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Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online 'TB-Profiler' tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing. [ABSTRACT FROM AUTHOR]

Background In mammalians, HIF is a master regulator of hypoxia gene expression through direct binding to DNA, while its role in microRNA expression regulation, critical in the hypoxia response, is not elucidated genome wide. Our aim is to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression. Methods MCF-7 cells were incubated at 1% Oxygen for 16, 32 and 48 h. SiRNA against HIF-1 α and HIF-2α were performed as previously published. MicroRNA and mRNA expression were assessed using microRNA microarrays, small RNA sequencing, gene expression microarrays and Real time PCR. The Kraken pipeline was applied for microRNA-seq analysis along with Bioconductor packages. Microarray data was analysed using Limma (Bioconductor), ChIPseq data were analysed using Gene Set Enrichment Analysis and multiple testing correction applied in all analyses. Results Hypoxia time course microRNA sequencing data analysis identified 41 microRNAs significantly up- and 28 down-regulated, including hsa-miR-4521, hsa-miR-145-3p and hsamiR-222-5p reported in conjunction with hypoxia for the first time. Integration of HIF-1α and HIF-2α ChIP-seq data with expression data showed overall association between binding sites and microRNA up-regulation, with hsa-miR-210-3p and microRNAs of miR- 27a/23a/24-2 and miR-30b/30d clusters as predominant examples. Moreover the expression of hsa-miR-27a-3p and hsa-miR-24-3p was found positively associated to a hypoxia gene signature in breast cancer. Gene expression analysis showed no full coordination between primiRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts involved in microRNA processing were found regulated by hypoxia, of which DICER (down-regulated) and AGO4 (up-regulated) were HIF dependent. DICER expression was found inversely correlated to hypoxia in breast cancer. Conclusions Integrated analysis of microRNA, mRNA and ChIP-seq data in a model cell line supports the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and posttranscriptional level, with the presence of HIF binding sites at microRNA genomic loci associated with up-regulation. The identification of hypoxia and HIF regulated microRNAs relevant for breast cancer is important for our understanding of disease development and design of therapeutic interventions. [ABSTRACT FROM AUTHOR]

Background: In animals, microRNAs (miRNA) are important genetic regulators. Animal miRNAs appear to have expanded in conjunction with an escalation in complexity during early bilaterian evolution. Their small size and high-degree of similarity makes them challenging for phylogenetic approaches. Furthermore, genomic locations encoding miRNAs are not clearly defined in many species. A number of studies have looked at the evolution of individual miRNA families. However, we currently lack resources for large-scale analysis of miRNA evolution. Results: We addressed some of these issues in order to analyse the evolution of miRNAs. We perform syntenic and phylogenetic analysis for miRNAs from 80 animal species. We present synteny maps, phylogenies and functional data for miRNAs across these species. These data represent the basis of our analyses and also act as a resource for the community. Conclusions: We use these data to explore the distribution of miRNAs across phylogenetic space, characterise their birth and death, and examine functional relationships between miRNAs and other genes. These data confirm a number of previously reported findings on a larger scale and also offer novel insights into the evolution of the miRNA repertoire in animals, and it’s genomic organization. [ABSTRACT FROM AUTHOR]

Background: A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. However, miRBase focuses on those species for which miRNAs have been directly confirmed. Secondly, specific miRNAs or their loci are sometimes not annotated even in well-covered species. We sought to address this problem by developing a computational system for automated mapping of miRNAs within and across species. Given the sequence of a known miRNA in one species it is relatively straightforward to determine likely loci of that miRNA in other species. Our primary goal is not the discovery of novel miRNAs but the mapping of validated miRNAs in one species to their most likely orthologues in other species. Results: We present MapMi, a computational system for automated miRNA mapping across and within species. This method has a sensitivity of 92.20% and a specificity of 97.73%. Using the latest release (v14) of miRBase, we obtained 10,944 unannotated potential miRNAs when MapMi was applied to all 21 species in Ensembl Metazoa release 2 and 46 species from Ensembl release 55. Conclusions: The pipeline and an associated web-server for mapping miRNAs are freely available on http://www. ebi.ac.uk/enright-srv/MapMi/. In addition precomputed miRNA mappings of miRBase miRNAs across a large number of species are provided. [ABSTRACT FROM AUTHOR]