ArticleDevelopment (Cambridge, England)2025
In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex.
Seishin Sakai, Yurie Maeda, Mai Saeki, Daijiro Konno, Keita Kawaji, Fumio Matsuzaki, Yutaka Suzuki, Yukiko Gotoh, Yusuke Kishi
Abstract read
In one paragraphArticle in Development (Cambridge, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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5 · Who and what moneyAuthors and funding
9 authors.
Seishin SakaiLaboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
Yurie MaedaLaboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
Mai SaekiLaboratory of Molecular Neurobiology, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.
Daijiro KonnoCellular and Molecular Bioengineering Laboratory, Graduate School of Science and Engineering, Kindai University, Osaka 577-8502, Japan.
Keita KawajiLaboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
Fumio MatsuzakiDepartment of Aging Science and Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan.
Yutaka SuzukiDepartment of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan.
Yukiko GotohLaboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
Yusuke KishiLaboratory of Molecular Biology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.ORCID 0000-0003-2846-5400 Funding
Asahi Glass FoundationAstellas Foundation for Research on Metabolic DisordersChugai Foundation for Innovative Drug Discovery ScienceHitachi Global FoundationJapan Agency for Medical Research and Development JP22gm6110021Japan Agency for Medical Research and Development JP23gm1310004Japan Society for the Promotion of Science 16H06279Japan Society for the Promotion of Science 16H06279, JP22H04687, 23H04214, and 24H01227Japan Society for the Promotion of Science 22gm6110021Japan Society for the Promotion of Science 22H00431Japan Society for the Promotion of Science 23gm1310004Japan Society for the Promotion of Science 23H04214Japan Society for the Promotion of Science 24H01227Japan Society for the Promotion of Science JP22H00431Japan Society for the Promotion of Science JP22H04687Kurata Memorial Hitachi Science and Technology FoundationMinistry of Education, Culture, Sports, Science and TechnologyNaito FoundationOno PharmaceuticalOno Pharmaceutical Foundation for Oncology, Immunology, and NeurologySecom Science and Technology FoundationSECOM Science and Technology FoundationTakeda Science FoundationUehara Memorial FoundationUniversity of Tokyo
6 · The paper itselfAbstract
During neuronal differentiation, gene transcription patterns change in response to both intrinsic and extrinsic cues. Chromatin regulation at regulatory elements plays a key role in this process. However, how chromatin accessibility evolves in vivo in cortical neurons remains unclear. Here, we established a method for labeling differentiating neurons with specific birthdates. Using this method, we traced the 4-day differentiation process of in vivo deep-layer excitatory neurons in the mouse embryonic cortex and examined changes in the genome-wide transcription pattern and chromatin accessibility using RNA sequencing and DNase sequencing, respectively. We found that genomic regions of genes linked to mature neuronal functions, including deep layer-specific and stimulus-responsive genes, became accessible even at the embryonic stage. Additionally, our results indicated the involvement of bivalent marks in neural precursor/stem cells and Dmrt3 and Dmrta2 in the regulation of chromatin accessibility during neuronal differentiation. These findings highlight the importance of chromatin regulation in embryonic neurons, enabling the timely activation of neuronal genes during maturation.
Indexed as
Cell DifferentiationChromatinNeocortexNeuronsAnimalsGene Expression Regulation, DevelopmentalMiceNeural Stem CellsNeurogenesisTranscription FactorsChromatinTranscription FactorsBivalent genesChromatin accessibilityCortical neuronsDifferentiationDmrtMouseTranscriptome
Identifiers
PMID40501413
PMCPMC12268177
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