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Helou, L.

Publications and source records attributed to Helou, L..

2 recordsLinked to original sources

The piggyBac derived transposase 5 (PGBD5) can interact with human piggyBac-like elements

PGBD5 is encoded by a gene domesticated at the chordate origin from a DNA transposon of the piggyBac family. During its evolution, PGBD5s sequence has been under strong purifying selection among vertebrate genomes. This suggests PGBD5 functions in the development and physiology of chordates, as recently demonstrated in mouse and human brain development, where it was implicated in double strand DNA breaks on neurons. However, biochemical PGBD5 activities remain undefined due to lack of appropriate in vitro model systems. Furthermore, coevolution of PGBD5 with hosts has likely reshaped some of its functions, resulting in differences between vertebrate PGBD5 and the insect piggybac transposase (PB). Recent studies have found that PGBD5 can interact with two different "species" of piggyBac-like transposon element (pble). Here, we show that human PGBD5 can interact with four "species" human pbles and to promote their chromosomal integration in cells, a property it shares with insect PB. Human PGBD5 can also bind to distinct chromosomal copies of human pble in cell type-specific manner, and to genomic loci containing inverted repeats in human cells akin to those found in subterminal insect pble ends. These findings expand the scope of potential biological activities of PGBD5 and other domesticated DNA transposases.

genomics↗

TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses

The advent of NGS has intensified the need for robust pipelines to perform high-performance automated analyses. The required softwares depend on the sequencing method used to produce raw data (e.g. Whole genome sequencing, Genotyping By Sequencing, RNASeq) as well as the kind of analyses to carry on (GWAS, population structure, differential expression). These tools have to be generic and scalable, and should meet the biologists needs.\n\nHere, we present the new version of TOGGLe (Toolbox for Generic NGS Analyses), a simple and highly flexible framework to easily and quickly generate pipelines for large-scale second-and third-generation sequencing analyses, including multi-threading support. TOGGLe comprises a workflow manager designed to be as effortless as possible to use for biologists, so the focus can remain on the analyses. Embedded pipelines are easily customizable and supported analyses are reproducible and shareable. TOGGLe is designed as a generic, adaptable and fast evolutive solution, and has been tested and used in large-scale projects with numerous samples and organisms. It is freely available at http://toggle.southgreen.fr/ under the GNU GPLv3/CeCill-C licenses) and can be deployed onto HPC clusters as well as on local machines.

bioinformatics↗