CLIP of mRNA capping enzyme CMTR2 in drosophila melanogaster
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE138868 | GEO | 2021/12/18
REPOSITORIES: GEO
Similar Datasets
Project description:The mRNA cap structure consists of the m7G "cap0" linked to the 5'-most nucleotide of the initial mRNA. The first two nucleotides of mRNA can be 2'-O-Ribose modified to form cap1 or cap2 structures. Here, mRNA was sequenced after CLIP with tagged recombinant CMTR1 and compared to input RNA.
2021-12-18 | GSE181321 | GEO
Project description:The mRNA cap structure is a major site of dynamic mRNA methylation. mRNA caps exist in either the Cap1 or Cap2 form, depending on the presence of 2’-O-methylation on the first, or both the first and second transcribed nucleotide, respectively. However, the identity of Cap2-containing mRNAs and the function of Cap2 are unclear. Here we describe CLAM-Cap-Seq, a method for transcriptome-wide mapping and quantification of Cap2. We find that unlike other epitranscriptomic modifications, Cap2 can occur on all mRNAs. Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol. As a result, Cap2 is enriched on long-lived mRNAs. We find that large increases in the abundance of Cap1 leads to activation of RIG-I, especially in conditions where RIG-I expression is increased. The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG-I. We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs. Overall, these results reveal an immunostimulatory role for Cap1, and that Cap2 functions to reduce activation of the innate immune response.
2022-12-12 | GSE196043 | GEO
Project description:Eukaryotic RNA pol II transcripts are capped at the 5′ end by the methylated guanosine (m7G) moiety. In higher eukaryotes, CMTR1 and CMTR2 catalyse cap-proximal ribose methylations on the first (cap1) and second (cap2) nucleotides, respectively. These modifications mark RNAs as ‘self’, blocking the activation of the innate immune response pathway. Here we show that loss of mouse Cmtr1 or Cmtr2 leads to embryonic lethality, with non-overlapping sets of transcripts being regulated, without activation of the interferon pathway. In contrast, Cmtr1 mutant adult mouse livers exhibit a chronic activation of the interferon pathway, with multiple interferon-stimulated genes (ISGs) being expressed. Conditional deletion of Cmtr1 in the male germline leads to infertility, while global translation is unaffected in the Cmtr1 mutant mouse liver and human cells. Thus, mammalian cap1 and cap2 modifications have an essential role in embryonic gene regulation that is independent of their established role in evading the innate immune system.
2023-07-14 | GSE235348 | GEO
Project description:Eukaryotic mRNA 5’ end is decorated with cap structure which plays multiple roles in the cell. Most importantly, protects transcript from exonucleolytic degradation and enables translation of encoded protein conducted by cap-dependent machinery. This is also a key feature in the process of recognizing RNA as self or non-self molecule by cellular innate immune system. Cap is composed of 7-methylguanosine linked by a 5′,5′-triphosphate chain to the first transcribed nucleotide, and is formed enzymatically during transcription. This m7GpppN structure, called cap0, can be further modified by CMTR1 methyltransferase to cap1 (m7GpppNm), which predominates in eukaryotic cells. Cap2, with additional 2′-O-methylation at the second transcribed nucleotide (m7GpppNmpNm) added by another methyltransferase CMTR2, also can be found at mRNA 5’ end. We present new tools allowing for in vitro synthesis of RNAs possessing cap2, i.e tetranucleotide cap analogues. Utilizing these for in vitro transcription reactions we obtained RNAs with 2′-O-methylation present at the second transcribed nucleotide. Due to that we investigated the role of cap2 in protein production from reporter mRNA protected with this structure in different conditions, normal or stress ones, or with CMTR1/2 down regulated level. We also assessed the affinity of eIF4E protein to differentially capped RNAs. Furthermore, we verified whether an additional 2′-O-methylation presence in capped RNA makes transcript more resistant to decapping enzyme action.
2022-09-08 | PXD028636 | Pride
Project description:Eukaryotic mRNA 5’ end is decorated with cap structure which plays multiple roles in the cell. Most importantly, protects transcript from exonucleolytic degradation and enables translation of encoded protein conducted by cap-dependent machinery. This is also a key feature in the process of recognizing RNA as self or non-self molecule by cellular innate immune system. Cap is composed of 7-methylguanosine linked by a 5′,5′-triphosphate chain to the first transcribed nucleotide, and is formed enzymatically during transcription. This m7GpppN structure, called cap0, can be further modified by CMTR1 methyltransferase to cap1 (m7GpppNm), which predominates in eukaryotic cells. Cap2, with additional 2′-O-methylation at the second transcribed nucleotide (m7GpppNmpNm) added by another methyltransferase CMTR2, also can be found at mRNA 5’ end. We present new tools allowing for in vitro synthesis of RNAs possessing cap2, i.e tetranucleotide cap analogues. Utilizing these for in vitro transcription reactions we obtained RNAs with 2′-O-methylation present at the second transcribed nucleotide. Due to that we investigated the role of cap2 in protein production from reporter mRNA protected with this structure in different conditions, normal or stress ones, or with CMTR1/2 down regulated level. We also assessed the affinity of eIF4E protein to differentially capped RNAs. Furthermore, we verified whether an additional 2′-O-methylation presence in capped RNA makes transcript more resistant to decapping enzyme action.
