The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length
FAIRDOMHub ID: https://fairdomhub.org/assays/245
Investigation: Gene expression in Trypanosoma brucei
Biological problem addressed: Model Analysis Type
Organisms: No organisms
Created: 31st Jul 2014 at 10:47
Last updated: 8th Nov 2017 at 15:21
The SilicoTryp project aims at the creation of a “Silicon Trypanosome”, a comprehensive, experiment-based, multi-scale mathematical model of trypanosome physiology.
Trypanosomes are blood-stream parasites transmitted by tsetse flies; they cause African sleeping sickness in humans and livestock. Currently available drugs have severe side effects, and the parasites are rapidly developing resistance.
In this project, we collect a wide range of new experimental data on the parasite in its various
Aim: To provide quantitative data that will allow modeling of gene expression for all enzymes of redox metabolism and the pentose phosphate pathway. Modeling will be used to predict enzyme levels based on the integration of an RNA degradation model with translation and protein degradation rates.
Plan: The amounts of a protein in a cell can be determined by the rates of transcription, mRNA processing, translation, mRNA turnover and protein degradation. In trypanosomes analysis is simpler because
Snapshots: No snapshots
Since over 40 enzymes will be investigated for their mRNA abundance, processing, and degradation kinetics, the less tedious and more accurate Next Generation Sequencing of the entire mRNA repertoire of the cell is employed. To optimise the proportion of useful sequence, while including RNA fragments that are products of of degradation, rRNA is depleted using the eukaryotic Ribominus kit (Ambion). Two biological replicates are treated with Sinefungin and Actinomycin D to inhibit RNA processing and
Person responsible: Christine Clayton
Snapshots: No snapshots
Investigations: Gene expression in Trypanosoma brucei
This files contains the parameter values, life-times, half-lives and errors associated with modeling the decay of the transcriptome, based on 3 models described in Deneke et al. "Complex degradation processes lead to non-exponential decay patters and age-dependent decay rates of messenger RNA". PLoS One. 2013;8(2):e55442
Date Published: 26th Aug 2014
Journal: Mol Microbiol
PubMed ID: 25145465