When is a Peak a Peak? (Claudio Cantù)
Epigenetics Podcast27 Heinä 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

Jaksot(168)

Development of Site-Specific ChIP Technologies (Hodaka Fujii)

Development of Site-Specific ChIP Technologies (Hodaka Fujii)

In this episode of the Epigenetics Podcast, we caught up with Dr. Hodaka Fujii, Professor of Biochemistry and Genome Biology at Hirosaki University Graduate School of Medicine and School of Medicine, ...

1 Loka 202042min

Regulation of Chromatin Organization by Histone Chaperones (Geneviève Almouzni)

Regulation of Chromatin Organization by Histone Chaperones (Geneviève Almouzni)

In this episode of the Epigenetics Podcast, we caught up with Geneviève Almouzni, Ph.D., Research Director at the CNRS at Institut Curie in Paris, to talk about her work on the regulation of chromatin...

17 Syys 202038min

How the "Fragile Nucleosome" Science Community Came to Life (Christine Cucinotta, Melvin Noe Gonzalez)

How the "Fragile Nucleosome" Science Community Came to Life (Christine Cucinotta, Melvin Noe Gonzalez)

In this episode of the Epigenetics Podcast, we caught up with Dr. Christine Cucinotta and Dr. Melvin Noe Gonzalez to talk about how they brought the #fragilenucleosome seminar series and Discord chann...

10 Syys 202041min

Epigenetic Influence on Memory Formation and Inheritance (Isabelle Mansuy)

Epigenetic Influence on Memory Formation and Inheritance (Isabelle Mansuy)

In this episode of the Epigenetics Podcast, we caught up with Professor Isabelle Mansuy, Ph.D., from the University of Zürich and the ETH Zürich, to talk about her work on epigenetic influences on mem...

3 Syys 202038min

Influence of Dynamic RNA Methylation on Gene Expression (Chuan He)

Influence of Dynamic RNA Methylation on Gene Expression (Chuan He)

In this episode of the Epigenetics Podcast, we caught up with Dr. Chuan He, John T. Wilson Distinguished Service Professor at University of Chicago, to talk about his work on the influence of dynamic ...

20 Elo 202041min

How to Publish in Nature: Lessons from the ENCODE Consortium (Michelle Trenkmann, Senior Editor at Nature)

How to Publish in Nature: Lessons from the ENCODE Consortium (Michelle Trenkmann, Senior Editor at Nature)

In this episode of the Epigenetics Podcast, we caught up with Dr. Michelle Trenkmann, Senior Editor at Nature. We discussed her work as an editor at Nature and how she contributed to the ENCODE 3 publ...

6 Elo 202035min

The Role of Non-Histone Proteins in Chromosome Structure and Function During Mitosis (Bill Earnshaw)

The Role of Non-Histone Proteins in Chromosome Structure and Function During Mitosis (Bill Earnshaw)

In this episode of the Epigenetics Podcast, we caught up with Professor Bill Earnshaw, Wellcome Trust Principal Research Fellow at the University of Edinburgh, to talk about his work on the role of no...

23 Heinä 20201h 4min

Effects of DNA Methylation on Chromatin Structure and Transcription (Dirk Schübeler)

Effects of DNA Methylation on Chromatin Structure and Transcription (Dirk Schübeler)

In this episode of the Epigenetics Podcast, we caught up with Dr. Dirk Schübeler, Director of the Friedrich Miescher Institute (FMI) in Basel, Switzerland, to talk about his work on the effects of DNA...

2 Heinä 202036min

Suosittua kategoriassa Tiede

tiedekulma-podcast
rss-mita-tulisi-tietaa
rss-poliisin-mieli
docemilia
rss-duodecim-lehti
utelias-mieli
rss-astetta-parempi-elama-podcast
rss-luontopodi-samuel-glassar-tutkii-luonnon-ihmeita
filocast-filosofian-perusteet
rss-ammamafia
rss-tiedetta-vai-tarinaa
rss-lapsuuden-rakentajat-podcast
rss-sosiopodi