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      BCL7A‐containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation

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          Abstract

          Mammalian SWI/SNF/BAF chromatin remodeling complexes influence cell lineage determination. While the contribution of these complexes to neural progenitor cell (NPC) proliferation and differentiation has been reported, little is known about the transcriptional profiles that determine neurogenesis or gliogenesis. Here, we report that BCL7A is a modulator of the SWI/SNF/BAF complex that stimulates the genome‐wide occupancy of the ATPase subunit BRG1. We demonstrate that BCL7A is dispensable for SWI/SNF/BAF complex integrity, whereas it is essential to regulate Notch/Wnt pathway signaling and mitochondrial bioenergetics in differentiating NPCs. Pharmacological stimulation of Wnt signaling restores mitochondrial respiration and attenuates the defective neurogenic patterns observed in NPCs lacking BCL7A. Consistently, treatment with an enhancer of mitochondrial biogenesis, pioglitazone, partially restores mitochondrial respiration and stimulates neuronal differentiation of BCL7A‐deficient NPCs. Using conditional BCL7A knockout mice, we reveal that BCL7A expression in NPCs and postmitotic neurons is required for neuronal plasticity and supports behavioral and cognitive performance. Together, our findings define the specific contribution of BCL7A‐containing SWI/SNF/BAF complexes to mitochondria‐driven NPC commitment, thereby providing a better understanding of the cell‐intrinsic transcriptional processes that connect metabolism, neuronal morphogenesis, and cognitive flexibility.

          Abstract

          Neurogenic gene expression and Notch/Wnt signaling in differentiating neural progenitor cells depend on BCL7A‐mediated BRG1 chromatin occupancy.

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          Most cited references105

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            BEDTools: a flexible suite of utilities for comparing genomic features

            Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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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
                daniele.bano@dzne.de
                Journal
                EMBO J
                EMBO J
                10.1002/(ISSN)1460-2075
                EMBJ
                embojnl
                The EMBO Journal
                John Wiley and Sons Inc. (Hoboken )
                0261-4189
                1460-2075
                28 October 2022
                December 2022
                28 October 2022
                : 41
                : 23 ( doiID: 10.1002/embj.v41.23 )
                : e110595
                Affiliations
                [ 1 ] German Center for Neurodegenerative Diseases (DZNE) Bonn Germany
                [ 2 ] Institute of Reconstructive Neurobiology University of Bonn Medical Faculty and University Hospital Bonn Bonn Germany
                [ 3 ] Cell Programming Core Facility University of Bonn Medical Faculty Bonn Germany
                [ 4 ] PRECISE Platform for Single Cell Genomics and Epigenomics German Center for Neurodegenerative Diseases (DZNE) and the University of Bonn Bonn Germany
                [ 5 ] Department for Genomics and Immunoregulation, LIMES Institute University of Bonn Bonn Germany
                Author notes
                [*] [* ]Corresponding author. Tel: +0049 228 43302 510; Fax: +0049 228 43302 689; E‐mail: daniele.bano@ 123456dzne.de
                Author information
                https://orcid.org/0000-0002-2203-408X
                https://orcid.org/0000-0002-3838-0294
                https://orcid.org/0000-0001-5795-3505
                https://orcid.org/0000-0001-5777-4240
                https://orcid.org/0000-0002-1277-0980
                https://orcid.org/0000-0003-1175-7466
                https://orcid.org/0000-0002-9617-5504
                Article
                EMBJ2022110595
                10.15252/embj.2022110595
                9713712
                36305367
                f2497f51-2efb-42ba-a8f2-a22fab6a826f
                © 2022 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 21 September 2022
                : 04 January 2022
                : 07 October 2022
                Page count
                Figures: 14, Tables: 1, Pages: 27, Words: 26258
                Funding
                Funded by: Deutsche Forschungsgemeinschaft (DFG) , doi 10.13039/501100001659;
                Award ID: EXC2151 – 390873048
                Funded by: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) , doi 10.13039/501100005224;
                Funded by: Innovative Medicines Initiative 2
                Award ID: 821522
                Funded by: The European Union's Horizon 2020 Research and Innovation Program and EFPIA
                Categories
                Article
                Articles
                Custom metadata
                2.0
                1 December 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.1 mode:remove_FC converted:01.12.2022

                Molecular biology
                bcl7a,cognitive function,mitochondrial oxphos,neural progenitor cells (npcs),swi/snf/baf complex,chromatin, transcription & genomics,neuroscience

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