Proceeding talk – Theme: Genes.
Abstract
Transcription factor (TF) binding can be studied accurately in vivo with ChIP-exo and ChIP-Nexus experiments. Accurate knowledge of TF binding locations and patterns is key to understanding binding not explained by PWM-models. ChIP-exo/Nexus can also offer insight on the effect of SNPs at TF binding sites on expression of the target genes. This is an important mechanism of action for disease-causing SNPs at non-coding genomic regions. We describe a peak caller PeakXus that is specifically designed to leverage the increased resolution of ChIP-exo/Nexus and developed with the aim of making minimal amount of assumptions of the data. We show that PeakXus consistently finds more verifiable peaks than published methods. We also demonstrate how PeakXus can be coupled with Unique Molecular Identifiers to measure the effect of a SNP overlapping with a TF binding site on the binding of the TF.
Authors
Tuomo Hartonen, University of Helsinki, Finland
Biswajyoti Sahu, University of Helsinki, Finland
Kashyap Dave, Karolinska Institutet, Sweden
Teemu Kivioja, University of Helsinki, Finland
Jussi Taipale, Karolinska Institutet, University of Helsinki, Sweden