Epigenetic regulation of Wnt7b expression by the<i>cis</i>-acting long noncoding RNA lnc-Rewind in muscle stem cells

Cipriano, Andrea; Macino, Martina; Buonaiuto, Giulia; Santini, Tiziana; Biferali, Beatrice; Peruzzi, Giovanna; Colantoni, Alessio; Mozzetta, Chiara; Ballarino, Monica

doi:10.1101/2020.01.03.894519

Cited by 6 publications

(7 citation statements)

References 57 publications

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“…Thus, we cannot exclude that pharmacological inhibition of G9a/GLP might also affect differentiation of myogenic progenitors. G9a has been recently implicated in preserving MuSCs' capacity to proliferate and to expand ex vivo by repressing Wnt signaling pathway (66). However, if this also happens in vivo, then it needs further exploration.…”

Section: Discussionmentioning

confidence: 99%

Prdm16-mediated H3K9 methylation controls fibro-adipogenic progenitors identity during skeletal muscle repair

et al. 2021

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H3K9 methylation maintains cell identity orchestrating stable silencing and anchoring of alternate fate genes within the heterochromatic compartment underneath the nuclear lamina (NL). However, how cell type–specific genomic regions are specifically targeted to the NL is still elusive. Using fibro-adipogenic progenitors (FAPs) as a model, we identified Prdm16 as a nuclear envelope protein that anchors H3K9-methylated chromatin in a cell-specific manner. We show that Prdm16 mediates FAP developmental capacities by orchestrating lamina-associated domain organization and heterochromatin sequestration at the nuclear periphery. We found that Prdm16 localizes at the NL where it cooperates with the H3K9 methyltransferases G9a/GLP to mediate tethering and silencing of myogenic genes, thus repressing an alternative myogenic fate in FAPs. Genetic and pharmacological disruption of this repressive pathway confers to FAP myogenic competence, preventing fibro-adipogenic degeneration of dystrophic muscles. In summary, we reveal a druggable mechanism of heterochromatin perinuclear sequestration exploitable to reprogram FAPs in vivo.

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Section: Discussionmentioning

confidence: 99%

Prdm16-mediated H3K9 methylation controls fibro-adipogenic progenitors identity during skeletal muscle repair

et al. 2021

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“…In addition, the cotranscription of the 1700018A04Rik lncRNA gene with Foxf2 may play a role in repressing Foxq1 gene expression in the developing palatal mesenchyme in wildtype embryos (Figure 8A). A few lncRNAs have been shown to recruit regulatory complexes through RNA-protein interactions to repress nearby genes in cis (Maamar et al, 2013;McHugh et al, 2015;Cipriano et al, 2021). Transcription of some lncRNA genes has also been shown to repress expression of a nearby gene in cis through transcriptional interference independently of the lncRNA transcript (Houseley et al, 2008;Latos et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Cis-Repression of Foxq1 Expression Affects Foxf2-Mediated Gene Expression in Palate Development

Liu

Lan

et al. 2021

Front. Cell Dev. Biol.

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Disruption of FOXF2, encoding a member of the Forkhead family transcription factors, has been associated with cleft palate in humans and mice. FOXF2 is located in a conserved gene cluster containing FOXQ1, FOXF2, and FOXC1. We found that expression of Foxq1 is dramatically upregulated in the embryonic palatal mesenchyme in Foxf2–/– mouse embryos. We show here that the Foxf2 promoter-deletion mutation caused dramatically increased expression of the cis-linked Foxq1 allele but had little effect on the Foxq1 allele in trans. We analyzed effects of the Foxf2 mutation on the expression of other neighboring genes and compared those effects with the chromatin domain structure and recently identified enhancer-promoter associations as well as H3K27ac ChIP-seq data. We show that the Foxf2 mutation resulted in significantly increased expression of the Foxq1 and Exoc2 genes located in the same topologically associated domain with Foxf2 but not the expression of the Foxc1 and Gmds genes located in the adjacent chromatin domain. We inactivated the Foxq1 gene in mice homozygous for a Foxf2 conditional allele using CRISPR genome editing and generated (Foxf2/Foxq1)+/– mice with loss-of-function mutations in Foxf2 and Foxq1 in cis. Whereas the (Foxf2/Foxq1)–/– mice exhibited cleft palate at birth similar as in the Foxf2–/– mice, systematic expression analyses of a large number of Foxf2-dependent genes revealed that the (Foxf2/Foxq1)–/– embryos exhibited distinct effects on the domain-specific expression of several important genes, including Foxf1, Shox2, and Spon1, in the developing palatal shelves compared with Foxf2–/– embryos. These results identify a novel cis-regulatory effect of the Foxf2 mutation and demonstrate that cis-regulation of Foxq1 contributed to alterations in palatal gene expression in Foxf2–/– embryos. These results have important implications for interpretation of results and mechanisms from studies of promoter- or gene-deletion alleles. In addition, the unique mouse lines generated in this study provide a valuable resource for understanding the cross-regulation and combinatorial functions of the Foxf2 and Foxq1 genes in development and disease.

