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Pristionchus pacificus daf-16/FOXO is Essential for Dauer Formation but Dispensable for Mouth Form Dimorphism
Akira Ogawa, Gilberto Bento, Gabi Bartelmes, Christoph Dieterich, and Ralf J Sommer
CYNTENATOR manuscript accepted
CYNTENATOR: Progressive gene order alignment of 17 vertebrate genomes
Active turnover modulates mature microRNA activity in Caenorhabditis elegans
MicroRNAs (miRNAs) constitute a large class of regulatory RNAs that repress target messenger RNAs to control various biological processes1. Accordingly, miRNA biogenesis is highly regulated, controlled at both transcriptional and post-transcriptional levels2, and overexpression and underexpression of miRNAs are linked to various human diseases, particularly cancers1, 3. As RNA concentrations are generally a function of biogenesis and turnover, active miRNA degradation might also modulate miRNA accumulation, and the plant 3'right arrow5' exonuclease SDN1 has been implicated in miRNA turnover4. Here we report that degradation of mature miRNAs in the nematode Caenorhabditis elegans, mediated by the 5'right arrow3' exoribonuclease XRN-2, affects functional miRNA homeostasis in vivo. We recapitulate XRN-2-dependent miRNA turnover in larval lysates, where processing of precursor-miRNA (pre-miRNA) by Dicer, unannealing of the miRNA duplex and loading of the mature miRNA into the Argonaute protein of the miRNA-induced silencing complex (miRISC) are coupled processes that precede degradation of the mature miRNA. Although Argonaute:miRNA complexes are highly resistant to salt, larval lysate promotes efficient release of the miRNA, exposing it to degradation by XRN-2. Release and degradation can both be blocked by the addition of miRNA target RNA. Our results therefore suggest the presence of an additional layer of regulation of animal miRNA activity that might be important for rapid changes of miRNA expression profiles during developmental transitions and for the maintenance of steady-state concentrations of miRNAs. This pathway might represent a potential target for therapeutic intervention on miRNA expression.
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Alvarado AS, Kempa S, Dieterich C, Rajewsky N, Chen W. Max-Delbrück-Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Robert Rössle Straße 10, Berlin 13125, Germany;
Helicos BioSciences Announces the First Ever Single-Molecule View of Whole Human Genome
Study Performed at Stanford University Published in Nature Biotechnology.
Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover - accepted
Chromosome conformation capture primer design
Our paper "Rapid design of optimal primers for chromosome conformation capture assays" by Fröhler and Dieterich was accepted for publication in BMC Genomics.
Proteogenomics of Pristionchus pacificus manuscript accepted
the manuscript will appear in Genome Research
doRiNA: a database of RNA interactions in post-transcriptional regulation
The doRiNA database was published online in NAR on 15 Nov 2012 and will be part of the database issue 2012
ACCUSA - Accurate SNP calling on draft genomes manuscript accepted
Next generation sequencing technologies facilitate genome-wide analysis of several biological processes. We are interested in whole-genome genotyping. To our knowledge, none of the existing SNP callers consider the quality of the reference genome, which is not necessary for high quality assemblies of well-studied model organisms. However, most genome projects will remain in draft status with little to no genome assembly improvement due to time and financial constraints. Here we present a simple yet elegant solution ('ACCUSA'), which considers both, the read qualities as well as the reference genome's quality using a Bayesian framework. We demonstrate that ACCUSA is as good as current SNP calling software in detecting true SNPs. More important, ACCUSA does not call spurious SNPs, which originate from a poor reference sequence.
doRiNA: a database of RNA interactions in post-transcriptional regulation
