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

Autor(es)

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

• Tipo de documento: Artigo Científico
• Fonte: BRIEFINGS IN BIOINFORMATICS; v. 25, n. 2, p. 15-pg., 2024-01-22.

Resumo

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)

• Processo FAPESP: 18/23693-5 - Mecanismos de ação de RNAs longos não-codificadores envolvidos nos programas de ativação gênica em eucariotos
• Beneficiário: Sergio Verjovski Almeida
• Modalidade de apoio: Auxílio à Pesquisa - Temático
• Processo FAPESP: 22/11192-7 - Análise dos mecanismos de regulação transcricional mediados pelo lincRNA PVT1 em modelo de cancer de prostata
• Beneficiário: Fábio Nunes de Mello
• Modalidade de apoio: Bolsas no Brasil - Mestrado
• Processo FAPESP: 20/02976-9 - Caracterização dos sítios de interação no genoma do lincRNA PVT1 associado ao receptor de andrógeno em linhagem de Câncer de Próstata
• Beneficiário: Maria Gabriela Berzoti Coelho
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado