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Meis1 isoform diversity orchestrates neural progenitor differentiation by regulating ATOH1 degradation at distinct subcellular compartments.

Code ↔ Paper

5 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 5 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Results › Comprehensive long-read cDNA sequencing of cerebellar granule cell progenitors reveals extensive isoform diversity ↔ meis1_isoform_code/scripts/06_venn_gene_sets.R, lines 1–42 · score 0.82 · Venn diagram, high isoform diversity, Mus musculus, diversity genes, Brain Development, transcription factors
  2. [2] § Results › Identification of transcription factors with extensive isoform diversity in GCPs ↔ meis1_isoform_code/scripts/06_venn_gene_sets.R, lines 1–42 · score 0.77 · Venn diagram, high isoform diversity, Brain Development, transcription factors, GO, gene
  3. [3] § Results › Meis1 gene produces two major, spatially separated protein isoforms in GCPs ↔ meis1_isoform_code/scripts/05_plot_protein_domains_drawProteins.R, lines 1–72 · score 0.58 · ENSMUST00000068264.14, transcript10374.11.nic, MEIS1 isoforms, protein
  4. [4] § Results › Comprehensive long-read cDNA sequencing of cerebellar granule cell progenitors reveals extensive isoform diversity ↔ meis1_isoform_code/scripts/02_run_isoquant.sh, the whole file · a weak match · score 0.57 · cerebellar GCPs, GCP samples, cDNA, Nanopore
  5. [5] § Materials and methods › Long-read cDNA sequencing data analysis ↔ meis1_isoform_code/scripts/03_run_sqanti3.sh, the whole file · a weak match · score 0.50 · IsoQuant, curation, peaked, Sqanti3, GTF, transcript

Paper

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The authors' code

R · 93 lines · 3.3 KB · no license · 2 matches

  1. #!/usr/bin/env Rscript
  3. # Generate a Venn diagram for high-isoform-diversity genes, transcription factors,
  4. # and brain development genes (GO:0007420), and print genes shared by all three lists.
  6. suppressPackageStartupMessages({
  7. library(readr)
  8. library(dplyr)
  9. library(ggvenn)
  10. library(ggplot2)
  11. })
  13. # -----------------------------------------------------------------------------
  14. # Input/output paths
  15. # -----------------------------------------------------------------------------
  16. file_isoform_rich <- "processed/genes_with_5_or_more_isoforms_after_TPM_filter.tsv"
  17. file_tf <- "processed/Mus_musculus_TF.txt"
  18. file_brain_dev <- "processed/GO0007420.tsv"
  19. output_dir <- "results/gene_set_overlap"
  20. output_venn_diagram_file <- file.path(output_dir, "gene_list_overlap_venn.png")
  21. output_common_genes_file <- file.path(output_dir, "common_genes_all_three.tsv")
  23. dir.create(output_dir, showWarnings = FALSE, recursive = TRUE)
  25. # -----------------------------------------------------------------------------
  26. # Read gene lists
  27. # -----------------------------------------------------------------------------
  28. message("Reading gene lists...")
  30. # High-isoform-diversity genes. Expected column: gene_name
  31. genes_isoform_rich <- read_tsv(file_isoform_rich, show_col_types = FALSE) %>%
  32. pull(gene_name) %>%
  33. unique() %>%
  34. na.omit()
  35. message("Isoform-rich genes: ", length(genes_isoform_rich))
  37. # Mouse transcription factor list. Expected column: Symbol
  38. genes_tf <- read_tsv(file_tf, show_col_types = FALSE) %>%
  39. pull(Symbol) %>%
  40. unique() %>%
  41. na.omit()
  42. message("Transcription factors: ", length(genes_tf))
  44. # Brain development GO:0007420 gene list.
  45. # Expected format: no header, gene symbol in the first column.
  46. genes_brain_dev <- read_tsv(file_brain_dev, col_names = FALSE, show_col_types = FALSE) %>%
  47. pull(X1) %>%
  48. unique() %>%
  49. na.omit()
  50. message("Brain development genes: ", length(genes_brain_dev))
  52. # Standardize symbols for overlap analysis.
  53. genes_isoform_rich_upper <- toupper(genes_isoform_rich)
  54. genes_tf_upper <- toupper(genes_tf)
  55. genes_brain_dev_upper <- toupper(genes_brain_dev)
  57. data_for_venn <- list(
  58. `High Isoform Diversity (TPM > 1, >=5 isoforms)` = genes_isoform_rich_upper,
  59. `Transcription Factors` = genes_tf_upper,
  60. `Brain Development (GO:0007420)` = genes_brain_dev_upper
  61. )
  63. # -----------------------------------------------------------------------------
  64. # Venn diagram
  65. # -----------------------------------------------------------------------------
  66. message("Creating Venn diagram...")
  68. venn_plot <- ggvenn(
  69. data_for_venn,
  70. columns = names(data_for_venn),
  71. fill_color = c("skyblue", "lightgreen", "salmon"),
  72. stroke_size = 0.5,
  73. set_name_size = 4,
  74. text_size = 3.5,
  75. show_percentage = FALSE
  76. ) +
  77. labs(title = "Overlap of Gene Sets in Neural Development") +
  78. theme(plot.title = element_text(hjust = 0.5, face = "bold"))
  80. ggsave(output_venn_diagram_file, plot = venn_plot, width = 8, height = 6, dpi = 300)
  81. message("Saved: ", output_venn_diagram_file)
  83. # -----------------------------------------------------------------------------
  84. # Common genes
  85. # -----------------------------------------------------------------------------
  86. common_all_three <- sort(Reduce(intersect, data_for_venn))
  87. message("Genes common to all three lists:")
  88. print(common_all_three)
  90. write_tsv(tibble(gene_symbol = common_all_three), output_common_genes_file)
  91. message("Saved: ", output_common_genes_file)
  93. sessionInfo()

