Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers
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Abstract
Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. Here we show by snRNA-seq and snATAC-seq that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we show that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential panel of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a previously undefined mechanism of coordination of gene expression in a syncytium.
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Multiplexed immunofluorescence and FISH can visualize whether the entire nucleolar assembly line is expanding or a specific sub-compartment is bottlenecked.
“By simultaneously tagging Pol I (initiation), fibrillarin (processing in the DFC), and nucleophosmin (assembly in the GC), researchers can visualize whether the entire nucleolar assembly line is expanding or if a specific sub-compartment is bottlenecked [79,80].”
From Ribosome Biogenesis as a Putative Bottleneck to Skeletal Muscle Hypertrophy: Mechanisms, Human Evidence, and Practical Modulators (2026) · cites this paper as [80]
The Methods section describes multiplex fluorescent FISH to visualize myofiber transcripts, and the Results use it to examine fMyh expression during development. Our copy does not address simultaneous tagging of Pol I, fibrillarin, and nucleophosmin or using those markers to distinguish nucleolar expansion from a sub-compartment bottleneck (searched those markers and nucleolar terms). (LLM, conf=0.77)
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LINCing Nuclear Mechanobiology With Skeletal Muscle Mass and Function
van Ingen, M. J. A., & Kirby, T. J. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.690577 · Cited by 26 · see citing works
Muñoz López, M., López-Gil, J. F., Ramírez de la piscina Viúdez, X., Baz-Valle, E., & Tornero Aguilera, J. F. (2026) · Cells · doi:10.3390/cells15111041 · Cited by 1 · see citing works
“By simultaneously tagging Pol I (initiation), fib-rillarin (processing in the DFC), and nucleophosmin (assembly in the GC), researchers can visualize whether the entire nucleolar assembly line is expanding or if a specific sub-compartment is bottlenecked [79,80].”
Influential
- Authors
- Dos Santos, M., Backer, S., Saintpierre, B., Izac, B., Andrieu, M., Letourneur, F., Relaix, F., Sotiropoulos, A., & Maire, P.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Maire, Pascal
- ORCID
- Venue
- Nature Communications
- Published
- 2020-10-09
- Volume
- 11
- Issue
- 1
- Pages
- 5102-5102
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7547110
- OpenAlex
- W3092065379
- Cited by
- 259
- References
- 85
- Citations by year
- 2026: 39 · 2025: 37 · 2024: 50 · 2023: 44 · 2022: 47 · 2021: 38 · 2020: 4
- FWCI
- 11.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Agence Nationale de la Recherche (17-EURE-0013, Myolinc, ANR R17062KK)
- AFM-Téléthon (17406)
- Institut National de la Santé et de la Recherche Médicale
- Centre National de la Recherche Scientifique
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Muscle Physiology and Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- skeletal muscle fibers, myonuclei, gene expression coordination, syncytium, single-nucleus RNA sequencing, single-nucleus ATAC-seq, myosin heavy chain isoforms, MUTYH, hybrid muscle fibers, myofiber type, neuromuscular junction, myotendinous junction, chromatin state, transcription factors, postnatal muscle development, innervation, muscle-specific gene expression
- MeSH terms
- Animals, Cell Nucleus, Female, Gene Expression Regulation, Mice, Inbred C57BL, Neuromuscular Junction, Tendons, Transcription, Genetic, In Situ Hybridization, Fluorescence, Sequence Analysis, RNA, Muscle, Skeletal, Muscle Fibers, Skeletal, Myosin Heavy Chains, Single-Cell Analysis
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