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The Unique Function of Runx1 in Skeletal Muscle Differentiation and Regeneration is Mediated by an ETS Interaction Domain (ATAC-Seq)

ABSTRACT: The conserved Runt-related (RUNX) transcription factor family are well-known master regulators of developmental and regenerative processes. Both Runx1 and Runx2 are expressed in satellite cells (SC) and skeletal myotubes. Conditional deletion of Runx1 in adult SC negatively impacted self-renewal, and skeletal muscle maintenance was impaired; Runx1-deficient SC cannot support muscle regeneration in response to injury. To determine the unique molecular functions of Runx1 that cannot be compensated by Runx2 we deleted Runx1 in C2C12 that retain Runx2 expression and established that myoblasts differentiation was blocked in vitro due in part to ectopic expression of Mef2c, a target repressed by Runx1. Structure-function analysis demonstrated that the Ets-interacting MID/EID region of Runx1 absent from Runx2 is critical to regulating myoblasts proliferation, differentiation, and fusion. Analysis of in-house and published ChIP-seq datasets from Runx1 (T-cells, muscle) versus Runx2 (preosteoblasts) dependent tissue identified enrichment for a Ets:Runx composite site in Runx1-dependent tissues. Comparing ATACseq datasets from WT and Runx1KO C2C12 cells showed that the Ets:Runx composite motif was enriched in peaks open exclusively in WT cells compared to peaks unique to Runx1KO cells. Thus, engagement of a set of targets by the RUNX1/ETS complex define the non-redundant functions of Runx1

ORGANISM(S): Mus musculus

PROVIDER: GSE248044 | GEO | 2023/11/17

REPOSITORIES: GEO

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The Unique Function of Runx1 in Skeletal Muscle Differentiation and Regeneration is Mediated by an ETS Interaction Domain (RNA-Seq)

Project description:The conserved Runt-related (RUNX) transcription factor family are well-known master regulators of developmental and regenerative processes. Both Runx1 and Runx2 are expressed in satellite cells (SC) and skeletal myotubes. Conditional deletion of Runx1 in adult SC negatively impacted self-renewal, and skeletal muscle maintenance was impaired; Runx1-deficient SC cannot support muscle regeneration in response to injury. To determine the unique molecular functions of Runx1 that cannot be compensated by Runx2 we deleted Runx1 in C2C12 that retain Runx2 expression and established that myoblasts differentiation was blocked in vitro due in part to ectopic expression of Mef2c, a target repressed by Runx1. Structure-function analysis demonstrated that the Ets-interacting MID/EID region of Runx1 absent from Runx2 is critical to regulating myoblasts proliferation, differentiation, and fusion. Analysis of in-house and published ChIP-seq datasets from Runx1 (T-cells, muscle) versus Runx2 (preosteoblasts) dependent tissue identified enrichment for a Ets:Runx composite site in Runx1-dependent tissues. Comparing ATACseq datasets from WT and Runx1KO C2C12 cells showed that the Ets:Runx composite motif was enriched in peaks open exclusively in WT cells compared to peaks unique to Runx1KO cells. Thus, engagement of a set of targets by the RUNX1/ETS complex define the non-redundant functions of Runx1

2023-11-17 | GSE248045 | GEO

Critical Role of Runx Transcription Factors in Maintaining Epididymal Epithelial Differentiation [RNA-seq II]

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Comprehensive analysis of the proteome, phosphoproteome and N-linked sialylated glycoproteome of C2C12 myoblasts

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Project description:This study aimed to interrogate the interrelationship between 3D genome organization and global gene expression during muscle development using a mouse C2C12 cell line as an in vitro model. The C2C12 cell line is a well-established and extensively studied in vitro model derived from serial passage of myoblasts cultured from the thigh muscle of C3H mice after a crush injury. C2C12 cells divide when mitogens are present in the culture medium and spontaneously differentiate into muscle-like multinucleated (myotubes) cells if the medium is depleted of mitogens (i.e. serum; (Bischoff 1986)). C2C12 cells were either harvested as: 1) proliferating myoblasts (Myoblasts); 2) myotubes that were not treated with AraC (as such these myotubes contained myoblasts) - Myotubes(Day3); or 3) myotubes which were treated with AraC (myoblasts were largely depleted from these myotube cultures; Myotubes(Day7+AraC).

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Cluster regulation of RUNX family by "gene switch" triggers a profound tumor regression of diverse origins.

