Hierarchical chromatin regulation during blood formation uncovered by single-cell sortChIC

Abstract

Post-translational histone modifications modulate chromatin packing to regulate gene expression. How chromatin states, at euchromatic and heterochromatic regions, underlie cell fate decisions in single cells is relatively unexplored. We develop sort assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in hematopoietic stem and progenitor cells (HSPCs), and mature blood cells in the mouse bone marrow. During differentiation, HSPCs acquire distinct active chromatin states that depend on the specific cell fate, mediated by cell type-specifying transcription factors. By contrast, most regions that gain or lose repressive marks during differentiation do so independent of cell fate. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin-repressed states. This suggests hierarchical chromatin regulation during hematopoiesis: heterochromatin dynamics define differentiation trajectories and lineages, while euchromatin dynamics establish cell types within lineages.

SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data

“…Several approaches have been developed for data integration across modalities 13, 49 and are likely to exhibit improved performance when applied at the metacell level. Given the kernel representation, SEACells should generalize to other modalities such as CUT&Tag 50, 51 or other single-cell chromatin modification measurements 52 with appropriate preprocessing.…”

Single-cell profiling of transcriptome and histone modifications with EpiDamID

“…The limited handling prior to individual cell capture offers opportunities to integrate upstream steps of other protocols that are compatible with the final processing steps of scDamID. Powerful future method integrations may involve combining scDamID with scChIC-seq (Ku et al, 2019) or sortChIC (Zeller et al, 2021) to measure two genome-wide profiles in the same cell, or the incorporation of the CITE-seq approach to obtain quantitative single-cell measurements of protein abundance, transcriptomics and histone PTM profiles. This latter combination offers the exciting prospect to study gene expression across the central dogma of gene regulation.…”

“…However, the general requirement of high numbers of input cells consequently provides a population-average view of the assayed histone PTM that belies the complexity of many biological systems. As a response, several low-input methods have been developed that can assay histone PTMs in individual cells (Ai et al, 2019;Hainer et al, 2019;Harada et al, 2019;Ku et al, 2019;Rotem et al, 2015;Zeller et al, 2021). While these singlecell methods offer a first understanding of the epigenetic heterogeneity between cells, it remains challenging to establish a direct link to other measurable outputs such as transcription or cellular state.…”

Single-cell profiling of transcriptome and histone modifications with EpiDamID

“…However, the requirement of high numbers of input cells consequently provides a population-average view, which disregards the complexity of most biological systems. As a result, several low-input methods have been developed that can assay histone PTMs in individual cells, including but not limited to Drop-ChIP ( Rotem et al., 2015 ), ChIL-seq ( Harada et al., 2019 ), ACT-seq ( Carter et al., 2019 ), single-cell ChIP-seq ( Grosselin et al., 2019 ), single-cell ChIC-seq ( Ku et al., 2019 ), single-cell adaptation of CUT&RUN ( Hainer et al., 2019 ), CUT&Tag ( Kaya-Okur et al., 2019 ), CoBATCH ( Wang et al., 2019 ), single-cell itChIP ( Ai et al., 2019 ), and sortChIC ( Zeller et al., 2021 ). While these techniques offer an understanding of the epigenetic heterogeneity between cells, they do not provide a direct link to other measurable outputs.…”