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Context-dependent deposition and regulation of mRNAs in P-bodies.

eLife | Jan 3, 2018

Cells respond to stress by remodeling their transcriptome through transcription and degradation. Xrn1p-dependent degradation in P-bodies is the most prevalent decay pathway, yet, P-bodies may facilitate not only decay, but also act as a storage compartment. However, which and how mRNAs are selected into different degradation pathways and what determines the fate of any given mRNA in P-bodies remain largely unknown. We devised a new method to identify both common and stress-specific mRNA subsets associated with P-bodies. mRNAs targeted for degradation to P-bodies, decayed with different kinetics. Moreover, the localization of a specific set of mRNAs to P-bodies under glucose deprivation was obligatory to prevent decay. Depending on its client mRNA, the RNA-binding protein Puf5p either promoted or inhibited decay. Furthermore, the Puf5p-dependent storage of a subset of mRNAs in P-bodies under glucose starvation may be beneficial with respect to chronological lifespan.

Pubmed ID: 29297464 RIS Download

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This is a list of tools and resources that we have found mentioned in this publication.


GE Healthcare

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Addgene

A non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Addgene’s mission is to accelerate research and discovery by improving access to useful research materials and information. We facilitate the sharing of high-quality scientific materials, research reproducibility, and open science by archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Our repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.

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Imaris

Interactive Vision In The Life SciencesCombining speed, precision and ease-of-use, Imaris provides an impressive range of capabilities for working with three-dimensional images. Move easily between simple and advanced 3D views. Use flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition.BitPlane, Inc. also releases the following companion products:- ImarisXT is a multi-functional two-way interface from Imaris to both classic programming languages and to Matlab.- Imaris MeasurementPro and Imaris Track provide the ability to segment and follow the movement of independent objects in a 3D image over time. Objects can either be Surface Objects or Spots, created automatically or manually.- ImarisColoc enables users to easily isolate, visualize, and quantify regional overlap in 3D and 4D images and automates the process of selecting colocalized image areas.

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Ambion Inc.

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Bio-Rad Laboratories

A commercial instrument and chemical vendor.

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Thermo Fisher Scientific

Commercial vendor and service provider of laboratory reagents and antibodies.

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AxioVision

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Gene Expression Omnibus

Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.

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Bioconductor

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

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ggplot2

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

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Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.

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edgeR

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

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htseq-count

Script distributed with the HT-Seq Python framework for processing RNA-seq or DNA-seq data.

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GOstat

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Bowtie

Software tool for aligning short DNA sequences to large genomes. Bowtie 2 supports gapped, local, and paired end alignment modes.

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BioMart Project

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Covance

A contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia)

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Ensembl

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

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