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      Mitochondria-to-nucleus retrograde signaling drives formation of cytoplasmic chromatin and inflammation in senescence

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          Abstract

          In this study, Vizioli et al. investigated the upstream signaling events that promote cytoplasmic formation of chromatin fragments (CCFs), which are extruded from the nucleus of senescent cells and trigger the senescence-associated secretory phenotype (SASP). They show that dysfunctional mitochondria, linked to down-regulation of nuclear-encoded mitochondrial oxidative phosphorylation genes, trigger a ROS–JNK retrograde signaling pathway that drives CCF formation and hence the SASP.

          Abstract

          Cellular senescence is a potent tumor suppressor mechanism but also contributes to aging and aging-related diseases. Senescence is characterized by a stable cell cycle arrest and a complex proinflammatory secretome, termed the senescence-associated secretory phenotype (SASP). We recently discovered that cytoplasmic chromatin fragments (CCFs), extruded from the nucleus of senescent cells, trigger the SASP through activation of the innate immunity cytosolic DNA sensing cGAS–STING pathway. However, the upstream signaling events that instigate CCF formation remain unknown. Here, we show that dysfunctional mitochondria, linked to down-regulation of nuclear-encoded mitochondrial oxidative phosphorylation genes, trigger a ROS–JNK retrograde signaling pathway that drives CCF formation and hence the SASP. JNK links to 53BP1, a nuclear protein that negatively regulates DNA double-strand break (DSB) end resection and CCF formation. Importantly, we show that low-dose HDAC inhibitors restore expression of most nuclear-encoded mitochondrial oxidative phosphorylation genes, improve mitochondrial function, and suppress CCFs and the SASP in senescent cells. In mouse models, HDAC inhibitors also suppress oxidative stress, CCF, inflammation, and tissue damage caused by senescence-inducing irradiation and/or acetaminophen-induced mitochondria dysfunction. Overall, our findings outline an extended mitochondria-to-nucleus retrograde signaling pathway that initiates formation of CCF during senescence and is a potential target for drug-based interventions to inhibit the proaging SASP.

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          Most cited references67

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          The Hallmarks of Aging

          Aging is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death. This deterioration is the primary risk factor for major human pathologies, including cancer, diabetes, cardiovascular disorders, and neurodegenerative diseases. Aging research has experienced an unprecedented advance over recent years, particularly with the discovery that the rate of aging is controlled, at least to some extent, by genetic pathways and biochemical processes conserved in evolution. This Review enumerates nine tentative hallmarks that represent common denominators of aging in different organisms, with special emphasis on mammalian aging. These hallmarks are: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication. A major challenge is to dissect the interconnectedness between the candidate hallmarks and their relative contributions to aging, with the final goal of identifying pharmaceutical targets to improve human health during aging, with minimal side effects. Copyright © 2013 Elsevier Inc. All rights reserved.
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            Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms

            High-throughput mRNA sequencing (RNA-Seq) holds the promise of simultaneous transcript discovery and abundance estimation 1-3 . We introduce an algorithm for transcript assembly coupled with a statistical model for RNA-Seq experiments that produces estimates of abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 million paired 75bp RNA-Seq reads from a mouse myoblast cell line representing a differentiation time series. We detected 13,692 known transcripts and 3,724 previously unannotated ones, 62% of which are supported by independent expression data or by homologous genes in other species. Analysis of transcript expression over the time series revealed complete switches in the dominant transcription start site (TSS) or splice-isoform in 330 genes, along with more subtle shifts in a further 1,304 genes. These dynamics suggest substantial regulatory flexibility and complexity in this well-studied model of muscle development.
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              TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

              TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat.
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                Author and article information

                Journal
                Genes Dev
                Genes Dev
                genesdev
                genesdev
                GAD
                Genes & Development
                Cold Spring Harbor Laboratory Press
                0890-9369
                1549-5477
                1 March 2020
                : 34
                : 5-6
                : 428-445
                Affiliations
                [1 ]Cancer Research UK Beatson Institute, Glasgow G61 1BD, United Kingdom;
                [2 ]Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, United Kingdom;
                [3 ]Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
                [4 ]Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA;
                [5 ]Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA;
                [6 ]Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;
                [7 ]Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota 55905, USA;
                [8 ]Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne NE4 5PL, United Kingdom;
                [9 ]MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh EH1 64TJ, United Kingdom;
                [10 ]Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
                Author notes
                [11]

                These authors contributed equally to this work.

                Article
                8711660
                10.1101/gad.331272.119
                7050483
                32001510
                188a9c97-e359-4265-a188-36d657263923
                © 2020 Vizioli et al.; Published by Cold Spring Harbor Laboratory Press

                This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

                History
                : 2 August 2019
                : 24 December 2019
                Page count
                Pages: 18
                Funding
                Funded by: National Institute on Aging
                Award ID: P01 AG031862-11
                Funded by: Glenn Foundation for Medical Research Postdoctoral Fellowships
                Award ID: PD18082
                Award ID: PD19131
                Award ID: F32 AG066459
                Funded by: Ted Nash Foundation
                Funded by: Cancer Research UK Beatson Institute Core funding
                Award ID: A171196
                Funded by: Wellcome Trust , open-funder-registry 10.13039/100010269;
                Award ID: WT107492Z
                Funded by: National Institutes of Health , open-funder-registry 10.13039/100000002;
                Award ID: K99AG053406
                Award ID: P01 AG031862-11
                Categories
                Research Paper

                cytoplasmic chromatin,inflammation,mitochondria,senescence

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