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PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

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Variation in the 3' untranslated region (3'UTR) of the HLA-C locus determines binding of the microRNA Hsa-miR-148a, resulting in lower cell surface expression of alleles that bind miR-148a relative to those alleles that escape its binding. The HLA-C 3'UTR ...

Natl Acad Sciences2013

RNA-Protein interactions at AU-rich elements

Ramona Pauchard-Batschulat

The expression of many proto-oncogenes, nuclear transcription factors and cytokines is regulated post-transcriptionally by specific interactions between distinct cis-elements within the mRNA and trans-acting factors that bind to these elements and thereby ...

EPFL2013

Kinetic Analysis of Transcriptional and Post-Transcriptional Processes During Circadian Cycles

Laura Symul

Every morning the sun rises, flooding the earth with its light and heat and every night it disappears leaving the Earth in the darkness of the night. Organisms living on this planet have adapted to this solar rhythm and have spread their activities through ...

EPFL2013

Searching the coding region for microRNA targets

Jiri Vanicek, Ray Marcel Marin Florez, Miroslav Sulc

Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for ...

2013

Highly Specific Methods for the Prediction of Genes Regulated by MicroRNAs

Ray Marcel Marin Florez

MicroRNAs (miRNAs) comprise a large set of short noncoding RNAs that bind to messenger RNAs (mRNAs) to reduce their translation into functional proteins. Computational prediction of miRNA targets is the first stage in the discovery and validation of new re ...

EPFL2012

Real-Time mRNA Measurement during an

Sebastian Maerkl, Henrike Marie Niederholtmeyer

In vitro transcription and translation reactions have become popular for a bottom-up approach to synthetic biology. Concentrations of the mRNA intermediate are rarely determined, although knowledge of synthesis and degradation rates could facilitate ration ...

Amer Chemical Soc2012

Unique Cell-Type-Specific Distributions and Functions of Brain MicroRNAs

Ana Jovicic

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional regulation of gene expression. The first miRNA was discovered less than 20 years ago in the context of studying Caenorabditis elegans development. The discovery of the second miR ...

EPFL2011

Alterations of the 5 ' Untranslated Region of SLC16A12 Lead to Age-Related Cataract

PURPOSE. Knowledge of genetic factors predisposing to age-related cataract is very limited. The aim of this study was to identify DNA sequences that either lead to or predispose for this disease. ...

2010

An Interface Formalism for Web Services

Dirk Thilo Beyer

Web application development using distributed components and web services presents new software integration challenges, because solutions often cross vendor, administrative, and other boundaries across which neither binary nor source code can be shared. We ...

2007

Destabilization of interleukin-6 mRNA requires a putative RNA stem-loop structure, an AU-rich element, and the RNA-binding protein AUF1

Lukas Kühn, Barbara Grisoni-Neupert

Interleukin-6 mRNA is unstable and degraded with a half-life of 30 min. Instability determinants can entirely be attributed to the 3' untranslated region. By grafting segments of this region to stable green fluorescent protein mRNA and subsequent scanning ...

2006