06_venn_gene_sets.R at commit 8087fc8, no license · at the source

Overview

Authors: Tomoo Owa1, Toma Adachi1, Ryo Shiraishi1, Kentaro Ichijo1,2, Kaiyuan Ji1,3, Minami Mizuno1,3,4, Kyoka Suyama1,3, Kayo Nishitani1, Ikuko Hasegawa1, Masaki Sone4, Daisuke Kawauchi1,5, Tomoki Nishioka6, Shinichiro Taya1, Yutaka Suzuki7, Kozo Kaibuchi6, Satoshi Miyashita1, Mikio Hoshino1,3
ORCID iDs: Mikio Hoshino
  1. Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
  2. Department of Otolaryngology and Head and Neck Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
  3. Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, Tokyo, Japan
  4. Department of Biomolecular Science, Faculty of Science, Toho University, Chiba, Japan
  5. Department of Neuro-oncology, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Aichi, Japan
  6. International Center for Brain Sciences, Fujita Health University, Aichi, Japan
  7. Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
Institutions: National Center of Neurology and Psychiatry (Japan); The University of Tokyo (Japan); Institute of Science Tokyo (Japan); Toho University (Japan); Nagoya City University (Japan); Fujita Health University (Japan)
Journal: PLoS biology, volume 24, issue 7, article e3003897
Dates: received 4 January 2026; accepted 24 June 2026; published online 13 July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pbio.3003897 · PMID 42441717 · PMCID PMC13379096 · OpenAlex W7168158075
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), developmental (subfield)
Methods: Statistics, Evoked potentials, fMRI & imaging
MeSH: Basic Helix-Loop-Helix Proteins*, Myeloid Ecotropic Viral Integration Site 1 Protein*, Neural Stem Cells*, Animals, Cell Differentiation, Cerebellum, Cullin Proteins, Mice, Neurogenesis, Protein Isoforms, Proteolysis, Ubiquitination (* major topic)
Topic: Ubiquitin and proteasome pathways (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Japan Agency for Medical Research and Development (JPMXP1323015483, 24wm0425005h0004, 22H04925, 25ek0109764h0002); Japan Health Research Promotion Bureau (2020-B-07, 2024‐D‐01); National Center of Neurology and Psychiatry; Japan Society for the Promotion of Science (22H02730, 22H04925 (PAGS), 22H04925, 25K02372, JPMXP1323015483, 22K15211)
Citations: not cited yet (Europe PMC); 68 references in the paper
Research resources: RRID:Addgene_22542

Abstract

The development of the complex nervous system is strictly controlled by diverse isoforms produced from individual genes, but the underlying machinery remains unclear. Our long-read cDNA sequencing of mouse cerebellar granule cell progenitors (GCPs) identifies more than 700 genes with high isoform diversity. One such gene, Meis1, produces MEIS1-FL and MEIS1-HdL isoforms, which include and lack the homeodomain, respectively. Our previous study showed that MEIS1-FL localizes to nuclei and promotes ATOH1 protein degradation through transcriptional regulation, thereby promoting GCP differentiation. In contrast, our in vivo electroporation experiments in the postnatal mouse cerebellum show that MEIS1-HdL inhibits GCP differentiation. MEIS1-HdL localizes in the cytoplasm and inhibits the degradation of ATOH1 mediated by CUL3, which is a newly identified E3 ligase for ATOH1. MEIS1-HdL enhances the binding of the COP9 signalosome to CUL3, which suppresses ATOH1 polyubiquitination. This study demonstrates that functionally antagonistic isoforms derived from a single gene cleverly control neural progenitor differentiation.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 5 matches between paragraphs and lines of code.

