A Core Subunit of Polycomb Repressive Complex 1 Is Broadly Conserved In

Total Page:16

File Type:pdf, Size:1020Kb

A Core Subunit of Polycomb Repressive Complex 1 Is Broadly Conserved In A core subunit of Polycomb repressive complex 1 is PNAS PLUS broadly conserved in function but not primary sequence Leslie Y. Beha,1, Lucy J. Colwellb,c, and Nicole J. Francisa,2 aDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;bApplied Mathematics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138; andcMedical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom Edited by Jerry L. Workman, Stowers Institute for Medical Research, Kansas City, MO, and accepted by the Editorial Board February 3, 2012 (received for review November 15, 2011) Polycomb Group (PcG) proteins mediate heritable gene silencing by (9), as reflected by sequence alignments of the SET domain in modifying chromatin structure. An essential PcG complex, PRC1, diverse genomes (10). Another PcG complex, Polycomb Repres- compacts chromatin and inhibits chromatin remodeling. In Droso- sive Complex 1 (PRC1), consists of four “core” subunits: RING, phila melanogaster, the intrinsically disordered C-terminal region Posterior sex combs (PSC), Polycomb (PC), and Polyhomeotic of PSC (PSC-CTR) mediates these noncovalent effects on chromatin, (PH), all of which are essential in Drosophila (11, 12). Several and is essential for viability. Because the PSC-CTR sequence is in vitro activities have been described for PRC1, all of which en- poorly conserved, the significance of its effects on chromatin out- tail the noncovalent modification of chromatin structure. These side of Drosophila was unclear. The absence of folded domains include chromatin compaction (13), inhibition of chromatin re- modeling (14), and repression of transcription from DNA and also made it difficult to understand how the sequence of PSC-CTR — encodes its function. To determine the mechanistic basis and extent chromatin templates in vitro (14). Two PRC1 subunits RING and PSC—are also present in a distinct complex, dRAF, which of conservation of PSC-CTR activity, we identified 17 metazoan functions as an E3 ligase to stimulate the covalent modification PSC-CTRs spanning chordates to arthropods, and examined their of chromatin through H2A ubiquitination (15). sequence features and biochemical properties. PSC-CTR sequences The PRC1 subunit PSC is sufficient for its noncovalent effects are poorly conserved, but are all highly charged and structurally on chromatin structure (11, 13, 16). PSC is a large protein with a — disordered. We show that active PSC-CTRs which bind DNA conserved motif near its N terminus containing a RING and tightly and inhibit chromatin remodeling efficiently—are distin- RAWUL domain (17–19). This region is important for assembly guished from less active ones by the absence of extended nega- of PSC into PRC1 and likely its activity in Polycomb complexes tively charged stretches. PSC-CTR activity can be increased by (17, 20). The C-terminal region (CTR) of the protein is necessary dispersing its contiguous negative charge, confirming the impor- and sufficient for PSC effects on chromatin structure. Nonsense tance of this property. Using the sequence properties defined as mutations that encode truncations of most of the CTR are severe important for PSC-CTR activity, we predicted the presence of active hypomorphs, and disrupt PcG-dependent gene silencing in vivo PSC-CTRs in additional diverse genomes. Our analysis reveals broad (16, 21). The truncated proteins also lack PSC’s effects on conservation of PSC-CTR activity across metazoans. This conclusion chromatin in vitro, indicating that these biochemical activities are BIOCHEMISTRY could not have been determined from sequence alignments. We central to its biological function. further find that plants that lack active PSC-CTRs instead possess The primary sequence of PSC-CTR is poorly conserved even a functionally analogous PcG protein, EMF1. Thus, our study sug- within the dipterans (20), rendering it difficult to identify con- gests that a disordered domain with dispersed negative charges served sequence features that encode its biochemical activities. — underlies PRC1 activity, and is conserved across metazoans and In addition, a paralogue of PSC in Drosophila melanogaster — plants. Suppressor 2 of zeste [Su(z)2] has a CTR of similar biochemical function to PSC-CTR, even though their primary sequences are intrinsically disordered protein ∣ protein evolution poorly conserved, according to Lo et al. (20). Su(z)2 shares high sequence similarity with PSC only in the N-terminal domain (20, 22, 23). The CTRs of PSC and Su(z)2 share unusual amino acid egulation of chromatin structure occurs through covalent compositions, and are both predicted to be disordered, leading Rmodification of histone proteins, and noncovalent effects on to the hypothesis that these