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“…For example, we wanted to understand the role of LncRewind in the context of the activation and proliferation of satellite cells (Cipriano et al, 2021), so we performed co-staining with Pax7, a specific marker for satellite cells, and Ki67, a marker for proliferation, on the single myofibers isolated from five mice. To obtain statistically significant results, we suggest quantifying at least 50 fibers per condition, isolated from a minimum of three mice.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, to infer the function of lncRNAs along the different stages of satellite cell-mediated myogenesis, it is important to rely on an experimental model that allows for monitoring of satellite cell activation from the quiescent state to their expansion and commitment to differentiation, and even to self-renewal (Mozzetta, 2016). To this end, we optimized previous protocols to isolate intact and viable single myofibers (Pasut et al, 2013;Mozzetta, 2016;Pegoli et al, 2020) from the extensor digitorum longus (EDL) muscle of wild-type mice for the purposes of subsequent manipulation of lncRNAs expression and phenotypical characterization by EdU incorporation and immunostaining (Cipriano et al, 2021). This isolation procedure preserves satellite cells within their physiological niche underneath the surrounding basal lamina.…”

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confidence: 99%

Targeting the Expression of Long Noncoding RNAs in Murine Satellite Cells from Single Myofibers

Macino¹,

Biferali²,

Cipriano³

et al. 2021

BIO-PROTOCOL

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LncRNAs have been recently implicated in the epigenetic control of muscle differentiation and their functional characterization has traditionally relied upon in vitro models of myogenic differentiation. However, the use of experimental paradigms to specifically target lncRNAs expression in muscle stem cells (MuSCs), also known as satellite cells, represents an important requisite to interrogate their function in more physiological contexts. Since isolation and culture of single myofibers preserves satellite cells within their physiological niche underneath the surrounding basal lamina, this procedure represents the optimal approach to follow satellite cell dynamics ex-vivo, such as activation from quiescence, expansion of committed progenitors, differentiation, and self-renewal. Here, we detail an optimized protocol to isolate viable single myofibers from the extensor digitorum longus (EDL) skeletal muscle of adult mice and to manipulate the expression of lncRNAs by antisense LNA GapmeRsmediated knock-down (KD). Furthermore, we describe a method of EdU incorporation that, coupled to lncRNA KD and subsequent immunofluorescence analysis of proliferating, differentiating, and satellite cell-specific markers, permits the inference of lncRNAs function on muscle stem cells dynamics.www.bio-protocol.org/e4209Bio-protocol 11(21): e4209.

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Epigenetic regulation of Wnt7b expression by thecis-acting long noncoding RNA lnc-Rewind in muscle stem cells

Cited by 6 publications

References 57 publications

Prdm16-mediated H3K9 methylation controls fibro-adipogenic progenitors identity during skeletal muscle repair

Prdm16-mediated H3K9 methylation controls fibro-adipogenic progenitors identity during skeletal muscle repair

Cis-Repression of Foxq1 Expression Affects Foxf2-Mediated Gene Expression in Palate Development

Targeting the Expression of Long Noncoding RNAs in Murine Satellite Cells from Single Myofibers

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