OSCR

The <i>Sox2</i> regulatory region 42 produces enhancer RNAs that influence neuronal migration during cortical development.

Overview

Authors: Satoe Banno1,2, Tsukasa Sanosaka1, Ryo Tomooka1,2, Noriko Mizota1,2, Akinori Tokunaga3, Hideyuki Okano1,4, Jun Kohyama1,2,5
ORCID iDs: Jun Kohyama
  1. Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
  2. Laboratory of Stem Cell Biology, Faculty of Human Sciences, Waseda University, Tokorozawa, Saitama 359-1192, Japan
  3. Division of Laboratory Animal Resources, Life Science Research Laboratory, University of Fukui, Eiheiji, Fukui 910-1193, Japan
  4. Keio University Regenerative Medicine Research Center, 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
  5. Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
Institutions: Waseda University (Japan); Keio University (Japan); University of Fukui (Japan)
Journal: iScience, volume 29, issue 9, article 117332
Dates: received 21 July 2025; accepted 10 August 2026; published online 26 August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.isci.2026.117332 · PMID 42699760 · PMCID PMC13544347 · OpenAlex W7204252153
Open access: gold, a free copy (OpenAlex)
Status: code on request
Categories: genetics / omics (modality), mouse (organism), developmental (subfield)
Methods: Spectral & time-frequency, Statistics, Smoothing, state filtering, decompositions, Machine learning
Keywords: mouse, cortex, neural stem cells, neuronal migration, snRNA-seq, snATAC-seq, enhancer, eRNAs
Topic: Developmental Biology and Gene Regulation (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Japan Society for the Promotion of Science (19H03623, 24K02571); Waseda University (GRC-kyoten-05)
Citations: not cited yet (Europe PMC); 88 references in the paper
Research resources: Anti-SatB2 RRID:AB_10563678, Anti-Tbr2 RRID:AB_10615604, Anti-β-galactosidase RRID:AB_10697365, Anti-Ctip2 RRID:AB_2064130, Anti-Sox2 RRID:AB_2286684, Anti-NeuN RRID:AB_2298772, Anti-Cleaved Caspase-3 RRID:AB_2341188, Anti-BrdU RRID:AB_305426, Anti-Phospho-Histone H3 (pH3) RRID:AB_331535, Anti-GAPDH RRID:AB_561053, Anti-Nestin RRID:AB_94911, GenomicRanges RRID:SCR_000025, R (v4.1.3, or v4.4.1) RRID:SCR_001905, Bioconductor RRID:SCR_006442, Imaris (11.0) RRID:SCR_007370, ZEN microscopy software (v3.10) RRID:SCR_013672, Seurat (v4.0.3, or v5.2.1) RRID:SCR_016341, Monocle 3 (v1.0.0) RRID:SCR_018685, Signac (v1.0.3, or v1.14.0) RRID:SCR_021158, Design and Analysis (2.8.0) RRID:SCR_026962

Abstract

Precise regulation of neural progenitor states and neuronal positioning is essential for cortical development. Here, we identified Sox2 regulatory region 42 (SRR42), a regulatory region located 42 kb downstream of the Sox2 transcription start site that exhibits open chromatin, active histone modifications, and bidirectional transcription of enhancer RNAs (eRNAs). Using transgenic reporter mice, we found that SRR42 is active in neural progenitor cells in the developing cortex. CRISPR-Cas9-mediated deletion of SRR42 combined with single-cell multiome analysis revealed alterations in progenitor-state dynamics, neuronal migration, and cortical lamination without detectable changes in Sox2 expression. Furthermore, in vivo knockdown of SRR42-derived eRNAs impaired neuronal migration. These findings identify SRR42-derived RNAs as regulators of neuronal migration during cortical development and highlight enhancer-associated transcription as a functional component of neurodevelopmental gene regulation.

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

Code

The paper says that its authors' code is available on request: it was not published with the paper, so there is nothing to verify.

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

Tracing map

A tracing map links a paper to the code its authors published: this paper has none (its code is available on request), so it has no map.

Data

Datasets cited

Other data links

Data and code availability

The high-throughput data used in this study have been deposited in the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). The single-cell multiome dataset is available under accession number GEO: GSE282390 (https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE282390), the CAGE dataset for mouse cortex under accession number GEO: GSE296925 (https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE296925), and the CAGE dataset for hiPSC-derived neurospheres under accession number GEO: GSE297056 (https://ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE297056).

This paper does not report original code.

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), 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 2, 28 September 2026

  • Authors: added Jun Kohyama (0000-0001-8168-8588); removed Jun Kohyama

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 8 keywords, 2 funders, 88 references, 20 RRIDs.

Cite

This paper

Banno, S., Sanosaka, T., Tomooka, R., Mizota, N., Tokunaga, A., Okano, H., & Kohyama, J. (2026). The <i>Sox2</i> regulatory region 42 produces enhancer RNAs that influence neuronal migration during cortical development. iScience, 29(9), 117332. https://doi.org/10.1016/j.isci.2026.117332

BibTeX

@article{banno2026lt,
author = {Banno, Satoe and Sanosaka, Tsukasa and Tomooka, Ryo and Mizota, Noriko and Tokunaga, Akinori and Okano, Hideyuki and Kohyama, Jun},
title = {{The \<i\>Sox2\</i\> regulatory region 42 produces enhancer RNAs that influence neuronal migration during cortical development}},
journal = {iScience},
year = {2026},
month = aug,
volume = {29},
number = {9},
pages = {117332},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.117332},
url = {https://doi.org/10.1016/j.isci.2026.117332},
pmid = {42699760},
pmcid = {PMC13544347}
}

RIS

TY - JOUR
AU - Banno, Satoe
AU - Sanosaka, Tsukasa
AU - Tomooka, Ryo
AU - Mizota, Noriko
AU - Tokunaga, Akinori
AU - Okano, Hideyuki
AU - Kohyama, Jun
TI - The <i>Sox2</i> regulatory region 42 produces enhancer RNAs that influence neuronal migration during cortical development
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/08/26
VL - 29
IS - 9
SP - 117332
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.117332
UR - https://doi.org/10.1016/j.isci.2026.117332
LA - en
ER -

CSL-JSON

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