Single-cell profiling of transcriptome and histone modifications with EpiDamID

Abstract

Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, including various combinations of transcriptome, genome and epigenome. However, comprehensive profiling of the histone post-translational modifications that influence gene expression at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of genetically engineered proteins. By fusing Dam to single-chain variable fragment antibodies, engineered chromatin reader domains, or endogenous chromatin-binding proteins, we render the DamID technology and all its implementations compatible with the genome-wide identification of histone post-translational modifications. Importantly, this enables the joint analysis of chromatin marks and transcriptome in a variety of biological systems at the single-cell level. In this study, we use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. We further demonstrate the applicability of this method to in vivo systems by mapping H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specifically in the notochord. Overall, EpiDamID is a new addition to a vast existing toolbox for obtaining systematic insights into the role of chromatin states during dynamic cellular processes.

Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis

“…If the sensitivity can be further improved, additional chromatin states might become visible that are indistinguishable from scRNA-seq. Future multi-omics studies integrating the detection of chromatin modifications with transcription [72][73][74] should further facilitate the integrated analysis of diverse histone modifications and allow us to more clearly understand how these multiple layers of gene regulation are related.…”

H3K27me3 dictates atypical genome-nuclear lamina interactions and allelic asymmetry during early embryogenesis

“…We chose to profile 1) H3K9me3 that is often present in LADs, 2) H3K27me3 which plays an essential role in repressing genes during embryonic development and 3) open chromatin that tends to anticorrelate with LADs. To this end, the fusion constructs Dam-Cbx1 (chromodomain tuple) and Dam-H3K27me3 (scFv) 22 as well as the untethered Dam were used, respectively. The profiles obtained with these constructs were comparable to published 2-cell stage ChIP-seq and ATACseq data (Figure 3a and Extended Data Figure 4a).…”

Combinatorial single-cell profiling of all major chromatin types with MAbID

“…The recent advancement of multi-omics strategies at single-cell resolution has created ample opportunity to obtain a deeper understanding of gene regulatory processes [9][10][11]16,19 . However, measuring multiple epigenetic modifications in a combined setting remains a challenge.…”

“…In recent years, there has been a vast advancement of multi-omic strategies that enable the profiling of several modalities in single cells. Most prominently among these are methods linking transcriptional heterogeneity to variations in DNA methylation [8][9][10] , chromatin accessibility 9,11,12 , protein-DNA binding 13,14 , nuclear architecture [13][14][15] and histone PTMs [16][17][18][19][20] . However, these techniques can generally only profile one of these modalities in combination with transcription, while methods that can simultaneously measure multiple gene-regulatory components are limited.…”