Coding and noncoding gene expression of human blood cells from healthy donors (Agilent-021441)

Long non-coding RNAs (lncRNAs) and miRNAs have emerged as crucial regulators of gene expression and cell fate decisions. Here we present an integrated analysis of the ncRNA-landscape of purified human hematopoietic stem cells (HSCs) and their differentiated progenies, including granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors. For each blood cell population, RNA from 5 healthy donors was hybridized onto three microarray platforms (Arraystar lncRNA V2.0, NCode™-miRNA/-ncRNA), yielding a coverage of more than 40,000 lncRNAs, 25,000 mRNAs and 900 miRNAs on 146 arrays. T-distributed stochastic neighbor embedding (t-SNE) on noncoding genes structured the dataset into groups of samples that matched the input populations, demonstrating their unique lncRNA expression profiles. Self-organizing maps (SOMs) revealed clusters of lncRNAs and mRNAs that were coordinately expressed in HSCs and during lineage commitment. Using a “guilt-by-association” approach we assigned putative functions to lncRNAs regulated during differentiation, which predicted LINC00173 as a novel non-coding regulator of granulopoiesis. We knocked down LINC00173 using two independent shRNA constructs, which resulted in diminished granulocytic in vitro differentiation, myeloid colony-formation and function. Next, we uncovered a strong and highly coordinated upregulation of miRNAs, small nucleolar RNAs (snoRNAs) and lncRNAs within the DLK1-DIO3 locus on chromosome 14 (hsa14) during megakaryocytic maturation. shRNA-mediated knock-down of noncoding members of the locus reduced erythroid colony-formation and megakaryocytic cell proliferation in vitro implicating the functional importance of this ncRNA locus in megakaryopoiesis. Mature blood cells (granulocytes, monocytes, T-cells, NK-cells, B-cells, megakaryocytes and erythroid precursors) and hematopoietic stem and progenitor cells from healthy donors were FACS-purified and total RNA was subjected to Microarray Analysis on the Agilent-021441 NCode Human Long Non-coding RNA microarrays (GPL18348)