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We are analyzing https://www.nature.com/articles/s41594-019-0218-x.

Title:
Genome-wide identification of mRNA 5-methylcytosine in mammals | Nature Structural & Molecular Biology
Description:
Accurate and systematic transcriptome-wide detection of 5-methylcytosine (m5C) has proved challenging, and there are conflicting views about the prevalence of this modification in mRNAs. Here we report an experimental and computational framework that robustly identified mRNA m5C sites and determined sequence motifs and structural features associated with the modification using a set of high-confidence sites. We developed a quantitative atlas of RNA m5C sites in human and mouse tissues based on our framework. In a given tissue, we typically identified several hundred exonic m5C sites. About 62–70% of the sites had low methylation levels (<20% methylation), while 8–10% of the sites were moderately or highly methylated (>40% methylation). Cross-species analysis revealed that species, rather than tissue type, was the primary determinant of methylation levels, indicating strong cis-directed regulation of RNA methylation. Combined, these data provide a valuable resource for identifying the regulation and functions of RNA methylation. A quantitative atlas of RNA m5C sites in human and mouse tissues based on a new discovery pipeline allows the identification of sequence motifs and structural features associated with the modification and provides a resource for future studies.
Website Age:
30 years and 10 months (reg. 1994-08-11).

Matching Content Categories {πŸ“š}

  • Education
  • Science
  • Technology & Computing

Content Management System {πŸ“}

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Custom-built

No common CMS systems were detected on Nature.com, and no known web development framework was identified.

Traffic Estimate {πŸ“ˆ}

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πŸŒ† Monumental Traffic: 20M - 50M visitors per month


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Display Ads {🎯}


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$536,300 per month
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Keywords {πŸ”}

article, google, scholar, sites, cas, rna, nature, data, methylation, nsun, supplementary, shown, human, cell, mouse, nat, reads, windows, samples, number, analysis, mrna, sequencing, transcripts, levels, access, res, cells, sample, rnas, fig, gene, control, conversion, replicates, hela, site, information, methylcytosine, tissues, genes, biol, editing, content, based, methods, mapping, studies, selected, molecular,

Topics {βœ’οΈ}

nature portfolio journals permissions reprints nature portfolio privacy policy web-based tools sequencing service advertising zymo research social media sun yat-sen university development simulating rna-seq datasets nsun2-mediated m5c methylation nsun2-mediated cytosine-5 methylation bs-seq data generated rna-dependent chromatin targeting nature+ nature 534 nature 554 nature 462 nature 538 nature 550 nature 485 nature cross-species analysis revealed rna editing single base deletion /sysu-zhanglab/rna-m5c systematic transcriptome-wide detection high-throughput sequencing reads c-cutoff filter based rna sequencing data simulated paired-end reads springerlink instant access subjects computational biology gene-specific conversion rates permissions fast gapped-read alignment high-confidence m5c sites raw sequencing data manuscript editing bs-seq protocols high-confidence sites called m5c rip-seq yeast reveals m5c messenger rna modifications author correspondence standard deviation based rna methylation pathways c-position coverage cutoffs

Schema {πŸ—ΊοΈ}

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         headline:Genome-wide identification of mRNA 5-methylcytosine in mammals
         description:Accurate and systematic transcriptome-wide detection of 5-methylcytosine (m5C) has proved challenging, and there are conflicting views about the prevalence of this modification in mRNAs. Here we report an experimental and computational framework that robustly identified mRNA m5C sites and determined sequence motifs and structural features associated with the modification using a set of high-confidence sites. We developed a quantitative atlas of RNA m5C sites in human and mouse tissues based on our framework. In a given tissue, we typically identified several hundred exonic m5C sites. About 62Ҁ“70% of the sites had low methylation levels (<20% methylation), while 8Ҁ“10% of the sites were moderately or highly methylated (>40% methylation). Cross-species analysis revealed that species, rather than tissue type, was the primary determinant of methylation levels, indicating strong cis-directed regulation of RNA methylation. Combined, these data provide a valuable resource for identifying the regulation and functions of RNA methylation. A quantitative atlas of RNA m5C sites in human and mouse tissues based on a new discovery pipeline allows the identification of sequence motifs and structural features associated with the modification and provides a resource for future studies.
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      headline:Genome-wide identification of mRNA 5-methylcytosine in mammals
      description:Accurate and systematic transcriptome-wide detection of 5-methylcytosine (m5C) has proved challenging, and there are conflicting views about the prevalence of this modification in mRNAs. Here we report an experimental and computational framework that robustly identified mRNA m5C sites and determined sequence motifs and structural features associated with the modification using a set of high-confidence sites. We developed a quantitative atlas of RNA m5C sites in human and mouse tissues based on our framework. In a given tissue, we typically identified several hundred exonic m5C sites. About 62Ҁ“70% of the sites had low methylation levels (<20% methylation), while 8Ҁ“10% of the sites were moderately or highly methylated (>40% methylation). Cross-species analysis revealed that species, rather than tissue type, was the primary determinant of methylation levels, indicating strong cis-directed regulation of RNA methylation. Combined, these data provide a valuable resource for identifying the regulation and functions of RNA methylation. A quantitative atlas of RNA m5C sites in human and mouse tissues based on a new discovery pipeline allows the identification of sequence motifs and structural features associated with the modification and provides a resource for future studies.
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