DOCSLIB.ORG

Loss of the Neural-Specific BAF Subunit ACTL6B Relieves PNAS PLUS Repression of Early Response Genes and Causes Recessive Autism

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Loss of the Neural-Specific BAF Subunit ACTL6B Relieves PNAS PLUS Repression of Early Response Genes and Causes Recessive Autism Loss of the neural-specific BAF subunit ACTL6B relieves PNAS PLUS repression of early response genes and causes recessive autism Wendy Wenderskia,b,c,d, Lu Wange,f,g,1, Andrey Krokhotina,b,c,d,1, Jessica J. Walshh, Hongjie Lid,i, Hirotaka Shojij, Shereen Ghoshe,f,g, Renee D. Georgee,f,g, Erik L. Millera,b,c,d, Laura Eliasa,b,c,d, Mark A. Gillespiek, Esther Y. Sona,b,c,d, Brett T. Staahla,b,c,d, Seung Tae Baeke,f,g, Valentina Stanleye,f,g, Cynthia Moncadaa,b,c,d, Zohar Shiponya,b,c,d, Sara B. Linkerl, Maria C. N. Marchettol, Fred H. Gagel, Dillon Chene,f,g, Tipu Sultanm, Maha S. Zakin, Jeffrey A. Ranishk, Tsuyoshi Miyakawaj, Liqun Luod,i, Robert C. Malenkah, Gerald R. Crabtreea,b,c,d,2, and Joseph G. Gleesone,f,g,2 aDepartment of Pathology, Stanford Medical School, Palo Alto, CA 94305; bDepartment of Genetics, Stanford Medical School, Palo Alto, CA 94305; cDepartment of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305; dHoward Hughes Medical Institute, Stanford University, Palo Alto, CA 94305; eDepartment of Neuroscience, University of California San Diego, La Jolla, CA 92037; fHoward Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037; gRady Children’s Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037; hNancy Pritztker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford Medical School, Palo Alto, CA 94305; iDepartment of Biology, Stanford University, Palo Alto, CA 94305; jDivision of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, 470-1192 Toyoake, Aichi, Japan; kInstitute for Systems Biology, Seattle, WA 98109; lLaboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037; mDepartment of Pediatric Neurology, Institute of Child Health, Children Hospital Lahore, 54000 Lahore, Pakistan; and nClinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, 12311 Cairo, Egypt Edited by Arthur L. Beaudet, Baylor College of Medicine, Houston, TX, and approved March 9, 2020 (received for review May 20, 2019) Synaptic activity in neurons leads to the rapid activation of genes Although present in all cells, BAF complexes orchestrate cell involved in mammalian behavior. ATP-dependent chromatin type-specific functions through combinatorial assembly of ∼15 remodelers such as the BAF complex contribute to these responses subunits from the products of 29 genes (5). During neural and are generally thought to activate transcription. However, the “ ” mechanisms keeping such early activation genes silent have NEUROSCIENCE been a mystery. In the course of investigating Mendelian recessive Significance autism, we identified six families with segregating loss-of-function mutations in the neuronal BAF (nBAF) subunit ACTL6B (originally Autism is a complex neurodevelopmental disorder whose named BAF53b). Accordingly, ACTL6B was the most significantly causative mechanisms are unclear. Taking advantage of a mutated gene in the Simons Recessive Autism Cohort. At least 14 unique cohort with recessively inherited autism, we identified subunits of the nBAF complex are mutated in autism, collectively six families with biallelic mutation of the neuronal-specific making it a major contributor to autism spectrum disorder (ASD). subunit of the BAF complex, ACTL6B (also known as BAF53b). Patient mutations destabilized ACTL6B protein in neurons and Relative to all other genes, ACTL6B was the most statistically rerouted dendrites to the wrong glomerulus in the fly olfactory significant mutated gene in the recessive autism cohort. We system. Humans and mice lacking ACTL6B showed corpus callosum describe autism-relevant phenotypes in human brain organoids hypoplasia, indicating a conserved role for ACTL6B in facilitating and in mouse and fly models. We foresee the outcomes from neural connectivity. Actl6b knockout mice on two genetic back- this study will be the following: 1) a link between neuronal