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(167)

Gene Dosage Alterations in Evolution and Ageing (Claudia Keller Valsecchi)

Gene Dosage Alterations in Evolution and Ageing (Claudia Keller Valsecchi)

In this episode of the Epigenetics Podcast, we caught up with Claudia Keller Valsecchi from the Institute for Molecular Biology in Mainz to talk about her work on gene dosage alterations in evolution ...

29 Kesä 202331min

Structural Analysis of Nucleosomes During Transcription (Lucas Farnung)

Structural Analysis of Nucleosomes During Transcription (Lucas Farnung)

In this episode of the Epigenetics Podcast, we caught up with Lucas Farnung from Harvard Medical School to talk about his work on the structural analysis of nucleosomes during transcription. Lucas Far...

15 Kesä 202333min

DNA Methylation Alterations in Neurodegenerative Diseases (Paula Desplats)

DNA Methylation Alterations in Neurodegenerative Diseases (Paula Desplats)

In this episode of the Epigenetics Podcast, we caught up with Paula Desplats from the University of California San Diego to talk about her work on DNA Methylation Alterations in Neurodegenerative Dise...

1 Kesä 202340min

scDamID, EpiDamID and Lamina Associated Domains (Jop Kind)

scDamID, EpiDamID and Lamina Associated Domains (Jop Kind)

In this episode of the Epigenetics Podcast, we caught up with Jop Kind from Hubrecht Institute to talk about his work on single cell DamID, EpiDamID, and Lamina Associated Domains (LADs). Jop Kind sta...

17 Touko 202351min

Circulating Epigenetic Biomarkers in Cancer (Charlotte Proudhon)

Circulating Epigenetic Biomarkers in Cancer (Charlotte Proudhon)

In this episode of the Epigenetics Podcast, we caught up with Charlotte Proudhon from the Institut Curie to talk about her work on circulating tumor DNA and circulating Epi-mutations as biomarkers in ...

4 Touko 202338min

Epigenetic Landscapes During Cancer (Luciano Di Croce)

Epigenetic Landscapes During Cancer (Luciano Di Croce)

In this episode of the Epigenetics Podcast, we caught up with Luciano Di Croce from the Center of Genomic Regulation in Barcelona to talk about his work on epigenetic landscapes in cancer. The Di Croc...

20 Huhti 202348min

Formation of CenH3-deficient Kinetochores (Ines Drinnenberg)

Formation of CenH3-deficient Kinetochores (Ines Drinnenberg)

In this episode of the Epigenetics Podcast, we caught up with Ines Drinnenberg from Institute Curie to talk about her work on the formation of CenH3-deficient kinetochores. The laboratory of Ines Drin...

6 Huhti 202334min

Effects of Environmental Cues on the Epigenome and Longevity (Paul Shiels)

Effects of Environmental Cues on the Epigenome and Longevity (Paul Shiels)

In this episode of the Epigenetics Podcast, we caught up with Paul Shiels from the University of Glasgow to talk about his work on the effects of environmental cues on the epigenome and longevity. Pau...

23 Maalis 202347min

Suosittua kategoriassa Tiede

rss-mita-tulisi-tietaa
rss-poliisin-mieli
rss-lihavuudesta-podcast
utelias-mieli
rss-duodecim-lehti
tiedekulma-podcast
rss-opeklubi
docemilia
mielipaivakirja
hippokrateen-vastaanotolla
radio-antro
rss-mental-race
rss-luontopodi-samuel-glassar-tutkii-luonnon-ihmeita
rss-sosiopodi