2022-09-08 | PXD028635 | Pride
Project description:CLIP of mRNA capping enzyme CMTR1 in Drosophila melanogaster
| PRJNA751571 | ENA
Project description:CLIP of mRNA capping enzyme CMTR2 in drosophila melanogaster
| PRJNA577645 | ENA
Project description:Eukaryotic messenger RNAs (mRNAs) possess a 5’-end N7-methyl guanosine (m7G) cap that promotes their translation and stability. However, it was recently demonstrated that eukaryotic mRNAs can also carry a 5' end nicotinamide adenine dinucleotide (NAD+) cap that promotes mRNA decay mediated by the NAD+ decapping enzyme DXO1. However, the dynamic regulation of NAD+ capping in plant remains unknown. Here, we describe the global landscape of NAD+-capped RNAs in Arabidopsis thaliana, and demonstrate that DXO1 is responsible for removal of these 5’-end modifications and facilitates mRNA degradation in plant transcriptomes. We also reveal that in the absence of DXO1 NAD+-capped mRNAs are unstable and processed into smRNAs. Furthermore, we find that Abscisic Acid (ABA) remodel the landscape of RNA cap epitransciptome, and the mRNA lost their NAD+ cap contribute to their stability under ABA. Overall, our results support a link between ABA response and RNA NAD+ capping.
2020-11-23 | GSE142389 | GEO
Project description:Eukaryotic messenger RNAs (mRNAs) possess a 5’-end N7-methyl guanosine (m7G) cap that promotes their translation and stability. However, it was recently demonstrated that eukaryotic mRNAs can also carry a 5' end nicotinamide adenine dinucleotide (NAD+) cap that promotes mRNA decay mediated by the NAD+ decapping enzyme DXO1. However, the dynamic regulation of NAD+ capping in plant remains unknown. Here, we describe the global landscape of NAD+-capped RNAs in Arabidopsis thaliana, and demonstrate that DXO1 is responsible for removal of these 5’-end modifications and facilitates mRNA degradation in plant transcriptomes. We also reveal that in the absence of DXO1 NAD+-capped mRNAs are unstable and processed into smRNAs. Furthermore, we find that Abscisic Acid (ABA) remodel the landscape of RNA cap epitransciptome, and the mRNA lost their NAD+ cap contribute to their stability under ABA. Overall, our results support a link between ABA response and RNA NAD+ capping.
2020-11-23 | GSE142388 | GEO
Project description:The analysis of capped RNAs by massively parallel sequencing has identified a large number of previously unknown transcripts, some of which are small RNAs and others are 5M-bM-^@M-^Y truncated forms of RefSeq genes. The latter may be generated by endonuclease cleavage or by stalling of Xrn1 at defined sites. With the exception of promoter-proximal transcripts the caps on all of these are added post-transcriptionally by a cytoplasmic capping enzyme complex that includes capping enzyme and a kinase that converts 5M-bM-^@M-^Y-monophosphate ends to a diphosphate capping substrate. We previously described a modified form of capping enzyme with dominant negative activity against cytoplasmic capping (DN-cCE). A tet-inducible form of this was used to identify substrates for cytoplasmic capping by treating cytoplasmic RNA from control and induced cells with and without Xrn1. Surviving RNA was analyzed on Affymetrix Human Exon 1.0 arrays and scored for changes in probe intensity as a function of its position on each RefSeq gene to derive a factor (alpha) that could be compared between sets. Notably, transcriptome-wide changes were not evident unless RNA was treated with Xrn1. This analysis identified 2,666 uncapped mRNAs in uninduced cells, 672 mRNAs that appeared in the uncapped pool in cells expressing DN-cCE, and 835 mRNAs that were in both populations. Changes in cap status of 10 re-capping targets and 5 controls were assessed by 3 independent measures; susceptibility to Xrn1, recovery with a biotin-tagged DNA primer after ligating a complementary RNA oligonucleotide to uncapped 5M-bM-^@M-^Y ends, and binding or exclusion from a high affinity cap-binding matrix comprised of immobilized eIF4E and the corresponding binding domain of eIF4G. 3 biological replicates of 4 different samples comparing XRN1 treatment/non-treatment and Dox induction/non-induction of K294A
2012-12-20 | E-GEOD-36729 | biostudies-arrayexpress