Zenodo 20581171

License: CC-BY-4.0
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: tidyverse (3 files), ggplot2 (2 files), data.table (1 file), Matplotlib (1 file), NumPy (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
6 files
At the source: doi.org/10.5281/zenodo.20581171

hoshino-lab/meis1-isoform-code

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 8087fc855bb7fcb0d93dbbdfbe7f262071e96f3a, 7 June 2026
Languages: R (3), Shell (2), Python (1)
Size: 15 files, 6 scripts
Software Heritage: not archived
Found in: the Zenodo archive record
Holds: README, license file, environment (meis1_isoform_code/environment.yml)
Not found: CITATION.cff, tests, continuous integration, documentation
Tools: tidyverse (3 files), ggplot2 (2 files), data.table (1 file), Matplotlib (1 file), NumPy (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
6 files
At the source: github.com/Hoshino-lab/meis1-isoform-code/tree/v1.0.1

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;
  • 12 scripts, each with its path and the digest of its content;
  • 5 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

The long-read cDNA sequencing data generated in this study have been deposited in the DNA Data Bank of Japan (DDBJ) under accession number PRJDB15106. The accession numbers for the individual BioSamples are SAMD00572392, SAMD00572393, and SAMD00572394. Custom code used for long-read cDNA-seq quality control, IsoQuant/SQANTI3 processing, isoform structure visualization, protein domain visualization, and gene-set overlap analysis is publicly available at Zenodo: https://doi.org/10.5281/zenodo.20581171. All other relevant data are within the paper and its Supporting information files.

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

Versions

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Version 2, 28 September 2026

  • Funding: added Japan Agency for Medical Research and Development: JPMXP1323015483, 24wm0425005h0004, 22H04925, 25ek0109764h0002; Japan Health Research Promotion Bureau: 2020-B-07, 2024‐D‐01; National Center of Neurology and Psychiatry; Japan Society for the Promotion of Science: 22H02730, 22H04925 (PAGS), 22H04925, 25K02372, JPMXP1323015483, 22K15211

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 17 authors, 12 MeSH terms, 68 references, 1 RRID.

Cite

This paper

Owa, T., Adachi, T., Shiraishi, R., Ichijo, K., Ji, K., Mizuno, M., Suyama, K., Nishitani, K., Hasegawa, I., Sone, M., Kawauchi, D., Nishioka, T., Taya, S., Suzuki, Y., Kaibuchi, K., Miyashita, S., & Hoshino, M. (2026). Meis1 isoform diversity orchestrates neural progenitor differentiation by regulating ATOH1 degradation at distinct subcellular compartments. PLoS biology, 24(7), e3003897. https://doi.org/10.1371/journal.pbio.3003897

BibTeX

@article{owa2026meis1,
author = {Owa, Tomoo and Adachi, Toma and Shiraishi, Ryo and Ichijo, Kentaro and Ji, Kaiyuan and Mizuno, Minami and Suyama, Kyoka and Nishitani, Kayo and Hasegawa, Ikuko and Sone, Masaki and Kawauchi, Daisuke and Nishioka, Tomoki and Taya, Shinichiro and Suzuki, Yutaka and Kaibuchi, Kozo and Miyashita, Satoshi and Hoshino, Mikio},
title = {{Meis1 isoform diversity orchestrates neural progenitor differentiation by regulating ATOH1 degradation at distinct subcellular compartments}},
journal = {PLoS biology},
year = {2026},
month = jul,
volume = {24},
number = {7},
pages = {e3003897},
publisher = {PLOS},
issn = {1544-9173},
doi = {10.1371/journal.pbio.3003897},
url = {https://doi.org/10.1371/journal.pbio.3003897},
pmid = {42441717},
pmcid = {PMC13379096}
}

RIS

TY - JOUR
AU - Owa, Tomoo
AU - Adachi, Toma
AU - Shiraishi, Ryo
AU - Ichijo, Kentaro
AU - Ji, Kaiyuan
AU - Mizuno, Minami
AU - Suyama, Kyoka
AU - Nishitani, Kayo
AU - Hasegawa, Ikuko
AU - Sone, Masaki
AU - Kawauchi, Daisuke
AU - Nishioka, Tomoki
AU - Taya, Shinichiro
AU - Suzuki, Yutaka
AU - Kaibuchi, Kozo
AU - Miyashita, Satoshi
AU - Hoshino, Mikio
TI - Meis1 isoform diversity orchestrates neural progenitor differentiation by regulating ATOH1 degradation at distinct subcellular compartments
T2 - PLoS biology
J2 - PLoS Biol
PY - 2026
DA - 2026/07/13
VL - 24
IS - 7
SP - e3003897
SN - 1544-9173
PB - PLOS
DO - 10.1371/journal.pbio.3003897
UR - https://doi.org/10.1371/journal.pbio.3003897
LA - en
ER -

CSL-JSON

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