Effect of CFB2 depletion in Trypanosoma brucei
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina MiSeq, none
ORGANISM(S): Trypanosoma brucei brucei
SUBMITTER: Esteban Erben
PROVIDER: E-MTAB-9700 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Bloodstream-form trypanosomes with inducible RNAi targeting ZC3H28 were incubated with the tetracycline inducer for 10h, cells without tetracycline were used as controls. This experiment was done in triplicates. In another similar experiment, bloodstream-form trypanosomes with inducible RNAi targeting ZC3H28 were incubated with the tetracycline inducer for 14h, 16h, and 24h. Cells without tetracycline (named ''no tet'' or ''0h'') were used as controls. This experiment was done in duplicates.
2021-07-31 | E-MTAB-10751 | biostudies-arrayexpress
Project description:Gradient fractions of RNAi of XAC1 (Tb927.7.2780) in Trypanosoma brucei bloodstream forms. RNAi was induced using tetracycline and cell extracts were fractionated into polysomal and monosome-non-ribosome-associated fractions.
2017-12-16 | E-MTAB-6239 | biostudies-arrayexpress
Project description:Trypanosome RNA polymerase II transcription is polycistronic, individual mRNAs being excised by trans splicing and polyadenylation. In this study, we refined the previously published mathematical model for bloodstream form parasites and extended it to the procyclic form. We used the model, together with known mRNA half-lives, to predict the abundances of individual mRNAs, assuming rapid, unregulated mRNA processing; then we compared the results with measured mRNA abundances. Remarkably, the abundances of most mRNAs in procyclic forms are predicted quite well by the model, being largely explained by variations in mRNA decay rates and length. In bloodstream forms substantially more mRNAs are less abundant than predicted. We list mRNAs that are likely to show particularly slow or inefficient processing, either in both forms or with developmental regulation. We also measured ribosome occupancies of all mRNAs in trypanosomes grown in the same conditions as were used to measure mRNA turnover. In procyclic forms there was a weak positive correlation between ribosome density and mRNA half-life, suggesting cross-talk between translation and mRNA decay; ribosome density was related to the proportion of the mRNA on polysomes, indicating control of translation initiation. Ribosomal protein mRNAs in procyclics appeared to be exceptionally rapidly processed but poorly translated. Through this study, we conclude that lLevels of mRNAs in procyclic form trypanosomes are determined mainly by length and mRNA decay, with some control of precursor processing. In bloodstream forms variations in nuclear events play a larger role in transcriptome regulation, suggesting acquisition of new control mechanisms during adaptation to mammalian parasitism.
2016-03-16 | GSE79208 | GEO
Project description:RBP9-TAP was expressed in bloodstream T. brucei and bound mRNA was pulled down using IgG beads and eluted via TEV-protease cleavage. rRNA was depleted using RNAseH and rRNA hybridizing oligos.
2020-05-30 | E-MTAB-9093 | biostudies-arrayexpress
Project description:Trypanosomes are a globally important group of parasites which together kill and debilitate millions of people world-wide. In trypanosomes, genes do not have individual promoters, rather ~10000 genes share ~200 promoters and all gene expression is thus regulated post-transcriptionally. While effector proteins which modulate the expression of many genes have been described, the mechanisms by which trypanosomes sense changes in their environment and manifest changes in gene expression remain elusive. This study demonstrates that trypanosomes sense changes in their environment through temperature sensitive RNA secondary structure. We show that the majority of observed mRNA abundance changes which distinguish insect adapted and bloodstream adapted life cycle stages can be explained through change in temperature alone.
2016-06-14 | E-MTAB-3335 | biostudies-arrayexpress
Project description:Trypanosomes are a globally important group of parasites which together kill and debilitate millions of people world-wide. In trypanosomes, genes do not have individual promoters, rather ~10000 genes share ~200 promoters and all gene expression is thus regulated post-transcriptionally. While effector proteins which modulate the expression of many genes have been described, the mechanisms by which trypanosomes sense changes in their environment and manifest changes in gene expression remain elusive. This study demonstrates that trypanosomes sense changes in their environment through temperature sensitive RNA secondary structure. We show that the majority of observed mRNA abundance changes which distinguish insect adapted and bloodstream adapted life cycle stages can be explained through change in temperature alone.
2017-06-15 | E-MTAB-4859 | biostudies-arrayexpress
Project description:Cy3 and Cy5 direct labelled RNA from Bloodstream MiTat1.1 trypanosomes and Procyclic 427 Lister were hybridized onto JCVI Trypanosoma brucei oligoarrays (version2). Procyclic RNA were used as control for data analysis.
2010-01-01 | E-MEXP-2028 | biostudies-arrayexpress
Project description:mRNAs associates with HnRNPF/H in Trypanosoma brucei bloodstream forms
2021-08-31 | E-MTAB-10708 | biostudies-arrayexpress
Project description:ZC3H5 was knocked down in bloodstream form T.brucei by RNAi for 0h and 12h. WT bloodstream form cells were used as control. Polysome fractionation was performed, RNA was purified from each fraction and fractions were pooled the following: F=free fraction; M=monosomes; L=light polysomes; H=heavy polysomes. RNA was depleted and RNA-Seq was performed.
2019-06-28 | E-MTAB-8069 | biostudies-arrayexpress
Project description:Trypanosome RNA polymerase II transcription is polycistronic, individual mRNAs being excised by trans splicing and polyadenylation. In this study, we refined the previously published mathematical model for bloodstream form parasites and extended it to the procyclic form. We used the model, together with known mRNA half-lives, to predict the abundances of individual mRNAs, assuming rapid, unregulated mRNA processing; then we compared the results with measured mRNA abundances. Remarkably, the abundances of most mRNAs in procyclic forms are predicted quite well by the model, being largely explained by variations in mRNA decay rates and length. In bloodstream forms substantially more mRNAs are less abundant than predicted. We list mRNAs that are likely to show particularly slow or inefficient processing, either in both forms or with developmental regulation. We also measured ribosome occupancies of all mRNAs in trypanosomes grown in the same conditions as were used to measure mRNA turnover. In procyclic forms there was a weak positive correlation between ribosome density and mRNA half-life, suggesting cross-talk between translation and mRNA decay; ribosome density was related to the proportion of the mRNA on polysomes, indicating control of translation initiation. Ribosomal protein mRNAs in procyclics appeared to be exceptionally rapidly processed but poorly translated. Through this study, we conclude that lLevels of mRNAs in procyclic form trypanosomes are determined mainly by length and mRNA decay, with some control of precursor processing. In bloodstream forms variations in nuclear events play a larger role in transcriptome regulation, suggesting acquisition of new control mechanisms during adaptation to mammalian parasitism. Ribosome profiling and mRNA libraries were constructed in triplicate from in vitro PCF and in duplicate from in vitro T. brucei Lister427, to understand global differntial gene transcription.
2016-03-16 | E-GEOD-79208 | biostudies-arrayexpress