OSCR

Single-base resolution atlas reveals moderate conservation and regulatory diversity of m6A modifications across mammals.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and methods › Animal samples ↔ transcript_num_m6a.R, the whole file · a weak match · score 0.77 · tree shrews, sugar gliders, toed hedgehogs, bats, liver, brain
  2. [2] § Materials and methods › Sequencing, assembly, and annotation of the four-toed hedgehog and the sugar glider genome ↔ transcript_num_m6a.R, the whole file · a weak match · score 0.65 · sugar glider, toed hedgehog, filled, library, species

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

R · 72 lines · 3.2 KB · MIT · 2 matches

  1. #m6A number in a single transcript
  2. library(ggplot2)
  4. data <- read.table("1transcript_num_m6a", header = FALSE)
  6. colnames(data) <- c("Species", "Tissue", "Number")
  8. species_names <- c("Monkey", "Mouse", "Rat", "Tree shrew", "Cattle", "Sheep", "Llama", "Dog", "Cat", "Horse",
  9. "Ferret", "Four-toed hedgehog", "Sugar glider", "Hyrax", "Pig", "Rabbit", "Guinea pig",
  10. "Horseshoe bat", "Myotis bat", "Hipposideros bat", "Donkey")
  11. tissue_names <- c("liver", "kidney", "brain")
  14. data$Species <- factor(data$Species, levels = 1:21, labels = species_names)
  15. data$Tissue <- factor(data$Tissue, levels = 1:3, labels = tissue_names)
  18. p <- ggplot(data, aes(x = Tissue, y = Number, fill = Tissue)) +
  19. geom_bar(stat = "identity", position = "dodge") +
  20. facet_wrap(~ Species, scales = "free_y") +
  21. theme_minimal() +
  22. labs(x = "Tissue", y = "Number", title = "Number by Species and Tissue") +
  23. theme(
  24. legend.position = "none",
  25. axis.text.x = element_text(angle = 45, hjust = 1),
  26. strip.text = element_text(size = 10, face = "bold"),
  27. panel.grid.major = element_blank(),
  28. panel.grid.minor = element_blank(),
  29. panel.border = element_rect(colour = "black", fill = NA, size = 1)
  30. ) +
  31. scale_fill_manual(values = c("#C56C66","#D6B36C", "#82B6CE"))
  32. ggsave(p, file='1transcript_num_m6a.pdf', width=8,height=8)
  34. #violin plot
  35. # Load required libraries
  36. library(ggplot2)
  38. # Read data
  39. data <- read.table("/media/tower/zhangxx/m6a/0data/eventalign/1transcript_num_m6a", header = FALSE)
  41. # Rename columns
  42. colnames(data) <- c("Group", "Subgroup", "Value")
  44. # Convert Subgroup to factor and replace with corresponding tissue names
  45. data$Subgroup <- factor(data$Subgroup, levels = c(1, 2, 3), labels = c("liver", "kidney", "brain"))
  47. # Calculate the mean for each Subgroup
  48. means <- aggregate(Value ~ Subgroup, data, mean)
  50. # Set colors: liver = #82B6CE, kidney = #D6B36C, brain = #C56C66
  51. colors <- c("liver" = "#C56C66", "kidney" = "#D6B36C", "brain" = "#82B6CE")
  53. # Create violin plot with scatter points and mean lines
  54. p <- ggplot(data, aes(x = Subgroup, y = Value)) +
  55. geom_violin(trim = FALSE, aes(color = Subgroup), fill = NA, size = 1) + # Violin plot outline
  56. geom_jitter(aes(color = Subgroup), shape = 16, position = position_jitter(0.2)) + # Scatter plot
  57. geom_segment(data = means, aes(x = as.numeric(Subgroup) - 0.2, xend = as.numeric(Subgroup) + 0.2,
  58. y = Value, yend = Value), color = "black", size = 1) + # Mean horizontal line
  59. geom_text(data = means, aes(x = Subgroup, y = Value, label = round(Value, 2)),
  60. vjust = -1.5, color = "black") + # Mean annotation
  61. scale_color_manual(values = colors) + # Custom outline and scatter point colors
  62. theme_minimal() +
  63. labs(title = "Violin plot with means and jittered points",
  64. x = "Tissue",
  65. y = "Value") +
  66. theme(legend.position = "none", # Hide legend
  67. axis.line = element_line(color = "black"), # Add axis lines
  68. axis.ticks = element_line(color = "black"), # Add tick marks
  69. axis.title.x = element_text(size = 12), # Set x-axis title size
  70. axis.title.y = element_text(size = 12)) # Set y-axis title size
  72. ggsave(p, file='1transcript_num_m6a.Violin.pdf', width=4, height=4)

