Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells

• Published in: Nature biotechnology Vol. 37; no. 7; pp. 766 - 772
• Main Authors: Rooijers, Koos, Markodimitraki, Corina M., Rang, Franka J., de Vries, Sandra S., Chialastri, Alex, de Luca, Kim L., Mooijman, Dylan, Dey, Siddharth S., Kind, Jop
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.07.2019; Nature Publishing Group
• Subjects: 631/337/100; 631/337/176; 631/337/386; 631/337/572; Adenine; Agriculture; Animals; Bioinformatics; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Cell Line; Cells; Chromatin; Deoxyribonucleic acid; DNA; DNA methyltransferase; DNA sequencing; DNA-Binding Proteins - metabolism; Embryo cells; Gene expression; Gene Expression Regulation; Genetic aspects; Genetic transcription; Genomes; Heterogeneity; Letter; Life Sciences; mRNA; Observations; Polycomb group proteins; Protein Binding; Protein-protein interactions; Proteins; Single-Cell Analysis - methods; Site-specific DNA methyltransferase (adenine-specific); Stem cell transplantation; Stem cells; Transcription; Transcriptome; United States; Netherlands; Germany
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/s41587-019-0150-y

Protein–DNA interactions are critical to the regulation of gene expression, but it remains challenging to define how cell-to-cell heterogeneity in protein–DNA binding influences gene expression variability. Here we report a method for the simultaneous quantification of protein–DNA contacts by combining single-cell DNA adenine methyltransferase identification (DamID) with messenger RNA sequencing of the same cell (scDam&T-seq). We apply scDam&T-seq to reveal how genome–lamina contacts or chromatin accessibility correlate with gene expression in individual cells. Furthermore, we provide single-cell genome-wide interaction data on a polycomb-group protein, RING1B, and the associated transcriptome. Our results show that scDam&T-seq is sensitive enough to distinguish mouse embryonic stem cells cultured under different conditions and their different chromatin landscapes. Our method will enable the analysis of protein-mediated mechanisms that regulate cell-type-specific transcriptional programs in heterogeneous tissues. scDamID&T combines DNA adenine methyltransferase-based labeling of protein–DNA contact sites with transcriptome sequencing to analyze regulatory programs in single cells.