properties underlie their conserved chromatin structure and folding (1, 2). Chromatin modifying en- activity. The poor sequence conservation of the PSC-CTR has zymes add or remove posttranslational modifications of histone also made it difficult to determine the extent of its evolutionary proteins through structured domains, which are readily identified conservation beyond Drosophila (20). through sequence alignments and predicted structure compari- To determine essential sequence properties encoding PSC- sons. On the other hand, proteins that alter chromatin folding CTR activity, and to assess the extent of its evolutionary conser- and compaction frequently use intrinsically disordered regions. vation, we identified 17 metazoan PSC-CTRs and compared their These domains tend to evolve more rapidly, making it difficult to sequences and biochemical activities. We find that biochemically track their activity across evolution using sequence alignments (1). active PSC-CTRs are present in widely diverged species despite An essential set of chromatin-based regulators are the Poly- comb Group (PcG) proteins, which mediate heritable gene silen- cing through the modification of chromatin structure (2). They Author contributions: L.Y.B., L.J.C., and N.J.F. designed research; L.Y.B. and L.J.C. performed have been implicated in a wide variety of biological processes, research; L.Y.B. and L.J.C. analyzed data; and L.Y.B., L.J.C., and N.J.F. wrote the paper. ranging from genome imprinting (3), cell cycle regulation (4), The authors declare no conflict of interest. mammalian X-chromosome inactivation (5), and the mainte- This article is a PNAS Direct Submission. J.L.W. is a guest editor invited by the Editorial nance of stem cell identity (6). PcG proteins are also misregulated Board. in cancer and contribute to cancer progression (7). PcG proteins 1Present address: Department of Ecology and Evolutionary Biology, Princeton University, assemble into multiprotein complexes, with different biochemical NJ 08544 activities toward chromatin (2). One PcG complex, PRC2, methy- 2To whom correspondence should be addressed. E-mail: [email protected]. lates histone H3 on lysine 27 through the SET domain of one of See Author Summary on page 6798 (volume 109, number 18). its subunits, Enhancer of Zeste [E(Z)] (8). PRC2 and its enzy- This article contains supporting information online at www.pnas.org/lookup/suppl/ matic activity are clearly conserved across metazoans and plants doi:10.1073/pnas.1118678109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1118678109 PNAS ∣ Published online April 18, 2012 ∣ E1063–E1071 Downloaded by guest on September 27, 2021 the lack of sequence similarity, indicating they are broadly con- Fig. S1B). Importantly, they did not alter the level of background served in function but not primary sequence. We identified restriction enzyme digestion by HhaI when incubated with chro- sequence properties shared by active PSC-CTRs, which bind matin template in the absence of chromatin remodeler (compare DNA tightly and inhibit chromatin remodeling efficiently. Impor- first and second lanes in Fig. S1B). This indicates that chromatin tantly, we determined that the presence of extended contiguous remodeling, and not restriction enzyme digestion, is specifically negative charge impairs PSC-CTR activity. Our work illustrates inhibited. The 15 PSC-CTRs that bound DNA most tightly also the importance of using empirical measurements, rather than inhibited chromatin remodeling with high efficiency, with 50% sequence alignments, to assess the functional properties of inhibition points from 1 to 7 nM. In contrast, D. pulex PSC1- PSC-like proteins. The mechanistic and evolutionary features CTR and PSC2-CTR required concentrations of 34 nM and of PSC-CTR uncovered in this study may be generally relevant 159 nM, respectively, to achieve 50% inhibition of remodeling, to chromatin-binding proteins, which commonly possess similar corresponding to an approximately 17 and approximately intrinsically disordered regions (24). 80-fold lower efficiency than D. melanogaster PSC-CTR. A mod- est correlation was observed between the affinity for DNA and Results the efficiency of inhibition of chromatin remodeling among Large, Intrinsically Disordered PSC-CTRs Are Present in a Wide Sam- repressive PSC-CTRs (r ¼ 0.532, P ¼ 0.041). Intuitively, this pling of Invertebrate Taxa. To assess the conservation of PSC-CTR correlation is expected since chromatin binding is likely mediated sequence and function, we assembled a comprehensive set of at least in part by DNA binding, and must be important for in- PSC-CTRs by querying 30 diverse metazoan and plant genomes hibition of chromatin remodeling. However, the weak correlation
Recommended publications
  • Specification in Embryonic Stem Cells Through Activation and Repression