grounds exhibited ASD-related behaviors, including social and activity-dependent transcriptional repression and autism; 2) a memory impairments, repetitive behaviors, and hyperactivity. Sur- characterization of mouse and fly models to study ACTL6B prisingly, mutation of Actl6b relieved repression of early response mutant autism; and 3) an understanding the role of ACTL6B genes including AP1 transcription factors (Fos, Fosl2, Fosb, and and nBAF complexes in neuronal transcriptional regulation. Junb), increased chromatin accessibility at AP1 binding sites, and transcriptional changes in late response genes associated with Author contributions: W.W., J.J.W., H.L., H.S., E.L.M., L.E., F.H.G., T.M., L.L., R.C.M., G.R.C., early response transcription factor activity. ACTL6B loss is thus and J.G.G. designed research; W.W., L.W., A.K., J.J.W., H.L., H.S., S.G., L.E., M.A.G., E.Y.S., B.T.S., C.M., S.B.L., M.C.N.M., T.S., M.S.Z., and J.G.G. performed research; W.W., L.W., an important cause of recessive ASD, with impaired neuron- S.T.B., V.S., Z.S., F.H.G., J.A.R., T.M., L.L., R.C.M., G.R.C., and J.G.G. contributed new re- specific chromatin repression indicated as a potential mechanism. agents/analytic tools; W.W., L.W., A.K., J.J.W., H.L., H.S., R.D.G., M.A.G., E.Y.S., B.T.S., S.T.B., V.S., C.M., Z.S., D.C., and J.G.G. analyzed data; W.W., G.R.C., and J.G.G. wrote the paper; A.K. helped to write a section of the paper; and S.G. contributed preliminary autism | mouse model | recessive | BAF | activity dependent data that helped inform our decision to switch to the brain organoid system. Competing interest statement: G.R.C. is a founder of Foghorn Therapeutics. utism spectrum disorder (ASD) represents a heterogeneous This article is a PNAS Direct Submission. Agroup of neurodevelopmental disorders that are character- This open access article is distributed under Creative Commons Attribution-NonCommercial- ized by social deficits and restricted or repetitive behaviors, and NoDerivatives License 4.0 (CC BY-NC-ND). ∼ affect 1% of children worldwide (1, 2). The heritability of ASD Data deposition: The exome-sequencing data from individuals in this study have been is estimated to be ∼80% (3), implicating genetic mutation as the deposited in the Database of Genotypes and Phenotypes (dbGaP), https://www.ncbi.nlm. prominent cause of autism. Indeed, exome-sequencing studies nih.gov/gap/ (accession no. phs000288.v2.p2) and are available upon reasonable request. have identified hundreds of genetic mutations that substantially The raw RNA- and ATAC-sequencing data have been deposited in the Gene Expression Omnibus (GEO) database, https://www.ncbi.nlm.nih.gov/geo (accession no. GSE147056). increase ASD risk (4). Among the most frequently mutated genes The processed RNA-sequencing dataset is included as Dataset S1 and ATAC-sequencing in ASD are subunits of the mammalian SWI/SNF (BAF) ATP- dataset as Dataset S2. dependent chromatin remodeling complex (4). BAF complexes 1L.W. and A.K. contributed equally to this work. facilitate dynamic changes in gene expression by controlling DNA 2To whom correspondence may be addressed. Email: [email protected] or accessibility to the transcriptional machinery (5). To accomplish this, [email protected]. BAF complexes mobilize nucleosomes, evict polycomb repressive This article contains supporting information online at https://www.pnas.org/lookup/suppl/ complexes, and recruit type II topoisomerases that decatenate doi:10.1073/pnas.1908238117/-/DCSupplemental. DNA (6–9). www.pnas.org/cgi/doi/10.1073/pnas.1908238117 PNAS Latest Articles | 1of12 Downloaded by guest on September 24, 2021 development, exit from the cell cycle is accompanied by BAF Appendix, Fig. S1C) (25). Individuals with recessive ASD-like subunit exchange: neural progenitor (np) subunits ACTL6A phenotypes linked to biallelic ACTL6B mutations have also (BAF53a), DPF2/PHF10 (BAF45a/d), and SS18 are exchanged been identified in recent case studies (29, 40, 41). Cumulatively, for neuron-specific (n) subunits ACTL6B (BAF53b), DPF1/3 these findings implicate mutations in ACTL6B as an important (BAF45b/c), and SS18L1 (CREST), respectively (10–13). Subunit cause of recessive autism. exchange is critical for neuronal function, as genetic deletion of Focusing on ACTL6B, we more closely examined the patient either ACTL6B or SS18L1 impairs activity-dependent dendritic phenotype and sought to understand how mutations in this gene arborization (14, 15). Furthermore, expression of the two microRNAs, give rise to autism. Six families representing 4.4% of the SRAC miR9* and miR124, which control BAF subunit switching, is sufficient cohort demonstrated homozygous variants in ACTL6B with fully to convert fibroblasts into neurons (13). penetrant recessive inheritance (Fig. 1D and SI Appendix, Table Recent findings link mutations in nearly every constitutive S1). Variants were not present in ExAC or gnomAD databases, member of the BAF complex to ASD or intellectual disability (ID), nor in ethnically matched controls from the Greater Middle East including syndromic forms such as Coffin–Siris and Nicolaides– – Variome or the cohort of 256 controls (42, 43), indicating that Baraitser syndromes (16 18). Implicated subunits include the fol- they are rare variants. Subjects exhibited nonverbal autism with ARID1B ARID1A lowing (protein/gene): BAF250b/ , BAF250a/ , stereotypies, as well as ID, developmental delay, hyperactivity, BAF200/ARID2,BCL11A/BCL11A,BRG1/SMARCA4,BRM/ and mild spasticity (SI Appendix, Table S2 and Movie S1). There SMARCA2, BAF155/SMARCC1, BAF170/SMARCC2, BAF45a/ were no syndromic features that would have identified these PHF10, BAF45d/DPF2 BAF47/SMARCB1, BAF57/SMARCE1, SI Ap- BAF53a/ACTL6A, BAF53b/ACTL6B, BAF60a/SMARCD1, and patients as unique a priori from other SRAC subjects ( β-actin/ACTB (17, 19–29). BAF mutant forms of ASD share over- pendix, Table S2 and Supplementary Text). Epilepsy was seen in lapping clinical features such as corpus callosal hypoplasia, epilepsy, all subjects, presenting at 2 wk to 5 y of age, and generally ID, lack of speech, craniofacial abnormalities, developmental de- responded to anticonvulsant medication.
Load more

Recommended publications
  • ACTL6A Promotes the Proliferation of Esophageal Squamous Cell Carcinoma Cells and Correlates with Poor Clinical Outcomes
    OncoTargets and Therapy Dovepress open access to scientific and medical research Open Access Full Text Article ORIGINAL RESEARCH ACTL6A Promotes the Proliferation of Esophageal Squamous Cell Carcinoma Cells and Correlates with Poor Clinical Outcomes This article was published in the following Dove Press journal: OncoTargets and Therapy Rui-zhe Li1 Background: ACTL6A, a regulatory subunit of ATP-dependent chromatin-remodeling Yun-yun Li1,2 complexes SWI/SNF, has been identified as a central oncogenic driver in many tumor types. Hui Qin1 Materials and Methods: We used immunohistochemistry (IHC) to detect ACTL6A Shan-shan Li1 expression in esophageal squamous cell carcinoma (ESCC) tissues. Then, the effect of ACTL6A on proliferation and DNA synthesis was explored by using cell counting kit 8 1 Department of Pathology, School of (CCK8) and EdU retention assays. The potential oncogenic mechanism of ACTL6A in Basic Medical Sciences, Zhengzhou University and First Affiliated Hospital of ESCC cells was also analyzed by flow cytometry and Western blotting. We further estab­ Zhengzhou University, Zhengzhou, lished an ESCC xenograft mouse model to validate the in vitro results. Henan 450000, People’s Republic of China; 2Department of Stomatology, First Results: ACTL6A expression, localized in cancer cell nuclei, was markedly higher in ESCC Affiliated Hospital of Zhengzhou tissues than in the corresponding noncancerous tissues (P<0.001) and was positively asso­ University, Zhengzhou, Henan 450000, ciated with tumor size, histological differentiation, T stage and tumor-node-metastasis People’s Republic of China (TNM) stage. Kaplan–Meier analysis revealed that high ACTL6A expression was signifi­ cantly associated with poor overall survival (OS) (P = 0.008, HR= 2.562, 95% CI: 1.241–­ 5.289), and decision curve analysis (DCA) demonstrated that ACTL6A could increase the clinical prognostic efficiency of the original clinical prediction model.
