Similar Datasets
Project description:Background: Colorectal cancer (CRC) is a harmful cancer with high morbidity and poor prognosis. There is growing evidence that RNA methylation is closely related to the occurrence of cancer and its malignant biological behavior. N6-methyladenosine (m6A) methylation is the most common RNA modification in eukaryotes, and its multiple regulatory mechanisms in CRC have been elucidated from multiple perspectives. At the same time, the role of 5-methylcytosine (m5C), another important and widely distributed methylation modification, in CRC is far from being elucidated. Methods: In this study, we used RNA immunoprecipitation sequencing combined with bioinformatics methods to identify the m5C peaks on messenger RNA (mRNA) in HCT15 cells and sh-NSUN2 HCT15 cells, understand which transcripts are modified by m5C, and characterize the distribution of m5C modifications. In addition, we performed further bioinformatics analysis of the detected data to initially clarify the potential function of these m5C-modified transcripts. Results: We found significant differences in the distribution of m5C between HCT15 cells and sh-NSUN2 HCT15 cells, suggesting that m5C is likely to play a key role in the occurrence and development of CRC. Furthermore, Gene Ontology (GO) enrichment analysis showed that genes altered by m5C were mainly enriched in phylogeny, synaptic membrane, and transcription factor binding.The Kyoto Encyclopedia of Genes and Genomes（KEGG）pathway analysis showed that the genes altered by m5C are enriched in ECM receptor interaction pathway, the circadian pathway, and the cAMP signaling pathway. Conclusions: Here, our study preliminarily revealed the different distribution patterns of m5C between HCT15 cell and sh-NSUN2 HCT15 cell. Our results open a new window to understand the role of m5C RNA methylation of mRNA in the development of CRC.
2023-03-02 | GSE226129 | GEO
Project description:5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. falciparum) malaria parasites transcriptome and depicted a comprehensive characterization landscape of m5C mRNA modification at single-nucleotide resolution (RNA-BisSeq) from asexual replicating stage to gametocyte development. Through transcriptome-wide profiling of mRNA m5C modification, we found that m5C modified mRNA displayed higher stability than non-m5C modified mRNA during the development of Plasmodium. We identified Plasmodium ortholog of NSUN2 as an mRNA m5C methyltransferase in malaria parasites. LC–MS/MS and RNA-BisSeq analysis revealed a large decrease in mRNA m5C modification at transcriptome-wide level upon Nsun2 knockout. Absence of Nsun2 severely reduced gametocyte production in either rodent (P. yoelii) or human (P. falciparum) malaria parasites. Meanwhile, some genes related to gametocytogenesis displayed a great reduction of m5C modification. Together, our data provides comprehensive mRNA m5C profiles in Plasmodium genus and reveals m5C modification-mediated mRNA stability as a novel mechanism regulating sexual differentiation of a unicellular eukaryote.
2022-02-08 | GSE159126 | GEO
Project description:5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. falciparum) malaria parasites transcriptome and depicted a comprehensive characterization landscape of m5C mRNA modification at single-nucleotide resolution (RNA-BisSeq) from asexual replicating stage to gametocyte development. Through transcriptome-wide profiling of mRNA m5C modification, we found that m5C modified mRNA displayed higher stability than non-m5C modified mRNA during the development of Plasmodium. We identified Plasmodium ortholog of NSUN2 as an mRNA m5C methyltransferase in malaria parasites. LC–MS/MS and RNA-BisSeq analysis revealed a large decrease in mRNA m5C modification at transcriptome-wide level upon Nsun2 knockout. Absence of Nsun2 severely reduced gametocyte production in either rodent (P. yoelii) or human (P. falciparum) malaria parasites. Meanwhile, some genes related to gametocytogenesis displayed a great reduction of m5C modification. Together, our data provides comprehensive mRNA m5C profiles in Plasmodium genus and reveals m5C modification-mediated mRNA stability as a novel mechanism regulating sexual differentiation of a unicellular eukaryote.
2022-02-08 | GSE159125 | GEO
Project description:5-methylcytosine (m5C) is emerging as an important epi-transcriptome modification involving RNA stability and translation efficiency in various biological processes. However, it remains unclear how m5C contributes to the dynamic regulation of transcriptome during the development of Plasmodium. Here, we identified the presence of 5-methylcytosine (m5C) modification in rodent (P. yoelii) and human (P. falciparum) malaria parasites transcriptome and depicted a comprehensive characterization landscape of m5C mRNA modification at single-nucleotide resolution (RNA-BisSeq) from asexual replicating stage to gametocyte development. Through transcriptome-wide profiling of mRNA m5C modification, we found that m5C modified mRNA displayed higher stability than non-m5C modified mRNA during the development of Plasmodium. We identified Plasmodium ortholog of NSUN2 as an mRNA m5C methyltransferase in malaria parasites. LC–MS/MS and RNA-BisSeq analysis revealed a large decrease in mRNA m5C modification at transcriptome-wide level upon Nsun2 knockout. Absence of Nsun2 severely reduced gametocyte production in either rodent (P. yoelii) or human (P. falciparum) malaria parasites. Meanwhile, some genes related to gametocytogenesis displayed a great reduction of m5C modification. Together, our data provides comprehensive mRNA m5C profiles in Plasmodium genus and reveals m5C modification-mediated mRNA stability as a novel mechanism regulating sexual differentiation of a unicellular eukaryote.
