Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIP-Seq). Mus musculus

Long non-coding RNAs (lncRNAs) have recently emerged as new players in gene expression regulation. Whether and how lncRNAs might control hematopoietic stem cell (HSC) function remains largely unknown. Here, we profiled the transcriptome of purified long-term HSCs by deep RNA-sequencing and identified thousands of un-annotated transcripts of which 323 are predicted to be lncRNAs. Comparison of their expression in differentiated lineages represented by B cells (B220+) and Granulocytes (Gr1+), revealed that 159 are likely to be HSC-specific. Knockdown of two such non-coding genes (LincHSC-1 and LincHSC-2) indicated that they regulate HSC lineage differentiation, possibly via targeting cell cycle regulators and chromatin modification enzymes. Taken together, we comprehensively identify lncRNAs in HSC and show to examples that play important roles in HSC function. Overall design: (I) Mouse Granulocytes mRNA profile were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. (II) To identify LncHSC target gene, mouse progenitor Sca-1+ cells were isolated from 5-FU injected mice and transduced with GFP+ retrovitus construct to knockdown lncHSC expression, and after in vitro culture for 2 days, KSL-GFP+ cells were sorted for mRNA profiling. (III) Mouse B-cells mRNA profile were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. (IV) Mouse HSC H3K4me1 and H3K27ac ChIP-seq were generated using 50,000-100,000 primary HSCs by deep sequencing using Illumina Hiseq 2000.