Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

• Published in: Nature biotechnology Vol. 39; no. 7; pp. 825 - 835
• Main Authors: Bartosovic, Marek, Kabbe, Mukund, Castelo-Branco, Gonçalo
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.07.2021; Nature Publishing Group
• Subjects: 631/114/2114; 631/136/368/2430; 631/1647/2210/2211; 631/1647/48; 631/378/2596/1705; Agriculture; Analysis; Animals; Bioinformatics; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Brain - metabolism; Central nervous system; Chromatin; Cluster Analysis; Cohesin; Deoxyribonucleic acid; DNA; Enhancers; Gene expression; Gene Expression Regulation; Genetic aspects; Histones; Histones - metabolism; Humans; Identification and classification; Life Sciences; Methods; Mice; Nervous system; Neural networks; Occupancy; Olig2 protein; Single-Cell Analysis - methods; Structure; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Sweden
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/s41587-021-00869-9

In contrast to single-cell approaches for measuring gene expression and DNA accessibility, single-cell methods for analyzing histone modifications are limited by low sensitivity and throughput. Here, we combine the CUT&Tag technology, developed to measure bulk histone modifications, with droplet-based single-cell library preparation to produce high-quality single-cell data on chromatin modifications. We apply single-cell CUT&Tag (scCUT&Tag) to tens of thousands of cells of the mouse central nervous system and probe histone modifications characteristic of active promoters, enhancers and gene bodies (H3K4me3, H3K27ac and H3K36me3) and inactive regions (H3K27me3). These scCUT&Tag profiles were sufficient to determine cell identity and deconvolute regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter–enhancer connectivity. We also used scCUT&Tag to investigate the single-cell chromatin occupancy of transcription factor OLIG2 and the cohesin complex component RAD21. Our results indicate that analysis of histone modifications and transcription factor occupancy at single-cell resolution provides unique insights into epigenomic landscapes in the central nervous system. An improved method for single-cell analysis of histone modifications is applied to the mouse brain.