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      The Neuron-specific Chromatin Regulatory Subunit BAF53b is Necessary for Synaptic Plasticity and Memory

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          Abstract

          Recent exome sequencing studies have implicated polymorphic BAF complexes (mammalian SWI/SNF chromatin remodeling complexes) in several human intellectual disabilities and cognitive disorders. However, it is currently unknown how mutations in BAF complexes result in impaired cognitive function. Post mitotic neurons express a neuron specific assembly, nBAF, characterized by the neuron-specific subunit BAF53b. Mice harboring selective genetic manipulations of BAF53b have severe defects in longterm memory and long-lasting forms of hippocampal synaptic plasticity. We rescued memory impairments in BAF53b mutant mice by reintroducing BAF53b in the adult hippocampus, indicating a role for BAF53b beyond neuronal development. The defects in BAF53b mutant mice appear to derive from alterations in gene expression that produce abnormal postsynaptic components, such as spine structure and function, and ultimately lead to deficits in synaptic plasticity. Our studies provide new insight into the role of dominant mutations in subunits of BAF complexes in human intellectual and cognitive disorders.

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            DAVID: Database for Annotation, Visualization, and Integrated Discovery.

            Functional annotation of differentially expressed genes is a necessary and critical step in the analysis of microarray data. The distributed nature of biological knowledge frequently requires researchers to navigate through numerous web-accessible databases gathering information one gene at a time. A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information. Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://www.david.niaid.nih.gov) addresses this need via four web-based analysis modules: 1) Annotation Tool - rapidly appends descriptive data from several public databases to lists of genes; 2) GoCharts - assigns genes to Gene Ontology functional categories based on user selected classifications and term specificity level; 3) KeggCharts - assigns genes to KEGG metabolic processes and enables users to view genes in the context of biochemical pathway maps; and 4) DomainCharts - groups genes according to PFAM conserved protein domains. Analysis results and graphical displays remain dynamically linked to primary data and external data repositories, thereby furnishing in-depth as well as broad-based data coverage. The functionality provided by DAVID accelerates the analysis of genome-scale datasets by facilitating the transition from data collection to biological meaning.
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              Is Open Access

              The UCSC Genome Browser database: update 2011

              The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.
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                Author and article information

                Journal
                9809671
                21092
                Nat Neurosci
                Nat. Neurosci.
                Nature neuroscience
                1097-6256
                1546-1726
                21 August 2013
                24 March 2013
                May 2013
                01 November 2013
                : 16
                : 5
                : 552-561
                Affiliations
                [1 ]University of California, Irvine; Department of Neurobiology & Behavior; Irvine, CA
                [2 ]Center for the Neurobiology of Learning & Memory; Irvine, CA
                [3 ]Oregon Health and Science University; Portland, OR
                [4 ]University of California, Irvine; Department of Anatomy and Neurobiology; Irvine, CA
                [5 ]University of California, Irvine; Department of Pediatrics; Irvine, CA
                [6 ]University of California, Irvine; Department of Computer Science; Irvine, CA
                [7 ]Institute for Genomics and Bioinformatics; Irvine, CA
                [8 ]Howard Hughes Medical Institute, Department of Developmental Biology and Department of Pathology; Stanford University School of Medicine; Stanford, CA
                [9 ]University of California, Irvine; Department of Psychiatry and Human Behavior; Irvine, CA
                Author notes
                [* ]Correspondence to: Marcelo A. Wood, PhD, University of California, Irvine, Department of Neurobiology & Behavior, Center for the Neurobiology of Learning & Memory, 301 Qureshey Research Labs, Irvine, CA 92697-3800, mwood@ 123456uci.edu , Phone: (949) 824-2259
                Article
                NIHMS447739
                10.1038/nn.3359
                3777648
                23525042
                6181e9b5-8663-4b5c-ae40-e8e126aaddc5

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                History
                Funding
                Funded by: National Institute of Neurological Disorders and Stroke : NINDS
                Award ID: R01 NS028912 || NS
                Funded by: National Institute of Mental Health : NIMH
                Award ID: R01 MH081004 || MH
                Funded by: National Institute of Mental Health : NIMH
                Award ID: R01 MH073136 || MH
                Funded by: National Institute on Drug Abuse : NIDA
                Award ID: R01 DA025922 || DA
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                Neurosciences
                Neurosciences

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