    [Show full text]
  • Defining Functional Interactions During Biogenesis of Epithelial Junctions
    ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
    [Show full text]
  • Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade
    Published OnlineFirst May 4, 2017; DOI: 10.1158/2159-8290.CD-17-0292 RESEARCH ARTICLE Modeling Renal Cell Carcinoma in Mice: Bap1 and Pbrm1 Inactivation Drive Tumor Grade Yi-Feng Gu1,2, Shannon Cohn1,2, Alana Christie2, Tiffani McKenzie2,3, Nicholas Wolff1,2, Quyen N. Do4, Ananth J. Madhuranthakam4, Ivan Pedrosa2,4, Tao Wang2,5, Anwesha Dey6, Meinrad Busslinger7, Xian-Jin Xie2,8, Robert E. Hammer9, Renée M. McKay1,2, Payal Kapur2,3, and James Brugarolas1,2 Downloaded from cancerdiscovery.aacrjournals.org on September 26, 2021. © 2017 American Association for Cancer Research. 17-CD-17-0292_p900-917.indd 900 7/20/17 10:05 AM Published OnlineFirst May 4, 2017; DOI: 10.1158/2159-8290.CD-17-0292 ABSTRACT Clear cell renal cell carcinoma (ccRCC) is characterized by BAP1 and PBRM1 muta- tions, which are associated with tumors of different grade and prognosis. However, whether BAP1 and PBRM1 loss causes ccRCC and determines tumor grade is unclear. We conditionally targeted Bap1 and Pbrm1 (with Vhl ) in the mouse using several Cre drivers. Sglt2 and Villin proximal convoluted tubule drivers failed to cause tumorigenesis, challenging the conventional notion of ccRCC origins. In contrast, targeting with PAX8, a transcription factor frequently overexpressed in ccRCC, led to ccRCC of different grades. Bap1 -defi cient tumors were of high grade and showed greater mTORC1 activation than Pbrm1 -defi cient tumors, which exhibited longer latency. Disrupting one allele of the mTORC1 negative regulator, Tsc1 , in Pbrm1 -defi cient kidneys triggered higher grade ccRCC. This study establishes Bap1 and Pbrm1 as lineage-specifi c drivers of ccRCC and histologic grade, implicates mTORC1 as a tumor grade rheostat, and suggests that ccRCCs arise from Bowman capsule cells.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • C/EBP Creates Elite Cells for Ipsc Reprogramming by Upregulating
    ARTICLES C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4 Bruno Di Stefano1,2,8,9,10, Samuel Collombet3,8, Janus Schou Jakobsen4,5,6,8, Michael Wierer7, Jose Luis Sardina1,2, Andreas Lackner1,2,9, Ralph Stadhouders1,2, Carolina Segura-Morales1,2, Mirko Francesconi1,2, Francesco Limone1,2, Matthias Mann7, Bo Porse4,5,6, Denis Thieffry3 and Thomas Graf1,2,10 Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) is typically inefficient and has been explained by elite-cell and stochastic models. We recently reported that B cells exposed to a pulse of C/EBPα (Bα0 cells) behave as elite cells, in that they can be rapidly and efficiently reprogrammed into iPSCs by the Yamanaka factors OSKM. Here we show that C/EBPα post-transcriptionally increases the abundance of several hundred proteins, including Lsd1, Hdac1, Brd4, Med1 and Cdk9, components of chromatin-modifying complexes present at super-enhancers. Lsd1 was found to be required for B cell gene silencing and Brd4 for the activation of the pluripotency program. C/EBPα also promotes chromatin accessibility in pluripotent cells and upregulates Klf4 by binding to two haematopoietic enhancers. Bα0 cells share many properties with granulocyte/macrophage progenitors, naturally occurring elite cells that are obligate targets for leukaemic transformation, whose formation strictly requires C/EBPα. The ability to reprogram somatic into pluripotent cells has revolu- complex process, where multiple players synergistically establish new tionized stem cell research with major implications for almost all transcriptional networks and remove epigenetic barriers14. Among the fields of modern biology.
