Single-cell profiling of histone modifications in the mouse brain

Abstract

The development of the mouse central nervous system (CNS) involves coordinated execution of transcriptional and epigenetic programs. These programs have been extensively studied through single-cell technologies in a pursuit to characterize the underlying cell heterogeneity. However, histone modifications pose additional layers of both positive and negative regulation that defines cellular identity. Here we show that the Cut&Tag technology can be coupled with a droplet-based single cell library preparation platform to produce high quality chromatin modifications data at a single cell resolution in tens of thousands of cells. We apply single-cell Cut&Tag (scC&T) to probe histone modifications characteristic of active promoters (H3K4me3), active promoters and enhancers (H3K27ac), active gene bodies (H3K36me3) and inactive regions (H3K27me3) and generate scC&T profiles for almost 50,000 cells. scC&T profiles of each of these histone modifications were sufficient to determine cell identity and deconvolute at single cell level regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter-enhancer connectivity. Moreover, we used scC&T 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 a single cell resolution can provide unique insights of epigenomic landscapes in the CNS. We also provide an online resource that can be used to interactively explore the data at https://castelobranco.shinyapps.io/BrainCutAndTag2020/.

Deep learning-based enhancement of epigenomics data with AtacWorks

“…We also demonstrate that AtacWorks can be adapted for crossmodality prediction of transcription factor footprints and ChIP-seq peaks from low-input ATAC-seq. As such, we anticipate this framework may be broadly useful for other deep learning applications in genomics, such as DNase, MNase, ChIP-seq, and the recently-developed method CUT&RUN 20 , which has comparable high-throughput single-cell adaptations 32,33 Finally, the robustness and speed of AtacWorks enable its application to high-throughput single-cell ATAC-seq datasets of heterogeneous tissues. We show that our method can be used on small subsets of rare lineage-priming cells to denoise signal and identify accessible regulatory regions at previously-unattainable genomic resolution.…”

Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

“…In addition to the Methods presented in this article, we are maintaining an online protocol to aid the research community in further development and adoption of TEA-seq on the Protocols.io platform ( https://doi.org/10.17504/protocols.io.bqagmsbw ). Additional development could allow simultaneous measurement of additional aspects of cell biology (e.g., CpG sequencing methods, scCUT&Tag; Bartosovic et al, 2020 ), as well as improvements to the modalities in the TEA-seq trio (e.g., s3-ATAC, Mulqueen et al, 2021 ). In direct comparisons of TEA-seq to existing methods (CITE-seq and scATAC-seq), we found that the sensitivity of gene detection was lower and distributions of antibody detections were altered relative to CITE-seq; however, ATAC-seq data quality remained comparable to the standalone assay ( Figure 4—figure supplement 4 ).…”

Simultaneous profiling of multiple chromatin proteins in the same cells

“…We and others have previously demonstrated the ability of methods adapted from CUT&RUN or CUT&Tag to map TFs and histone modifications in single cells (Bartlett et al, 2021;Bartosovic et al, 2020;Carter et al, 2019;Kaya-Okur et al, 2019;Skene and Henikoff, 2017;Wang et al, 2019;Wu et al, 2020;Xiong et al, 2020;Zhu et al, 2021). Critically, in single cell protocols that utilize transposition by Tn5, many of the enzymatic steps and washes can be performed in bulk cell populations, followed by single cell isolation and barcoding using any of several different methods (Bartlett et al, 2021;Bartosovic et al, 2020;Kaya-Okur et al, 2019;Wu et al, 2020). Based in part on these previous advances, we next developed a simple strategy to adapt multi-CUT&Tag to profile multiple chromatin factors in high throughput within the same single cells.…”