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39 papers found.
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Mapping Functional Associations in the Entire Genome of Drosophila melanogaster Using Fusion Analysis

We have previously shown that the detection of gene fusion events can contribute towards the elucidation of functional associations of proteins within entire genomes. Here we have analysed the entire genome of Drosophila melanogaster using fusion analysis and two additional constraints that improve the reliability of the predictions, viz. low sequence similarity and low degree of...

Estimation of Synteny Conservation and Genome Compaction Between Pufferfish (Fugu) and Human

Background: Knowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergence. The vertebrate Fugu rubripes (pufferfish) has a small genome with little repetitive sequence which makes it attractive as a model genome. Genome compaction and synteny conservation between human and Fugu were studied using data...

Chimira: analysis of small RNA sequencing data and microRNA modifications

Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences...

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences

Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and...

Exploring regulatory networks of miR-96 in the developing inner ear

1SA, UKMorag A. Lewis, Annalisa Buniello, Jennifer M. Hilton, Fei Zhu, William I. Zhang, Stephanie Evans & Karen P. SteelEMBL EBI, Hinxton, Cambridge CB10 1SD.Stijn van Dongen & Anton J. Enright ... Stephanie Evans in:Nature Research journals • PubMed • Google ScholarSearch for Stijn van Dongen in:Nature Research journals • PubMed • Google ScholarSearch for Anton J. Enright in:Nature Research journals

Large-scale analysis of microRNA evolution

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...

SylArray: a web server for automated detection of miRNA effects from expression data

Summary: A useful step for understanding the function of microRNAs (miRNA) or siRNAs is the detection of their effects on genome-wide expression profiles. Typically, approaches look for enrichment of words in the 3′UTR sequences of the most deregulated genes. A number of tools are available for this purpose, but they require either in-depth computational knowledge, filtered 3′UTR...

MapMi: automated mapping of microRNA loci

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...

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion

Background Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear. We sought insights into the possible functions of META1 by studying its evolutionary origins. Results Using multiple criteria including sequence similarity...

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis

Background RNA inhibition by siRNAs is a frequently used approach to identify genes required for specific biological processes. However RNAi screening using siRNAs is hampered by non-specific or off target effects of the siRNAs, making it difficult to separate genuine hits from false positives. It is thought that many of the off-target effects seen in RNAi experiments are due to...

An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway

In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad...

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation

Background Synapse formation and the development of neural networks are known to be controlled by a coordinated program of mRNA synthesis. microRNAs are now recognized to be important regulators of mRNA translation and stability in a wide variety of organisms. While specific microRNAs are known to be involved in neural development, the extent to which global microRNA and mRNA...

MiR-221 Influences Effector Functions and Actin Cytoskeleton in Mast Cells

Mast cells have essential effector and immunoregulatory functions in IgE-associated allergic disorders and certain innate and adaptive immune responses, but the role of miRNAs in regulating mast cell functions is almost completely unexplored. To examine the role of the activation-induced miRNA miR-221 in mouse mast cells, we developed robust lentiviral systems for miRNA...

Annotation of mammalian primary microRNAs

Background MicroRNAs (miRNAs) are important regulators of gene expression and have been implicated in development, differentiation and pathogenesis. Hundreds of miRNAs have been discovered in mammalian genomes. Approximately 50% of mammalian miRNAs are expressed from introns of protein-coding genes; the primary transcript (pri-miRNA) is therefore assumed to be the host transcript...

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia

Carme Camps 0 Harpreet K Saini David R Mole Hani Choudhry 0 Martin Reczko 1 Jos Afonso Guerra-Assuno Ya-Min Tian Francesca M Buffa Adrian L Harris Artemis G Hatzigeorgiou 1 Anton J Enright Jiannis

MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs

Background miRNAs are a class of small non-coding RNAs that regulate gene expression and have critical functions in various biological processes. Hundreds of miRNAs have been identified in mammalian genomes but only a small number of them have been functionally characterized. Recent studies also demonstrate that some miRNAs have important roles in reprogramming somatic cells to...

Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines

Small RNAs such as microRNAs play important roles in embryonic stem cell maintenance and differentiation. A broad range of microRNAs is expressed in embryonic stem cells while only a fraction of their targets have been identified. We have performed large-scale identification of embryonic stem cell microRNA targets using a murine embryonic stem cell line deficient in the...

miRBase: tools for microRNA genomics

miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. miRBase provides a range of data to facilitate studies of miRNA genomics: all miRNAs...

Protein families and Tribes in genome sequence space

Anton J. Enright 0 Victor Kunin 0 Christos A. Ouzounis 0 0 Computational Genomics Group, The European Bioinformatics Institute , EMBL Cambridge Outstation, Cambridge CB10 1SD, UK Accurate detection

A logic-based diagram of signalling pathways central to macrophage activation

Background The complex yet flexible cellular response to pathogens is orchestrated by the interaction of multiple signalling and metabolic pathways. The molecular regulation of this response has been studied in great detail but comprehensive and unambiguous diagrams describing these events are generally unavailable. Four key signalling cascades triggered early-on in the innate...