Dataset Information

ATAC-seq in Ranbp2 Wild-type and knockout 10T1/2 cells

ABSTRACT: Mitochondria regulate cellular processes through direct and indirect interactions with other organelles. A well-studied example is contact with the endoplasmic reticulum at mitochondrial-associated ER membranes (MAMs), which control pathways including redox and calcium homeostasis. Recent studies also reported direct mitochondria–nuclear membrane contacts in cancer cells and yeast that promote pro-survival signaling, but how exchange occurs across two largely impermeable membranes remains unclear. Here, we describe the existence of direct interactions between the nuclear pore and the mitochondria. In two unbiased proteomic screens, GST pulldown and BioID, VDAC1 was the top mitochondrial candidate that interacts with the nuclear pore protein RANBP2. In vitro RANBP2 CRISPR knock-out, RANBP2 truncation, or site directed mutagenesis of RANBP2-interacting amino acids in VDAC1 resulted in reduced mitochondria-nucleus proximity and decreased nuclear ATP and phosphocreatine levels. This was accompanied by a decline in levels of the nuclear phosphoproteome, and downregulation of pathways involved in histone modification, cellular differentiation and transcriptional regulation in vitro. We show differential ATAC peaks in Ranbp2 Wildtype and knockout cells in 10T1/2. Moreover, deletion of RANBP2 C-terminal domain in vivo in mice resulted in embryonic lethality due to cardiac and neural crest differentiation defects. Collectively, these results describe a mechanism by which mitochondria directly interact with the NPC, a phenomenon which is critical for regulation nuclear energetics and cellular differentiation during embryonic development.

ORGANISM(S): Mus musculus

PROVIDER: GSE324952 | GEO | 2026/03/17

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:SEPN1 is a type II protein of the endoplasmic reticulum (ER) whose loss of function gives rise to a collection of debilitating autosomal recessive myopathies gathered under the umbrella term of SEPN1-related myopathy (RM). At the moment, SEPN1-RM lacks an effective pharmacological treatment; thus, the medical management of the disease is only supportive. The potentially fatal diaphragmatic weakness leading to respiratory insufficiency in patients still ambulant is the main reason for medical concerns. Thus, studies on SEPN1-RM pathogenesis are necessary to implement a targeted pharmacological therapy aimed at relieving the general muscle weakness and the more worrisome diaphragmatic dysfunction. Here, we show a physical and functional interaction between SEPN1 and the ER stress mediator ERO1 alpha (henceforth, ERO1). Both SEPN1 and ERO1 are involved in the redox regulation of proteins into the ER, although in an opposite way SEPN1 imposes a less oxidant ER poise while ERO1 a more oxidant one, conceivable with a reductase function of SEPN1 and an oxidase one of ERO1. Furthermore, both are mainly localized in a region of the ER in close contact with mitochondria termed mitochondria-associated membranes (MAMs) and their loss impacts oppositely on the short-range MAMs, thereby impinging ER-mitochondria Ca2+ dynamics, OXPHOS, and bioenergetics. We find that ERO1 depletion restores the impaired short-range MAMs due to SEPN1 loss together with mitochondrial ATP. ERO1 knockout in a mouse background of SEPN1 loss blunts ER stress and the consequent Unfolded Protein Response (UPR) while it rescues the diaphragmatic weakness by improving ER/mitochondria contacts, calcium dynamics, and OXPHOS. Importantly, treatments of SEPN1 knock out mice with the chemical chaperone tauroursodeoxycholic acid (TUDCA) mimic the results of ERO1 loss improving calcium dynamics, OXPHOS, ER/mitochondria contacts, thereby rescuing diaphragmatic weakness as well. In addition, TUDCA-treated SEPN1-RM patients-derived myoblasts show a dynamic dose-dependent increase in ATP levels under ER stress conditions suggesting improved mitochondrial function. Thus, our findings point to the ERO1 axis in the pathogenesis of SEPN1-RM thereby impinging on MAMs and mitochondria bioenergetics and recall for the efficacy of a pharmacology therapy with ad hoc ER stress/ERO1 inhibitors for SEPN1-RM.

Project description:Mitochondria are subcellular organelles that are more than just the powerhouse of cells, they also dictate if a cell dies or survives. The mitochondrial outer-membrane voltage-dependent anion channel 1 (VDAC1) has been shown to play a crucial role in metabolism and apoptosis, however its involvement in ischemic pathologies and cancer is not clear. Transcriptome analysis of Vdac1-/- mouse embryonic fibroblasts (MEF) highlighted cancer and inflammation as top diesases but also activation of the HIF-1 signaling pathway in normoxia. HIF-1α protein was stable due to ROS accumulation that decreased respiration and glycolysis and maintained basal apoptosis. However, in hypoxia increased activation of ERK in combination with maintenance of respiration and increased glycolysis counterbalanced the deleterious effects of ROS, thereby allowing Vdac1-/- MEF to proliferate better than wild-type MEF. Xenografts of RAS-transformed Vdac1-/- MEF in mice showed stabilization of both HIF-1α and HIF-2α which led to blood vessel destabilization and a strong inflammatory response. Moreover, expression of Cdkn2a, a HIF-1-target and tumor suppressor gene, was strongly decreased. Consequently RAS-transformed Vdac1-/- MEF tumors grew faster than wild-type MEF tumors. These findings provide new perspectives into the understanding of VDAC1 in the function of mitochondria not only in cancer but also in inflammatory diseases. Profiling of VDAC1-/- and wild-type (Wt) Mouse Embryonic Fibroblasts (MEFs) was performed using whole genome mouse microarrays. in normoxic or hypoxic conditions. MEF (Wt and Vdac1-/-) were incubated in normoxia (Nx, ie: 20% O2) or hypoxia (Hx, ie: 1% O2) for 72h and then lysed prior to RNA isolation, labelling and hybridization on microarrays. One color experiment with 2 biological replicates (marked 1 or 2) of the 4 experimental conditions. One condition (MEF WT Nx2) has been removed from the statistical analysis after microarray quality check due to high background. Total of 7 samples.

Dataset Information

ATAC-seq in Ranbp2 Wild-type and knockout 10T1/2 cells

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets