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Life stage specific poly(A) site selection regulated by Trypanosoma brucei DRBD18

ABSTRACT: Life stage specific poly(A) site selection regulated by Trypanosoma brucei DRBD18

PROVIDER: PRJNA1076464 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27965858.fastq.gz	Fastqsanger.gz
	SRR27965859.fastq.gz	Fastqsanger.gz
	SRR27965860.fastq.gz	Fastqsanger.gz
	SRR27965861.fastq.gz	Fastqsanger.gz
	SRR27965862.fastq.gz	Fastqsanger.gz

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Life stage specific poly(A) site selection regulated by Trypanosoma brucei DRBD18

Project description:In this work, we examine the function of DRBD18 in T. brucei, here using single cell RNA sequencing (scRNAseq) of uninduced and induced DRBD18 knockdowns. In insect procyclic form, we identified one major and one minor population of cells that dramatically increased upon DRBD18 knockdown. Both of these cell populations were significantly enriched for transcripts that are normally upregulated in the quiescent stumpy bloodstream form and metacyclic (MF) life cycle stages, consistent with a role for DRBD18 in life cycle progression. Furthermore, the 3’ end bias of our sequencing technique allowed us to investigate the effect of DRBD18 on poly(A) site selection, and extension of gene annotations permitted a comprehensive analysis of these changes. We found that 3’UTR shortening upon DRBD18 depletion was prevalent, with over 1500 transcripts exhibiting this this phenotype, and RIPseq analyses showed significant overlap between bound transcripts and those with 3’UTR shortening

2024-07-25 | GSE255758 | GEO

RNAi against DRBD18 in Trypanosoma brucei bloodstream forms

Project description:RNAi against DRBD18 in Trypanosoma brucei bloodstream forms

2021-06-29 | E-MTAB-9783 | biostudies-arrayexpress

RIP-seq to investigate RNAs associated with TAP-DRBD18 in Trypanosoma brucei bloodstream forms

Project description:RIP-Seq of DRBD18 in Trypanosoma brucei bloodstream forms

2021-07-31 | E-MTAB-10735 | biostudies-arrayexpress

Poly(A) binding KPAF4/5 in Trypanosoma brucei

Project description:Raw file submission for publication 'Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei'

2020-03-27 | MSV000085175 | MassIVE

RNAi against DRBD18 in Trypanosoma brucei bloodstream forms

Project description:RNAi against DRBD18 in Trypanosoma brucei bloodstream forms

| PRJEB41419 | ENA

Impact of overexpression of DRBD18 and its methyl mutants on the gene expression pattern of T. brucei: A transcriptomic approach

Project description:Arginine methylation of RNA-binding proteins (RBPs) plays a crucial role in the post-transcriptional regulation of gene expression in Trypanosoma brucei, the causative agent of African trypanosomiasis. This protozoan has evolved intricate mechanisms to regulate gene expression at the mRNA level, allowing it to adapt to diverse environmental conditions encountered during its complex life cycle. The process of arginine methylation involves the addition of methyl groups to specific arginine residues within RNA-binding domains of proteins. This modification can profoundly impact the binding affinity of RBPs to their target mRNAs, thereby influencing mRNA stability, localization, and translation efficiency. DRBD18 is one of the RNA-binding proteins (RBPs) in T. brucei that undergoes arginine methylation and has been involved in various aspects of mRNA metabolism and post-transcriptional gene regulation. Studies have shown that arginine methylation of DRBD18 can modulate its interaction with target mRNAs, leading to differential regulation of gene expression. Here, we have done a comprehensive transcriptomic analysis of T. brucei overexpressing DRBD18 and its methyl mutants R->F (methylmimic) and R->K (hypomethylated), aiming to elucidate the regulatory mechanisms orchestrated by DRBD18 and its potential impact on the parasite's gene expression landscape. We identified specific mRNA targets exhibiting differential expression patterns in response to DRBD18, R->F and R->K overexpression, providing insights into the regulatory pathways modulated by this RBP.

2025-04-01 | GSE262448 | GEO

Trypanosoma brucei brucei Doxycycline induced DRBD18 knockdown whole cell RNA and cytoplasmic RNA

Project description:Trypanosoma brucei brucei Doxycycline induced DRBD18 knockdown whole cell RNA and cytoplasmic RNA

| PRJNA665716 | ENA

Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state

Project description:Trypanosoma brucei occupies distinct niches throughout its life cycle, both within the vertebrate host (fat tissue, bloodstream, central nervous system) and within the insect host, the tsetse fly (taken up with a bloodmeal and passing through the midgut, and migrating to the salivary glands). The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. Whereas most well-studied organisms rely on transcriptional control as the main regulator of gene expression, post-transcriptional control mechanisms are particularly important in T. brucei, and these are often mediated by RNA-binding proteins. DRBD18 is a T. brucei RNA binding protein that interacts with ribosomal proteins and translation factors. Here, we tested a role for DRBD18 in translational control. We show that DRBD18 depletion by RNA interference leads to altered polysomal profiles with a specific depletion of heavy polysomes. RiboSeq analysis reveals that 101 transcripts change in translational efficiency (TE) upon DRBD18 depletion: 41 of them exhibit decreased TE and 60 increased TE. A further 66 transcripts are buffered, i.e. changes in transcript abundance are compensated by changes in TE such that the total translational output is expected not to change. Proteomic analysis validates much of these data. In DRBD18 depleted cells, a cohort of transcripts that code for procyclic form specific proteins are translationally repressed while, conversely, transcripts that code for bloodstream form specific proteins are translationally enhanced. These data suggest that DRBD18 contributes to the maintenance of the procyclic state through both positive and negative translational control of specific mRNAs.

2024-01-26 | PXD039064 | Pride

Trypanosoma brucei brucei Doxycycline induced DRBD18 knockdown whole cell RNA and cytoplasmic RNA

Project description:DRBD18 (Tb927.11.14090) was knocked down by 19 hour doxycycline treatment. Whole cell RNA and cytoplasmic RNA was isolated and sequenced.

2020-09-26 | GSE158584 | GEO

Transcriptomes of new Trypanosoma brucei brucei

Project description:Trypanosoma brucei were isolated from cattle, in Bunya, Uganda (Tb065BAPC) or Apuru, Uganda (Tb098AAPC). Parasites were stored as stabilities after a single mouse passage. After a further mouse passage the parasites were grown in rats to the parasitaemias indicated, isolated on DEAE cellulose and RNA was prepared. We also compared rRNA depletion with poly(A) selection.

2020-07-16 | E-MTAB-9320 | biostudies-arrayexpress

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