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Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum

MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied...

miRBase: annotating high confidence microRNAs using deep sequencing data

Ana Kozomara 0 Sam Griffiths-Jones 0 0 Faculty of Life Sciences, University of Manchester , Manchester , M13 9PT, UK We describe an update of the miRBase database (http://www.mirbase.org/), the

Conserved Temporal Patterns of MicroRNA Expression in Drosophila Support a Developmental Hourglass Model

Maria Ninova 0 Matthew Ronshaugen 0 Sam Griffiths-Jones 0 0 Faculty of Life Sciences, University of Manchester , Manchester, United Kingdom The spatiotemporal control of gene expression is crucial

Bias in microRNA functional enrichment analysis

Motivation: Many studies have investigated the differential expression of microRNAs (miRNAs) in disease states and between different treatments, tissues and developmental stages. Given a list of perturbed miRNAs, it is common to predict the shared pathways on which they act. The standard test for functional enrichment typically yields dozens of significantly enriched functional...

Intron Evolution in Saccharomycetaceae

Introns in protein-coding genes are very rare in hemiascomycetous yeast genomes. It has been suggested that these species have experienced extensive intron loss during their evolution from the postulated intron-rich fungal ancestor. However, no intron-devoid yeast species have been identified and some of the introns remaining within the genomes of intron-poor species, such as...

Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa

The prevalence of long non-coding RNAs (lncRNA) and natural antisense transcripts (NATs) has been reported in a variety of organisms. While a consensus has yet to be reached on their global importance, an increasing number of examples have been shown to be functional, regulating gene expression at the transcriptional and post-transcriptional level. Here, we use RNA sequencing...

Detection of microRNAs in color space

Antonio Marco 0 Sam Griffiths-Jones 0 Associate Editor: Martin Bishop 0 Faculty of Life Sciences, University of Manchester , Michael Smith Building, Oxford Road, M13 9PT Manchester, UK Motivation

Clusters of microRNAs emerge by new hairpins in existing transcripts

Genetic linkage may result in the expression of multiple products from a polycistronic transcript, under the control of a single promoter. In animals, protein-coding polycistronic transcripts are rare. However, microRNAs are frequently clustered in the genomes of animals, and these clusters are often transcribed as a single unit. The evolution of microRNA clusters has been the...

Target Repression Induced by Endogenous microRNAs: Large Differences, Small Effects

Ninova 0 Sam Griffiths-Jones 0 Matthew Ronshaugen 0 A. Aziz Aboobaker, University of Oxford, United Kingdom 0 Faculty of Life Sciences, The University of Manchester , Manchester , United Kingdom

Mitochondrial Pseudogenes in the Nuclear Genomes of Drosophila

Mitochondrial pseudogenes in nuclear chromosomes (numts) have been detected in the genomes of a diverse range of eukaryotic species. However, the numt content of different genomes and their properties is not uniform, and study of these differences provides insight into the mechanisms and dynamics of genome evolution in different organisms. In the genus Drosophila, numts have...

miRBase: integrating microRNA annotation and deep-sequencing data

Ana Kozomara 0 Sam Griffiths-Jones 0 0 Faculty of Life Sciences, University of Manchester , Michael Smith Building, Oxford Road, Manchester , M13 9PT, UK miRBase is the primary online repository for

Conservation and Losses of Non-Coding RNAs in Avian Genomes

Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We...

Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods

In Drosophila melanogaster, the iab-4/iab-8 locus encodes bi-directionally transcribed microRNAs that regulate the function of flanking Hox transcription factors. We show that bi-directional transcription, temporal and spatial expression patterns and Hox regulatory function of the iab-4/iab-8 locus are conserved between fly and the beetle Tribolium castaneum. Computational...

Sex-Biased Expression of MicroRNAs in Schistosoma mansoni

Schistosomiasis is an important neglected tropical disease caused by digenean helminth parasites of the genus Schistosoma. Schistosomes are unusual in that they are dioecious and the adult worms live in the blood system. MicroRNAs play crucial roles during gene regulation and are likely to be important in sex differentiation in dioecious species. Here we characterize 112...

RALEE—RNA ALignment Editor in Emacs

Summary: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The...

The Evolution of tRNA Genes in Drosophila

Hubert H. Rogers 0 Casey M. Bergman 0 Sam Griffiths-Jones 0 0 Faculty of Life Sciences, University of Manchester , Manchester, United Kingdom The structure and function of transfer RNA (tRNA) genes

The microRNA Registry

Sam Griffiths-Jones 0 0 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 9SA, UK The miRNA Registry provides a service for the assignment of miRNA gene

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...

Functional Shifts in Insect microRNA Evolution

MicroRNAs (miRNAs) are short endogenous RNA molecules that regulate gene expression at the posttranscriptional level and have been shown to play critical roles during animal development. The identification and comparison of miRNAs in metazoan species are therefore paramount for our understanding of the evolution of body plans. We have characterized 203 miRNAs from the red flour...

The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs

Sam Griffiths-Jones 0 Alex Bateman 0 0 The Wellcome Trust Sanger Institute , Hinxton, Cambridge CB10 1SA , UK Motivation: The best quality multiple sequence alignments are generally considered to