Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a method, Chromatin Velocity, that identifies the trajectories of epigenetic modifications at the single-cell level. Chromatin Velocity uncovered paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.

Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin

Giannese, Francesca;Catalano, Irene;Grassi, Elena;Zanella, Eugenia R;Bertotti, Andrea;Trusolino, Livio;Cittaro, Davide;Tonon, Giovanni
2022

Abstract

Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a method, Chromatin Velocity, that identifies the trajectories of epigenetic modifications at the single-cell level. Chromatin Velocity uncovered paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.
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Chromatin; Epigenesis, Genetic; Humans; Transposases; Euchromatin; Heterochromatin
Tedesco, Martina; Giannese, Francesca; Lazarević, Dejan; Giansanti, Valentina; Rosano, Dalia; Monzani, Silvia; Catalano, Irene; Grassi, Elena; Zanella, Eugenia R; Botrugno, Oronza A; Morelli, Leonardo; Panina Bordignon, Paola; Caravagna, Giulio; Bertotti, Andrea; Martino, Gianvito; Aldrighetti, Luca; Pasqualato, Sebastiano; Trusolino, Livio; Cittaro, Davide; Tonon, Giovanni
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2318/1869160
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