    [Show full text]
  • Increased ACTL6A Occupancy Within Mswi/SNF Chromatin Remodelers
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.22.435873; this version posted March 22, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Increased ACTL6A Occupancy Within mSWI/SNF Chromatin Remodelers Drives Human Squamous Cell Carcinoma Chiung-Ying Chang1,2,7, Zohar Shipony3,7, Ann Kuo1,2, Kyle M. Loh4,5, William J. Greenleaf3,6, Gerald R. Crabtree1,2,5* 1Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA. 2Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA. 3Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA. 4Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA. 5Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA. 6Department of Applied Physics, Stanford University, Stanford, California 94305, USA. 7These authors contributed equally. *Corresponding author: Gerald R. Crabtree, [email protected] Summary Mammalian SWI/SNF (BAF) chromatin remodelers play dosage-sensitive roles in many human malignancies and neurologic disorders. The gene encoding the BAF subunit, ACTL6A, is amplified at an early stage in the development of squamous cell carcinomas (SCCs), but its oncogenic role remains unclear. Here we demonstrate that ACTL6A overexpression leads to its stoichiometric assembly into BAF complexes and drives its interaction and engagement with specific regulatory regions in the genome. In normal epithelial cells, ACTL6A was sub-stoichiometric to other BAF subunits. However, increased ACTL6A levels by ectopic expression or in SCC cells led to near-saturation of ACTL6A within BAF complexes.
    [Show full text]
  • Transcriptional Control of Tissue-Resident Memory T Cell Generation
    Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells.
    [Show full text]
  • 1 Canonical BAF Complex in Regulatory T Cells 2 3 Chin
    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.964981; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 A genome-wide CRISPR screen reveals a role for the BRD9-containing non- 2 canonical BAF complex in regulatory T cells 3 4 Chin-San Loo1,3,#, Jovylyn Gatchalian2,#, Yuqiong Liang1, Mathias Leblanc1, Mingjun 5 Xie1, Josephine Ho2, Bhargav Venkatraghavan1, Diana C. Hargreaves2*, and Ye 6 Zheng1* 7 8 1. NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for 9 Biological Studies 10 2. Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies 11 3. Division of Biological Sciences, University of California, San Diego 12 # Co-first authors 13 * Co-corresponding authors 14 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.26.964981; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 15 Summary 16 Regulatory T cells (Tregs) play a pivotal role in suppressing auto-reactive T cells 17 and maintaining immune homeostasis. Treg development and function are 18 dependent on the transcription factor Foxp3. Here we performed a genome-wide 19 CRISPR/Cas9 knockout screen to identify the regulators of Foxp3 in mouse 20 primary Tregs. The results showed that Foxp3 regulators are highly enriched in 21 genes encoding SWI/SNF and SAGA complex subunits. Among the three 22 SWI/SNF-related complexes, the non-canonical or ncBAF (also called GBAF or 23 BRD9-containing BAF) complex promoted the expression of Foxp3, whereas the 24 PBAF complex repressed its expression.
    [Show full text]
  • Swi/Snf Chromatin Remodeling/Tumor Suppressor Complex Establishes Nucleosome Occupancy at Target Promoters
    Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters Michael Y. Tolstorukova,b,1,2, Courtney G. Sansamc,d,e,1, Ping Luc,d,e,1, Edward C. Koellhofferc,d,e, Katherine C. Helmingc,d,e, Burak H. Alvera, Erik J. Tillmanc,d,e, Julia A. Evansc,d,e, Boris G. Wilsonc,d,e, Peter J. Parka,b,3, and Charles W. M. Robertsc,d,e,3 aCenter for Biomedical Informatics, Harvard Medical School, Boston, MA 02115; bDivision of Genetics, Brigham and Women’s Hospital, Boston, MA 02115; cDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115; dDivision of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115; and eDepartment of Pediatrics, Harvard Medical School, Boston, MA 02115 Edited by Mark Groudine, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved May 2, 2013 (received for review February 6, 2013) Precise nucleosome-positioning patterns at promoters are thought Brg1 haploinsufficient mice are tumor prone, establishing these to be crucial for faithful transcriptional regulation. However, the subunits of the complex as bona fide tumor suppressors (1, 12–17). mechanisms by which these patterns are established, are dynam- It is noteworthy that recent exome sequencing of 35 human SNF5- ically maintained, and subsequently contribute to transcriptional deficient rhabdoid tumors identified a remarkably low rate of control are poorly understood. The switch/sucrose non-fermentable mutations, with loss of SNF5 being essentially the sole recurrent event (18). Indeed, in two of the cancers, there were no other chromatin remodeling complex, also known as the Brg1 associated fi factors complex, is a master developmental regulator and tumor identi ed mutations.