    Article Polycomb Regulates Mesoderm Cell Fate- Specification in Embryonic Stem Cells through Activation and Repression Mechanisms Graphical Abstract Authors Lluis Morey, Alexandra Santanach, Enrique Blanco, ..., Elphe` ge P. Nora, Benoit G. Bruneau, Luciano Di Croce Correspondence [email protected] (L.M.), [email protected] (L.D.C.) In Brief Morey et al. reveal that Mel18, a Polycomb-complex-associated protein, is an essential epigenetic regulator of cardiac differentiation. During directed differentiation of embryonic stem cells, Morey et al. find that Mel18-PRC1 complexes exchange subunits in a stage- specific manner and instruct sequential gene activation and repression programs to specify mesoderm fate, prevent alternate lineage commitment, and promote cardiac differentiation. Highlights Accession Numbers d Mel18 is required for PRC1 stability and maintenance of gene GSE67868 repression in ESCs d Mel18 is essential for ESC differentiation into early cardiac- mesoderm precursors d Different Mel18-PRC1 complexes are assembled during cardiac differentiation d Distinctive PRC1 complexes bind to highly active and repressed genes in MES cells Morey et al., 2015, Cell Stem Cell 17, 300–315 September 3, 2015 ª2015 Elsevier Inc. http://dx.doi.org/10.1016/j.stem.2015.08.009 Cell Stem Cell Article Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms Lluis Morey,1,2,6,* Alexandra Santanach,1,2 Enrique Blanco,1,2 Luigi Aloia,1,2 Elphe` ge P. Nora,3,4 Benoit G. Bruneau,3,4
    [Show full text]
  • Polycomb Group Proteins Ring1a/B Are Functionally Linked to the Core Transcriptional Regulatory Circuitry to Maintain ES Cell Identity Mitsuhiro Endoh1, Takaho A
    Development ePress online publication date 13 March 2008 RESEARCH ARTICLE 1513 Development 135, 1513-1524 (2008) doi:10.1242/dev.014340 Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity Mitsuhiro Endoh1, Takaho A. Endo2, Tamie Endoh1, Yu-ichi Fujimura1, Osamu Ohara1, Tetsuro Toyoda2, Arie P. Otte3, Masaki Okano4, Neil Brockdorff5, Miguel Vidal1,6 and Haruhiko Koseki1,* The Polycomb group (PcG) proteins mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes 1 (PRC1) and 2 (PRC2). Although PRC2 has been shown to share target genes with the core transcription network, including Oct3/4, to maintain embryonic stem (ES) cells, it is still unclear whether PcG proteins and the core transcription network are functionally linked. Here, we identify an essential role for the core PRC1 components Ring1A/B in repressing developmental regulators in mouse ES cells and, thereby, in maintaining ES cell identity. A significant proportion of the PRC1 target genes are also repressed by Oct3/4. We demonstrate that engagement of PRC1 at target genes is Oct3/4-dependent, whereas engagement of Oct3/4 is PRC1-independent. Moreover, upon differentiation induced by Gata6 expression, most of the Ring1A/B target genes are derepressed and the binding of Ring1A/B to their target loci is also decreased. Collectively, these results indicate that Ring1A/B-mediated Polycomb
    [Show full text]
  • PCGF2 Monoclonal Antibody (M07A), Clone 4E5
    PCGF2 monoclonal antibody (M07A), clone 4E5 Catalog # : H00007703-M07A 規格 : [ 200 uL ] List All Specification Application Image Product Mouse monoclonal antibody raised against a partial recombinant Western Blot (Recombinant protein) Description: PCGF2. ELISA Immunogen: PCGF2 (AAH04858.1, 236 a.a. ~ 294 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Sequence: LTLATVPTPSEGTNTSGASECESVSDKAPSPATLPATSSSLPSPATPSH GSPSSHGPPA Host: Mouse Reactivity: Human Isotype: IgG2a Kappa Quality Control Antibody Reactive Against Recombinant Protein. Testing: Western Blot detection against Immunogen (32.23 KDa) . Storage Buffer: In ascites fluid Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Instruction: MSDS: Download Datasheet: Download Applications Western Blot (Recombinant protein) Protocol Download ELISA Gene Information Entrez GeneID: 7703 GeneBank BC004858 Page 1 of 2 2020/6/25 Accession#: Protein AAH04858.1 Accession#: Gene Name: PCGF2 Gene Alias: MEL-18,MGC10545,RNF110,ZNF144 Gene polycomb group ring finger 2 Description: Omim ID: 600346 Gene Ontology: Hyperlink Gene Summary: The protein encoded by this gene contains a RING finger motif and is similar to the polycomb group (PcG) gene products. PcG gene products form complexes via protein-protein interaction and maintain the transcription repression of genes involved in embryogenesis, cell cycles, and tumorigenesis. This protein was shown to act as a negative regulator of transcription and has tumor suppressor activity. The expression of this gene was detected in various tumor cells, but is limited in neural organs in normal tissues. Knockout studies in mice suggested that this protein may negatively regulate the expression of different cytokines, chemokines, and chemokine receptors, and thus plays an important role in lymphocyte differentiation and migration, as well as in immune responses.
