The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping

Author(s)

de Mello, Fabio N. ; Tahira, Ana C. ; Berzoti-Coelho, Maria Gabriela ; Verjovski-Almeida, Sergio

• Document type: Journal article
• Source: BRIEFINGS IN BIOINFORMATICS; v. 25, n. 2, p. 15-pg., 2024-01-22.

Abstract

Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a recent development for epigenome mapping, but its unique methodology can hamper proper quantitative analyses. As traditional normalization approaches have been shown to be inaccurate, we sought to determine endogenous normalization factors based on the human genome regions of constant nonspecific signal. This constancy was determined by applying Shannon's information entropy, and the set of normalizer regions, which we named the 'Greenlist', was extensively validated using publicly available datasets. We demonstrate here that the greenlist normalization outperforms the current top standards, and remains consistent across different experimental setups, cell lines and antibodies; the approach can even be applied to different species or to CUT&Tag. Requiring no additional experimental steps and no added cost, this approach can be universally applied to CUT&RUN experiments to greatly minimize the interference of technical variation over the biological epigenome changes of interest. (AU)

• FAPESP's process: 18/23693-5 - Mechanisms of action of long non-coding RNAs involved with gene activation programs in eukaryotes
• Grantee: Sergio Verjovski Almeida
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 22/11192-7 - Analysis of the transcriptional regulation mechanisms mediated by the lincRNA PVT1 in a prostate cancer model
• Grantee: Fábio Nunes de Mello
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 20/02976-9 - Characterization of the interaction sites in the genome of the PVT1 lincRNA associated with the androgen receptor in Prostate Cancer lineages
• Grantee: Maria Gabriela Berzoti Coelho
• Support Opportunities: Scholarships in Brazil - Post-Doctoral