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Determination of MHV RNA poly(A) tail length and 3' end additions upon NCTC cells infection

ABSTRACT: The mouse hepatitis virus (MHV) genomic and sub-genomic RNAs have 3’ poly(A) tails. The terminal addition of uridines to poly(A) tails has been shown to be a widespread modification. Here, we investigated the presence of 3' end additions on the MHV RNA poly(A) tails. To this end, we infected NCTC cells with MHV and isolated RNA at 24-hours post-infection (hpi). While the median poly(A) tail length of the MHV RNAs is around 50 nucleotides, we observed a peak of uridylation in transcripts with poly(A) tails about 40 nucleotides long

ORGANISM(S): Mus musculus

PROVIDER: GSE200414 | GEO | 2023/03/23

REPOSITORIES: GEO

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Determination of MHV RNA poly(A) tail length and 3' end additions upon 17-CL1 cells infection [17-CL1_WT]

Project description:The mouse hepatitis virus (MHV) genomic and sub-genomic RNAs are 3’ polyadenylated. The length of the 3’ poly(A) tail is known to change during infection, but little is known about the molecular mechanisms driving this change. Here, we investigate the presence of terminal uridylation and terminal guanylation on the MHV poly(A) tail during infection. We infected 17-CL1 cells with MHV and isolated RNA at 24- and 48-hour post-infection (hpi). We observed that MHV RNAs poly(A) tails shortened during infection and that short poly(A) tails of about 20 nucleotides are highly uridylated.

2023-03-23 | GSE200412 | GEO

Determination of MHV virion genome poly(A) tail length and 3' end additions.

Project description:The mouse hepatitis virus (MHV) genomic RNA has a poly(A) tail required for replication. Here we investigated the presence of terminal poly(A) tail uridylation and guanylation in the virion RNA. After isolating the viral RNA followed by sequencing, we found a mean poly(A) tail of 66 nucleotides long with a peak of terminal uridylation on tails 55 to 66 nucleotides long.

2023-03-23 | GSE200415 | GEO

Role of TUT4 and TUT7 on the regulation of MHV poly(A) tail length and 3' end additions [17-CL1_Mutants]

Project description:Terminal uridylation of mRNAs poly(A) tails by Terminal Uridylyl Transferases (TUTs) promote transcript decay. Here, we investigate the role of two functionally redundant mammalian TUTs, TUT4 and TUT7 (TUT4/7), in mouse hepatitis virus (MHV) RNA processing. We generated a TUT4/7 knock-down 17-CL1 cell line using lentivirus encoding shRNAs against Tut4 and Tut7 transcripts (shTUT4/7) and a control 17-CL1 cell line (shCTL) with a non-targeting shRNA. We then infected the shCTL and shTUT4/7 cells with MHV and isolated RNA at 24- and 48-hours post-infection (hpi). We found that viral RNA poly(A) tails of about 20 and 40 nucleotides are highly uridylated and that the uridylation of the 20 nucleotide long tails is dependent on TUT4/7. Depletion of TUT4/7 also resulted in an accumulation of the viral RNA.

2023-03-23 | GSE200413 | GEO

Next generation sequencing identifies polyadenylated species of hTR

Project description:The paired-end next-generation sequencing of all hTR versions of less than 200 nucleotides in length was used to analyze the 3’ end distribution of hTR associated to Flag-tagged versions of PABPN1, hTERT and Dyskerin. In total, we obtained 2,716,342, 3,152,013, and 3,077,395 hTR-specific reads for the PABPN1, hTERT, and Dyskerin purifications, respectively. We found that the majority of polyadenylated telomerase RNA recovered in the PABPN1, hTERT, and Dyskerin purifications had poly(A) tails starting immediately after the annotated hTR 3’ end. However, a greater proportion of poly(A) tails were found on genome-encoded 3’-extentions in the PABPN1-bound fraction compared to the population of hTR that was copurified with hTERT and DKC1: 15.5% for PABPN1, 6.9% for hTERT, and 6.5% for Dyskerin. Notably, the population of polyadenylated telomerase RNA recovered with PABPN1 was significantly different in terms of poly(A) tail length compared to polyadenylated hTR retrieved in the hTERT- and Dyskerin-bound fractions (P-value=5.551e-16, Kolmogorov-Smirnov test), showing a tendency toward longer poly(A) tails in the PABPN1-bound fraction. The enrichment of telomerase RNA with long poly(A) tails in the PABPN1-bound fraction is consistent with a role of PABPN1 in a maturation pathway that depends on hTR 3’ end polyadenylation. Moreover, our results indicate that a fraction of hTERT and Dyskerin are associated with polyadenylated versions of hTR.

2015-10-21 | GSE74186 | GEO

Determination of MHV RNA poly(A) tail length and 3' end additions in infected 17-CL1 and NCTC cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-03-23 | GSE200416 | GEO

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Project description:Ribonucleotidyl transferases (rNTases) add non-templated ribonucleotides to diverse RNAs. We developed a screening strategy in S. cerevisiae to identify sequences added by candidate enzymes from different organisms at single-nucleotide resolution. The rNTase activities of 19 previously unexplored enzymes were determined. In addition to poly(A)- and poly(U)-adding enzymes, we identified a C-adding enzyme that is likely part of a two-enzyme system that adds CCA to tRNAs in a eukaryote; a nucleotidyl transferase that adds nucleotides to RNA without apparent nucleotide preference; and a poly(UG) polymerase, C. elegans MUT-2, which adds alternating U and G nucleotides to form poly(UG) tails. MUT-2 is known to be required for certain forms of RNA silencing, and mutations in the enzyme that are defective in silencing also fail to add poly(UG) tails in our assay. We propose that MUT-2 poly(UG) polymerase activity is required to promote genome integrity and RNA silencing.

2018-12-08 | GSE123478 | GEO

Transcription profiling of mouse brain tissue from three strains infected with mouse hepatitis virus (MHV) for 2 or 5 days

Project description:In this study we explored the antiviral gene expression induced in the CNS of MHV-infected mice, by performing whole-genome expression profiling. Three different mouse strains (BALB/c, 129SvEv and 129SvEv IFNAR-/- mice), differing in their susceptibility to infection with MHV, were used.

2009-10-01 | E-MEXP-2081 | biostudies-arrayexpress

Regulation of poly(A) tail and translation during the somatic cell cycle

Project description:Poly(A) tails are critical for mRNA stability and translation. However, recent studies have challenged this view, showing that poly(A) tail length and translation efficiency are decoupled in non-embryonic cells. Using TAIL-seq and ribosome profiling, we investigate poly(A) tail dynamics and translational control in the somatic cell cycle. We find dramatic changes in poly(A) tail lengths of cell cycle regulatory genes like CDK1, TOP2A, and FBXO5, explaining their translational repression in M phase. We also find that poly(A) tail length is coupled to translation when the poly(A) tail is <20 nucleotides. However, as most genes have >20 nucleotide poly(A) tails, their translation is regulated mainly via poly(A) tail length-independent mechanisms during the cell cycle. Specifically, we find that terminal oligopyrimidine (TOP) tract-containing transcripts escape global translational suppression in M phase and are actively translated. Our quantitative and comprehensive data provide a revised view of translational control in the somatic cell cycle. HeLa cells were synchronized at S or M phase, and subject to RNA-seq, ribosome profiling and TAIL-seq analysis.

2016-04-04 | E-GEOD-79664 | biostudies-arrayexpress

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