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Essential roles of RNA cap-proximal ribose methylation in mammalian embryonic development and fertility

ABSTRACT: Essential roles of RNA cap-proximal ribose methylation in mammalian embryonic development and fertility

PROVIDER: PRJNA985729 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24972800_1.fastq.gz	Fastqsanger.gz
	SRR24972800_2.fastq.gz	Fastqsanger.gz
	SRR24972801_1.fastq.gz	Fastqsanger.gz
	SRR24972801_2.fastq.gz	Fastqsanger.gz
	SRR24972802_1.fastq.gz	Fastqsanger.gz

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Essential roles of RNA cap-proximal ribose methylation in mammalian embryonic development and fertility

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

The mammalian cap-specific m6Am RNA methyltransferase PCIF1 regulates transcript levels in mouse tissues

Project description:The 5' end of eukaryotic mRNAs is protected by the m7G-cap structure. The transcription start site nucleotide is ribose methylated (Nm) in many eukaryotes, while an adenosine at this position is further methylated at the N6 position (m6A) by the mammalian Phosphorylated CTD-interacting Factor 1 (PCIF1) to generate m6Am. Here we show that while loss of cap-specific m6Am in mice does not affect viability or fertility, the Pcif1 mutants display reduced body-weight. Transcriptome analyses of mutant mouse tissues support a role for the cap-specific m6Am modification in stabilizing transcripts. In contrast, the Drosophila Pcif1 is catalytically-dead, but like its mammalian counterpart it retains the ability to associate with the Ser5-phosphorylated CTD of RNA pol II. Finally, we show that the Trypanosoma Pcif1 is an m6Am methylase that contributes to the N6,N6,2?-O-trimethyladenosine (m62Am) in the hypermethylated cap4 structure of Trypanosomatids. Thus, PCIF1 has evolved to function in catalytic and non-catalytic roles.

2020-08-28 | GSE151229 | GEO

Cap 2’-O-ribose methylation is required for reward learning in Drosophila melanogaster

Project description:Cap 2’-O-ribose methylation is required for reward learning in Drosophila melanogaster

| PRJNA477785 | ENA

PAB5 regulation of plant fertility and 5' cap efficiency in pollen development

Project description:PAB5 regulation of plant fertility and 5' cap efficiency in pollen development

| PRJNA398402 | ENA

CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing

Project description:The nuclear cap-binding complex (CBC) stimulates multiple steps in several RNA maturation pathways, but how it functions in humans is incompletely understood. For small capped RNAs like pre-snRNAs, the CBC recruits PHAX. Here, we identify the CBCAP complex, composed of CBC, Ars2 and PHAX, and show that both CBCAP and CBC-Ars2 complexes can be reconstituted from recombinant proteins. Ars2 stimulates PHAX binding to the CBC as well as snRNAs 3'-end processing, hereby coupling maturation with export. In vivo, CBC and Ars2 bind similar capped non-coding and coding RNAs, and stimulate their 3M-bM-^@M-^Y-end processing. Strongest effects are displayed for cap-proximal polyadenylation sites, thereby favoring premature transcription termination. Ars2 functions in part through the mRNA 3M-bM-^@M-^Y-end cleavage factor CLP1, which binds RNA Polymerase II through PCF11. Ars2 is thus a major CBC effector that stimulates functional and cryptic 3'-end processing sites. In total 12 samples; 4 control IP, 2 Flag- Ars2 IP and 2 Flag-CBP20 IP; 2 control FFL siRNA and 2 siRNA Ars2

2013-11-08 | E-GEOD-52131 | biostudies-arrayexpress

Cap 2’-O-ribose methylation is required for reward learning in Drosophila melanogaster

Project description:RNA-seq Quant-seq FWD performed on cap-adjacent methylatransferase mutants and wildtype of drosophila melanogaster.

2021-12-18 | GSE116212 | GEO

CBC-ARS2 stimulates 3'-end maturation of multiple RNA families and favors cap-proximal processing

Project description:The nuclear cap-binding complex (CBC) stimulates multiple steps in several RNA maturation pathways, but how it functions in humans is incompletely understood. For small capped RNAs like pre-snRNAs, the CBC recruits PHAX. Here, we identify the CBCAP complex, composed of CBC, Ars2 and PHAX, and show that both CBCAP and CBC-Ars2 complexes can be reconstituted from recombinant proteins. Ars2 stimulates PHAX binding to the CBC as well as snRNAs 3'-end processing, hereby coupling maturation with export. In vivo, CBC and Ars2 bind similar capped non-coding and coding RNAs, and stimulate their 3’-end processing. Strongest effects are displayed for cap-proximal polyadenylation sites, thereby favoring premature transcription termination. Ars2 functions in part through the mRNA 3’-end cleavage factor CLP1, which binds RNA Polymerase II through PCF11. Ars2 is thus a major CBC effector that stimulates functional and cryptic 3'-end processing sites.

2013-11-08 | GSE52131 | GEO

Transcription profiling by array of Lactobacillus sakei strains grown on ribose or glucose to study ribose catabolism

Project description:We used a whole-genome microarray based on the sequenced strain Lactobacillus sakei 23K to study ribose catabolism in three Lactobacillus sakei strains by screening for differentially expressed genes when grown on ribose compared to glucose

2010-12-01 | E-MEXP-2892 | biostudies-arrayexpress

Ribose utilization by the human commensal Bifidobacterium breve UCC2003

Project description:Growth of B. breve UCC2003 on ribose leads to the transcriptional induction of the rbsACBDK gene cluster. Generation and phenotypic analysis of an rbsA insertion mutant established that the rbs gene cluster is essential for ribose utilization, and that its transcription is likely regulated by a LacI-type regulator encoded by rbsR, located immediately upstream of rbsA. Gel mobility shift assays using purified RbsRHis indicate that the promoter upstream of rbsABCDK is negatively controlled by RbsRHis binding to an 18-bp inverted repeat and that RbsRHis binding activity is modulated by D-ribose. The rbsK gene of the rbs operon of B. breve UCC2003 was shown to specify a ribokinase (EC 2.7.1.15), which specifically directs its phosphorylating activity towards D-ribose, converting this pentose sugar to ribose-5-phosphate. In order to investigate differences in global gene expression upon growth of B. breve UCC2003 on ribose, or a combination of ribose and glucose, as compared to glucose, DNA microarray experiments were performed. Total RNA was isolated from B. breve UCC2003 cultures grown on ribose, a combination of ribose and glucose, or glucose. All experiments were performed in duplicate. A dye swap was performed in one of the two biological replicates.

2010-05-19 | E-GEOD-17325 | biostudies-arrayexpress

Trinucleotide cap analogs with N6-adenosine modifications: interaction partners in HEK293F cell line

Project description:A series of trinucleotide cap analogs functionalized with an amine-terminated linker at the guanosine ribose and immobilized on BrCN-activated Sepharose was prepared. These affinity resins AR-1 (Am), AR-2 (m6Am), and AR-3 (Bn6Am) were incubated with HEK293F cell extract in the presence of GTP to limit non-specific interactions. The pulled-down proteins were eluted with the corresponding trinucleotide cap analog (m7GpppAmpG for AR-1, m7Gpppm6AmpG for AR-2, and m7GpppBn6AmpG for AR-3), digested with trypsin, labeled with isobaric tags (TMT), and analyzed by shotgun proteomics. This experiment was performed in order to assess binding preferences of proteins to the resins AR-1, AR-2, and AR-3.

2024-03-08 | PXD046838 | Pride

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