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CLIP of mRNA capping enzyme CMTR2 in drosophila melanogaster

ABSTRACT: CLIP of mRNA capping enzyme CMTR2 in drosophila melanogaster

PROVIDER: PRJNA577645 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10279650.fastq.gz	Fastqsanger.gz
	SRR10279652.fastq.gz	Fastqsanger.gz
	SRR10279656.fastq.gz	Fastqsanger.gz
	SRR10279658.fastq.gz	Fastqsanger.gz

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CLIP of mRNA capping enzyme CMTR1 in Drosophila melanogaster

Project description:CLIP of mRNA capping enzyme CMTR1 in Drosophila melanogaster

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CLIP of mRNA capping enzyme CMTR2 in drosophila melanogaster

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 CMTR2 enzyme and compared to input RNA.

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CLIP of mRNA capping enzyme CMTR1 in Drosophila melanogaster

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Identification of re-capping substrates for the cytoplasmic capping enzyme complex

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

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Genome-wide study of the MSL1 effect on gene expression and mRNA capping efficiency

Project description:Measurement of capping efficiency (by 5'CAP and 5'noCAP sequencing) in male (S2) and female (Kc) Drosophila melanogaster cells upon depletion of MSL1 by dsRNA compared to the eGFP RNAi control. The measurement of capping efficiency was combined with gene expression measurement by strand specific RNA-Seq in female (Kc) Drosophila melanogaster cells

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Identification of re-capping substrates for the cytoplasmic capping enzyme complex

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 5’ 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 5’-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 5’ ends, and binding or exclusion from a high affinity cap-binding matrix comprised of immobilized eIF4E and the corresponding binding domain of eIF4G.

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Project description:The 5’ cap, catalyzed by capping enzyme, RNGTT, is a vital mRNA modification for the functionality of mRNAs and dysregulated in cancer cells. The m6A writer METTL3 is a regulator of mRNA stability and protein translation, and its expression is altered in various cancers, including lung cancer cells. We identified a METTL3 motif in the mRNA of RNGTT and investigated whether METTL3 could regulate the expression of RNGTT. Knock down of METTL3 resulted in destabilizing RNGTT mRNA, reduced protein expression and activity. Sequencing of capped mRNAs and m7G immunoprecipitation identified an underrepresentation of ribosomal protein mRNA.

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A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function with the Larp7 family member Pof8 in the biogenesis of telomerase

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