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      FMRP attenuates activity dependent modifications in the mitochondrial proteome

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          Abstract

          Homeostatic plasticity is necessary for the construction and maintenance of functional neuronal networks, but principal molecular mechanisms required for or modified by homeostatic plasticity are not well understood. We recently reported that homeostatic plasticity induced by activity deprivation is dysregulated in cortical neurons from Fragile X Mental Retardation protein (FMRP) knockout mice (Bulow et al. in Cell Rep 26: 1378-1388 e1373, 2019). These findings led us to hypothesize that identifying proteins sensitive to activity deprivation and/or FMRP expression could reveal pathways required for or modified by homeostatic plasticity. Here, we report an unbiased quantitative mass spectrometry used to quantify steady-state proteome changes following chronic activity deprivation in wild type and Fmr1 −/y cortical neurons. Proteome hits responsive to both activity deprivation and the Fmr1 −/y genotype were significantly annotated to mitochondria. We found an increased number of mitochondria annotated proteins whose expression was sensitive to activity deprivation in Fmr1 −/y cortical neurons as compared to wild type neurons. These findings support a novel role of FMRP in attenuating mitochondrial proteome modifications induced by activity deprivation.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s13041-021-00783-w.

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          Most cited references67

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          Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

          Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.
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            The PRIDE database and related tools and resources in 2019: improving support for quantification data

            Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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              ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

              Summary: We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes. ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two lists of genes and comprehensively visualizes functionally grouped terms. A one-click update option allows ClueGO to automatically download the most recent GO/KEGG release at any time. ClueGO provides an intuitive representation of the analysis results and can be optionally used in conjunction with the GOlorize plug-in. Availability: http://www.ici.upmc.fr/cluego/cluegoDownload.shtml Contact: jerome.galon@crc.jussieu.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                pwenner@emory.edu
                gary.bassell@emory.edu
                vfaunde@emory.edu
                Journal
                Mol Brain
                Mol Brain
                Molecular Brain
                BioMed Central (London )
                1756-6606
                30 April 2021
                30 April 2021
                2021
                : 14
                : 75
                Affiliations
                [1 ]GRID grid.189967.8, ISNI 0000 0001 0941 6502, Department of Cell Biology, , Emory University School of Medicine, ; Atlanta, GA 30322 USA
                [2 ]GRID grid.189967.8, ISNI 0000 0001 0941 6502, Department of Physiology, , Emory University School of Medicine, ; Atlanta, GA 30322 USA
                Author information
                http://orcid.org/0000-0002-2114-5271
                Article
                783
                10.1186/s13041-021-00783-w
                8086361
                33931071
                bc735669-e044-4bdc-a0c9-d8db313ba2ee
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 24 January 2021
                : 21 April 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: 1R01MH109026
                Award ID: R01NS065992
                Award ID: 1RF1AG060285
                Award Recipient :
                Categories
                Research
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                © The Author(s) 2021

                Neurosciences
                fmrp,homeostatic plasticity,mitochondria,proteomics,neurodevelopmental disorder,autism
                Neurosciences
                fmrp, homeostatic plasticity, mitochondria, proteomics, neurodevelopmental disorder, autism

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