Project description:Although Runt-related transcription factor 1 (RUNX1) has been generally considered to be a tumor suppressor, a growing body of evidence strongly suggests its pro-oncogenic property in acute myeloid leukemia (AML), Here we demonstrate that anti-leukemic effect mediated by RUNX1 depletion is highly dependent on a functional p53-mediated cell death pathway. Based on our present findings, anti-tumor effect elicited by RUNX1 silencing was compensated by the other RUNX family members such as RUNX2 and RUNX3, and a simultaneous attenuation of whole RUNX family members as a cluster displayed a much stronger anti-tumor effect relative to their individual suppression. Notably, switching off RUNX cluster utilizing the novel alkylating agent-conjugated pyrrole-imidazole (PI) polyamides, which specifically bound to the consensus RUNX-binding sequences, was highly effective against leukemia as well as dismal-prognostic solid tumors arising from diverse origins in vivo without any significant adverse events. Together, this work identifies the crucial role of RUNX cluster in the maintenance and the progression of cancer cells, and the indicated gene switch technology-dependent its modulation would be a novel strategy to control malignancies.

2017-03-26 | GSE94835 | GEO

Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation

Project description:We report that differentiation of the C2C12 myoblast line on patterened hydrogels results in the increased expression of muscle sarcomere genes and more closely models expression changes that happen in in vivo muscle differentiation than do C2C12 myoblasts cultured on unpatterened substrates.

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Expression data for C2C12 differentiation disrupted by Lrrfip1 knockdown

Project description:C2C12 myoblasts differentiation is a precise controlled process. Splicing of many genes changes during the differentiation process. Some muscle-specific splicing isoforms play important role in myogenesis. We used microarrays to detail the global programme of gene expression underlying defect of lrrfip1a, a muscle specific splicing isoform of Lrrfip1. Differentiated C2C12 myoblasts shLUCI or shLrrfip1a were collected and extracted RNA, then hybridizated on Affymetrix. We sought to obtain the different expressed genes between shLUCI and shLrrfip1a samples.

2015-04-01 | E-GEOD-66924 | biostudies-arrayexpress

Characteristics of the transcriptome of a nurse cell harboring muscle larva of Trichinella spiralis

Project description:Muscle larva of a parasitic nematode Trichinella spp. lives a portion of muscle fiber transformed to a nurse cell (NC). The NC is formed from miss-differentiated muscle satellite cells which have fused with a parasite-invaded degenerating myofiber. Though originating from muscle cells, the NC is of non-muscular type.The NC is multinuclear and hypertrophic. Molecular mechanism of the NC development remains largely unknown. The microarray project was aimed at characterization of the NC transcriptome. The NCs were isolated by enzymatic digestion from infected mouse striated muscles. Murine C2C12 myogenic cell line (ATCC) was cultured in vitro. Differentiation of myoblasts into myotubes was carried out for 6 days in a high-glucose DMEM supplemented with 2% heat-inactivated horse serum, on the plates covered with laminin and collagen IV.The NC transcriptome was referred to the transcriptomes of C2C12 myoblasts and C2C12 myotubes in two sets of camparative expression microarray hybridization experiments, NC vs myoblasts and NC vs myotubes, respectively.

2022-07-26 | E-MTAB-12042 | biostudies-arrayexpress

Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion.

Project description:Runx2 is a metastatic transcription factor (TF) increasingly expressed during prostate cancer (PCa) progression. Using PCa cells conditionally expressing Runx2, we previously identified Runx2-regulated genes with known roles in epithelial-mesenchymal transition, invasiveness, angiogenesis, extracellular matrix proteolysis and osteolysis. To map Runx2-occupied regions (R2ORs) in PCa cells, we first analyzed regions predicted to bind Runx2 based on the expression data, and found that recruitment to sites upstream of the KLK2 and CSF2 genes was cyclical over time. Genome-wide ChIP-seq analysis at a time of maximum occupancy at these sites revealed 1,603 high-confidence R2ORs, enriched with cognate motifs for RUNX, GATA and ETS TFs. The R2ORs were distributed with little regard to annotated transcription start sites (TSSs), mainly in introns and intergenic regions. Runx2-upregulated genes, however, displayed enrichment for R2ORs within 40 kb of their TSSs. The main annotated functions enriched in 98 Runx2-upregulated genes with nearby R2ORs were related to invasiveness and membrane trafficking/secretion. Indeed, using SDS-PAGE, mass spectrometry and western analyses, we show that Runx2 enhances secretion of several proteins, including fatty acid synthase and metastasis-associated laminins. Thus, combined analysis of Runx2’s transcriptome and genomic occupancy in PCa cells lead to defining its novel role in regulating protein secretion. Examination of Runx2 in Prostate Cancer cells

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