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

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

PROVIDER: PRJNA295973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2352570_1.fastq.gz	Fastqsanger.gz
	SRR2352570_2.fastq.gz	Fastqsanger.gz
	SRR2352571_1.fastq.gz	Fastqsanger.gz
	SRR2352571_2.fastq.gz	Fastqsanger.gz
	SRR2352572_1.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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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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Genome-wide DNA methylation change due to H19 knockdown and TET3 knockdown in UtLM

Project description:We used Methyl-MiniSeq platform from Zymo Research company to identify genome-wide methylation changes affected by H19 knockdown and TET3 knockdown in human UtLM. Following H19 and TET3 knockdown, we observed extensive genome-wide methylation pattern changes relative to siCon cells, with some genes showing increased methylation, others showing decreased methylation, and a third group with no significant change.

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Project description:Long non-coding RNAs (lncRNAs) regulate diverse cellular processes and are associated with many age-associated diseases. However, the function of lncRNAs in cellular senescence remains largely unknown. Here we characterize the role of lncRNA H19 in senescence. We show that H19 levels decline as cells undergo senescence, and depletion of H19 results in premature senescence. We find that repression of H19 is triggered by the loss of CTCF and prolonged activation of p53 as part of the senescence pathway. Mechanistically, the loss of H19 drives senescence via increased let7b mediated targeting of EZH2. We further demonstrate that H19 is required for senescence inhibition by the mTOR inhibitor rapamycin, where it maintains lncRNA H19 levels throughout the cellular lifespan and thus prevents the reduction of EZH2 that would otherwise lead to cellular senescence. Therefore, lncRNA H19 is crucial in maintaining the balance between sustained cell growth and the onset of senescence.

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

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

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

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