Abstract
BackgroundDigital gene expression (DGE) profiling has become an established tool to study RNA expression. Here, we provide an in-depth analysis of small RNA DGE profiles from two different rat strains (BN-Lx and SHR) from six different rat tissues (spleen, liver, brain, testis, heart, kidney). We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs.ResultsWe confirmed the expression of 588 known miRNAs (54 in antisense orientation) and identified 56 miRNAs homologous to known human or mouse miRNAs, as well as 45 new rat miRNAs. Furthermore, we confirmed specific A to I editing in brain for mir-376a/b/c and identified mir-377 as a novel editing target. In accordance with earlier findings, we observed a highly tissue-specific expression pattern for all tissues analyzed. The brain was found to express the highest number of tissue-specific miRNAs, followed by testis. Notably, our experiments also revealed robust strain-specific differential miRNA expression in the liver that is caused by genetic variation between the strains. Finally, we identified two types of germline-specific piRNAs in testis, mapping either to transposons or in strand-specific clusters.ConclusionsTaken together, the small RNA compendium described here advances the annotation of small RNAs in the rat genome. Strain and tissue-specific expression patterns furthermore provide a strong basis for studying the role of small RNAs in regulatory networks as well as biological process like physiology and neurobiology that are extensively studied in this model system.
Highlights
Digital gene expression (DGE) profiling has become an established tool to study RNA expression
The target spectrum of a miRNA is mostly defined by the seed, i.e. the 1st or 2nd 7 nt, which hybridizes to the target mRNA [5,6]. miRNAs can both act as developmental switches [7,8,9] or subtly tune expression, when tight regulation of a gene is required [10,11]
The libraries were sequenced on the SOLiD platform version 2 (ABI), generating 115 million small RNA sequence reads
Summary
Digital gene expression (DGE) profiling has become an established tool to study RNA expression. We describe the expression patterns of known and novel micro (mi)RNAs and piwi-interacting (pi)RNAs. miRNAs are ~22 nt-long, single stranded RNA molecules that mediate post-transcriptional regulation of gene expression by directing the RNA-induced Silencing Complex (RISC) to the 3' untranslated region (UTR) of target mRNAs [1,2]. A second developmentally vital class of small RNAs are the piwi-interacting (pi)RNAs [16,17], which play a role in the formation of the germ line. In mammals, these ~27 nt ssRNAs are expressed in the reproductive organs, mainly the testis [18,19], where two types can be distinguished. The function of these genomic clusters, remains elusive [18,19,20,21]
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