Next-generation sequencing identifies the natural killer cell microRNA transcriptome

ABSTRACT: Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g. granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate the translation of their mRNA targets, and are therefore candidates mediating this control process. While the expression and importance of miRNAs in T and B lymphocytes has been established, little is known about miRNAs in NK cells. Here, we utilized two next-generation sequencing (NGS) platforms to define the miRNA transcriptomes of resting and cytokine-activated primary murine NK cells, with confirmation by RT-qPCR and microarrays. We delineate a bioinformatics analysis pipeline that identified 302 known and 28 novel mature miRNAs from sequences obtained from NK cell small RNA libraries. These miRNAs are expressed over a broad range, exhibit isomiR complexity, and a subset is differentially expressed following cytokine-activation. Using this miRNA NGS data, miR-223 was identified as a mature miRNA present in resting NK cells with decreased expression following cytokine-activation. Further, we demonstrate that miR-223 specifically targets the 3’UTR of murine GzmB in vitro, indicating that this miRNA may contribute to control of GzmB translation in resting NK cells. Thus, the sequenced NK cell miRNA transcriptome provides a valuable framework for further elucidation of miRNA expression and function in NK cell biology. Illumina GA (SRR036363, SRR036364) and SOLiD (SRR036206, SRR036210) sequencing data have been submitted to the NCBI Sequence Read Archive (SRA).

ORGANISM(S): Mus musculus

PROVIDER: GSE21003 | GEO | 2010/10/01

SECONDARY ACCESSION(S): PRJNA125783

REPOSITORIES: GEO