Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions

Abstract

Development of the gastrointestinal system occurs after gut tube closure, guided by spatial and temporal control of gene expression. However, it remains unclear what forces regulate these spatiotemporal gene expression patterns. Here we perform single-cell chromatin profiling of the primitive gut tube to reveal organ-specific chromatin patterns that reflect the anatomical patterns of distinct organs. We generate a comprehensive map of epigenomic changes throughout gut development, demonstrating that dynamic chromatin accessibility patterns associate with lineage-specific transcription factor binding events to regulate organ-specific gene expression. Additionally, we show that loss of Sox2 and Cdx2, foregut and hindgut lineage-specific transcription factors, respectively, leads to fate shifts in epigenomic patterns, linking transcription factor binding, chromatin accessibility, and lineage fate decisions in gut development. Notably, abnormal expression of Sox2 in the pancreas and intestine impairs lineage fate decisions in both development and adult homeostasis. Together, our findings define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and adult homeostasis.

Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA

“…Due to the scarcity of cleavage events in an individual cell, most chromatin accessibility regions in a single cell have only one aligned fragment, making the potential influence of intrinsic cleavage biases more substantial in scATAC-seq data than in bulk ATAC-seq data. We collected scATAC-seq datasets generated using different platforms for different biological samples, human hematopoietic cells 37 , mixed human cell lines 21 , and mouse primitive gut tube 38 , and found that the scATAC-seq data contained similar intrinsic cleavage biases to bulk data with highly correlated bias scores estimated by SELMA (Supplementary Fig. 9a–c ).…”

Accurate estimation of intrinsic biases for improved analysis of bulk and single-cell chromatin accessibility sequencing data using SELMA

“…Due to the scarcity of cleavage events in an individual cell, most chromatin accessibility regions in a single cell have only one aligned fragment, making the potential influence of intrinsic cleavage biases more substantial in scATAC-seq data than in bulk ATAC-seq data. We collected scATAC-seq datasets generated using different platforms for different biological samples, human hematopoietic cells 37 , human cell lines 21 , and mouse primitive gut tube 38 , and found that the scATAC-seq data contained similar intrinsic cleavage biases to bulk data with highly correlated bias scores estimated by SELMA (Fig. S9a-c).…”

A statistical method for quantifying progenitor population reveals incipient cell fate commitments

“…S13a). It is known that the gut endoderm has a spatial pattern along the anterior-posterior axis at ~E7.5 and will form seven organs, including thyroid, thymus, lung, liver, pancreas, small intestine and colon, at ~E9.0 48,49 . Accordingly, it is expected that the gut endoderm cells of the two embryos are undergoing incipient fate commitments.…”