Ontology highlight
ABSTRACT:
PROVIDER: PRJNA727846 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription
| PRJNA484931 | ENA
Project description:Base J is a modified DNA base that is enriched at RNA polymerase II termination sites and telomeres. We previously found that base J functions to prevent readthrough transcription within gene clusters in T. brucei. We now identify a complex in Leishmania and T. brucei composed of PNUTS, PP1, Wdr82 and a J-binding protein (JBP3). We show the RNAi ablation of PNUTS in T. brucei leads to readthrough transcription and expression of downstream genes.
2020-01-14 | GSE135708 | GEO
Project description:Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of trypanosomatids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and play an essential role in chromosome ends protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its, previously described, DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression that plays a role in the control of antigenic variation in T. brucei.
2024-02-28 | GSE227504 | 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 brucei base J and H3.V transcription regulation
| PRJNA305332 | ENA
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:DNA replication initiation is spatiotemporally regulated to ensure highly-ordered genome duplication. While it is intriguing to find that DNA replication initiation correlates with actively transcribed regions in mammalian cells, it remains elusive how DNA replication initiation coordinates with transcription. Here we developed a high-resolution method, Nucleoside Analogues Incorporation Loci sequencing (NAIL-seq), to map early replication initiation zones (ERIZs). We found that ERIZs fall into non-transcribed regions of open chromatin compartments, mutually exclusive with transcription. Transcription blockage leads to the ERIZ signals, along with the replicative helicase MCM (mini-chromosome maintenance), infiltrating into active gene bodies. Moreover, pervasive transcription read-through shapes early DNA replication by placing them further downstream. Transcription barriers such as loop anchors and nuclease-dead Cas9 routinely facilitate DNA replication initiation. Therefore we propose a “transcription-dozer” model that transcription orchestrates DNA replication initiation via transcription-mediated redistribution of MCM to transcription-poor regions to avoid replication initiation-transcription collision.
| OEX002082 | NODE
Project description:DNA replication initiation is spatiotemporally regulated to ensure highly-ordered genome duplication. While it is intriguing to find that DNA replication initiation correlates with actively transcribed regions in mammalian cells, it remains elusive how DNA replication initiation coordinates with transcription. Here we developed a high-resolution method, Nucleoside Analogues Incorporation Loci sequencing (NAIL-seq), to map early replication initiation zones (ERIZs). We found that ERIZs fall into non-transcribed regions of open chromatin compartments, mutually exclusive with transcription. Transcription blockage leads to the ERIZ signals, along with the replicative helicase MCM (mini-chromosome maintenance), infiltrating into active gene bodies. Moreover, pervasive transcription read-through shapes early DNA replication by placing them further downstream. Transcription barriers such as loop anchors and nuclease-dead Cas9 routinely facilitate DNA replication initiation. Therefore we propose a “transcription-dozer” model that transcription orchestrates DNA replication initiation via transcription-mediated redistribution of MCM to transcription-poor regions to avoid replication initiation-transcription collision.
| OEX002081 | NODE