miRNomes of haematopoietic stem cells and dendritic cells identify miR-30b as a regulator of Notch1

Su, Xiaoping; Qian, Cheng; Zhang, Qian; Hou, Jin; Gu, Yan; Han, Yanmei; Chen, Yongjian; Jiang, Minghong; Cao, Xuetao

Results miRNomes in mouse HSCs and DC subsets. Using unique perfectly mapped reads, a total of 5,865,224, 5,928,841, 6,324,361 and 3,983,460 reads were sequenced from the HSCs, imDCs, maDCs and DCreg libraries respectively. We assigned each of the small RNAs a unique annotation according to its precursor and classified these small RNAs into different categories such as known miRNA, rRNA and so on (rRNA, tRNA, snRNA, snoRNA), repeat (LINE, SINE, LTR), mRNA (exons/introns) and unannotated small RNAs. All libraries showed a similar small RNA distribution. On average, 90.92% matched annotated miRNA hairpins; 7.06% matched rRNA, and so on.; 1.35% matched mRNAs; 0.33% matched repeat elements and 0.34% were previously uncharacterized small RNAs (Fig. 1a) . The mapping and categorizing of clean reads revealed that most small RNA reads were miRNAs during DC development and differentiation. miRNAs are differentially expressed at different DC stages. In order to obtain the abundance value for each miRNA in each small RNA library, miRNAs in mouse miRBase v.19 were analysed and normalized to 'transcripts per million (TPM)' for each library. In order to depict the dynamic expression patterns of markedly changed miRNAs during DC development and differentiation, 391 miRNAs (TPM410 in at least one small RNA library, acounting for B99.9% of miRNome) were selected. The miRNA with more than double of expression variation between two analysed cell types was determined as differentially expressed miRNA. We further classified these miRNAs into the 26 possible dynamic expression patterns and calculated the number of miRNAs in each pattern. Fisher exact test was used to determine the significantly enriched patterns (Fig. 1b) . Analysis showed that most miRNAs were expressed preferentially at one or two stages of DCs, and only a few of them were highly expressed in all the stages of DCs, suggesting miRNAs with specific functions may be more related to the biological characteristics of different DC stages.