Investigation of multi-footprints

In order to understand complex transcriptional regulatory networks we need to be able to identify where the transcription factors (TFs) are binding to the DNA. Since TFs can only bind to open areas of the chromatin, a first step is to locate the accessible areas of chromatin. Both DNase-seq and ATAC-seq are genome-wide techniques that elucidate the location of open chromatin regions. Downstream analysis of data generated from these methods, such as digital genomic footprinting, can be used to reveal TF binding sites and so help in developing our understanding of complex regulatory networks. Footprinting methods have already been used successfully to identify TFs involved in disease mechanisms.
Current footprinting methods are focused on identifying single footprints that relate to a single TF binding site. We have seen evidence within footprinting data in our research group of protein complexes that bind to the DNA via multiple binding sites in close sequential proximity on the DNA. Due to the close proximity of the binding sites of these multi-footprints, current methodologies do not identify all of these sites or do not identify these as separate entities.
We propose to develop a new methodology that is focused on identifying the multi-footprints that are associated with larger protein complexes that bind to the DNA using more than one binding site. In order to achieve this we will first examine data from different sample types and generated using both DNase-seq and ATAC-seq methods to identify which experimental protocol provides the better data set with which to perform this analysis.
Optimisation of the data generation will be followed by development of a tool that will identify the multi-footprints. This tool will need to account for the proximity of footprints and correct for bias that arises from biological mechanisms of the experimental protocol.