Une vue protéomique des tumeurs endocrines

As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available.This work is supported by grants from the Spanish Ministry of Economy and Competitiveness (BIO2014-57291-R) and co-funded with European Regional Development Funds (ERDF), AECID (D/016099/08) and from the Conselleria d’Educacio of the Valencian Community (PROMETEOII/2014/025). This work has been carried out in the context of the HPC4G initiative (http://www.hpc4g.org) and the Bull-CIPF Chair for Computational Genomics. Funding to pay the Open Access publication charges for this article was provided by grant BIO2014-57291-R from the Spanish Ministry of Economy and Competitiveness (MINECO), co-funded with European Regional Development Funds (ERDF)

Nucleolin interacts with US11 protein of herpes simplex virus 1 and is involved in its trafficking

Herpes simplex virus type 1 (HSV-1) infection induces profound nucleolar modifications at the functional and organizational levels, including nucleolar invasion by several viral proteins. One of these proteins is US11, which exhibits several different functions and displays both cytoplasmic localization and clear nucleolar localization very similar to that of the major multifunctional nucleolar protein nucleolin. To determine whether US11 interacts with nucleolin, we purified US11 protein partners by coimmunoprecipitations using a tagged protein, Flag-US11. From extracts of cells expressing Flag-US11 protein, we copurified a protein of about 100 kDa that was further identified as nucleolin. In vitro studies have demonstrated that nucleolin interacts with US11 and that the C-terminal domain of US11, which is required for US11 nucleolar accumulation, is sufficient for interaction with nucleolin. This association was confirmed in HSV-1-infected cells. We found an increase in the nucleolar accumulation of US11 in nucleolin-depleted cells, thereby revealing that nucleolin could play a role in US11 nucleocytoplasmic trafficking through one-way directional transport out of the nucleolus. Since nucleolin is required for HSV-1 nuclear egress, the interaction of US11 with nucleolin may participate in the outcome of infection