    [Show full text]
  • Estrogen Exposure Overrides the Masculinizing Effect of Elevated
    Díaz and Piferrer BMC Genomics (2017) 18:973 DOI 10.1186/s12864-017-4345-7 RESEARCH ARTICLE Open Access Estrogen exposure overrides the masculinizing effect of elevated temperature by a downregulation of the key genes implicated in sexual differentiation in a fish with mixed genetic and environmental sex determination Noelia Díaz1,2 and Francesc Piferrer1* Abstract Background: Understanding the consequences of thermal and chemical variations in aquatic habitats is of importance in a scenario of global change. In ecology, the sex ratio is a major population demographic parameter. So far, research that measured environmental perturbations on fish sex ratios has usually involved a few model species with a strong genetic basis of sex determination, and focused on the study of juvenile or adult gonads. However, the underlying mechanisms at the time of gender commitment are poorly understood. In an effort to elucidate the mechanisms driving sex differentiation, here we used the European sea bass, a fish species where genetics and environment (temperature) contribute equally to sex determination. Results: Here, we analyzed the transcriptome of developing gonads experiencing either testis or ovarian differentiation as a result of thermal and/or exogenous estrogen influences. These external insults elicited different responses. Thus, while elevated temperature masculinized genetic females, estrogen exposure was able to override thermal effects and resulted in an all-female population. A total of 383 genes were differentially expressed, with an overall downregulation in the expression of genes involved in both in testicular and ovarian differentiation when fish were exposed to Estradiol-17ß through a shutdown of the first steps of steroidogenesis.
    [Show full text]
  • Mammalian PRC1 Complexes: Compositional Complexity and Diverse Molecular Mechanisms
    International Journal of Molecular Sciences Review Mammalian PRC1 Complexes: Compositional Complexity and Diverse Molecular Mechanisms Zhuangzhuang Geng 1 and Zhonghua Gao 1,2,3,* 1 Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; [email protected] 2 Penn State Hershey Cancer Institute, Hershey, PA 17033, USA 3 The Stem Cell and Regenerative Biology Program, Penn State College of Medicine, Hershey, PA 17033, USA * Correspondence: [email protected] Received: 6 October 2020; Accepted: 5 November 2020; Published: 14 November 2020 Abstract: Polycomb group (PcG) proteins function as vital epigenetic regulators in various biological processes, including pluripotency, development, and carcinogenesis. PcG proteins form multicomponent complexes, and two major types of protein complexes have been identified in mammals to date, Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The PRC1 complexes are composed in a hierarchical manner in which the catalytic core, RING1A/B, exclusively interacts with one of six Polycomb group RING finger (PCGF) proteins. This association with specific PCGF proteins allows for PRC1 to be subdivided into six distinct groups, each with their own unique modes of action arising from the distinct set of associated proteins. Historically, PRC1 was considered to be a transcription repressor that deposited monoubiquitylation of histone H2A at lysine 119 (H2AK119ub1) and compacted local chromatin. More recently, there is increasing evidence that demonstrates the transcription activation role of PRC1. Moreover, studies on the higher-order chromatin structure have revealed a new function for PRC1 in mediating long-range interactions. This provides a different perspective regarding both the transcription activation and repression characteristics of PRC1.
