Identification of tissue-specific microRNAs from mouse
Few mammalian miRNAs were known and their tissue distribution was untested; this paper cloned about 21-nucleotide RNAs from mouse tissues and identified 34 novel miRNAs. A single miRNA dominated heart (miR-1, 45%), liver (miR-122 variants, 72%) and brain (miR-124, 25–48%), and nearly all were conserved in the human genome.
Key findings
- Cloning of approximately 21-nucleotide RNAs from nine adult mouse tissues, including heart, liver, spleen, colon, cortex, cerebellum and midbrain, identifies 34 novel miRNAs. Almost all are encoded in the human genome and are frequently found in nonmammalian vertebrate genomes such as pufferfish, which points to conserved function.
- In adult mouse liver, variants of miR-122 account for 72% of all cloned miRNAs, and miR-122 is undetected in all other tissues analyzed. The cloned variants (miR-122a, miR-122b and the shared 22-nucleotide core) differ only at the 3′ terminus.
- A single tissue-specifically expressed miRNA dominates the cloned miRNA population of several tissues: miR-1 accounts for 45% of mouse heart miRNAs (and is low in liver and midbrain), miR-124 variants for 25–48% of brain miRNAs, miR-143 for about 30% of spleen miRNAs and miR-142-as for about 30% of colon miRNAs. This pattern suggests roles for these miRNAs in tissue specification or cell lineage decisions.
- The mouse mir-30a precursor yields miRNAs from both strands. The originally described miR-30 is renamed miR-30a-as, and the miRNA from the opposite, 5′ arm of the precursor is miR-30a-s (equivalent to miR-97). The family members miR-30b, miR-30c and miR-30d are also cloned from mouse tissues.
- Mouse miR-125a and miR-125b are similar to the C. elegans lin-4 stRNA, differing mainly in the central region, and miR-125b has a readily identifiable Drosophila melanogaster ortholog expressed in pupae and adults but not in embryo or larvae. These are the proposed fruitfly and mammalian orthologs of lin-4.
Abstract
MicroRNAs (miRNAs) are a new class of noncoding RNAs, which are encoded as short inverted repeats in the genomes of invertebrates and vertebrates. It is believed that miRNAs are modulators of target mRNA translation and stability, although most target mRNAs remain to be identified. Here we describe the identification of 34 novel miRNAs by tissue-specific cloning of approximately 21-nucleotide RNAs from mouse. Almost all identified miRNAs are conserved in the human genome and are also frequently found in nonmammalian vertebrate genomes, such as pufferfish. In heart, liver, or brain, it is found that a single, tissue-specifically expressed miRNA dominates the population of expressed miRNAs and suggests a role for these miRNAs in tissue specification or cell lineage decisions. Finally, a miRNA was identified that appears to be the fruitfly and mammalian ortholog of C. elegans lin-4 stRNA.