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Linkages between 3D genome organization and transcriptome during muscle cell development

ABSTRACT: 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)).

ORGANISM(S): Mus musculus

PROVIDER: GSE84279 | GEO | 2017/04/07

SECONDARY ACCESSION(S): PRJNA328513

REPOSITORIES: GEO

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Transcriptome changes during the differentiation of myoblasts into myotubes

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).

2017-04-07 | GSE84158 | GEO

long read RNA-seq from C2C12 (ENCSR418ZYU)

Project description:Myoblast cell line derived from thigh muscle of C3H mice after crush injury For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2022-12-04 | GSE219813 | GEO

Novel RNA-binding activity of MYF5 enhances Ccnd1/Cyclin D1 mRNA translation during myogenesis

Project description:Skeletal muscle contains long multinucleated and contractile structures known as muscle fibers, which arise from the fusion of myoblasts into nucleated myotubes during myogenesis. The myogenic regulatory factor (MRF) MYF5 is the earliest to be expressed during myogenesis and functions as a transcription factor in muscle progenitor cells (satellite cells) and myocytes. In mouse C2C12 myocytes, MYF5 is implicated in the initial steps of myoblast differentiation into myotubes. Ribonucleoprotein immunoprecipitation (RIP) analysis showed that MYF5 bound a subset of myoblast mRNAs; prominent among them was Ccnd1 mRNA, which encodes the key cell cycle regulator CCND1 (Cyclin D1). Biotin-RNA pulldown, UV-crosslinking, and gel shift experiments indicated that MYF5 was capable of binding the 3' untranslated region (UTR) and the coding region (CR) of Ccnd1 mRNA. MYF5 silencing in proliferating growing myoblasts revealed that and MYF5 promoted CCND1 translation, and it also modestly increased transcription of Ccnd1 mRNA. Importantly, silencing MYF5 reduced myoblast growth as well as differentiation of myoblasts into myotubes, while overexpressing MYF5 in C2C12 cells upregulated CCND1 expression. We propose that MYF5 enhances early myogenesis in part by coordinately elevating Ccnd1 transcription and Ccnd1 mRNA translation. Four replicates were utilized from either Control (IgG) or MYF5-immunoprecipitated RNA samples from C2C12 cells growing in either growth medium (GM) or differentiation medium (DM) for a total of sixteen samples.

2016-08-08 | E-GEOD-73704 | biostudies-arrayexpress

The transcriptome and m6A-epitranscriptome during skeletal muscle differentiation

Project description:Mouse C2C12 myoblasts were used to mimic skeletal muscle differentiation in vitro.Using RNA-seq and MeRIP-seq, we generated the tascriptome and epitranscriptome data of undifferentited C2C12 myoblasts in growth medium (GM) and differentiated myotubes in differentitation medium for 4 days (D4).

2021-07-22 | GSE180431 | GEO

C2C12 Mouse Skeletal Muscle Cells Grown in Differentiation Medium for 5 Days.

Project description:C2C12 mouse skeletal muscle cells grown in differentiation medium for 5 days. Keywords: other

2005-12-09 | GSE3787 | GEO

A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation

Project description:To study the function of E3 ligase Huwe1 knockdown on C2C12 proliferation and differentiation, we use mRNA-seq to compare gene expression profiles between control wild-type C2C12 myoblasts and two Huwe1 knockdown C2C12 cell lines generated by different shRNAs on differentiation Day 0 (proliferation medium) and Day 6 (differentiation medium for 6 days). To study the potential roles of Huwe1 in maintainance of muscle morphology, we use mRNA-seq to compare gene expression profiles between control and Huwe1 knockdown myotubes. To study whether downregulation of USP10 deubiquitinase is of functional significance during muscle differentiation, we compare gene expression profiles between control wildtype and USP10 overexpressing C2C12 cells on differentiation Day 6.

2015-09-30 | GSE72105 | GEO

Transcription profiling of p68/72 deficient C2C12 cells cultured in either growth medium or differentiation medium to investigate the function of p68/p72 in muscle gene expression and skeletal C2C12 cell differentiation.

Project description:This project investigates the function of p68/p72 in muscle gene expression and skeletal C2C12 cell differentiation. p68/p72 in C2C12 cells cultured in either growth medium (GM) or differentiation medium (DM) was knocked down using shRNA p68/p72 retrovirus, and globle gene expression was profiled using Affymetrix MOE 430A and 430B GeneChip. Experiment Overall Design: The specific aim is to study muscle gene expression changes and skeletal muscle differenciation using RNA interference of p68/p72 in C2C12 cells.

2007-11-29 | E-GEOD-5305 | biostudies-arrayexpress

p68 SMC differentiation

2006-07-13 | GSE5305 | GEO

Changes in WT C2C12 Mouse Muscle Myoblast gene expression throughout differentiation.

Project description:Genesis of skeletal muscle relies on the differentiation and fusion of mono-nucleated muscle progenitor cells into the multi-nucleated muscle fiber syncytium. The temporally-controlled cellular and morphogenetic changes underlying this process are initiated by a series of highly coordinated transcription programs. Ultimately, highly specific coordination of these transcription programs is critical for their masterfully timed transitions, which in turn facilitate the intricate generation of skeletal muscle fibers from a naïve pool of progenitor cells. This work aims to categorize changes of gene expression in vitro in C2C12 mouse muscle myoblasts while they begin to form these multinucleated myotubes.

2024-04-03 | GSE247438 | GEO

Expression data from transfected C2C12 cell lines

Project description:Skeletal muscle differentiation is a highly coordinated multistep process in which proliferating mononucleated myoblasts ﬁrst withdraw from the cell cycle, then differentiate into postmitotic mononucleated myocytes, and subsequently fuse into multinucleated myotubes which ﬁnally bundle to form mature muscle ﬁbers. All these processes are controlled by the sequential activation of myogenic regulatory factors, and especially MYOD1 is activated in the early phase to promote the transcription of muscle-specific genes coding for muscle proteins such as alpha-actin, myosin heavy chain and muscle creatine kinase. We used microarrays to detail the global gene expression changes associated with MYOD1 L122R mutation and identified MYOD1 L122R blocked myogenic differentiation and had a MYC-like transcriptional potential. C2C12 mouse myoblast cells were introduced wild type MYOD1, MYOD1 L122R, MYC, and GFP by retroviral infection. For retrovirus production, the pcx4 and pBabe vectors system were used. Retroviruses were obtained by using 293T cells as packaging cells, and were infected into C2C12 cell line and selected with 500 μg/ml Zeocin (Invitrogen, Carlsbad, CA, USA). After selection, RNAs were extracted and processed at MSKCC according to procedures recommended by Affymetrix (Santa Clara, CA, USA).

2014-05-01 | E-GEOD-56079 | biostudies-arrayexpress

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