Description

Single-Cell Epigenomics Maps the Continuous Regulatory Landscape of Human

Hematopoietic Differentiation

Jason D Buenrostro^1,2, M Ryan Corces³, Beijing Wu⁴, Alicia N Schep⁴, Caleb A Lareau¹,

Ravindra Majeti^5,6, Howard Y. Chang³, William J. Greenleaf^3,4,7

¹Broad Institute of MIT and Harvard, Cambridge, MA, USA^{; 2}Harvard Society of Fellows, Harvard University, Cambridge, MA, USA^{; 3}Center for Personal Dynamic Regulomes, Stanford University, CA, USA; ⁴Department of Genetics, Stanford University, CA, USA; ⁵Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, CA, USA; ⁶Division of Hematology, Department of Medicine, Stanford University, CA, USA; ⁷Department of Applied Physics, Stanford University, CA, USA

Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden by ensemble averaging. We generated single-cell chromatin accessibility landscapes across 8 populations of immunophenotypically-defined human hematopoietic cell types. Using bulk chromatin accessibility profiles to scaffold our single-cell data analysis, we constructed an epigenomic landscape of human hematopoiesis and characterized epigenomic heterogeneity within phenotypically sorted populations to find epigenomic lineage-bias toward different developmental branches in multipotent stem cell states. We identify and isolate sub-populations within classically-defined granulocyte-macrophage progenitors (GMPs) and use ATAC-seq and RNA-seq to confirm that GMPs are epigenomically and transcriptomically heterogeneous. Furthermore, we identified transcription factors and cis-regulatory elements linked to changes in chromatin accessibility within cellular populations and across a continuous myeloid developmental trajectory, and observe relatively simple TF motif dynamics give rise to a broad diversity of accessibility dynamics at cis-regulatory elements. Overall, this work provides a template for exploration of complex regulatory dynamics in primary human tissues at the ultimate level of granular specificity – the single cell.

This work was supported by National Institutes of Health (NIH) P50HG007735 (to H.Y.C. and W.J.G.), U19AI057266 (to W.J.G.)