Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1216521 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32149600_1.fastq.gz | Fastqsanger.gz | |||
| SRR32149600_2.fastq.gz | Fastqsanger.gz | |||
| SRR32149601_1.fastq.gz | Fastqsanger.gz | |||
| SRR32149601_2.fastq.gz | Fastqsanger.gz | |||
| SRR32149602_1.fastq.gz | Fastqsanger.gz |
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Project description:Bloodstream-form African trypanosomes display mono-telomeric expression of a Variant Surface Glycoprotein (VSG) gene in an inter-chromosomally bridged transcription and splicing compartment, such that the dominant gene produces 10,000 times more transcript than excluded VSG genes. Antigenic variation, whereby parasites switch to express other VSGs, then underpins a robust host immune evasion strategy. Specific chromatin and RNA-associated factors are required to maintain VSG exclusion, but our understanding of the mechanisms involved remains incomplete. Here we show that the VSG transcript impacts allelic competition. We induced either specific translation blockade by recruiting MS2 coat protein to the active VSG 5'-untranslated region, or VSG transcript depletion using RNA interference. Neither perturbation substantially compromised exclusion of native VSGs, as determined by transcriptomic analyses. In contrast, exclusion of a VSG transgene was compromised when the native transcript was transiently depleted. Notably, while both perturbations blocked cytokinesis, an additional round of DNA replication and mitosis was observed when the transcript, known to be stabilized by a bloodstream-form specific cyclin-like F-box protein, was translationally blocked. We conclude that the VSG transcript is a bi-functional coding and non-coding RNA that participates in allelic competition, and possibly also in cell cycle control, to establish exclusion.
2025-03-11 | PXD060524 | Pride
Project description:The African trypanosome Trypanosoma brucei is a unicellular eukaryote, which relies on a protective Variant Surface Glycoprotein (VSG) coat for survival in the mammalian host. A single trypanosome has >2000 VSG genes and pseudogenes of which only one is expressed from one of ~15 telomeric bloodstream form expression sites (BESs). Infectious metacyclic trypanosomes present within the tsetse fly vector also express VSG from a separate set of telomeric metacyclic ESs (MESs). All MESs are silenced in bloodstream form T. brucei. As very little is known about how this is mediated, we performed a whole genome RNAi library screen to identify MES repressors. This allowed us to identify a novel SAP domain containing DNA binding protein which we called TbSAP. TbSAP is enriched at the nuclear periphery and binds both MESs and BESs. Knockdown of TbSAP in bloodstream form trypanosomes did not result in cells becoming more ‘metacyclic’-like. Instead, there was extensive global upregulation of transcripts including MES VSGs, VSGs within the silent VSG arrays as well as genes immediately downstream of BES promoters. TbSAP therefore appears to be a novel architectural chromatin protein playing an important role in silencing the extensive VSG repertoire of bloodstream form T. brucei.
2020-11-04 | GSE160713 | GEO
Project description:UPF1-like helicases play roles in telomeric heterochromatin formation and X-chromosome inactivation and we focus here on variant surface glycoprotein (VSG) exclusion-factor-2 (VEX2), a UPF1-related protein in the African trypanosome. This bloodstream parasite evades host immunity by employing monogenic and switchable VSG expression, a form of antigenic variation which involves transcription of one telomeric VSG gene at a time. A trans-splicing compartment and the single VSG transcription factory are juxtaposed and enriched for VEX1 and VEX2, respectively, but our understanding of the VSG exclusion mechanism remains otherwise incomplete. Here, we sought VEX2-interacting partners, using cryomilling and affinity purification followed my LC-MS/MS analysis. We confirmed previous observations that VEX2 interacts with VEX1 and CAF-1, but also found evidence for weaker interactions and/or spatial proximity to telomere binding proteins.
2023-11-20 | PXD040686 | Pride
Project description:The African trypanosome Trypanosoma brucei is a unicellular eukaryote, which relies on a protective Variant Surface Glycoprotein (VSG) coat for survival in the mammalian host. A single trypanosome has >2000 VSG genes and pseudogenes of which only one is expressed from one of ~15 telomeric bloodstream form expression sites (BESs). Infectious metacyclic trypanosomes present within the tsetse fly vector also express VSG from a separate set of telomeric metacyclic ESs (MESs). All MESs are silenced in bloodstream form T. brucei. As very little is known about how this is mediated, we performed a whole genome RNAi library screen to identify MES repressors. This allowed us to identify a novel SAP domain containing DNA binding protein which we called TbSAP. TbSAP is enriched at the nuclear periphery and binds both MESs and BESs. Knockdown of TbSAP in bloodstream form trypanosomes did not result in cells becoming more ‘metacyclic’-like. Instead, there was extensive global upregulation of transcripts including MES VSGs, VSGs within the silent VSG arrays as well as genes immediately downstream of BES promoters. TbSAP therefore appears to be a novel architectural chromatin protein playing an important role in silencing the extensive VSG repertoire of bloodstream form T. brucei.
