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Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome

ABSTRACT: Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome

PROVIDER: PRJEB21868 | ENA |

REPOSITORIES: ENA

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Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome.

Project description:R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localization was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the regions between coding sequences of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination the most widespread localization of R-loops in T. brucei suggests a novel correlation with pre-mRNA processing. Finally, we find little evidence for correlation between R-loop localization and mapped sites of DNA replication initiation.

| S-EPMC6294496 | biostudies-literature

Oxaboroles target trypanosome CPSF3

Project description:Oxaboroles target trypanosome CPSF3 - DDD85646 screen

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Function of Trypanosome brucei RBP10

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Oxaboroles target trypanosome CPSF3

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Diverged Trypanosome MICOS as a Hub for Mitochondrial Cristae Shaping and Protein Import

Project description:The mitochondrial contact site and cristae organization system (MICOS) is a complex responsible for proper cristae formation. Empirical data about this ubiquitous complex is limited to opisthokont models (e.g. yeast), impeding understanding of its core properties and adaptation potential to diverse cellular milieus. To close this knowledge gap, we characterized MICOS from the diverged excavate Trypanosoma brucei. These results allow the definition of fundamental MICOS properties, such as its role in maintaining both cristae and contacts between the inner and outer membranes plus its extrusion into the intermembrane space. Yet, surprising differences with opisthokonts indicate that MICOS can assume different forms. T. brucei MICOS contains a novel subunit involved in the import of intermembrane space proteins, including respiratory chain complex assembly factors. We propose an evidence-based hypothesis that T. brucei MICOS populates cristae membranes with proteins needed for respiration, supported by the complex's even distribution in cristae

2018-09-13 | PXD009601 | Pride

Oxaboroles target trypanosome CPSF3 - Acoziborole screen

Project description:Oxaboroles target trypanosome CPSF3 - Acoziborole screen

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A conserved transcriptional regulator governs fungal morphology in widely diverged species

Project description:This SuperSeries is composed of the following subset Series: GSE32550: A conserved transcriptional regulator governs fungal morphology in widely diverged species [expression data] GSE32557: A conserved transcriptional regulator governs fungal morphology in widely diverged species [ChIP-chip, Transcriptional regulation by Mit1 and orthologs] Refer to individual Series

2011-10-03 | E-GEOD-32558 | biostudies-arrayexpress

The roles of 3’-exoribonucleases and the exosome in trypanosome mRNA degradation

Project description:The roles of 3’-exoribonucleases and the exosome in trypanosome mRNA degradation; 30 min after actinomycin D +sinefungin, RNAi against CAf1, CNOT10, PAN2. These are really old data that hadn't been deposited.The datasets called RNA1, RNA2, RNA3 and RNA4 are almost certainly, from their location in the folder and from new alignment results, from the RRP45 RNAi.

2021-03-11 | E-MTAB-10260 | biostudies-arrayexpress

Evolution of sex-dependent gene expression in three recently diverged species of Drosophila

Project description:To identify the transcriptome divergence and sex roles underlying it in recently diverged Drosophia pseudoobscura group, we compare the global gene expression of 7-day-old whole body adults of pure species.

2010-01-12 | GSE17192 | GEO

Transcription profiling of mouse liver and spleen from strains that are susceptible and tolerant to trypanosome infection

Project description:Tissues were harvested from mice from two congenic strains (Tir1CC and Tir3CC) and their two control strains (Tir1AA and Tir3AA). The congenic strains were bred from inbred lines known to be susceptible (A/J) and tolerant (C57BL/6) to Trypanosome infection, such that C57BL/6 genomic regions underlying QTL for trypanotolerance were present in an A/J genetic background. Liver and spleen tissues were harvested. For each strain RNA was prepared from various tissues of twenty mice. For each condition, RNA extracts from individuals were pooled (5 per pool) prior to hybridisation.

2009-12-02 | E-TABM-865 | biostudies-arrayexpress

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