transcript_num_m6a.R at commit 61acb3a, under MIT · at the source

Overview

Authors: Xiaoxiao Zhang1,2, Zhan Zhang1,2, Weiqiang Liu1,3, Wenfu Liu1,2, Meng Li1, Weixiao Chen1,2, Gaoming Liu1, Yichen Dai4, Zihao Li1,2, Chunyan Hu1,2, Qi Pan1,2, Yang Yu5, Xiangye Liu1,2, Pingfen Zhu1, Xuming Zhou1
ORCID iDs: Weiqiang Liu, Xuming Zhou
  1. State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  2. University of Chinese Academy of Sciences, Beijing 100049, China
  3. Department of Neurology at Yale School of Medicine, Yale University, New Haven, CT 06510, United States
  4. School of Life Sciences, Fudan University, Shanghai 200438, China
  5. School of Life Sciences, University of Science and Technology of China, Anhui 230026, China
Institutions: Chinese Academy of Sciences (China); University of Chinese Academy of Sciences (China); Institute of Zoology (China); Yale University (United States); Fudan University (China); University of Science and Technology of China (China)
Journal: Nucleic acids research, volume 54, issue 10, article gkag544
Dates: received 8 November 2025; accepted 7 May 2026; published online 30 May 2026; in print May 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1093/nar/gkag544 · PMID 42216759 · PMCID PMC13221654 · OpenAlex W7162861319
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism)
Methods: Statistics, Connectivity
MeSH: Adenosine*, Mammals*, RNA, Messenger*, Animals, Brain, Epitranscriptome, Epitranscriptomics, Evolution, Molecular, Humans, Kidney, Liver, RNA Methylation, RNA Splicing, Sequence Analysis, RNA (* major topic)
Journal subjects: Data Resources and Analyses
Topic: RNA modifications and cancer (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Natural Science Foundation of China (National Science Foundation of China) (32270437); National Key Research and Development Projects of the Ministry of Science and Technology of China (2023YFC3304000); Institute of Zoology, Chinese Academy of Sciences (2023IOZ0104); Prevention and Control of Emerging and Major Infectious Diseases‐National Science and Technology Major Project (2026ZD01911000)
Citations: cited by 1 paper (Europe PMC); 110 references in the paper

Abstract

RNA methylation, notably m6A modification, is a predominant epitranscriptomic alteration in mRNA, yet its evolutionary properties and the selective constraints acting on it across mammals remain poorly understood. Here, we generated a single-base-resolution m6A modification atlas in liver, kidney, and brain tissues across 21 non-model mammals using Nanopore direct RNA sequencing. We found that 25.54–35.70% of orthologous transcripts across examined species harbor m6A modifications, with m6A-modified sites exhibiting significantly greater conservation than nearby unmodified regions, probably under purifying selection. While m6A sites were preferentially enriched in RNA loops rather than stems, an inverse correlation between overall m6A levels and RNA splicing complexity was observed, a pattern which is compatible with a model in which exon junction complex (EJC)-associated, splice-junction-proximal mechanisms contribute to suppression of nearby m6A deposition. Further analyses of m6A-modified genes and life history traits uncovered that genes with higher m6A modification ratios in long-lived mammals were mainly characterized by relaxed selection. This study explores the evolutionary landscape of m6A modifications in non-model organisms, underscoring their diverse regulatory roles and evolutionary significance across mammalian lineages.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

