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Characterization of the regulatory programs governed by ELAV-like proteins in Trypanosoma brucei

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Trypanosoma brucei Trypanosoma brucei brucei TREU927

PROVIDER: GSE46162 | GEO | 2013/04/18

SECONDARY ACCESSION(S): PRJNA197390

REPOSITORIES: GEO

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Characterization of the regulatory programs governed by ELAV-like proteins in Trypanosoma brucei

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-18 | E-GEOD-46162 | biostudies-arrayexpress

Characterization of the regulatory programs governed by ELAV-like proteins in Trypanosoma brucei

Project description:Characterization of the regulatory programs governed by ELAV-like proteins in Trypanosoma brucei

| PRJNA197390 | ENA

Phenotypic activation and repression of three ELAV-like proteins in Trypanosoma brucei

2013-04-18 | GSE46161 | GEO

Phenotypic activation and repression of three ELAV-like proteins in Trypanosoma brucei

Project description:Three potential ELAV-like proteins of T. brucei, including Tb927.3.2930, Tb927.7.5380, and Tb927.8.6650, were either inhibited by RNAi or phenotypically activated by over-expression, followed by microarray analysis of the transcriptome. The results indicated that these ELAV-like proteins regulate the abundance of a large number of T. brucei transcripts, potentially through regulation of mRNA stability. Each of the three ELAV-like proteins were either inhibited by RNAi or over-expressed, in stable transgenic procyclic form cell lines. Total RNA was extracted 48h after tetracycline induction of the constructs (except for total RNA from Tb927.8.6650 RNAi which was extracted 24h after tet-induction), and sent to NimbleGen for cDNA synthesis and hybridization. Non-induced cells were analyzed in parallel.

2013-04-18 | E-GEOD-46161 | biostudies-arrayexpress

RIP-Seq analysis of Trypanosoma brucei ELAV-like protein Tb927.8.6650

2013-04-18 | GSE46160 | GEO

Trypanosoma brucei brucei: thymine 7-hydroxylase-like proteins.

Project description:Two genes from Trypanosoma brucei brucei are predicted to encode Fe(II)- and alpha-ketoglutarate-dependent enzymes related to fungal thymine 7-hydroxylase. Transcription of the thymine hydroxylase-like genes is up-regulated in the bloodstream form of the parasite over the insect form, whereas Western blot analysis indicates more cross-reactive protein in the latter life stage. The genes were cloned, the proteins purified from Escherichia coli, and both proteins were shown to bind Fe(II) and alpha-ketoglutarate, confirming proper folding. The isolated proteins were incubated with Fe(II)- and alpha-ketoglutarate plus thymine, thymidine, and other putative substrates, but no activity was detected. Furthermore, no thymine 7-hydroxylase activity was detected in extracts of procyclic or bloodstream form cells. Although the functions of these proteins remain unknown, we conclude they are unlikely to be involved in thymine salvage.

| S-EPMC2824036 | biostudies-literature

Development of Trypanosoma brucei EATRO 1125 and Trypanosoma congolense IL3000 in the host bloodstream

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-10-01 | GSE114813 | GEO

The SPARC complex defines RNAPII promoters in Trypanosoma brucei

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-09-28 | GSE208037 | GEO

RIP-Seq analysis of Trypanosoma brucei ELAV-like protein Tb927.8.6650

Project description:A tagged ectopic version of the ELAV-like protein Tb927.8.6650 of T. brucei was expressed in stable cell lines and pulled down. Co-purifying transcripts were analyzed by sequencing to identify RNAs associated with Tb927.8.6650. Stable procyclic form cell lines expressing tetracycline-inducible TAP-tagged Tb927.8.6650 were created. Cells were harvested 48h after tet-induction, followed by tandem affinity purification of Tb927.8.6650, extraction of co-purified RNA, and sequencing.

2013-04-18 | E-GEOD-46160 | biostudies-arrayexpress

ELAV/Hu RNA binding proteins determine multiple programs of neural alternative splicing.

Project description:ELAV/Hu factors are conserved RNA binding proteins (RBPs) that play diverse roles in mRNA processing and regulation. The founding member, Drosophila Elav, was recognized as a vital neural factor 35 years ago. Nevertheless, little was known about its impacts on the transcriptome, and potential functional overlap with its paralogs. Building on our recent findings that neural-specific lengthened 3' UTR isoforms are co-determined by ELAV/Hu factors, we address their impacts on splicing. While only a few splicing targets of Drosophila are known, ectopic expression of each of the three family members (Elav, Fne and Rbp9) alters hundreds of cassette exon and alternative last exon (ALE) splicing choices. Reciprocally, double mutants of elav/fne, but not elav alone, exhibit opposite effects on both classes of regulated mRNA processing events in larval CNS. While manipulation of Drosophila ELAV/Hu RBPs induces both exon skipping and inclusion, characteristic ELAV/Hu motifs are enriched only within introns flanking exons that are suppressed by ELAV/Hu factors. Moreover, the roles of ELAV/Hu factors in global promotion of distal ALE splicing are mechanistically linked to terminal 3' UTR extensions in neurons, since both processes involve bypass of proximal polyadenylation signals linked to ELAV/Hu motifs downstream of cleavage sites. We corroborate the direct action of Elav in diverse modes of mRNA processing using RRM-dependent Elav-CLIP data from S2 cells. Finally, we provide evidence for conservation in mammalian neurons, which undergo broad programs of distal ALE and APA lengthening, linked to ELAV/Hu motifs downstream of regulated polyadenylation sites. Overall, ELAV/Hu RBPs orchestrate multiple broad programs of neuronal mRNA processing and isoform diversification in Drosophila and mammalian neurons.

| S-EPMC8055025 | biostudies-literature

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