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Real-time quantitative PCR analysis of primary human dermal fibroblasts_comparing two young samples (fibroblasts isolated from a 5 month old vs. those from a 1 year old)

ABSTRACT: Endogenous changes in the nuclear encoded genes of the mitochondrial ETC were analyzed using the mitochondrial energy metabolism profiler array from Qiagen to compare nuclear-encoded gene expression changes between fibroblasts isolated from two young patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE100409 | GEO | 2017/06/23

SECONDARY ACCESSION(S): PRJNA391585

REPOSITORIES: GEO

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Real-time quantitative PCR analysis of primary human dermal fibroblasts_comparing young (5 month old) and old (78 years old) samples treated with GC4419

Project description:To analyze the age-associated changes in the nuclear encoded genes of the mitochondrial ETC following treatment with a Superoxide dismutase mimetic GC4419 using the mitochondrial energy metabolism profiler array from Qiagen.

2017-07-08 | GSE100920 | GEO

Ophthalmologic findings in an 18-month-old boy with focal dermal hypoplasia.

Project description:Focal dermal hypoplasia is a rare X-linked dominant disorder with in utero lethality in males. Affected patients have been reported to have several different mutations in the PORCN gene on chromosome Xp11.23. Dysplastic mesodermal and ectodermal tissue causes clinical findings in the skin, skeleton, teeth, central nervous system, and eyes of affected patients. We describe the ophthalmologic findings in an 18-month-old boy with mosaicism of a novel mutation in PORCN.

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Anterograde Regulation of Nuclear-encoded Mitochondrial Genes and FGF21 Signaling by Hepatic Histone Demethylase LSD1

Project description:Mitochondrial biogenesis and function are controlled by anterograde regulatory pathways involving more than one thousand proteins encoded by nuclear genome. Transcriptional networks controlling the nuclear-encoded mitochondrial genes remain elucidated. Here we show that histone demethylase LSD1 knockout from adult mouse liver (LSD1-LKO) reduces one-third of all nuclear-encoded mitochondrial genes and decreases mitochondrial biogenesis and function. LSD1-modulated histone methylation epigenetically regulates nuclear-encoded mitochondrial genes. Furthermore, LSD1 targets methylation of nicotinamide mononucleotide adenylyltransferase 1 (NMNAT1), the rate-limiting enzyme for nuclear NAD+ synthesis. Hepatic LSD1 knockout reduces NAD+-dependent Sirt1 and Sirt7 deacetylase activity, leading to hyperacetylation and hypofunctioning of GABP and PGC-1, the major transcriptional factor/cofactor for nuclear-encoded mitochondrial genes. Despite the reduced mitochondrial function, LSD1-LKO mice are protected from diet-induced hepatic steatosis and glucose intolerance, partially due to induction of hepatokine FGF21. Thus, LSD1 orchestrates a core regulatory network involving epigenetic modifications and NAD+ synthesis to control mitochondrial function and hepatokine production.

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Global changes of transcriptomes between 3-month-old and 1-year-old human right atria

Project description:Previous study showed that there are more cell cycle active cardiomyocytes (CMs) in 3-month-old (3M) than1-year-old (1Y) human atria, and extracellular matrix (ECM) from mouse atria benefits neonatal CMs proliferation. We investigate the global changes of transcriptomes between 3M and 1Y human atria and whether ECM from 3M human atria improves myocardium infarct recovery. RNAseq results showed that the major changes between 3M and 1Y human atria were ECM. 3M –ECM increased CM cell cycle activities and rescue mouse heart from injury. We conclude that 3M-ECM hold a therapeutic effect on myocardium infarction.

2020-07-02 | PXD020148 |

Anterograde Regulation of Nuclear-encoded Mitochondrial Genes and FGF21 Signaling by Hepatic Histone Demethylase LSD1 [RNA-seq]

Project description:Mitochondrial biogenesis and function are controlled by anterograde regulatory pathways involving more than one thousand nuclear-encoded proteins. Transcriptional networks controlling the nuclear-encoded mitochondrial genes remain fully elucidated. Here we show that histone demethylase LSD1 knockout from adult mouse liver (LSD1-LKO) reduces one-third of all nuclear-encoded mitochondrial genes and decreases mitochondrial biogenesis and function. ChIP-seq analysis shows that LSD1 and LSD1-targeted H3K4me2 modulate the expression of mitochondrial genes in liver.

