Trypanosoma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA352420 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative genomic analysis of T. cruzi CLB vs Trypanosoma rangeli (strains SC, Choachí, C23, H14, R1625 and PIT10) and Trypanosoma conorhini
2023-04-11 | GSE229354 | GEO
Project description:Comparative genomic analysis of Trypanosoma cruzi G with Trypanosoma cruzi D11.
2022-03-06 | GSE197870 | GEO
Project description:Eukaryotes have an array of diverse mechanisms for organising and using their genomes, but the histones that make up chromatin are highly conserved. Unusually, histones from Kinetoplastids are highly divergent. The structural and functional consequences of this variation are unknown. Here, we have biochemically characterised nucleosome core particles (NCPs) from the Kinetoplastid parasite Trypanosoma brucei. A structure of the T. brucei NCP reveals that global histone architecture is conserved, but specific sequence alterations lead to distinct DNA and protein interaction interfaces. The T. brucei NCP is unstable and has weakened DNA binding overall. However, dramatic changes at the H2A-H2B interface introduce local reinforcement of DNA contacts. The T. brucei acidic patch has altered topology and is refractory to known binders, indicating that the nature of chromatin interactions in T. brucei may be unique. Overall, our results provide a detailed molecular basis for understanding evolutionary divergence in chromatin structure.
2023-08-30 | GSE226029 | GEO
Project description:5-Hydroxymethyluracil (5hmU) is a thymine modification existing in the genomes of a number of living organisms. The post-replicative formation of 5hmU occurs via hydroxylation of thymine, which can be mediated by the ten-eleven translocation (TET) dioxygenases in mammalian and J-binding proteins (JBPs) in protozoan genomes, respectively. In addition, 5hmU also can be generated through oxidation of thymine by reactive oxygen species or from deamination of 5hmC by activation-induced cytidine deaminase (AID) or APOBEC family enzymes. While the biological roles of 5hmU have not been fully explored, identifying its genomic location will assist in elucidating its functions. Herein, we report a method of enzyme-mediated bioorthogonal labeling to selectively enrich genomic regions containing 5hmU. 5hmU DNA kinase (5hmUDK) was utilized to selectively install an azide group or alkynyl group into the hydroxyl group of 5hmU followed by incorporation of the biotin linker through click chemistry and capture of 5hmU-containing DNA fragments via streptavidin pull-down. The enriched fragments were applied to deep sequencing to map the location of 5hmU. With this established enzyme-mediated bioorthogonal labeling strategy, we achieved the genome-wide mapping of 5hmU in Trypanosoma brucei (T. brucei) genomes. The method described here will allow for a better understanding of the functional roles and dynamics of 5hmU in genomes
2021-07-11 | GSE179809 | GEO
Project description:Since the initial publication of the trypanosomatid genomes, curation has been ongoing. Here we apply the technique of ribosome profiling to Trypanosoma brucei, identifying 223 new coding regions by virtue of ribosome occupancy in the corresponding transcripts. A small number of these putative genes correspond to extra copies of previously annotated genes but 85% are novel. The median size of these novels CDSs is small (74 aa) indicating that past annotation work has excelled at detecting large CDSs. Of the unique CDSs discovered here, over half have candidate orthologues in other trypanosomatid genomes, most of which were not yet annotated as genes. Still, approximately one-third of the new CDSs were found only in T. brucei subspecies. When combined with RNA-seq and spliced leader mapping, we were able to definitively revise the start sites for 430 CDSs as compared to the current gene models. Such data also allowed us to use a structured approach to eliminate 701 putative genes as protein-coding. Finally, the data pointed to several regions of the genome that had sequence errors that altered coding region boundaries.
2015-12-22 | GSE72463 | GEO
Project description:Genomic shotgun sequences of Trypanosoma brucei brucei from Uganda with minimal laboratory passage.
2020-11-22 | E-MTAB-9759 | biostudies-arrayexpress
Project description:Genomes of two new Trypanosoma brucei isolates
| PRJEB39254 | ENA
Project description:Antibody recognition of Trypanosoma cruzi conserved proteins was assessed by evaluating pools of patient IgG samples on microarrays of 400,000 peptides covering these proteins as 15-mers with an overlap of 13 amino acids.
2024-02-28 | GSE235074 | GEO
Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was performed to generate genome-wide binding maps of two U1-snRNP proteins: U1C and U1-70K in Trypanosoma brucei.
2014-05-16 | GSE43848 | GEO