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      Valproic Acid Causes Proteasomal Degradation of DICER and Influences miRNA Expression

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          Abstract

          Valproic acid (VPA) is a commonly used drug to treat epilepsy and bipolar disorders. Known properties of VPA are inhibitions of histone deacetylases and activation of extracellular signal regulated kinases (ERK), which cannot fully explain VPA’s clinical features. We found that VPA induces the proteasomal degradation of DICER, a key protein in the generation of micro RNAs. Unexpectedly, the concentration of several micro RNAs increases after VPA treatment, which is caused by the upregulation of their hosting genes prior to DICER degradation. The data suggest that a loss of DICER protein and changes in micro RNA concentration contributes to the clinical properties of VPA. VPA can be used experimentally to down regulate DICER protein levels, which likely reflects a natural regulation of DICER.

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          Defining the human deubiquitinating enzyme interaction landscape.

          Mathew Sowa, Eric J Bennett, Steven Gygi … (2009)
          Deubiquitinating enzymes (Dubs) function to remove covalently attached ubiquitin from proteins, thereby controlling substrate activity and/or abundance. For most Dubs, their functions, targets, and regulation are poorly understood. To systematically investigate Dub function, we initiated a global proteomic analysis of Dubs and their associated protein complexes. This was accomplished through the development of a software platform called CompPASS, which uses unbiased metrics to assign confidence measurements to interactions from parallel nonreciprocal proteomic data sets. We identified 774 candidate interacting proteins associated with 75 Dubs. Using Gene Ontology, interactome topology classification, subcellular localization, and functional studies, we link Dubs to diverse processes, including protein turnover, transcription, RNA processing, DNA damage, and endoplasmic reticulum-associated degradation. This work provides the first glimpse into the Dub interaction landscape, places previously unstudied Dubs within putative biological pathways, and identifies previously unknown interactions and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome pathway.
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            How to interpret LC3 immunoblotting.

            Noboru Mizushima, Tamotsu Yoshimori (2007)
            Microtubule-associated protein light chain 3 (LC3) is now widely used to monitor autophagy. One approach is to detect LC3 conversion (LC3-I to LC3-II) by immunoblot analysis because the amount of LC3-II is clearly correlated with the number of autophagosomes. However, LC3-II itself is degraded by autophagy, making interpretation of the results of LC3 immunoblotting problematic. Furthermore, the amount of LC3 at a certain time point does not indicate autophagic flux, and therefore, it is important to measure the amount of LC3-II delivered to lysosomes by comparing LC3-II levels in the presence and absence of lysosomal protease inhibitors. Another problem with this method is that LC3-II tends to be much more sensitive to be detected by immunoblotting than LC3-I. Accordingly, simple comparison of LC3-I and LC3-II, or summation of LC3-I and LC3-II for ratio determinations, may not be appropriate, and rather, the amount of LC3-II can be compared between samples.
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              Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing.

              Chryssa Kanellopoulou, Stefan Muljo, Andrew Kung … (2005)
              Dicer is the enzyme that cleaves double-stranded RNA (dsRNA) into 21-25-nt-long species responsible for sequence-specific RNA-induced gene silencing at the transcriptional, post-transcriptional, or translational level. We disrupted the dicer-1 (dcr-1) gene in mouse embryonic stem (ES) cells by conditional gene targeting and generated Dicer-null ES cells. These cells were viable, despite being completely defective in RNA interference (RNAi) and the generation of microRNAs (miRNAs). However, the mutant ES cells displayed severe defects in differentiation both in vitro and in vivo. Epigenetic silencing of centromeric repeat sequences and the expression of homologous small dsRNAs were markedly reduced. Re-expression of Dicer in the knockout cells rescued these phenotypes. Our data suggest that Dicer participates in multiple, fundamental biological processes in a mammalian organism, ranging from stem cell differentiation to the maintenance of centromeric heterochromatin structure and centromeric silencing.
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                Author and article information

                Contributors
                Sebastien Pfeffer: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, USA )
                ISSN (Electronic): 1932-6203
                Publication date Collection: 2013
                Publication date (Electronic): 17 December 2013
                Volume: 8
                Issue: 12
                Electronic Location Identifier: e82895
                Affiliations
                [1 ]Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
                [2 ]GenoSplice Technology, Hôpital Saint-Louis, Av Claude Vellefaux, Paris, France
                French National Center for Scientific Research - Institut de biologie moléculaire et cellulaire, France
                Author notes

                Competing Interests: The authors have the following interests: Frédéric Lemoine and Pierre de la Grange are owners and employees of GenoSplice Technology. Genosplice Technology carried out the bioinformatic analysis for this study. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

                Conceived and designed the experiments: DAA SS. Performed the experiments: ZZ XX PC MS SS. Analyzed the data: ZZ DAA SS. Contributed reagents/materials/analysis tools: FL PDG. Wrote the manuscript: DAA SS. Performed the bioinformatic analysis: FL PDG.

                Article
                Publisher ID: PONE-D-13-19230
                DOI: 10.1371/journal.pone.0082895
                PMC ID: 3866160
                PubMed ID: 24358235
                SO-VID: 29aee47c-19d1-4b74-98ea-c66f0a194f27
                Copyright statement: Copyright @ 2013
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 9 May 2013
                Date accepted : 7 November 2013
                Funding
                The work was supported by the NIH [RO1 GM083187 and 5P20RR020171- 08]; and a grant from the Muscular Dystrophy Association. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article

                ScienceOpen disciplines: Uncategorized
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                ScienceOpen disciplines: Uncategorized

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