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Dataset on the identification of differentially expressed genes by annealing control primer-based PCR in mitochondrial DNA-depleted myocytes.

ABSTRACT: Changes in the mitochondrial DNA (mtDNA) content are believed to initiate a stress signal that leads to alterations in nuclear gene expression. This article presents data on the identification of nuclear genes that are expressed differentially in response to changes in the mtDNA content in myocytes using annealing controlled primers (ACP)-based PCR technology. The data obtained from L6 GLUT4myc myocytes showed that a total of 19 ACPs produced differentially expressed PCR amplicons in the mtDNA-depleted myocytes. Among those, 13 amplicons were cloned, sequenced, and identified successfully based on the GenBank database. To validate the efficacy of ACP-based PCR analysis, three differentially expressed genes (DEG10, 22 and 26) were confirmed by PCR using the specific primers. The further analysis and detailed results of DEG22 and its functional significance can be found in "C1q tumor necrosis factor alpha-related protein isoform 5 is increased in mitochondrial DNA-depleted myocytes and activates AMP-activated protein kinase." [1].

SUBMITTER: Yang WM

PROVIDER: S-EPMC5320051 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Dataset on the identification of differentially expressed genes by annealing control primer-based PCR in mitochondrial DNA-depleted myocytes.

Yang Won-Mo WM Min Kyung-Ho KH Lee Wan W

Data in brief 20170213

Changes in the mitochondrial DNA (mtDNA) content are believed to initiate a stress signal that leads to alterations in nuclear gene expression. This article presents data on the identification of nuclear genes that are expressed differentially in response to changes in the mtDNA content in myocytes using annealing controlled primers (ACP)-based PCR technology. The data obtained from L6 GLUT4myc myocytes showed that a total of 19 ACPs produced differentially expressed PCR amplicons in the mtDNA-d ...[more]

PMID: 28243623

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Project description:In ventricular myocardium, extracellular matrix (ECM) remodeling is a hallmark of physiological and pathological growth, coincident with metabolic rewiring of cardiac myocytes. However, the direct impact of the biochemical and mechanical properties of the ECM on the metabolic function of cardiac myocytes is mostly unknown. Furthermore, understanding the impact of distinct biomaterials on cardiac myocyte metabolism is critical for engineering physiologically-relevant models of healthy and diseased myocardium. For these reasons, we systematically measured morphological and metabolic responses of neonatal rat ventricular myocytes cultured on fibronectin- or gelatin-coated polydimethylsiloxane (PDMS) of three elastic moduli and gelatin hydrogels with four elastic moduli. On all substrates, total protein content, cell morphology, and the ratio of mitochondrial DNA to nuclear DNA were preserved. Cytotoxicity was low on all substrates, although slightly higher on PDMS compared to gelatin hydrogels. We also quantified oxygen consumption rates and extracellular acidification rates using a Seahorse extracellular flux analyzer. Our data indicate that several metrics associated with baseline glycolysis and baseline and maximum mitochondrial function are enhanced when cardiac myocytes are cultured on gelatin hydrogels compared to all PDMS substrates, irrespective of substrate rigidity. These results yield new insights into how mechanical and biochemical cues provided by the ECM impact mitochondrial function in cardiac myocytes. STATEMENT OF SIGNIFICANCE: Cardiac development and disease are associated with remodeling of the extracellular matrix coincident with metabolic rewiring of cardiac myocytes. However, little is known about the direct impact of the biochemical and mechanical properties of the extracellular matrix on the metabolic function of cardiac myocytes. In this study, oxygen consumption rates were measured in neonatal rat ventricular myocytes maintained on several commonly-used biomaterial substrates to reveal new relationships between the extracellular matrix and cardiac myocyte metabolism. Several mitochondrial parameters were enhanced on gelatin hydrogels compared to synthetic PDMS substrates. These data are important for comprehensively understanding matrix-regulation of cardiac myocyte physiology. Additionally, these data should be considered when selecting scaffolds for engineering in vitro cardiac tissue models.

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Dataset Information

Dataset on the identification of differentially expressed genes by annealing control primer-based PCR in mitochondrial DNA-depleted myocytes.

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Dataset on the identification of differentially expressed genes by annealing control primer-based PCR in mitochondrial DNA-depleted myocytes.

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