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- Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels
African trypanosomes are an excellent system for quantitative modelling of post-transcriptional mRNA control. Transcription is constitutive and polycistronic; individual mRNAs are excised by trans splicing and polyadenylation. We here measure mRNA decay kinetics in two life cycle stages, bloodstream and procyclic forms, by transcription inhibition and RNASeq. Messenger RNAs with short half-lives tend to show initial fast degradation, followed by a slower phase; they are often stabilized by depletion of the 5'-3' exoribonuclease XRNA. Many longer-lived mRNAs show initial slow degradation followed by rapid destruction: we suggest that the slow phase reflects gradual deadenylation. Developmentally regulated mRNAs often show regulated decay, and switch their decay pattern. Rates of mRNA decay are good predictors of steady state levels for short mRNAs, but mRNAs longer than 3 kb show unexpectedly low abundances. Modelling shows that variations in splicing and polyadenylation rates can contribute to steady-state mRNA levels, but this is completely dependent on competition between processing and co-transcriptional mRNA precursor destruction.
SEEK ID: https://fairdomhub.org/publications/228
PubMed ID: 25145465
Projects: SilicoTryp
Journal: Mol Microbiol
Citation:
Date Published: 26th Aug 2014
Authors: Abeer Fadda, M. Ryten, D. Droll, Federico Rojas, V. Farber, Jurgen Haanstra, C. Merce, Barbara Bakker, Keith Matthews, Christine Clayton
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Projects: SilicoTryp, Multiscale modelling of state transitions in the host-microbiome-brain network, MESI-STRAT, PoLiMeR - Polymers in the Liver: Metabolism and Regulation
Institutions: University of Groningen
I am an Associate Professor in Systems Biology and the University Medical Centre Groningen. My research aims at understanding how energy metabolism is integrated and regulated. My work includes experimental, modelling as well as theoretical research. Recently I studied how metabolic regulation and gene-expression regulation work together towards in integrated response, e.g. when parasites are confronted with chemical inhibitors. Much of my work has been about the regulation of glycolysis and its
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Projects: SilicoTryp, IMOMESIC
Institutions: University of Groningen, VU University Amsterdam
Projects: SilicoTryp
Institutions: University of Heidelberg
Expertise: network inference, motif detection
Tools: Perl programming, Bioconductor Packages in R, HTML, MySQL
Projects: SilicoTryp
Institutions: University of Edinburgh
Roles: Postdoc
Expertise: Proteomics
Tools: Proteomics, Cell culture, Flow cytometry, Fluorescence and confocal microscopy, RNA / DNA Techniques, RNA interference, Proteomics (2D-PAGE)
I am a Postdoc at Keith Matthews lab in the Institute of Immunology and Infection Research, Edinburgh University. As part of the SilicoTryp project we are in charge of performing Targeted disruption and Overexpression of critical enzymes of Trypanosoma brucei redox metabolism enzymes and developmental perturbations to provide part of the necessary data for the construction of the model. Also generate consistent samples, so that data can be integrated and quantification results are guarateed to
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Projects: SilicoTryp
Institutions: University of Edinburgh
Projects: SilicoTryp
Institutions: University of Heidelberg
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
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Programme: SysMO
Public web page: http://silicotryp.ibls.gla.ac.uk/wiki/Main_Page
Organisms: Trypanosoma brucei
Genes are transcribed in polysictronic messages (pre-mRNA) that are destined for either maturation into mRNAs, or degradation. Since transcription regulation is non-existent with few exceptions, the rate of pre-mRNA processing, together with mRNA decay and translation rates, are believed to control gene expression. In this assay, 2T1 blood form trypanosomes are subject to treatment by ActinomycinD for 5 minutes, inhibiting transcription. The cells are harvested, depleted for ribosomal RNA, and
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Contributor: Abeer Fadda
Assay type: Transcriptomics
Technology type: Rna-seq
Snapshots: No snapshots
Investigation: Gene expression in Trypanosoma brucei
Study: Determination and integration of abundance, pro...
Organisms: Trypanosoma brucei : 2T1 (wild-type / wild-type) (batch)
SOPs: No SOPs
Data files: No Data files
This assay is designed to measure the decay kinetics of mRNA in T. brucei blood forms. T. brucei lacks the canonical transcriptional regulation employed by other eukaryotes through transcription factors, and relies almost entirely on regulation of mRNA decay and further downstream steps in order to control gene expression.
3 replicates of 8 time points were taken to measure mRNA abundance in the cell using RNA-seq. The first time point was fot WT, untreated cells; the second was 5 min after the
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Contributor: Abeer Fadda
Assay type: Transcriptomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Gene expression in Trypanosoma brucei
Study: Determination and integration of abundance, pro...
Organisms: Trypanosoma brucei : 2T1 (wild-type / wild-type)
SOPs: Sample preparation for mRNA decay study
Data files: Half life values for enzymes of redox and polya..., mRNA decay, mRNA half-lives
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
Contributor: Jurgen Haanstra
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Gene expression in Trypanosoma brucei
Study: Determination and integration of abundance, pro...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: mRNA decay, mRNA half-lives, precursor mRNA half-lives
Creator: Abeer Fadda
Contributor: Abeer Fadda
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
Creator: Abeer Fadda
Contributor: Abeer Fadda
The file contains the normalized relative read counts (RPM) of 2 mRNA decay experiments. Columns in blue correspond to experiment 1, columns in violet correspond to experiment 2. The time points are in column headers. The last 3 columns contain parameters and half lives calculated from an exponantial fit of all data points. Normalization was done in 2 steps :first by calculating RPM i.e. reads per million of aligned reads to unique ORFs, second by normalizing this to the total amount of mRNA
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Creator: Abeer Fadda
Contributor: Abeer Fadda
Investigations: Gene expression in Trypanosoma brucei
Studies: Determination and integration of abundance, pro...
Assays: mRNA decay assay