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Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

ABSTRACT: Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

PROVIDER: PRJNA610259 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11236400.fastq.gz	Fastqsanger.gz
	SRR11236401.fastq.gz	Fastqsanger.gz
	SRR11236402.fastq.gz	Fastqsanger.gz
	SRR11236403.fastq.gz	Fastqsanger.gz
	SRR11236404.fastq.gz	Fastqsanger.gz

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Similar Datasets

Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

Project description:The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a noncanonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5′-ends. The modification percentage of transcripts is low (<5%). NAD incorporation occurs mainly during transcription initiation by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3′-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs are not translatable in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be disadvantageous to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

2020-04-28 | GSE146368 | GEO

Extensive 5'-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast.

Project description:The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5'-ends. The modification percentage of transcripts is low (<5%). NAD incorporation occurs mainly during transcription initiation by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3'-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs are not translatable in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be disadvantageous to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

| S-EPMC7606564 | biostudies-literature

NADcapPro Seq and CircNAD –Methods for Accurate Profiling of NAD and Non-Canonical RNA Caps in Eukaryotes

Project description:Accurate identification of NAD-capped RNAs is essential for understanding their biological function. Previous transcriptome-wide methods used to profile NAD-capped RNAs contain inherent limitations of having hindered the accurate identification of NAD caps from eukaryotic RNAs. Herein we introduced two novel orthogonal methods to precisely identify NAD-capped RNAs. One is D-SPAAC, a copper-free click-chemistry-based approach, and the second is an intramolecular ligation-based circNAD to resolve implicit limitations of the previous methods, which enabled us to unravel unforeseen features of NAD RNAs in budding yeast. Contrary to previous reports, we find that 1) cellular NAD RNAs can be full-length and polyadenylated transcripts, 2) transcription start sites for NAD-capped and canonical m7G-capped RNAs are different, and 3) NAD caps can be added post-transcriptionally. Moreover, we uncovered a dichotomy of NAD RNAs in translation where NAD RNAs are detected with mitochondrial ribosomes but not cytoplasmic ribosomes indicating their propensity to be translated in mitochondria.

2023-03-17 | GSE217259 | GEO

NADcapPro Seq and CircNAD –Methods for Accurate Profiling of NAD and Non-Canonical RNA Caps in Eukaryotes

Project description:NADcapPro Seq and CircNAD –Methods for Accurate Profiling of NAD and Non-Canonical RNA Caps in Eukaryotes

| PRJNA898308 | ENA

Presence of NAD+-capped RNA in human cells: function and removal by the DXO deNADing Protein

Project description:Eukaryotic mRNAs generally possess an N7 methyl guanosine cap at their 5? end to promote their translation and stability. Here we demonstrate mammalian mRNAs can carry a 5'-end nicotinamide adenine dinucleotide (NAD+) cap. We further demonstrate fungal and mammalian noncanonical DXO family of decapping enzymes can efficiently remove NAD+ caps from mRNAs in vitro and cocrystal structures of DXO with 3´ phosphate NAD+ illuminates the molecular mechanism for the “deNADing” reaction. An NAD+ cap promotes mRNA decay in wild type mammalian cells and confers mRNA stability in the absence of DXO. Importantly, mammalian cells possess a capping mechanism that NAD+ caps a subset of intronic small nucleolar RNAs that are selectively enriched in DXO deficient cells. Our data establish NAD+ as a bona fide mammalian RNA cap and identifies the DXO proteins as potent deNADing enzymes that modulate the levels of NAD+-capped RNAs in cells.

2017-03-09 | GSE90884 | GEO

HIV-1 infection affects NAD capping of host cell snRNA and snoRNA

Project description:NAD besides its key role in cellular metabolism can serve as an alternative 5’ cap at several short non-coding RNAs. However, the function of the NAD cap remains elusive. Here, we investigate NAD capping of RNAs upon HIV-1 infection, which is associated with intracellular pellagra – depletion of NAD/NADH cellular pool. We applied NAD captureSeq on HIV-1 infected/noninfected cells and we revealed that four snRNAs (U1, U4ATAC, U5E and U7) and four snoRNAs (snord3G, snord102, snorA50A and snord3B) lost NAD cap upon HIV-1 infection. Interestingly, U1 snRNA was previously shown to be essential for HIV-1 replication. We provide evidence that the NAD cap reduces the stability of the U1 - HIV-1 pre-mRNA duplex. The importance of NAD RNA cap in HIV-1 infection was further supported by NAD decapping enzyme DXO overexpression, which led to increase in HIV-1 infectivity. This is the first example of NAD cap function in mammalian cells and suggests a general role of non-canonical RNA caps in antiviral innate immunity response.

2024-05-16 | GSE191019 | GEO

Decapping enzyme NUDT12 partners with BLMH for cytoplasmic surveillance of NAD-capped RNAs

Project description:RNA polymerase II transcripts receive a protective 5ʹ m7G cap early during transcription. An alternative cap can be acquired when RNA pol II initiation uses the redox cofactor nicotinamide adenine dinucleotide (NAD) to generate NAD-capped RNAs. The biology of mammalian NAD-RNAs, including its turnover and physiological roles are not completely understood. Here we identify NUDT12 as a cytosolic decapping enzyme for NAD-RNAs. Structural, biochemical and functional studies reveal how homodimerization modulates specificity of NUDT12 for NAD-RNAs as substrate. NUDT12 is localized within a few discrete cytoplasmic granules that are distinct from P-bodies. We identity Bleomycin hydrolase (BLMH) as a factor that associates with NUDT12 in a large ~600 kDa dodecamer complex, and we demonstrate that BLMH is required for correct localization of NUDT12 into these granules. This complex is functional in human cell cultures, as artificial tethering of BLMH to a reporter mRNA results in downregulation of reporter expression, similar to that seen with tethering of NUDT12. Analysis of mouse liver transcriptome from the Nudt12 knockout mouse reveals that a select set of RNAs are regulated, including a significant upregulation of circadian clock transcripts. Given that NAD biosynthesis is under circadian control, our study points to a physiological role for the cytosolic surveillance of NAD-RNAs.

2019-12-25 | GSE138019 | GEO

Transcription profiling of brains from honey bees guards of different subspecies and host colony environment

Project description:Expression profiling of guards brains as a function of individual genotype (AHB/EHB) and environment (AHB/EHB host colony)

2009-07-01 | E-TABM-606 | biostudies-arrayexpress

Transcriptional profiling of Xenopus laevis animal caps overexpressing MyoD

Project description:mRNa encoding for XtMyoD was overexpressed in animal caps and the transcriptional profile of uninjected and injected animal caps was compared.

2011-06-22 | E-MEXP-3273 | biostudies-arrayexpress

Xenopus laevis embryos and animal caps: Control vs PouV morpholino

Project description:Transcriptional profiling of Xenopus laevis embryos and ectoderm (animal caps) comparing embryos injected with control morpholino with embryos injected with the morpholino mixture PVD2, which knocks down all three Xenopus PouV proteins. Whole embryos (WE) or animal caps (AC) were collected at late blastula (9) or early gastrula (10) stages from Control and PVD2 morphants. Two conditions: Control vs. PouV morpholino; Two tissues: whole embryos, animal caps .Two timepoints: stage 9 and 10. Biological replicates: 2 control replicates at stage 9 and 10 for whole embryos, 2 control replicates at stage 9 and 10 for animal caps, 2 PVD2 morpholino replicates at stage 9 and 10 for whole embryos, 2 control replicates at stage 9 and 10 for animal caps

2013-11-12 | E-GEOD-47578 | biostudies-arrayexpress

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