When is a Peak a Peak? (Claudio Cantù)

<p class="md-end-block md-p">In this episode of the Epigenetics Podcast, we talked to Claudio Cantù from Linköping University about his work on peak blacklists, peak concordance and what is a peak in CUT&amp;RUN.</p> <p class="md-end-block md-p md-focus">Our host Stefan Dillinger and guest Claudio Cantù dive into the topic of when we can be sure that a peak is a peak. To help with this, Claudio Cantù's group has been working on defining a set of suspicious peaks that can be used as a "peak blacklist" and can be subtracted to clean up CUT&amp;RUN data sets. The lab also worked on a method called ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation) to help define peaks from a number of experimental replicates. By using this algorithm, the team is trying to discover the beta-catenin binding profile, not the tip of the beta-catenin binding iceberg, but the whole of the beta-catenin binding profile.</p> <p class="md-end-block md-p"> </p> <p class="md-end-block md-p">References</p> <ul class="ul-list"><li class="md-list-item"> <p class="md-end-block md-p">Zambanini, G., Nordin, A., Jonasson, M., Pagella, P., &amp; Cantù, C. (2022). A new CUT&amp;RUN low volume-urea (LoV-U) protocol optimized for transcriptional co-factors uncovers Wnt/β-catenin tissue-specific genomic targets. Development (Cambridge, England), 149(23), dev201124. <a href='https://doi.org/10.1242/dev.201124'>https://doi.org/10.1242/dev.201124</a></p> </li> <li class="md-list-item"> <p class="md-end-block md-p">Nordin, A., Zambanini, G., Pagella, P., &amp; Cantù, C. (2022). The CUT&amp;RUN Blacklist of Problematic Regions of the Genome [Preprint]. Genomics. <a href='https://doi.org/10.1101/2022.11.11.516118'>https://doi.org/10.1101/2022.11.11.516118</a></p> </li> <li class="md-list-item"> <p class="md-end-block md-p">Nordin, A., Pagella, P., Zambanini, G., &amp; Cantu, C. (2023). Exhaustive identification of genome-wide binding events of transcriptional regulators with ICEBERG [Preprint]. Genomics. <a href='https://doi.org/10.110