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/

RNA2017 – Prague

We are back from the RNA2107 in Prague. Very exciting talks!

One highlight, Adrian Krainer talked about SPINRAZA, a new therapy against spinal muscular atrophy (SMA) based on antisense oligos. SMA produces the loss of motor neurons that ends up in muscle wasting and early dead (the life expectation of a new born baby with type 1 SMA is ten months). The recently developed treatment treatment has shown excellent results in phase III clinical trials. Adrian guided us through the conception and development of the drug and included emotive videos of how SPINRAZA improves the life of children affected with SMA. An inspiring talk that demonstrates that basic science is fundamental for advancing applied research.

 

In their memory

With incredible sadness I received the terrible news that my colleagues and friends, Bernd Fischer and Katrin Eichelbaum, passed away. Bernd, Katrin and I formed a highly interdisciplinary team working from 2009 to 2014 at EMBL in Heidelberg. Bernd and I continued our close collaboration as independent group leaders. Together with other colleagues at EMBL, we achieved a long-standing challenge: the determination of the “near complete” atlas of human RNA-binding proteins. Katrin and Bernd were outstanding scientists and great friends.

I can only be grateful for having the opportunity to work with you. You are terribly missed.

Alfredo

Bernd Fischer

Katrin Eichelbaum

 

 

Celebrating our great success!

Explaining me why ENSEMBL IDs?