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Coordination and assembly of protein complexes encoded across mitochondrial and nuclear genomes is assisted by mtCLPXP in Arabidopsis thaliana

Project description:Protein homeostasis in eukaryotic organelles and their progenitor prokaryotes is regulated by a series of ATP-dependent proteases including the caseinolytic protease complex (ClpXP). In chloroplasts, ClpXP has essential roles in organelle biogenesis and maintenance , but the significance of the plant mitochondrial ClpXP remains unknown and factors that aid coordination of nuclear and mitochondrial encoded subunits for complex assembly in mitochondria await discovery. In this study, we generated knock-out lines of the single copy mitochondrial Clp protease subunit, CLPP2, in Arabidopsis thaliana. They have higher abundance of transcripts from mitochondrial genes encoding OXPHOS protein complexes, while transcripts for nuclear genes encoding other subunits of the same complexes showed no change in transcript abundance. In contrast, the protein abundance of specific nuclear-encoded subunits in OXPHOS complexes I and V increased in knockouts, without accumulation of mitochondrial-encoded counterparts in the same complex. Protein complexes mainly or wholly encoded in the nucleus were unaffected. Analysis of protein import, assembly and function of Complex I revealed that while function was retained, protein homeostasis was disrupted through slower assembly, leading to accumulation of soluble subcomplexes of nuclear-encoded subunits after import. It is proposed that CLPP contributes to the mitochondrial protein degradation network through supporting coordination and assembly of protein complexes encoded across mitochondrial and nuclear genomes.

2019-12-13 | GSE141942 | GEO

Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages [RNA-seq]

Project description:Mitochondrial biogenesis requires precise regulation of both mitochondrial-encoded and nuclear-encoded genes. Nuclear receptor Nur77 is known to regulate mitochondrial metabolism in macrophages and skeletal muscle cells. Here, we compared genome-wide Nur77 binding site and target gene expression in these two cell types, which revealed conserved roles for this nuclear receptor in the regulation of nuclear-encoded mitochondrial ribosomal proteins (MRP) and enrichment of motifs for the transcription factor Yin-Yang 1 (YY1). We show that Nur77 and YY1 interact, that YY1 increases Nur77 activity, and that their binding sites are co-enriched at MRP gene loci. Nur77 and YY1 co-expression synergistically increases mitochondrial abundance and activity in macrophages but not skeletal muscle. As such, we identify a macrophage-specific Nur77-YY1 interaction that enhances mitochondrial metabolism.

2024-05-07 | GSE263316 | GEO

Nuclear receptor Nur77 and Yin-Yang 1 synergistically increase mitochondrial abundance and activity in macrophages [ChIP-seq]

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tRNA Over-Expression in Breast Cancer

Project description:Increased proliferation and elevated levels of protein synthesis are characteristic of transformed and tumor cells. Though components of the translation machinery are often misregulated in cancers, how tRNA plays a role in cancer cells has not been explored. We compare genome-wide tRNA expression in tumorigenic versus non-tumorigenic breast cell lines, as well as tRNA expression in breast tumors versus normal breast tissues. In tumorigenic versus non-tumorigenic cell lines, nuclear-encoded tRNAs increase by up to 3-fold and mitochondrial-encoded tRNAs increase by up to 5-fold. In tumors versus normal breast tissues, both nuclear and mitochondrial-encoded tRNAs increase by up to 10-fold. This tRNA over-expression is selective and coordinates with the properties of cognate amino acids. Nuclear- and mitochondrial-encoded tRNAs exhibit distinct expression patterns, indicating that tRNAs can be used as biomarkers for breast cancer. We analyzed tRNA expression levels in 2 non-tumorigenic breast cell lines, 6 tumorigenic breast cancer cell lines, 3 normal breast tissue samples, and 9 breast tumor samples. We used a non-tumorigenic breast cell line (MCF10A) as a reference sample in all hybridizations. All data is dye-swapped.

2010-05-22 | E-GEOD-17945 | biostudies-arrayexpress

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