Low-input chromatin profiling reveals inter- and intra-lineage differences across immune cell types

Abstract Transcriptional regulation in cells is governed by myriad traits that allow specific responses to ever-changing environments. Inclusive of these regulatory factors are the histone proteins that compact the genome while additionally being decorated with diverse post-translational modifications (PTM) suggested to direct the cellular machinery to express / repress lineage- and context-specific loci. Our consortium recently performed a detailed analysis of chromatin accessibility (ATACseq) across multiple mouse immunocyte populations, which advanced our understanding of how cis-regulatory elements (CRE) control transcriptional programs in rarer immune cell types. Understanding the role of histone PTMs in this process has remained elusive due to the high cell-input demands of the gold-standard assay: ChIPseq. To this end, we developed a streamlined CUT&RUN approach to support robust profiling at 10K cells per target in ~100 sorted mouse immunologic populations. We have used this to map histone PTM states characteristic of active (H3K4me1/3, H3K27ac, H3K36me3) or repressed (H3K27me3) chromatin and architectural factors associated with genome organization (H3.3, CTCF), in tandem with RNA- and ATAC-seq. We further dissected the effect of genomic variation by utilizing a B6xCast/EiJ F1 hybrid mouse to understand how CRE variation at each allele independently impacts transcriptional regulation. Taken together, our data provides a deeper understanding of transcriptional regulation in the mouse immune system across differentiation and perturbation states.