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Transcriptome-wide mapping of internal mRNA N7-methylguanosine in sporulated and unsporulated oocysts of Eimeria tenella reveals stage-specific signatures

ABSTRACT: Transcriptome-wide mapping of internal mRNA N7-methylguanosine in sporulated and unsporulated oocysts of Eimeria tenella reveals stage-specific signatures

PROVIDER: PRJNA1124552 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29686904_1.fastq.gz	Fastqsanger.gz
	SRR29686904_2.fastq.gz	Fastqsanger.gz
	SRR29686905_1.fastq.gz	Fastqsanger.gz
	SRR29686905_2.fastq.gz	Fastqsanger.gz
	SRR29686906_1.fastq.gz	Fastqsanger.gz

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Transcriptome-wide mapping of internal mRNA N7-methylguanosine in sporulated and unsporulated oocysts of Eimeria tenella reveals stage-specific signatures

Project description:Growing evidence indicates that 7-methylguanosine (m7G) modification plays critical roles in epigenetic regulation. However, no data regarding m7G modification are currently available in Eimeria tenella, a highly virulent species causing coccidiosis in chickens. Thus, in the present study, we explored the distribution of internal mRNA m7G modification in sporulated and unsporulated oocysts of E. tenella as well as its biological functions during oocyst development. Our data showed that m7G peaks were detected throughout the whole mRNA body, and the coding DNA sequence (CDS) region displayed the most methylation modification. Compared with unsporulated oocysts, 7799 hypermethylated peaks and 1945 hypomethylated peaks were identified in sporulated oocysts. Further combined analysis of differentially methylated genes (DMGs) and differentially expressed genes (DEGs) showed that there was a positive correlation between m7G modification levels and gene transcript abundance. Unsurprisingly, the mRNA sequencing (RNA-seq) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) data showed a good consistence with the results of the quantitative reverse transcription PCR (RT-qPCR) and MeRIP-qPCR, respectively. Gene Ontology (GO) and pathway enrichment analysis of DEGs with altered m7G-methylated peaks were involved in diverse biological functions and pathways, including DNA replication, RNA transport, spliceosome, autophagy-yeast, and cAMP signaling pathway. Altogether, our findings revealed the potential significance of internal m7G modification in E. tenella oocysts, providing some directions and clues for later in-depth research.

2024-06-23 | GSE269982 | GEO

Quantitative phosphoproteomic analysis of Eimeria tenella six stages (unsporulated oocysts (USO), partial sporulated 7 h oocysts (SO7h), sporulated oocysts (SO), sporozoites (S), second generation merozoite (M2) and gametocyte (G))

Project description:we performed a comprehensive, quantitative phosphoproteomic profile analysis of six stages of the E. tenella life cycle: unsporulated oocysts (USO), partial sporulated 7 h oocysts (SO7h), sporulated oocysts (SO), sporozoites (S), second generation merozoite (M2) and gametocyte (G). The results revealed significant changes in the abundance of phosphoproteins during E. tenella development. The findings shed light on the key roles of protein phosphorylation and dephosphorylation in the E. tenella life cycle.

2022-02-16 | PXD029545 | Pride

Comprehensive analysis of mRNA N6-methyladenosine modification in Eimeria tenella unsporulated oocysts and sporulated oocysts

Project description:N6-methyladenosine (m6A) modification, one of the most abundant RNA modification forms, is associated with almost all the aspects of RNA metabolism. In the present study, we surveyed the transcriptome-wide prevalence of m6A in sporulated oocysts and unsporulated oocysts of E. tenella. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) analysis showed that m6A modifications were most abundant in the coding sequence, followed by stop codon. There were 3903 hypermethylated and 3178 hypomethylated mRNAs in sporulated oocysts compared with unsporulated oocysts. Further joint analysis suggested that m6A modifications of the majority of genes were positively correlated with mRNA expression. The mRNA relative expression and m6A level of the selected genes were confirmed by quantitative reverse transcription PCR (RT-qPCR) and MeRIP-qPCR. GO and KEGG analysis indicated that differentially m6A methylated genes with significant differences in expression were closely related to processes such as regulation of gene expression, epigenetic, microtubule, autophagy-other and TOR signaling. Moreover, a total of 96 differentially expressed m6A genes without significant differences in expression showed significant differences at protein level. GO and pathway enrichment analysis of the 96 genes showed that RNA methylation may be involved in cell biosynthesis and metabolism of E. tenella.

