heart-specific VISTA enhancers chromatin accessible regions.