Decapping host and viral RNAs

In a recent work with Yolanda Revilla’s lab (CBMSO, Madrid) published in the Journal of Virology, we investigated the role in RNA metabolism of a protein from a complex DNA virus, called African swine fever virus (ASFV). This protein exhibits high homology with cellular decapping enzymes and thus can potentially remove the cap structure from the RNA body triggering degradation.  We show that this protein interacts with viral and cellular mRNAs in infected cells. This interaction results in decreased levels of both types of transcripts, agreeing with a putative role as virus-encoded decapping activity. We propose that the degradation of RNA triggered by this protein is key to control gene expression in ASFV infected cells.

 

 

PhD position in Marseille

Our Colleague Juan Reguera, offers a PhD student position at the Viral Macromolecular Complexes Teat at the AFMB in Marseille. The aim of the project is the structural and functional characterisation of retrotrasposon integration in yeast. Interested candidates can send their CV and a motivation letter to reguera@afmb.univ-mrs.fr

Capture and proteomic analysis of single RNP species

It is challenging to determine the composition of a given ribonucleoprotein. We recently approached this problem by adapting the original RNA interactome capture protocol (Castello et al., Cell 2012), to the use of specific antisense LNA probes to capture specific RNA species. We use this method to elucidate the composition of luciferase containing reporters and ribosomal RNA in vitro and in vivo. We were able to recapitulate well-established protein-RNA interactions and to discover new ones.

Specific RNP capture with antisense LNA/DNA mixmers. Rogell B, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW. RNA. 2017 Aug;23(8):1290-1302. doi: 10.1261/rna.060798.117. Epub 2017 May 5.

Postdoctoral position in Genomics/Computational Biology

Our colleague Vicent Pelechano is looking for a postdoc in Genomics/Computational Biology to join his team at Karolinska Institutet – SciLifeLab.

The available postdoctoral position concerns developing and applying novel genomic and computational approaches to study ribosome dynamics and RNA metabolism, and its impact to cell-to-cell phenotypic heterogeneity. The candidate will focus on the computational analysis of newly developed methods to study ribosome dynamics, mRNA degradation and tRNA processing (e.g. Pelechano et al. Cell 2015). The candidate is expected to contribute to our common goal of understanding how RNA biology and post-transcriptional regulation contributes to the appearance of differences across clonal populations of cells.

The application deadline is October 2nd and you can find more information about this job here:  http://pelechanolab.com/2017/06/21/postdoctoral-stipend-in-genomics-computational-biology/