Stranded SNS-seq T. brucei
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ABSTRACT:
PROVIDER: PRJEB70708 | ENA |
REPOSITORIES: ENA
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Project description:Trypanosoma brucei, a member of the Excavates supergroup, falls in an evolutionarily ancient branch of eukaryotes. We have mapped nucleosome positions in T. brucei and identified a map that differs from that of other eukaryotes in several important ways. Unlike in other eukaryotes, the RNA polymerase II initiation regions in T. brucei do not exhibit pronounced nucleosome depletion, and show little evidence for defined -1 and +1 nucleosomes. In contrast, a well-positioned nucleosome is present directly on the splice acceptor sites within the polycistronic transcription units. The RNA polyadenylation sites were depleted of nucleosomes, with a single well-positioned nucleosome present immediately downstream of the predicted sites. The regions flanking the silent Variant Surface Glycoprotein (VSG) gene arrays showed extensive arrays of well-positioned nucleosomes, which may act to repress cryptic transcription initiation. The silent VSG genes themselves exhibited a less regular nucleosomal pattern in both bloodstream and procyclic form trypanosomes. The DNA replication origins, when present within arrays of silent VSG genes, displayed a defined nucleosomal organization compared with replication origins in other chromosomal core regions. Our results indicate that some organizational features of chromatin are evolutionarily ancient, and may already have been present in the last eukaryotic common ancestor.
2017-03-13 | GSE90593 | GEO
Project description:In Trypanosoma brucei, genes are arranged in Polycistronic Transcription Units (PTUs), which are demarcated by transcription start and stop sites. Transcription start sites are also binding sites of Origin Recognition Complex 1 (ORC1). These suggest that transcription and replication in trypanosomes must occur in highly ordered and cooperative manners. Not coincidently, our previous genetic screen, a LOss of transcription Silencing (LOS) screen, identified a T. brucei MCM-BP, which forms a complex with subunits of the replicative helicase MCM. Here, I show that TbMCM-BP is required for DNA replication and transcription. TbMCM-BP depletion causes a significant reduction of replicating cells in S phase and genome-wide impairments of replication origin activation. Moreover, levels of sense and antisense transcripts increase at boundaries of PTUs in the absence of TbMCM-BP. TbMCM-BP is also important for transcriptional repression of the specialized subtelomeric PTUs, the Bloodstream-form Expression-Sites (BESs), which house the gene of antigenic importance, VSG. In the absence of TbMCM-BP, expression of silent VSGs is elevated, silent promoter regions are derepressed, and antisense transcription increases downstream of the silent promoters. This study reveals that TbMCM-BP, a replication initiation protein, guides transcription to properly start and stop, and also helps it move in the correct direction.
2018-10-19 | GSE118232 | 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
Project description:The host range of African trypanosomes is influenced by innate protective molecules in the blood of primates. A subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I, apolipoprotein L-I, and haptoglobin-related protein is toxic to Trypanosoma brucei brucei but not the human sleeping sickness parasite Trypanosoma brucei rhodesiense. It is thought that T. b. rhodesiense evolved from a T. b. brucei-like ancestor and expresses a defense protein that ablates the antitrypanosomal activity of human HDL. To directly investigate this possibility, we developed an in vitro selection to generate human HDL-resistant T. b. brucei. Here we show that conversion of T. b. brucei from human HDL sensitive to resistant correlates with changes in the expression of the variant surface glycoprotein (VSG) and abolished uptake of the cytotoxic human HDLs. Complete transcriptome analysis of the HDL-susceptible and -resistant trypanosomes confirmed that VSG switching had occurred but failed to reveal the expression of other genes specifically associated with human HDL resistance, including the serum resistance-associated gene (SRA) of T. b. rhodesiense. In addition, we found that while the original active expression site was still utilized, expression of three expression site-associated genes (ESAG) was altered in the HDL-resistant trypanosomes. These findings demonstrate that resistance to human HDLs can be acquired by T. b. brucei. Keywords: Trypanosoma, VSG, antigenic switching, HDL-resistance
2007-07-04 | GSE8369 | 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:Trypanosoma brucei gambiense is the causative agent of the fatal human disease African sleeping sickness. Using Digital Gene Expression we have compared the transcriptome of a group 1 T.b.gambiense (Eliane) and a T.b.brucei (STIB 247).
2022-08-31 | GSE23885 | GEO
Project description:Trypanosoma brucei brucei edited mRNA transcriptomes
| PRJNA369536 | ENA
Project description:Trypanosoma brucei brucei Raw sequence reads
| PRJNA292451 | ENA
Project description:RNAseq of Trypanosoma brucei brucei EATRO1125 bloodstream forms without EIF4E2 compared with add-back
2021-08-31 | E-MTAB-10719 | biostudies-arrayexpress