2022-12-22 | GSE221214 | GEO

Comprehensive analysis of mRNA 5-methylcytosine modification in Eimeria tenella oocysts

Project description:5-methylcytosine (m5C) is a type of RNA modifications reported to regulate diverse biological processes. However, the distribution and biological functions of m5C in E. tenella mRNAs remain largely unknown. Herein, we report transcriptome-wide profiling of mRNA m5C in E. tenella by applying m5C RNA immunoprecipitation followed by a deep-sequencing approach (m5C-RIP-seq). Our data showed that m5C peaks were distributed across the whole mRNA body. There were 2813 hypermethylated and 1850 hypomethylated m5C peaks in sporulated oocysts compared with unsporulated oocysts. Further joint analysis showed a positive correlation between m5C modification and gene expression levels. The mRNA sequencing and m5C-RIP-seq data were consistent with the results of the quantitative reverse transcription PCR (RT-qPCR) and m5C-RIP-qPCR, respectively. Gene ontology (GO) and pathway enrichment analysis predicated diverse biological functions and pathways, including microtubule motor activity, helicase activity, cGMP-PKG signaling pathway, aminoacyl-tRNA biosynthesis, glycolysis/gluconeogenesis and spliceosome. Meanwhile, stage-specific gene expression signatures of m5C-related enzymes were observed. Altogether, our findings revealed the transcriptional significance of m5C modification in E. tenella oocysts, providing clues for in-depth research.

2023-12-19 | GSE249232 | GEO

Identification of potential readers for eukaryotic internal mRNA N7-methylguanosine (m7G) modification

Project description:The project aims to identify the RNA binding proteins that can specifically bind to mRNA internal modification N7-methylguanosine (m7G). N7-methylguanosine (m7G) methylation has been long identified as the essential cap modification for eukaryotic mRNA, but later has been identified internally in various types of RNAs, including tRNA, rRNA, miRNA, and mRNA. While the METTL1/WDR4 complex, responsible for tRNA m7G installation, has been suggested to be responsible for internal mRNA modification as well, little is known about the proteins that can identify and interact with m7G. To better understand its interaction with RNA binding proteins and further define its regulatory function in mRNA metabolism, we performed the experiment to pulldown proteins with different binding affinity on unmodified G and m7G and subject the enriched fractions to mass spectrometry.

2024-09-03 | PXD049390 | Pride

Transcriptome Mapping of Internal N7-methylguanosine modification via m7G MeRIP-seq [m7g.2]

Project description:Previous study found the presence of internal N7-methylguanosine (m7G) within mammalian mRNA. We performed antibody-based m7G MeRIP-seq for transcriptome-wide mapping the internal m7G sites in U2OS cells.

2023-05-17 | GSE192845 | GEO

Transcriptome Mapping of Internal N7-methylguanosine modification via m7G MeRIP-seq [m7g.1]

2023-05-17 | GSE192844 | GEO

Comprehensive analysis of mRNA N6-methyladenosine modification in Eimeria tenella unsporulated oocysts and sporulated oocysts

Project description:Comprehensive analysis of mRNA N6-methyladenosine modification in Eimeria tenella unsporulated oocysts and sporulated oocysts

| PRJNA913413 | ENA

Transcriptome Mapping of Internal N7-methylguanosine Methylome in Mammalian mRNA

Project description:N7-methylguanosine (m7G) is a positively charged, essential modification at the 5′ cap of eukaryotic mRNA, regulating mRNA export, translation, and splicing. m7G also occurs internally within tRNA and rRNA, but its existence and distribution within eukaryotic mRNA remain to be investigated. Here, we show the presence of internal m7G sites within mammalian mRNA. We then performed transcriptome-wide profiling of internal m7G methylome using m7G-MeRIP sequencing (MeRIP-seq). To map this modification at base resolution, we developed a chemical-assisted sequencing approach that selectively converts internal m7G sites into abasic sites, inducing misincorporation at these sites during reverse transcription. This base-resolution m7G-seq enabled transcriptome-wide mapping of m7G in human tRNA and mRNA, revealing distribution features of the internal m7G methylome in human cells. We also identified METTL1 as a methyltransferase that installs a subset of m7G within mRNA and showed that internal m7G methylation could affect mRNA translation.

2019-04-26 | GSE112276 | GEO

Comparative analysis of Gallus gallus cecal epithelia following Eimeria tenella infection

Project description:Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays. We used Affymetrix GeneChip chicken genome arrays to detail the chicken cecal epithelia gene expression in the control and E. tenella-infected birds.

2012-12-10 | GSE39602 | GEO

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