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Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers

ABSTRACT: Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers

PROVIDER: PRJNA631015 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11729338_1.fastq.gz	Fastqsanger.gz
	SRR11729338_2.fastq.gz	Fastqsanger.gz
	SRR11729339_1.fastq.gz	Fastqsanger.gz
	SRR11729339_2.fastq.gz	Fastqsanger.gz
	SRR11729340_1.fastq.gz	Fastqsanger.gz

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Single-nucleus RNA-seq and FISH reveal coordinated transcriptional activity in mammalian myofibers

Project description:Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. By snRNA-seq and snATAC-seq, we showed 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 showed that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential pane of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a unique mechanism of coordination of gene expression in a syncytium.

2020-05-08 | GSE150065 | GEO

Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers.

Project description: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.

| S-EPMC7547110 | biostudies-literature

Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers

Project description:While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology.

2020-10-11 | GSE147127 | GEO

Dystrophic single myofibers vs. control single myofibers

Project description:Dystrophic single myofibers vs. control single myofibers

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Dystrophic single myofibers vs control single myofibers

Project description:Dystrophic single myofibers vs control single myofibers

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Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers

Project description:Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers

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Dystrophic single myofibers vs control single myofibers

Project description:MicroRNA-expression profile of dystrophic single fibres vs wild type single fibers isolated from different muscle of mdx and c57bl mice. Myofibers were isolated from different muscle type (tibialis, diaphragm and quadriceps of gender- (male) and age- (3 month old and half) matched wt and dystrophic mice). 9 total samples per animal model, 3 replicates per muscle type sample

2012-12-21 | E-GEOD-21219 | biostudies-arrayexpress

Dystrophic single myofibers vs. control single myofibers

Project description:MicroRNA-expression profile of dystrophic single fibers compared to wild type single fibers isolated from different muscles of mdx and C57BL mice. Myofibers were isolated from different muscle types (tibialis, diaphragm and quadriceps) of gender- (male) and age- (3 month old and half) matched wt and dystrophic mice. 9 total samples per animal model (C57BL, mdx), 3 replicates per muscle type.

2015-11-25 | E-GEOD-21498 | biostudies-arrayexpress

Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis

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Project description:<p>Nucleic acid and histone modifications critically depend on tricarboxylic acid (TCA) cycle for substrates and co-factors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to operate in mitochondria. Here, we show that a part of the TCA cycle is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass-spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Nuclear localization of the latter enzyme, which produces succinyl-CoA, changed from pluripotency to differentiated state with accompanying changes in the nuclear protein succinylation. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus warranting a revision of the canonical view on metabolic compartmentalization.</p>

2022-06-15 | MTBLS2235 | MetaboLights

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