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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. Refer to individual Series

ORGANISM(S): Trypanosoma brucei

SUBMITTER: Hamed Najafabadi

PROVIDER: E-GEOD-46162 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

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.

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2012-05-29 | E-GEOD-37593 | biostudies-arrayexpress

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T. Brucei, Nup-1 Depletion

Project description:Organization of the genome into compacted chromatin is a eukaryotic innovation facilitating increased sophistication in transcriptional regulation. In metazoa coiled-coil lamin proteins are major components of the chromatin organizer at the nuclear periphery and maintain nuclear integrity. While identifiable lamin homologues are restricted to metazoans, morphologically analogous structures maintaining nuclear organization in other eukaryotic lineages are known, but the molecular constituents remain undefined. Trypanosoma brucei NUP-1 is a large coiled-coil protein associated with fibrils at the inner face of the nuclear envelope. Using transcriptome analysis in combination with RNA interference and various imaging techniques, we demonstrate that NUP-1 forms a stable immobile cage around the nucleus, is required for viability and nuclear structural integrity, directs the positional organization of nuclear pore complexes, and serves to organize chromatin and specifically repress genes located at the nuclear periphery involved in immune evasion. Based on architectural similarity and functionality, we propose that NUP-1 is a novel, highly divergent lamin The effect of Nup-1 depletion on the transcriptome was examined in three independent experiments (A, B, & C). T. brucei cultures were either treated with RNAi (plus) or left untreated (minus) and RNA was extracted from each sample at the indicated time point (0h, 6h, 12h, 24h, or 48h). Two color microarrays were performed comparing treated and untreated samples at each time point. Dye swaps were performed and are indicated. Replicates of t=12h and t=24h for sample B were also included.

2011-12-15 | E-GEOD-26256 | biostudies-arrayexpress

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2023-05-10 | PXD039684 | Pride

The mitogen-activated protein kinase kinase 5 regulates the proliferation and biosynthetic processes in procyclic forms of Trypanosoma brucei

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2017-10-20 | PXD007910 | Pride

Dynamic mRNA Expression analysis of cells undergoing synchronous life-cycle differentiation in Trypanosoma brucei

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