Gene

RUNX1

Cell biology

Haematopoiesis

Biology

Epigenetics

Long non-coding RNA

Stem cell

Operating system

Cancer research

Computer science

DNA methylation

Computational biology

Downregulation and upregulation

Hematopoietic stem cell

Genetics

Embryonic stem cell

Transcription factor

Cell

Gene expression

Profiling (computer programming)

Cell stem cell

The generation of hematopoietic stem cells (HSCs) from embryonic endothelial precursors and pre-HSCs is precisely regulated by signaling pathways and transcription factors. Nevertheless, regulatory roles of non-coding RNAs remain unknown. Taking advantage of our ability to capture rare pre-HSCs and HSCs in vivo, we generated a single-cell landscape of long non-coding RNAs (lncRNAs) during HSC development. Combining bioinformatics and functional screening, we identified 6 lncRNAs influencing hematopoiesis in vitro. We further revealed that H19 lncRNA is pivotal for in vivo HSC emergence in aorta-gonads-mesonephros region. Early H19 lncRNA deficiency blocked endothelial-to-hematopoietic transition, which was independent of the H19-derived miR, miR-675. Moreover, H19-deficient pre-HSCs displayed promoter hypermethylation and concomitant downregulation of several master hematopoietic transcription factors, including Runx1 and Spi1. H19 deficiency increased the activity of S-adenosylhomocysteine hydrolase, a regulator of DNA methylation, which partially contributed to the observed hematopoietic defect. Our findings provide a resource for further analysis of lncRNAs in embryonic HSC development.

Combined Single-Cell Profiling of lncRNAs and Functional Screening Reveals that H19 Is Pivotal for Embryonic Hematopoietic Stem Cell Development