Massively parallel single-cell profiling of transcriptome and multiple epigenetic proteins in cell fate regulation

Abstract

Sculpting the epigenome with a combination of histone modifications and transcription factor (TF) occupancy determines gene transcription and cell fate specification. Here we first develop uCoTarget, utilizing a split-pool barcoding strategy for realizing ultra-high throughput single-cell joint profiling of multiple epigenetic proteins. Through extensive optimization for sensitivity and multimodality resolution, we demonstrate that uCoTarget enables simultaneous detection of five histone modifications (H3K27ac, H3K4me3, H3K4me1, H3K36me3 and H3K27me3) in 19,860 single cells. We applied uCoTarget to the in vitro generation of hematopoietic stem/progenitor cells (HSPCs) from human embryonic stem cells, presenting multimodal epigenomic profiles in 26,418 single cells. uCoTarget with high sensitivity per modality reveals establishment of pairing of HSPC enhancers (H3K27ac) and promoters (H3K4me3) along the differentiation trajectory and RUNX1 engagement priming for the H3K27ac activation along the HSPC path. We then develop uCoTargetX, an expansion of uCoTarget to simultaneously measure transcriptome and multiple epigenome targets. Together, our methods enable generalizable, versatile multi-modal profiles for reconstructing comprehensive epigenome and transcriptome landscapes and analyzing the regulatory interplay at single-cell level.

Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

“…The rise of powerful single-cell epigenomic technologies has now made this level of profiling attainable. Single-cell studies covering DNA methylation 25 and individual histone modifications [26][27][28][29][30][31][32][33][34][35][36] have started elucidating these epigenetic landscapes in the mouse adult CNS; however the exploration of the adult human CNS remains limited and currently only DNA methylation and chromatin architecture have been analysed at the single cell level 37 . Regarding histone modifications, current datasets are restricted to single cell analysis of H3K27me3 of a glioblastoma tumour from one patient 30 and bulk characterization of glioblastoma tumours 18 , or specific fluorescent-activated nuclei sorted subpopulations in the human cortex 38 , while multi-modal single-cell profiling of the different cell states in the adult human CNS is still lacking.…”