XiaoxiaoZhang57/Evolutionary-analysis-of-m6A-in-mammals

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 61acb3ae1355ce5489141c4aa1c06fc77b19564d, 8 May 2026
Languages: Python (4), R (3), Shell (1)
Size: 13 files, 8 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README, license file, environment (requirements.txt)
Not found: CITATION.cff, tests, continuous integration, documentation
Tools: ggplot2 (3 files), Biopython (2 files), nlme (1 file), SAMtools (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
10 files
At the source: github.com/XiaoxiaoZhang57/Evolutionary-analysis-of-m6A-in-mammals.git

Zenodo 20085328

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (3 files), Biopython (2 files), nlme (1 file), SAMtools (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
10 files
At the source: doi.org/10.5281/zenodo.20085328

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 16 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data availability

All data are available in the main text or the supplementary data. Materials and reagents described in this study are either commercially available or available on request from the corresponding author. The Oxford Nanopore DRS sequencing data and NGS data are deposited in the Genome Sequence Archive in the National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (accession no. GSA: CRA015510 for all species) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa.

The original code has been deposited at https://github.com/XiaoxiaoZhang57/Evolutionary-analysis-of-m6A-in-mammals.git and Zenodo at https://doi.org/10.5281/zenodo.20085328.

Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 15 authors, 14 MeSH terms, 4 funders, 109 references.

Cite

This paper

Zhang, X., Zhang, Z., Liu, W., Liu, W., Li, M., Chen, W., Liu, G., Dai, Y., Li, Z., Hu, C., Pan, Q., Yu, Y., Liu, X., Zhu, P., & Zhou, X. (2026). Single-base resolution atlas reveals moderate conservation and regulatory diversity of m6A modifications across mammals. Nucleic acids research, 54(10), gkag544. https://doi.org/10.1093/nar/gkag544

BibTeX

@article{zhang2026single,
author = {Zhang, Xiaoxiao and Zhang, Zhan and Liu, Weiqiang and Liu, Wenfu and Li, Meng and Chen, Weixiao and Liu, Gaoming and Dai, Yichen and Li, Zihao and Hu, Chunyan and Pan, Qi and Yu, Yang and Liu, Xiangye and Zhu, Pingfen and Zhou, Xuming},
title = {{Single-base resolution atlas reveals moderate conservation and regulatory diversity of m6A modifications across mammals}},
journal = {Nucleic acids research},
year = {2026},
month = may,
volume = {54},
number = {10},
pages = {gkag544},
publisher = {Oxford University Press},
issn = {0305-1048},
doi = {10.1093/nar/gkag544},
url = {https://doi.org/10.1093/nar/gkag544},
pmid = {42216759},
pmcid = {PMC13221654}
}

RIS

TY - JOUR
AU - Zhang, Xiaoxiao
AU - Zhang, Zhan
AU - Liu, Weiqiang
AU - Liu, Wenfu
AU - Li, Meng
AU - Chen, Weixiao
AU - Liu, Gaoming
AU - Dai, Yichen
AU - Li, Zihao
AU - Hu, Chunyan
AU - Pan, Qi
AU - Yu, Yang
AU - Liu, Xiangye
AU - Zhu, Pingfen
AU - Zhou, Xuming
TI - Single-base resolution atlas reveals moderate conservation and regulatory diversity of m6A modifications across mammals
T2 - Nucleic acids research
J2 - Nucleic Acids Res
PY - 2026
DA - 2026/05/01
VL - 54
IS - 10
SP - gkag544
SN - 0305-1048
PB - Oxford University Press
DO - 10.1093/nar/gkag544
UR - https://doi.org/10.1093/nar/gkag544
LA - en
ER -

