Tracking single cell evolution via clock-like chromatin accessibility

Abstract

Single cell chromatin accessibility sequencing (scATAC) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Here we show a simple, accurate and phenotypic-neutral measure of cell developmental hierarchy – the fraction of accessible clock-like differential methylation loci (ClockDML). As cell undergone mitosis, heterogeneity of chromatin accessibility on ClockDML reduced, providing a measure of mitotic age. We developed a method, EpiTrace, that counts the fraction of opened ClockDML from scATAC data to determine cell age and perform lineage tracing. EpiTrace derived cell age shows concordance to known developmental hierarchies, correlates well with DNA methylation-based clocks, and is complementary with mutation-based lineage tracing, RNA velocity, and stemness predictions. Applying EpiTrace to human scATAC data revealed a multitude of novel biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification. Our work discovered a universal epigenomic hallmark during cellular development, which facilitates the study of cellular hierarchies and organismal aging.

A universal molecular mechanism driving aging

“…We found that G4s tend to gradually accumulate in accessible chromatin (Extended Data Fig. 1), and the fraction of G4 reads within the aging-associated ATAC peak, determined as the ATAC peaks that gradually open during aging 7 , linearly increases as the cell number increases (Fig. 1b).…”

“…2a). We calculated aging-associated chromatin opening kinetics as the Z-scaled correlation coefficient between ATAC peak reads and sample age 7 (hereinafter termed the "aging coefficient" for simplicity). The genes that showed a significant correlation between TSS chromatin accessibility and sample age (defined as those with an aging coefficient >= 3) were termed "aging genes", which showed a significantly greater gain of chromatin opening during aging (Fig.…”

“…To test whether chromatin openings in G4 regions exhibit clock-like behavior, we used EpiTrace 7 to estimate the total number of opened G4 loci in bulk or single-cell ATAC-seq data from in vitro passaged pMEFs or primary mouse astrocytes (pASTs). A linear correlation between the total number of opened G4 loci and cell age was found for different cell types across the different assays (Fig.…”

“…The multiplex anchored PCR bisulfite sequencing data of mouse primary embryonic fibroblasts generated using the MM285/347 ClockDML primer set were obtained from a previous publication 7 .…”

“…Transcription factor activity was computed by ChromVAR in ArchR (1.0.1) from the pMEF SHARE-seq dataset from a previous publication 7 . Single-cell ages were estimated from the same dataset using EpiTrace.…”