    [Show full text]
  • A Chromosome-Centric Human Proteome Project (C-HPP) To
    computational proteomics Laboratory for Computational Proteomics www.FenyoLab.org E-mail: [email protected] Facebook: NYUMC Computational Proteomics Laboratory Twitter: @CompProteomics Perspective pubs.acs.org/jpr A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17 † ‡ § ∥ ‡ ⊥ Suli Liu, Hogune Im, Amos Bairoch, Massimo Cristofanilli, Rui Chen, Eric W. Deutsch, # ¶ △ ● § † Stephen Dalton, David Fenyo, Susan Fanayan,$ Chris Gates, , Pascale Gaudet, Marina Hincapie, ○ ■ △ ⬡ ‡ ⊥ ⬢ Samir Hanash, Hoguen Kim, Seul-Ki Jeong, Emma Lundberg, George Mias, Rajasree Menon, , ∥ □ △ # ⬡ ▲ † Zhaomei Mu, Edouard Nice, Young-Ki Paik, , Mathias Uhlen, Lance Wells, Shiaw-Lin Wu, † † † ‡ ⊥ ⬢ ⬡ Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Gilbert S. Omenn, , Ronald C. Beavis, † # and William S. Hancock*, ,$, † Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States ‡ Stanford University, Palo Alto, California, United States § Swiss Institute of Bioinformatics (SIB) and University of Geneva, Geneva, Switzerland ∥ Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States ⊥ Institute for System Biology, Seattle, Washington, United States ¶ School of Medicine, New York University, New York, United States $Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia ○ MD Anderson Cancer Center, Houston, Texas, United States ■ Yonsei University College of Medicine, Yonsei University,
    [Show full text]
  • Agricultural University of Athens
    ΓΕΩΠΟΝΙΚΟ ΠΑΝΕΠΙΣΤΗΜΙΟ ΑΘΗΝΩΝ ΣΧΟΛΗ ΕΠΙΣΤΗΜΩΝ ΤΩΝ ΖΩΩΝ ΤΜΗΜΑ ΕΠΙΣΤΗΜΗΣ ΖΩΙΚΗΣ ΠΑΡΑΓΩΓΗΣ ΕΡΓΑΣΤΗΡΙΟ ΓΕΝΙΚΗΣ ΚΑΙ ΕΙΔΙΚΗΣ ΖΩΟΤΕΧΝΙΑΣ ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ ΑΘΗΝΑ 2020 ΔΙΔΑΚΤΟΡΙΚΗ ΔΙΑΤΡΙΒΗ Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Genome-wide association analysis and gene network analysis for (re)production traits in commercial broilers ΕΙΡΗΝΗ Κ. ΤΑΡΣΑΝΗ ΕΠΙΒΛΕΠΩΝ ΚΑΘΗΓΗΤΗΣ: ΑΝΤΩΝΙΟΣ ΚΟΜΙΝΑΚΗΣ Τριμελής Επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Επταμελής εξεταστική επιτροπή: Aντώνιος Κομινάκης (Αν. Καθ. ΓΠΑ) Ανδρέας Κράνης (Eρευν. B, Παν. Εδιμβούργου) Αριάδνη Χάγερ (Επ. Καθ. ΓΠΑ) Πηνελόπη Μπεμπέλη (Καθ. ΓΠΑ) Δημήτριος Βλαχάκης (Επ. Καθ. ΓΠΑ) Ευάγγελος Ζωίδης (Επ.Καθ. ΓΠΑ) Γεώργιος Θεοδώρου (Επ.Καθ. ΓΠΑ) 2 Εντοπισμός γονιδιωματικών περιοχών και δικτύων γονιδίων που επηρεάζουν παραγωγικές και αναπαραγωγικές ιδιότητες σε πληθυσμούς κρεοπαραγωγικών ορνιθίων Περίληψη Σκοπός της παρούσας διδακτορικής διατριβής ήταν ο εντοπισμός γενετικών δεικτών και υποψηφίων γονιδίων που εμπλέκονται στο γενετικό έλεγχο δύο τυπικών πολυγονιδιακών ιδιοτήτων σε κρεοπαραγωγικά ορνίθια. Μία ιδιότητα σχετίζεται με την ανάπτυξη (σωματικό βάρος στις 35 ημέρες, ΣΒ) και η άλλη με την αναπαραγωγική
    [Show full text]
  • Supplementary Material Localizing Regions in the Genome
    Supplementary Material Localizing regions in the genome contributing to ADHD, aggressive and antisocial behavior Running title: Genetic overlap between ADHD, aggression and antisocial behavior Mariana Lizbeth Rodríguez López1, Barbara Franke1,2*, Marieke Klein1,3 1 Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Human Genetics, Nijmegen, The Netherlands 2 Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Department of Psychiatry, Nijmegen, The Netherlands 3 University Medical Center Utrecht, UMC Utrecht Brain Center, Department of Psychiatry, Utrecht, the Netherlands Supplementary Tables: 5 Supplementary Figures: 2 Supplementary Table 1 | Category traits from LDHub GWAS-ss database. Category Number of traits Aging 3 Anthropometric 22 Autoimmune 11 Bone 5 Brain Volume 7 Cancer 5 Cardiometabolic 2 Cognitive 1 Education 5 Glycemic 8 Haemotological 3 Hormone 2 Kidney 6 Lipids 4 Lung Function 8 Metabolites 107 Metal 2 Neurological 3 Other 1 Personality 4 Psychiatric 11 Reproductive 4 Sleeping 5 Smoking 4 Behaviour Uric Acid 1 Total 234 A list of all categories from all the traits LDHub platform. We performed genetic correlation analyses for all traits with both AGG and ASB, giving a total of 234 rg scores for each one of our two traits. Supplementary Table 2 | Summary of data from GTEx project (https://gtexportal.org/home/). GTEx - Gene expression in 12 brain-related tissues Anterior Caudate Frontal cingulate (basal Cerebellar Cortex Nucleus Substantia
