RNA immunoprecipitation coupled to RNA-sequencing of Plasmodium berghei NAB2::mCherry parasites.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB46559 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6352540.fastq.gz | Fastqsanger.gz | |||
| ERR6352538.fastq.gz | Fastqsanger.gz | |||
| ERR6352539.fastq.gz | Fastqsanger.gz |
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Project description:Identification of RNAs directly bound by malarial NAB2
2021-09-03 | E-MTAB-10773 | biostudies-arrayexpress
Project description:RNA immunoprecipitation of Plasmodium berghei coupled to RNA-sequencing of GBP2::mCherry parasites.
| PRJEB46557 | ENA
Project description:Identification of RNAs directly bound by malarial GBP2
2021-09-03 | E-MTAB-10775 | biostudies-arrayexpress
Project description:The quality control and export of mRNA by RNA-binding proteins are necessary for the survival of malaria parasites, which have complex life cycles. Malarial nuclear poly(A) binding protein 2 (NAB2), ALWAYS EARLY (ALY) and serine/arginine-rich (SR) proteins, such as nucleolar protein 3 (NPL3), G-strand binding protein 2 (GBP2) and SR1, are involved in nuclear mRNA export in malaria parasites. However, their functions and cellular localization are not fully understood. In this study, we found that NAB2 and SR1, but not ALY, NPL3 or GBP2, played essential roles in the asexual development of malaria parasites, while GBP2 was involved in gametocyte production. Moreover, GBP2 localized to both the nucleus and cytoplasm of malaria parasites and interacted with the proteins ALBA4, DOZI and CITH, which play roles in translational repression. Our findings suggest that malarial GBP2 may be involved in the recruitment of ALBA4, DOZI and CITH. Immunoprecipitation coupled to mass spectrometry (IP-MS) revealed that PHAX domain-containing protein, an adaptor protein for exportin-1, also interacted with GBP2, suggesting that mRNA export occurs via the PHAX domain-containing protein pathway in malaria parasites. Fluorescence live cell imaging revealed that malarial NAB2 localized at the nuclear periphery and co-localized with NUP205. Moreover, using IP-MS, we found that malarial NAB2 interacted with transportin. RNA immunoprecipitation coupled to RNA sequencing revealed that malarial NAB2 bound directly to 143 mRNAs, including those encoding 40S and 60S ribosomal proteins. This indicates that malarial NAB2 is involved in general mRNA assembly and is shuttled between the nucleus and cytoplasm. Our findings suggest that unique mRNA export and post-transcriptional gene regulation mediated by RNA-binding proteins occur in malaria parasites.
2021-11-03 | PXD027302 | Pride
Project description:Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3’-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export. We use Genome-wide analysis of expression of a conditional degron nab2 mutant that allows the depletion of the protein in 15 minutes, to demosntrate that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is not the result of a secondary effect. Our results identify primary targets of nab2 revealing novel functions for Nab2 in transcription and metabolism of most types of RNAs, not only poly(A) mRNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, being a central player in the general and coordinated control of gene expression from transcription elongation to translation initiation.
2011-12-01 | GSE19302 | GEO
Project description:Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3’-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export. We use Genome-wide analysis of expression of nab2-1 mutant to demosntrate that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is not the result of a secondary effect. Our results identify primary targets of nab2 revealing novel functions for Nab2 in transcription and metabolism of most types of RNAs, not only poly(A) mRNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, being a central player in the general and coordinated control of gene expression from transcription elongation to translation initiation.
2011-12-01 | GSE26303 | GEO
Project description:Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3M-bM-^@M-^Y-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export. We use Genome-wide analysis of expression of nab2-1 mutant to demosntrate that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is not the result of a secondary effect. Our results identify primary targets of nab2 revealing novel functions for Nab2 in transcription and metabolism of most types of RNAs, not only poly(A) mRNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, being a central player in the general and coordinated control of gene expression from transcription elongation to translation initiation. Three repeats of the wild type and nab2-1 mutant
2011-12-01 | E-GEOD-26303 | biostudies-arrayexpress
Project description:Gene expression in eukaryotes is an essential process that includes transcription, pre-RNA processing and RNA export. All these steps are coupled and normally, any failure in one step affects the other steps and could cause nuclear mRNA retention. One important player in this interface is the poly(A)-RNA binding protein Nab2, which regulates the poly(A)-tail length of mRNAs protecting their 3M-bM-^@M-^Y-ends from a second round of polyadenylation and facilitating their nucleo-cytoplasmic export. Interestingly, here we show that Nab2 has additional roles in mRNA transcription elongation, tRNA metabolism and rRNA export. We use Genome-wide analysis of expression of a conditional degron nab2 mutant that allows the depletion of the protein in 15 minutes, to demosntrate that the role of Nab2 in RNAPII transcription and RNAPIII metabolism is not the result of a secondary effect. Our results identify primary targets of nab2 revealing novel functions for Nab2 in transcription and metabolism of most types of RNAs, not only poly(A) mRNAs, indicating that Nab2 function is more ubiquitous than previously anticipated, being a central player in the general and coordinated control of gene expression from transcription elongation to translation initiation. Two and three repeats of the wild type control and the nab2-td mutant respectively at time 0, 30 and 75 minutes after the degron induction.
2011-12-01 | E-GEOD-19302 | biostudies-arrayexpress
Project description:Nab2 encodes a polyadenosine RNA-binding protein (RBP) with broad roles in post-transcriptional regulation, including in RNA export, poly(A) tail length control, and mRNA splicing, and loss of its human ortholog ZC3H14 gives rise to a form of autosomal recessive intellectual disability. Understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part, because no comprehensive identification of metazoan-Nab2-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships likely remain unidentified. Here we present evidence that Drosophila melanogaster Nab2 interacts with the RBP Ataxin-2 (Atx2), a neuronal translational regulator, and implicate these proteins in coordinate regulation of neuronal morphology and adult viability. We then present the first high-throughput identifications of RNAs associating with Nab2 and Atx2 in Drosophila brain neurons using an RNA immunoprecipitation-sequencing (RIP-Seq) approach. Critically, the RNA interactomes of each RBP overlap. The identities of shared associated transcripts (e.g. drk, me31B, stai) and of transcripts specific to Nab2 or Atx2 (e.g. Arpc2, tea, respectively) promise insight into the neuronal functions of and interactions between each RBP. Significantly, we find Nab2 exhibits high specificity in its RNA associations in neurons in vivo, associating with only a fraction of all polyadenylated RNAs. These Nab2-associated RNAs are overrepresented for internal A-rich motifs, suggesting such sequences may partially mediate Nab2 target selection. Taken together, these data demonstrate 1)Nab2 opposingly regulates neuronal morphology and shares associated neuronal RNAs with Atx2 and 2)Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.
2021-02-05 | GSE165677 | GEO
Project description:Transcription profiling was performed on the time course of Nab2 protein depletion in THC-Nab2 strain at 0h, 7h, 12h in biological triplicates to access its affect on the composition and structure of mRNA in budding yeast. For the protein depletion experiment THC-NAB2 (THJ collection Y2484, THC-NAB2:KAN tTA:URA, Open Biosystems) strain was used, where expression of the NAB2 gene is under control of a tetracyclin-repressible promoter.
2013-01-11 | E-MTAB-981 | biostudies-arrayexpress