CSL-JSON

{
"id": "10.1093/nar/gkag544",
"type": "article-journal",
"title": "Single-base resolution atlas reveals moderate conservation and regulatory diversity of m6A modifications across mammals",
"container-title": "Nucleic acids research",
"author": [
{
"family": "Zhang",
"given": "Xiaoxiao"
},
{
"family": "Zhang",
"given": "Zhan"
},
{
"family": "Liu",
"given": "Weiqiang"
},
{
"family": "Liu",
"given": "Wenfu"
},
{
"family": "Li",
"given": "Meng"
},
{
"family": "Chen",
"given": "Weixiao"
},
{
"family": "Liu",
"given": "Gaoming"
},
{
"family": "Dai",
"given": "Yichen"
},
{
"family": "Li",
"given": "Zihao"
},
{
"family": "Hu",
"given": "Chunyan"
},
{
"family": "Pan",
"given": "Qi"
},
{
"family": "Yu",
"given": "Yang"
},
{
"family": "Liu",
"given": "Xiangye"
},
{
"family": "Zhu",
"given": "Pingfen"
},
{
"family": "Zhou",
"given": "Xuming"
}
],
"container-title-short": "Nucleic Acids Res",
"volume": "54",
"issue": "10",
"page": "gkag544",
"DOI": "10.1093/nar/gkag544",
"PMID": "42216759",
"PMCID": "PMC13221654",
"ISSN": "0305-1048",
"publisher": "Oxford University Press",
"URL": "https://doi.org/10.1093/nar/gkag544",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
1
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1186/s12864-026-12863-z [code]
Chromosome-level genome assembly of the nematophagous flatworm Luticola nematophagus: revealing molecular adaptations for predation and its biocontrol potential against nematode diseases.
Journal: BMC genomics
In common: 11 references
[2] doi:10.1038/s42003-026-10402-w [code]
Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model.
Journal: Communications biology
In common: SAMtools, ggplot2, tidyverse, 8 references
[3] doi:10.1038/s41531-026-01362-3
The epitranscriptomic m6A RNA modification modulates the synapse in ageing and in a mouse model of synucleinopathy.
Journal: NPJ Parkinson's disease
In common: 9 references
[4] doi:10.1038/s41597-026-07102-9
Chromosome-level genome assembly and annotation of the moon jellyfish Aurelia coerulea.
Journal: Scientific data
In common: 8 references
[5] doi:10.7554/elife.107393 [code]
Chromosome-scale genome assembly of the European common cuttlefish &lt;i&gt;Sepia officinalis&lt;/i&gt;.
Journal: eLife
In common: SAMtools, ggplot2, tidyverse, 4 references
[6] doi:10.1093/molbev/msag159 [code]
Genomic signature of repeated transitions to diurnality in spiders.
Journal: Molecular biology and evolution
In common: 6 references
[7] doi:10.1038/s41467-026-76675-1 [code]
Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.
Journal: Nature communications
In common: Biopython, SAMtools, ggplot2, 1 other tool, 2 references
[8] doi:10.1038/s41598-026-51674-w
FTO-mediated m6A demethylation regulates PGC-1α-dependent mitochondrial biogenesis to attenuate aluminum-induced neuronal senescence.
Journal: Scientific reports
In common: 5 references
[9] doi:10.1038/s42003-026-10957-8 [code]
Brain defence by the extracellular matrix protein Cochlin.
Journal: Communications biology
In common: Biopython, nlme, SAMtools, 2 other tools
[10] doi:10.1111/jne.70203 [code]
Nonapeptide molecular evolution during the adaptive radiation of Tanganyika cichlids.
Journal: Journal of neuroendocrinology
In common: Biopython, SAMtools, tidyverse, 2 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.