When is a Peak a Peak? (Claudio Cantù)
Epigenetics Podcast27 Juli 2023

When is a Peak a Peak? (Claudio Cantù)

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&RUN.

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&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.

References

  • Zambanini, G., Nordin, A., Jonasson, M., Pagella, P., & Cantù, C. (2022). A new CUT&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. https://doi.org/10.1242/dev.201124

  • Nordin, A., Zambanini, G., Pagella, P., & Cantù, C. (2022). The CUT&RUN Blacklist of Problematic Regions of the Genome [Preprint]. Genomics. https://doi.org/10.1101/2022.11.11.516118

  • Nordin, A., Pagella, P., Zambanini, G., & Cantu, C. (2023). Exhaustive identification of genome-wide binding events of transcriptional regulators with ICEBERG [Preprint]. Genomics. https://doi.org/10.1101/2023.06.29.547050

Related Episodes

Contact

Avsnitt(168)

Polycomb Proteins, Gene Regulation, and Genome Organization in Drosophila (Giacomo Cavalli)

Polycomb Proteins, Gene Regulation, and Genome Organization in Drosophila (Giacomo Cavalli)

In this episode of the Epigenetics Podcast, we talked with Giacomo Cavalli from the Institute of Human Genetics in Montpellier about his work on critical aspects of epigenetic regulation, particularly...

13 Feb 202544min

The Interplay of Nutrition, Metabolic Pathways, and Epigenetic Regulation (Ferdinand von Meyenn)

The Interplay of Nutrition, Metabolic Pathways, and Epigenetic Regulation (Ferdinand von Meyenn)

In this episode of the Epigenetics Podcast, we talked with Ferdinand von Meyenn from ETH Zürich about his work on the interplay of nutrition, metabolic pathways, and epigenetic regulation. To start Dr...

23 Jan 202548min

Single-Molecule Adenine Methylated Oligonucleosome Sequencing Assay (SAMOSA) (Vijay Ramani)

Single-Molecule Adenine Methylated Oligonucleosome Sequencing Assay (SAMOSA) (Vijay Ramani)

In this episode of the Epigenetics Podcast, we talked with Vijay Ramani from the Gladstone Institute about his work on Single-Molecule Adenine Methylated Oligonucleosome Sequencing Assay (SAMOSA). Our...

9 Jan 202552min

Epigenetic Consequences of DNA Methylation in Development (Maxim Greenberg)

Epigenetic Consequences of DNA Methylation in Development (Maxim Greenberg)

In this episode of the Epigenetics Podcast, we talked with Maxim Greenberg from the Institute Jacob Monot about his work on epigenetic consequences of DNA methylation in development. In this interview...

19 Dec 202444min

R-Loop Biology in Health and Disease (Natalia Gromak)

R-Loop Biology in Health and Disease (Natalia Gromak)

In this episode of the Epigenetics Podcast, we talked with Natalia Gromak from the University of Oxford about her work on R-Loop biology in health and disease. In this interview Dr. Gromak delves into...

5 Dec 202429min

The Menin-MLL Complex and Small Molecule Inhibitors (Yadira Soto-Feliciano)

The Menin-MLL Complex and Small Molecule Inhibitors (Yadira Soto-Feliciano)

In this episode of the Epigenetics Podcast, we talked with Yadira Soto-Feliciano from MIT about her work on the Menin-MLL complex and the effect of small molecules on its stability in leukemia. We exp...

21 Nov 202440min

Grant Writing in Academia and Industry – Tips for Success (Mary Anne Jelinek)

Grant Writing in Academia and Industry – Tips for Success (Mary Anne Jelinek)

In this episode of the Epigenetics Podcast, we talked with Mary Anne Jelinek Associate Director of R&D at Active Motif about writing and reviewing grants in academia and industry. Learn from Dr. Jelin...

14 Nov 202439min

DNase Hypersensitive Sites and Chromatin Remodeling Enzymes (Carl Wu)

DNase Hypersensitive Sites and Chromatin Remodeling Enzymes (Carl Wu)

In this episode of the Epigenetics Podcast, we talked with Carl Wu from John's Hopkins University about his work on nucleosome remodeling, histone variants, and the role of single-molecule imaging in ...

31 Okt 202455min

Populärt inom Vetenskap

p3-dystopia
svd-nyhetsartiklar
pojkmottagningen
dumma-manniskor
allt-du-velat-veta
kapitalet-en-podd-om-ekonomi
det-morka-psyket
rss-vetenskapsradion
rss-ufo-bortom-rimligt-tvivel
rss-experimentet
paranormalt-med-caroline-giertz
medicinvetarna
bildningspodden
halsorevolutionen
rss-vetenskapsradion-2
4health-med-anna-sparre
rss-spraket
hacka-livet
rss-broccolipodden-en-podcast-som-inte-handlar-om-broccoli
sexet