2022-02-08 | GSE159124 | GEO
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
Project description:The 5-methylcytosine (m5C) modification is present at appreciable amounts in the mammalian transcriptome, but its precise location and function is still poorly understood. Here, we identify high m5C levels and map their locations in a model retrovirus, the murine leukemia virus, and show that the ALYREF m5C reader protein regulates viral replication. Our results reveal a single-nucleotide m5C profile in a virus and its function in a eukaryotic mRNA.
2020-04-14 | GSE139606 | GEO
Project description:5-methylcytosine modification profiling of messenger RNA in breast cancer brain metastasis
| PRJNA1034491 | ENA
Project description:Compared with the well-studied 5-methylcytosine (m5C) in DNA, the role of m5C in mRNA remains elusive as existing studies of RNA m5C are largely confined to rRNA and tRNA. Using bisulfite sequencing (BS-Seq) approach, we profiled transcriptome-wide m5C and found that RNA m5C modification is enriched and conserved at 5’UTRs in human and mouse. Through a comparative analysis of the mRNA and DNA methylome, we demonstrate that like DNA methylation, RNA m5C methylation exhibits a strong clustering. Surprisingly, mRNA Cytosine-5 methylation inversely correlates with DNA methylation under CpG context, which suggests a synergic regulatory effect. Importantly, comparison of the global RNA m5C methylome of breast cancer cells with normal mammary epithelial cells revealed that breast cancer methylome is predominantly hypomethylated and several breast cancer-related genes are differentially methylated. Despite global hypomethylation, 5’UTR of differentially methylated genes contain higher percentage of m5C. Taken together, this study provides a first-in-depth characterization of transcriptome-wide m5C modification. Furthermore, our findings showing differential m5C methylation pattern in normal and cancer cells suggest a vital role m5C methylation may play in the post transcriptional regulation of key pro-tumorigenic genes. Sample Preparation and RNA Bisulfite Sequencing: MCF10A and MDA-MB-468 (MDA468) cells were obtained from ATCC. Cells were cultured and maintained in DMEM media as per ATCC instructions. For BS-Seq total RNA was isolated from MCF10A and MDA_MB-468 cells and was enriched for polyA+ RNA using poly-A selection kits. The purified RNA is subjected to sodium bisulfite treatment at 60 degrees for 8 hours. The bisulfite-treated RNA was then reverse transcribed was subjected to deep-sequencing using Illumina RNA-Seq protocol.
2017-07-11 | GSE84230 | GEO
Project description:In order to fulfil a wide range of cellular functions, RNA molecules contain, in addition to the four canonical bases, a large number of chemically modified structures. Among those, the methylation of carbon-5 of cytosines (m5C) is an abundant, widespread mark in different classes of RNAs. m5C is catalysed by DNMT2 and by seven members of the NSUN family of enzymes. While some m5C-methyltransferases have been studied individually and implicated in phenotypes observed in organisms ranging from yeast to humans, it remains unclear how the m5C methylome acts to sustain development in homeostasis and stress. Here, using Caenorhabditis elegans as a model organism, we developed the first organism devoid of detectable m5C in RNA, providing strong evidence that this modification and its derivatives are non-essential for the nematode’s development and fertility under standard laboratory conditions. We further used this genetic tool to determine the localisation of m5C sites in different RNA classes, and showed that NSUN-4 acts as a multisite-specific tRNA/rRNA methyltransferase in the mitochondria. In addition, we show that m5C is required for adaptation to temperature changes, as animals devoid of this modification present temperature-sensitive fertility defects. At the molecular level, we show that loss of m5C leads to increased ribosome pausing at triplets encoding for leucine and proline, the most frequently methylated tRNA isoacceptors in C. elegans. This is correlated with reduced translation efficiency of transcripts enriched in these amino acids. Finally, we found translation of Leu-UUG codons to be the most strongly affected upon heat shock, suggesting a role of m5C wobble methylation in the adaptation to heat stress.
2020-06-30 | GSE146256 | GEO
Project description:In order to fulfil a wide range of cellular functions, RNA molecules contain, in addition to the four canonical bases, a large number of chemically modified structures. Among those, the methylation of carbon-5 of cytosines (m5C) is an abundant, widespread mark in different classes of RNAs. m5C is catalysed by DNMT2 and by seven members of the NSUN family of enzymes. While some m5C-methyltransferases have been studied individually and implicated in phenotypes observed in organisms ranging from yeast to humans, it remains unclear how the m5C methylome acts to sustain development in homeostasis and stress. Here, using Caenorhabditis elegans as a model organism, we developed the first organism devoid of detectable m5C in RNA, providing strong evidence that this modification and its derivatives are non-essential for the nematode’s development and fertility under standard laboratory conditions. We further used this genetic tool to determine the localisation of m5C sites in different RNA classes, and showed that NSUN-4 acts as a multisite-specific tRNA/rRNA methyltransferase in the mitochondria. In addition, we show that m5C is required for adaptation to temperature changes, as animals devoid of this modification present temperature-sensitive fertility defects. At the molecular level, we show that loss of m5C leads to increased ribosome pausing at triplets encoding for leucine and proline, the most frequently methylated tRNA isoacceptors in C. elegans. This is correlated with reduced translation efficiency of transcripts enriched in these amino acids. Finally, we found translation of Leu-UUG codons to be the most strongly affected upon heat shock, suggesting a role of m5C wobble methylation in the adaptation to heat stress.
2020-11-06 | GSE144822 | GEO