Extended Data Fig. 6: Characterization of feature chromatin states during mouse preimplantation development.
From: Genome-coverage single-cell histone modifications for embryo lineage tracing
(a) Annotation of genic and non-genic elements for each ChromHMM-trainned chromatin state. Chromatin state definitions are labeled on the left for each synthetic cell. (b) Emission probabilities for random control synthetic cells by single-cell ChromHMM. Random control synthetic cells are generated via randomly merging interpolated cells, rather than based on hierarchical clustering. Chromatin state definitions (left) and genome coverage (right) for each state are annotated. (c) Violin plots displaying histone modifications on multivalent regions for all single cells at the zygotic stage. Histone modifications are also calculated in a list of random regions at the same length as multivalent regions, served as a control. (d) Genomic annotation of multivalent regions. (e) Sankey diagram showing chromatin state dynamics of multivalent regions. Each line represents a 200-bp bin categorized by ChromHMM. Multi, multivalent; Pr-W, promoter (weak); Pr-s, promoter (strong); En-W, enhancer (weak); En-S, enhancer (strong); Ge-P, gene body (poised); Ge-A, gene body (active); He-P, heterochromatin (polycomb); He-K9, heterochromatin (H3K9me3); He, heterochromatin (K27 + K9); Quies, quiescent/low. (f) Emission probabilities for GV-oocyte, Zygote, and 2-cell by ChromHMM. Low-input ChIP-seq profiles are either downloaded from GSE76687, GSE71434, GSE207222, GSE112834, GSE98149, or obtained with itChIP-seq in this work. (g) TF motifs identified from chromatin regions annotated as promoters, enhancers or gene bodies for synthetic cells. Representative known regulators for totipotency and pluripotency are shown. Chromatin regions annotated as promoters, enhancers or gene bodies were intersected with ATAC-seq peaks to refine the regions for TF motif enrichment analysis via Homer. P value, one-sided binomial test.