    [Show full text]
  • SUPPLEMENTARY APPENDIX Exome Sequencing Reveals Heterogeneous Clonal Dynamics in Donor Cell Myeloid Neoplasms After Stem Cell Transplantation
    SUPPLEMENTARY APPENDIX Exome sequencing reveals heterogeneous clonal dynamics in donor cell myeloid neoplasms after stem cell transplantation Julia Suárez-González, 1,2 Juan Carlos Triviño, 3 Guiomar Bautista, 4 José Antonio García-Marco, 4 Ángela Figuera, 5 Antonio Balas, 6 José Luis Vicario, 6 Francisco José Ortuño, 7 Raúl Teruel, 7 José María Álamo, 8 Diego Carbonell, 2,9 Cristina Andrés-Zayas, 1,2 Nieves Dorado, 2,9 Gabriela Rodríguez-Macías, 9 Mi Kwon, 2,9 José Luis Díez-Martín, 2,9,10 Carolina Martínez-Laperche 2,9* and Ismael Buño 1,2,9,11* on behalf of the Spanish Group for Hematopoietic Transplantation (GETH) 1Genomics Unit, Gregorio Marañón General University Hospital, Gregorio Marañón Health Research Institute (IiSGM), Madrid; 2Gregorio Marañón Health Research Institute (IiSGM), Madrid; 3Sistemas Genómicos, Valencia; 4Department of Hematology, Puerta de Hierro General University Hospital, Madrid; 5Department of Hematology, La Princesa University Hospital, Madrid; 6Department of Histocompatibility, Madrid Blood Centre, Madrid; 7Department of Hematology and Medical Oncology Unit, IMIB-Arrixaca, Morales Meseguer General University Hospital, Murcia; 8Centro Inmunológico de Alicante - CIALAB, Alicante; 9Department of Hematology, Gregorio Marañón General University Hospital, Madrid; 10 Department of Medicine, School of Medicine, Com - plutense University of Madrid, Madrid and 11 Department of Cell Biology, School of Medicine, Complutense University of Madrid, Madrid, Spain *CM-L and IB contributed equally as co-senior authors. Correspondence:
    [Show full text]
  • A Systems Immunology Approach Identifies the Collective Impact of Five Mirs in Th2 Inflammation Supplementary Information
    A systems immunology approach identifies the collective impact of five miRs in Th2 inflammation Supplementary information Ayşe Kılıç, Marc Santolini, Taiji Nakano, Matthias Schiller, Mizue Teranishi,Pascal Gellert, Yuliya Ponomareva, Thomas Braun, Shizuka Uchida, Scott T. Weiss, Amitabh Sharma and Harald Renz Corresponding Author: Harald Renz, MD Institute of Laboratory Medicine Philipps University Marburg 35043 Marburg, Germany Phone +49 6421 586 6235 [email protected] 1 Kılıç A et. al. 2018 A B C D PBS OVA chronic PAS PAS (cm H2O*s/ml (cm Raw Sirius Red Sirius Supplementary figure 1: Characteristic phenotype of the acute and chronic allergic airway inflammatory response in the OVA-induced mouse model. (a) Total and differential cell counts determined in BAL and cytospins show a dominant influx of eosinophils. (b) Serum titers of OVA-specific immunoglobulins are elevated. (c) Representative measurement of airway reactivity to increasing methacholine (Mch) responsiveness measured by head-out body plethysmography. (d) Representative lung section staining depicting airway inflammation and mucus production (PAS, original magnification x 10) and airway remodeling (SiriusRed; original magnification x 20). Data are presented as mean ± SEM and are representative for at least 3 independent experiments with n=8-10 animals per group. Statistical analyses have been performed with one-way ANOVA and Tukey’s post-test and show *p<0.05, **p<0.01 and ***p<0.001. 2 Kılıç A et. al. 2018 lymphocytes A lung activated CD4+-cells CD4+-T-cell-subpopulations SSC FSC ST2 live CD69 CD4 CXCR3 B spleen Naive CD4+- T cells DAPI FSC single cells SSC CD62L CD4 CD44 FSC FSC-W Supplementary figure 2.