2020-11-06 | PXD022397 | Pride
Project description:We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ten subjects. RNA sequencing techniques were designed to detect both coding and non-coding RNA, splice isoform composition, and allelic expression. Brain regions were selected from five subjects with a documented history of smoking and five non-smokers. Paired-end RNA sequencing was performed on SOLiD instruments to a depth of >40 million reads, using linearly amplified, ribosomally depleted RNA. 12 thousand protein coding and 2 thousand lncRNA transcripts were detectable at a conservative threshold. Of the aligned reads, 52% were exonic, 34% intronic and 14% intergenic. A majority of protein coding genes (65%) was expressed in all regions, whereas ncRNAs displayed a more restricted distribution. Profiles of RNA isoforms varied across brain regions and subjects at multiple gene loci, with neurexin 3 (NRXN3) a prominent example. Allelic RNA ratios deviating from unity were identified in > 400 genes, detectable in both protein-coding and non-coding genes, indicating the presence of cis-acting regulatory variants. RNA sequencing identifies distinct and consistent differences in gene expression between brain regions, with non-coding RNA displaying greater diversity between brain regions than mRNAs. Numerous RNAs exhibit robust allele selective expression, proving a means for discovery of cis-acting regulatory factors with potential clinical relevance. Sequenced whole transcriptomes of 10 brain regions from 10 individuals, 5 smokers and 5 nonsmokers
2015-09-01 | E-GEOD-68559 | biostudies-arrayexpress
Project description:Bacterial non-coding RNAs excised from within protein-coding transcripts
| PRJEB27518 | ENA
Project description:Trypanosoma brucei spp. develop into mammalian-infectious metacyclic trypomastigotes inside tsetse salivary glands. Besides acquiring a variant surface glycoprotein (VSG) coat, little is known about the metacyclic expression of invariant surface antigens. Proteomics analyses of saliva from T. brucei-infected flies identified, in addition to VSG and Brucei Alanine-Rich Protein (BARP) peptides, a family of GPIanchored surface proteins herein named Metacyclic Invariant Surface Proteins (MISP). The MISP family is encoded by five paralog genes with >80% protein identity, which are exclusively expressed by salivary gland stages of the parasite and peak in metacyclic stage, as shown by confocal microscopy and immuno-high resolution scanning electron microscopy. Crystallographic analysis of a MISP isoform (MISP360) and a high confidence model of BARP revealed a triple helical bundle architecture commonly found in other trypanosome surface proteins. Molecular modelling combined with live fluorescent microscopy suggests that MISP N-termini are extended above the VSG coat. However, vaccination with recombinant MISP360 isoform did not protect mice against a T. brucei infectious tsetse bite. Lastly, both RNAi knock down and CRISPR-Cas9-driven knock out of all MISP paralogues suggest they are not essential for parasite development in the tsetse vector. We speculate that MISP may be relevant during trypanosome inoculation or establishment in the vertebrate’s skin.
2023-05-10 | PXD039684 | Pride
Project description:Polycomb preferentially targets stalled promoters of coding and non-coding transcripts
| PRJNA132651 | ENA
Project description:We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ten subjects. RNA sequencing techniques were designed to detect both coding and non-coding RNA, splice isoform composition, and allelic expression. Brain regions were selected from five subjects with a documented history of smoking and five non-smokers. Paired-end RNA sequencing was performed on SOLiD instruments to a depth of >40 million reads, using linearly amplified, ribosomally depleted RNA. 12 thousand protein coding and 2 thousand lncRNA transcripts were detectable at a conservative threshold. Of the aligned reads, 52% were exonic, 34% intronic and 14% intergenic. A majority of protein coding genes (65%) was expressed in all regions, whereas ncRNAs displayed a more restricted distribution. Profiles of RNA isoforms varied across brain regions and subjects at multiple gene loci, with neurexin 3 (NRXN3) a prominent example. Allelic RNA ratios deviating from unity were identified in > 400 genes, detectable in both protein-coding and non-coding genes, indicating the presence of cis-acting regulatory variants. RNA sequencing identifies distinct and consistent differences in gene expression between brain regions, with non-coding RNA displaying greater diversity between brain regions than mRNAs. Numerous RNAs exhibit robust allele selective expression, proving a means for discovery of cis-acting regulatory factors with potential clinical relevance.
2015-09-01 | GSE68559 | GEO
Project description:Antigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded from a large repertoire of ~2,000 alleles. T. brucei express multiple, sometimes closely related, VSGs in a population at any one time, and the ability to resolve and analyse this diversity has been limited. We applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from batches of mice sacrificed at time points (days 3, 6, 10 and 12) post-infection with T. brucei TREU927. The data showed that long read sequencing is reliable for resolving allelic differences between VSGs, and demonstrated that there is significant expressed diversity (449 VSGs detected across 20 mice) and across the timeframe of study there was a clear semi-reproducible pattern of expressed diversity (median of 27 VSGs per sample at day 3 post infection (p.i.), 82 VSGs at day 6 p.i., 187 VSGs at day 10 p.i. and 132 VSGs by day 12 p.i.). There was also consistent detection of one VSG dominating expression across replicates at days 3 and 6, and emergence of a second dominant VSG across replicates by day 12, providing further evidence for hierarchical VSG expression, a conclusion that was confirmed by the novel application of diversity analysis to VSG expression. Our results indicate that long read analysis is a reliable tool for resolving diverse allele expression profiles, and provides novel insights into the complexity and nature of VSG expression in trypanosomes, revealing significantly higher diversity than previously shown and identifying mosaic gene formation unprecedentedly early during the infection process.
2018-11-01 | GSE114843 | GEO