    [Show full text]
  • Serum Albumin OS=Homo Sapiens
    Protein Name Cluster of Glial fibrillary acidic protein OS=Homo sapiens GN=GFAP PE=1 SV=1 (P14136) Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 Cluster of Isoform 3 of Plectin OS=Homo sapiens GN=PLEC (Q15149-3) Cluster of Hemoglobin subunit beta OS=Homo sapiens GN=HBB PE=1 SV=2 (P68871) Vimentin OS=Homo sapiens GN=VIM PE=1 SV=4 Cluster of Tubulin beta-3 chain OS=Homo sapiens GN=TUBB3 PE=1 SV=2 (Q13509) Cluster of Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 (P60709) Cluster of Tubulin alpha-1B chain OS=Homo sapiens GN=TUBA1B PE=1 SV=1 (P68363) Cluster of Isoform 2 of Spectrin alpha chain, non-erythrocytic 1 OS=Homo sapiens GN=SPTAN1 (Q13813-2) Hemoglobin subunit alpha OS=Homo sapiens GN=HBA1 PE=1 SV=2 Cluster of Spectrin beta chain, non-erythrocytic 1 OS=Homo sapiens GN=SPTBN1 PE=1 SV=2 (Q01082) Cluster of Pyruvate kinase isozymes M1/M2 OS=Homo sapiens GN=PKM PE=1 SV=4 (P14618) Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 Clathrin heavy chain 1 OS=Homo sapiens GN=CLTC PE=1 SV=5 Filamin-A OS=Homo sapiens GN=FLNA PE=1 SV=4 Cytoplasmic dynein 1 heavy chain 1 OS=Homo sapiens GN=DYNC1H1 PE=1 SV=5 Cluster of ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide OS=Homo sapiens GN=ATP1A2 PE=3 SV=1 (B1AKY9) Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 Dihydropyrimidinase-related protein 2 OS=Homo sapiens GN=DPYSL2 PE=1 SV=1 Cluster of Alpha-actinin-1 OS=Homo sapiens GN=ACTN1 PE=1 SV=2 (P12814) 60 kDa heat shock protein, mitochondrial OS=Homo
    [Show full text]
  • WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US).
    [Show full text]
  • Snf2h-Mediated Chromatin Organization and Histone H1 Dynamics Govern Cerebellar Morphogenesis and Neural Maturation
    ARTICLE Received 12 Feb 2014 | Accepted 15 May 2014 | Published 20 Jun 2014 DOI: 10.1038/ncomms5181 OPEN Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation Matı´as Alvarez-Saavedra1,2, Yves De Repentigny1, Pamela S. Lagali1, Edupuganti V.S. Raghu Ram3, Keqin Yan1, Emile Hashem1,2, Danton Ivanochko1,4, Michael S. Huh1, Doo Yang4,5, Alan J. Mears6, Matthew A.M. Todd1,4, Chelsea P. Corcoran1, Erin A. Bassett4, Nicholas J.A. Tokarew4, Juraj Kokavec7, Romit Majumder8, Ilya Ioshikhes4,5, Valerie A. Wallace4,6, Rashmi Kothary1,2, Eran Meshorer3, Tomas Stopka7, Arthur I. Skoultchi8 & David J. Picketts1,2,4 Chromatin compaction mediates progenitor to post-mitotic cell transitions and modulates gene expression programs, yet the mechanisms are poorly defined. Snf2h and Snf2l are ATP-dependent chromatin remodelling proteins that assemble, reposition and space nucleosomes, and are robustly expressed in the brain. Here we show that mice conditionally inactivated for Snf2h in neural progenitors have reduced levels of histone H1 and H2A variants that compromise chromatin fluidity and transcriptional programs within the developing cerebellum. Disorganized chromatin limits Purkinje and granule neuron progenitor expansion, resulting in abnormal post-natal foliation, while deregulated transcriptional programs contribute to altered neural maturation, motor dysfunction and death. However, mice survive to young adulthood, in part from Snf2l compensation that restores Engrailed-1 expression. Similarly, Purkinje-specific Snf2h ablation affects chromatin ultrastructure and dendritic arborization, but alters cognitive skills rather than motor control. Our studies reveal that Snf2h controls chromatin organization and histone H1 dynamics for the establishment of gene expression programs underlying cerebellar morphogenesis and neural maturation.
    [Show full text]