    [Show full text]
  • BMI1 Is a Context-Dependent Tumor Suppressor That Is a Barrier to Dedifferentiation in Non-Small Cell Lung Adenocarcinoma
    BMI1 is a context-dependent tumor suppressor that is a barrier to dedifferentiation in non-small cell lung adenocarcinoma by Rachit Neupane B.A. Biology Bard College Submitted to the Department of Biology in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology at the Massachusetts Institute of Technology May 2019 © Massachusetts Institute of Technology All Rights Reserved Signature of the Author _________________________________________________________ Rachit Neupane Department of Biology May 23, 2019 Certified by __________________________________________________________________ Jacqueline A. Lees Professor of Biology May 23, 2019 Accepted by __________________________________________________________________ Amy Keating Professor of Biology Chairman, Graduate Committee May 23, 2019 0 BMI1 is a context-dependent tumor suppressor that is a barrier to dedifferentiation in non-small cell lung adenocarcinoma by Rachit Neupane Submitted to the Department of Biology on May 24, 2019 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology ABSTRACT Predictive value is expected when preclinical models of disease are used for research. However, not all models appropriately mimic the disease progression or the treatment paradigm in the clinic. This thesis addresses an epigenetic regulator, Bmi1, which acts in stem cells to maintain their proliferative and self-renewal capacity primarily through silencing of the Ink4a/Arf locus. Bmi1 has been proposed as a good therapeutic candidate in cancer because of its presumed role in maintaining tumor propagating cells (TPCs). This conclusion is based on the observed tumor suppressive effects of Bmi1 deletion in in vitro cell culture models, in vivo transplant models, and autochthonous models in which Bmi1 was absent throughout development.
    [Show full text]
  • RNA-Seq Analysis of Tgfβ3 Mice Ozturk Et Al
    Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFβ3-knockout mice alleles: RNA-Seq analysis of TGFβ3 Mice Ozturk et al. Ozturk et al. BMC Genomics 2013, 14:113 http://www.biomedcentral.com/1471-2164/14/113 Ozturk et al. BMC Genomics 2013, 14:113 http://www.biomedcentral.com/1471-2164/14/113 RESEARCH ARTICLE Open Access Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFβ3-knockout mice alleles: RNA-Seq analysis of TGFβ3 Mice Ferhat Ozturk1,4, You Li2, Xiujuan Zhu1, Chittibabu Guda2,3 and Ali Nawshad1* Abstract Background: In humans, cleft palate (CP) accounts for one of the largest number of birth defects with a complex genetic and environmental etiology. TGFβ3 has been established as an important regulator of palatal fusion in mice and it has been shown that TGFβ3-null mice exhibit CP without any other major deformities. However, the genes that regulate cellular decisions and molecular mechanisms maintained by the TGFβ3 pathway throughout palatogenesis are predominantly unexplored. Our objective in this study was to analyze global transcriptome changes within the palate during different gestational ages within TGFβ3 knockout mice to identify TGFβ3-associated genes previously unknown to be associated with the development of cleft palate. We used deep sequencing technology, RNA-Seq, to analyze the transcriptome of TGFβ3 knockout mice at crucial stages of palatogenesis, including palatal growth (E14.5), adhesion (E15.5), and fusion (E16.5). Results: The overall transcriptome analysis of TGFβ3 wildtype mice (C57BL/6) reveals that almost 6000 genes were upregulated during the transition from E14.5 to E15.5 and more than 2000 were downregulated from E15.5 to E16.5.
    [Show full text]