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Barrera, V.

Publications and source records attributed to Barrera, V..

2 recordsLinked to original sources

LaNt α31 modulates LM332 organisation during matrix deposition leading to cell-matrix adhesion and migration defects.

Laminin N-terminus 31 (LaNt 31), a member of the laminin superfamily, expressed at low levels in intact epithelium but upregulated during wound repair. Increased expression of LaNt 31 reduced migration rate of corneal keratinocytes through an unknown mechanism. Here, we investigated whether LaNt 31 influences cell behaviour through modulating laminin-mediated processes. Adenoviral delivery of LaNt 31 into corneal epithelial cells led to reduced migration speed and increased cell spreading and changed laminin 332 organisation from diffuse arcs to tight clusters. Enhanced recruitment of collagen XVII and bullous pemphigoid antigen 1e to {beta}4 integrin, indicating early maturation of hemidesmosomes, and changed focal adhesion distribution were also identified. LaNt 31 and laminin {beta}3 co-immunoprecipitated from doubly transduced cells and were deposited together in live imaging experiment. Moreover, LaNt 31 expression led to increased matrix metalloproteinase (MMP) activity and proteolytic processing of laminin 3, and the inhibition of MMP activity rescued the laminin and hemidesmosome phenotypes. Provision of cell-derived extracellular matrix rescued the cell spreading and motility effects. These findings reveal LaNt 31 as a new player in regulating cell-to-matrix adhesion through its ability to influence laminin organisation and proteolytic processing.

cell biology

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

BackgroundMicroRNAs (miRNAs) are small RNA molecules ([~]22 nucleotide long) involved in post-transcriptional gene regulation. Advances in high-throughput sequencing technologies led to the discovery of isomiRs, which are miRNA sequence variants. While many miRNA-seq analysis tools exist, a lack of consensus on miRNA/isomiR analyses exists, and the resulting diversity of output formats hinders accurate comparisons between tools and precludes data sharing and the development of common downstream analysis methods.\n\nFindingsTo overcome this situation, we present here a community-based project, miRTOP (miRNA Transcriptomic Open Project) working towards the optimization of miRNA analyses. The aim of miRTOP is to promote the development of downstream analysis tools that are compatible with any existing detection and quantification tool. Based on the existing GFF3 format, we first created a new standard format, mirGFF3, for the output of miRNA/isomiR detection and quantification results from small RNA-seq data. Additionally, we developed a command line Python tool, mirtop, to manage the mirGFF3 format. Currently, mirtop can convert into mirGFF3 the outputs of commonly used pipelines, such as seqbuster, miRge2.0, isomiR-SEA, sRNAbench, and Prost!, as well as BAM files. Its open architecture enables any tool or pipeline to output results in mirGFF3.\n\nConclusionsCollectively a comprehensive isomiR categorization system, along with the accompanying mirGFF3 and mirtop API provide a complete solution for the standardization of miRNA and isomiR analysis, enabling data sharing, reporting, comparative analyses, and benchmarking, while promoting the development of common miRNA methods focusing on downstream steps to miRNA detection, annotation, and quantification.

bioinformatics