Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: T. brucei transcription and replication

PROVIDER: PRJNA727846 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14459702_1.fastq.gz	Fastqsanger.gz
	SRR14459702_2.fastq.gz	Fastqsanger.gz
	SRR14459703_1.fastq.gz	Fastqsanger.gz
	SRR14459703_2.fastq.gz	Fastqsanger.gz
	SRR14459704_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 102

Similar Datasets

Well-positioned nucleosomes punctuate polycistronic Pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei

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

Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription

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

mtTF1: A Novel Factor Involved in Mitochondrial Gene Expression in Trypanosoma brucei

Project description:Mitochondrial DNA replication and gene expression are essential for cell survival. In Trypanosoma brucei, a protozoan animal and human parasite, the mitochondrial RNA polymerase (mtRNAP) plays roles in both transcription and DNA replication. This study identifies and characterizes the first mitochondrial transcription factor (mtTF1) in the Kinetoplastea. mtRNAP and mtTF1 form a high-molecular-weight complex that localizes to the kinetoplast DNA (kDNA) and is essential for parasite survival in both life cycle stages. Their localization is interdependent, and both proteins influence maxicircle replication, but not minicircle replication. Knockdown of either protein result in altered gene expression, particularly affecting the minor strand of the mitochondrial genome. Since mtTF1 is unique to the Kinetoplastea, it might prove to be a promising drug target.

2025-05-26 | GSE297664 | GEO

Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription

Project description:Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription

| PRJNA484931 | ENA

Base J binding protein (JBP3) is a Component of a Novel Trypanosomatid PNUTS-PP1 Phosphatase Complex involved in RNA Pol II Transcription Termination

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

UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes [ATAC-seq]

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

Genomic shotgun sequences of Trypanosoma brucei brucei from Uganda

Project description:Genomic shotgun sequences of Trypanosoma brucei brucei from Uganda with minimal laboratory passage.

2020-11-22 | E-MTAB-9759 | biostudies-arrayexpress

Trypanosoma brucei

Project description:Trypanosoma brucei brucei base J and H3.V transcription regulation

| PRJNA305332 | ENA

Protein Phosphatase PP1 Regulation of Pol II Phosphorylation is Linked to Transcription Termination and Allelic Exclusion of VSG Genes and TERRA in Trypanosomes.

Project description:Base J is a modified DNA base that is enriched at RNA polymerase II termination sites. We previously found that base J functions to prevent readthrough transcription within gene clusters via the PJW/PP1 complex. Analysis of the complex in T. brucei faild to identify the catalytic PP1 component. We now show the RNAi ablation of PP1-1 in T. brucei leads to readthrough transcription and expression of downstream genes.

2024-07-17 | GSE244975 | GEO

Histone divergence in Trypanosoma brucei results in unique alterations in nucleosome structure

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data