MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.

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Activation of the T cell-mediated immune response has been associated with changes in the expression of specific microRNAs (miRNAs). However, the role of miRNAs in the development of an effective immune response is just beginning to be explored. This study focuses on the functional role of miR-146a in T lymphocyte-mediated immune response and provides interesting clues on the transcriptional regulation of miR146a during T-cell activation. We show that miR-146a is low in human naive T cells and is abundantly expressed in human memory T cells; consistently, miR-146a is induced in human primary T lymphocytes upon T-cell receptor (TCR) stimulation. Moreover, we identified NF-kB and c-ETS binding sites as required for the induction of miR-146a transcription upon TCR engagement. Our results demonstrate that several signaling pathways, other than inflammation, are influenced by miR-146a. In particular, we provide experimental evidence that miR-146a modulates activation-induced cell death (AICD), acting as an antiapoptotic factor, and that Fasassociated death domain (FADD) is a target of miR-146a. Furthermore, miR146a enforced expression impairs both activator protein 1 (AP-1) activity and interleukin-2 (IL-2) production induced by TCR engagement, thus suggesting a role of this miRNA in the modulation of adaptive immunity. (Blood. 2010;115: 265-273) IntroductionDuring adaptive immune response T-cell receptor (TCR) engagement by the antigen triggers a signal cascade, which leads to the activation of 3 main transcription factors: AP-1, NF-kB, and NFAT, critically involved in cytokine production. In particular, these transcription factors regulate the expression of early cytokines, especially interleukin-2 (IL-2), that mediate the lymphocytic "clonal expansion" phase. 1 Once the foreign threat has been overcome and T lymphocytes have served their effector functions, they must be removed. The death of activated lymphocytes serves to limit the immune response by killing cells that are no longer needed or cells that may have developed the potential to recognize and generate a response to selfantigens. Deregulation of apoptotic pathways in T cells may lead to a spectrum of diseases, including autoimmune diseases and proliferative disorders. 2,3 MicroRNAs (miRNAs) recently came into focus as a novel class of posttranscriptional regulatory elements. They are small endogenous noncoding RNAs that repress mRNA translation by base pairing to 3Ј untranslated region (3ЈUTR) of the target genes. In particular, miRNAs are powerful tools that can be promptly expressed by the cell and have the potential to coordinately regulate a large number of different target genes. This suggests that they can be optimal candidates for the control of immune response, a process involving large regulative networks and fine prompt modulation.The first indication that miRNAs are involved in immunity has emerged by studies showing the selective expression of miR-223 in bone marrow and the involvement of miR-223, miR-155, and miR-146a in the differentiation ...

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The analysis of microbiota composition in humans, animals, and built environments is important because of emerging roles and applications in a broad range of disease and ecological phenotypes. Next Generation Sequencing is the current method of choice to characterize microbial community composition. The taxonomic profile of a microbial community can be obtained either by shotgun analysis of random DNA fragments or through 16S ribosomal RNA gene (rDNA) amplicon sequencing. It has been previously shown that the 16S rDNA amplicon sequencing approach yields quantitatively and qualitatively different results compared to shotgun metagenomics when the two techniques are used to assess microbial community composition on the same samples. However, most of such comparisons were either based on the recovery of 16S rDNA sequences in the shotgun metagenomics data or limited to a single microbiome or synthetic samples. Direct comparison of shotgun metagenomics and 16S rDNA amplicon sequencing on the same samples was performed only once in the recent literature, suggesting that the two methods yield comparable results. Here, we set out to compare the outcome of these two alternative approaches to the microbiome characterization in human gut microbiomes from stool samples. To this end, we processed six different samples with both techniques. We report here that shotgun next generation sequencing metagenomics allows much deeper characterization of the microbiome complexity, allowing identification of a larger number of species for each sample, compared to 16S rDNA amplicon sequencing. Further comparative studies in independent samples are called for.

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