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Mus musculus

ABSTRACT: Genome-wide DNA methylation change due to lncRNA H19 knockdown in myotubes

PROVIDER: PRJNA296100 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2397281_1.fastq.gz	Fastqsanger.gz
	SRR2397281_2.fastq.gz	Fastqsanger.gz
	SRR2397282_1.fastq.gz	Fastqsanger.gz
	SRR2397282_2.fastq.gz	Fastqsanger.gz

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Genome-wide DNA methylation change due to lncRNA H19 knockdown in myotubes

Project description:We used Methyl-MiniSeq platform from Zymo Research company to identify genome-wide methylation changes affected by lncRNA H19 knockdown in myotubes. Following H19 knockdown, we observed extensive genome-wide mthylation pattern changes relative to siCon cells, with some genes showing incresed methylation, others showing decreased methylation, and a third group with no significant change. Myotubes differentiated from mouse C3H myoblasts were transfected with either control siRNA or siH19, 48h later, cellular genomic DNA was extracted and subjected to genome-scale DNA methylation mapping using the platform of an improved version of Reduced Representation Bisulfite Sequencing (RRBS).

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Genome-wide DNA methylation change due to lncRNA H19 knockdown in myotubes

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Genome-wide DNA methylation change due to H19 knockdown and TET3 knockdown in UtLM

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Protein Identification and Post-translational Analysis of DMD and its associated Proteins in H19-proficient and -deficient Cells

Project description:Dystrophin proteomic regulation in Muscular Dystrophies (MD) remains unclear. We report that a long noncoding RNA (lncRNA) H19 associates with dystrophin. To investigate the biological roles of this interaction in vivo, we performed mass spectrometry analysis of dystrophin and its associated proteins in H19-proficient and -deficient C2C12 myotubes. Mass spectrometry data indicated that in H19-proficient myotubes, dystrophin associates with components of dystrophin-associated protein complex (DPC); however, in H19-deficient myotubes, dystrophin associated with UBA1, UB2G1, TRIM63 ubiquitin E3 ligase and ubiquitin. In H19-deficient myotubes, dystrophin was post-translationally modified with K48-linked poly-ubiquitination at Lys3577 (referred to as Ub-DMD). This mass spectrometry study demonstrated that lncRNA H19, associates with dystrophin and inhibits E3 ligase-dependent Ub-DMD formation and its subsequent proteasomal degradation. Based on this study, H19 RNA oligonucleotides conjugated with a muscle homing ligand Agrin (referred to as AGR-H19) and Nifenazone, a TRIM63-specific small molecule inhibitor, reverses the dystrophin degradation in iPSC-derived skeletal muscle cells from Becker Muscular Dystrophy patients. Furthermore,treatment of mdx mice with exon-skipping reagent, in combination with either AGR-H19 or Nifenazone, dramatically stablized dystrophin, preserved skeletal/cardiac muscle histology, and improved strength/heart function. In summary, this mass spectrometry study paves the way to meaningful targeted therapeutics for BMD and certain DMD patients.

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Project description:We used high throughput sequencing to analyze the transcriptional profiling of myotubes. By comparing the transcriptional profiling of myotubes with or without H19 knockdown,1131 genes or transcripts were found at least 1.5-fold up-regulated in siH19 relative to siCon cells, meanwhile 508 genes or transcripts were found at least 1.5-fold down-regulated in siH19 over siCon cells.

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