Early B-Cell Factors Are Required for Specifying Multiple Retinal Cell Types and Subtypes from Postmitotic Precursors
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
Synergetic Effect of Recoverin and Calmodulin on Regulation of Rhodopsin Kinase
Thomas Jefferson University Jefferson Digital Commons Department of Biochemistry and Molecular Department of Biochemistry and Molecular Biology Faculty Papers Biology 1-1-2012 Synergetic effect of recoverin and calmodulin on regulation of rhodopsin kinase. Ilya I Grigoriev Lomonosov Moscow State University Ivan I Senin Lomonosov Moscow State University Natalya K Tikhomirova Lomonosov Moscow State University Konstantin E Komolov Lomonosov Moscow State University; University of Oldenburg, Oldenburg, Germany; Department of FBiochemistrollow this andy and additional Molecular works Biology at: ,https:/ Thomas/jdc.jeff Jeffersonerson.edu/bmpfp University Ser geiPar tE of P theermy Medicalakov Biochemistry Commons, and the Medical Molecular Biology Commons LetInstitute us for knowBiological Instrumentationhow access of the tRussiano this Academy document of Sciences benefits ouy RecommendedSee next page for Citation additional authors Grigoriev, Ilya I; Senin, Ivan I; Tikhomirova, Natalya K; Komolov, Konstantin E; Permyakov, Sergei E; Zernii, Evgeni Yu; Koch, Karl-Wilhelm; and Philippov, Pavel P, "Synergetic effect of recoverin and calmodulin on regulation of rhodopsin kinase." (2012). Department of Biochemistry and Molecular Biology Faculty Papers. Paper 36. https://jdc.jefferson.edu/bmpfp/36 This Article is brought to you for free and open access by the Jefferson Digital Commons. The Jefferson Digital Commons is a service of Thomas Jefferson University's Center for Teaching and Learning (CTL). The Commons is a showcase for Jefferson books and journals, peer-reviewed scholarly publications, unique historical collections from the University archives, and teaching tools. The Jefferson Digital Commons allows researchers and interested readers anywhere in the world to learn about and keep up to date with Jefferson scholarship. This article has been accepted for inclusion in Department of Biochemistry and Molecular Biology Faculty Papers by an authorized administrator of the Jefferson Digital Commons. -
Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
Absence of S100A4 in the Mouse Lens Induces an Aberrant Retina-Specific Differentiation Program and Cataract
www.nature.com/scientificreports OPEN Absence of S100A4 in the mouse lens induces an aberrant retina‑specifc diferentiation program and cataract Rupalatha Maddala1*, Junyuan Gao2, Richard T. Mathias2, Tylor R. Lewis1, Vadim Y. Arshavsky1,3, Adriana Levine4, Jonathan M. Backer4,5, Anne R. Bresnick4 & Ponugoti V. Rao1,3* S100A4, a member of the S100 family of multifunctional calcium‑binding proteins, participates in several physiological and pathological processes. In this study, we demonstrate that S100A4 expression is robustly induced in diferentiating fber cells of the ocular lens and that S100A4 (−/−) knockout mice develop late‑onset cortical cataracts. Transcriptome profling of lenses from S100A4 (−/−) mice revealed a robust increase in the expression of multiple photoreceptor‑ and Müller glia‑specifc genes, as well as the olfactory sensory neuron‑specifc gene, S100A5. This aberrant transcriptional profle is characterized by corresponding increases in the levels of proteins encoded by the aberrantly upregulated genes. Ingenuity pathway network and curated pathway analyses of diferentially expressed genes in S100A4 (−/−) lenses identifed Crx and Nrl transcription factors as the most signifcant upstream regulators, and revealed that many of the upregulated genes possess promoters containing a high‑density of CpG islands bearing trimethylation marks at histone H3K27 and/or H3K4, respectively. In support of this fnding, we further documented that S100A4 (−/−) knockout lenses have altered levels of trimethylated H3K27 and H3K4. Taken together, -
Miami University – the Graduate School
MIAMI UNIVERSITY – THE GRADUATE SCHOOL CERTIFICATE FOR APPROVING THE DISSERTATION We hereby approve the Dissertation Of Elvis K. Tiburu Candidate for the Degree: Doctor of Philosophy Dr. Gary A. Lorigan, Director Dr. Christopher A. Makaroff, Reader Dr. Robert E. Minto, Reader Dr. Richard T. Taylor, Reader Dr. David G. Pennock Graduate School Representative ABSTRACT DEVELOPMENT OF NEW METHODS FOR THE ALIGNMENT OF LONGER CHAIN PHOSPHOLIPIDS IN BICELLES AND SOLID-STATE NMR STUDIES OF PHOSPHOLAMBAN by Elvis K. Tiburu Magnetically aligned phospholipid bilayers or bicelles are model systems that mimic biological membranes for magnetic resonance studies. A long chain phospholipid bilayer system that spontaneously aligns in a static magnetic field was characterized utilizing solid-state NMR spectroscopy. The oriented membrane system was composed of a mixture of the bilayer-forming phospholipid palmitoylstearoylphosphatidylcholine (PSPC) and the short-chain phospholipid dihexanoylphosphatidylcholine (DHPC) that breaks up the extended bilayers into bilayered micelles or bicelles that are highly hydrated. Traditionally, the shorter 14-carbon chain phospholipid dimyristoyl- phosphatidylcholine (DMPC) has been utilized as the bilayer-forming phospholipid in bicelle studies. The effect of cholesterol in bicelles containing chain perdeuterated 2 DMPC, a partially deuterated (a-[2,2,3,4,4,6- H6]) cholesterol, and stearic acid-d35 has been reported as a function of temperature using 2H solid-state NMR spectroscopy. The order parameters of the labeled probes were calculated and compared with values obtained from unoriented samples in the literature. In addition, 2H solid-state NMR spectroscopy was used to investigate the orientation and side chain dynamics of specific- labeled methyl groups of leucines in PLB in unoriented as well as in magnetically and mechanically aligned phospholipids bilayers. -
Biochemical Journal
www.biochemj.org Biochem. J. (2007) 405, 199–221 (Printed in Great Britain) doi:10.1042/BJ20070255 199 REVIEW ARTICLE Structures and metal-ion-binding properties of the Ca2+-binding helix–loop–helix EF-hand motifs Jessica L. GIFFORD*, Michael P. WALSH† and Hans J. VOGEL*1 *Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4, and †Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1 The ‘EF-hand’ Ca2+-binding motif plays an essential role in interaction site or structure formation from a molten-globule eukaryotic cellular signalling, and the proteins containing this apo state. EF-hand proteins exhibit various sensitivities to Ca2+, motif constitute a large and functionally diverse family. The EF- reflecting the intrinsic binding ability of the EF-hand as well as hand is defined by its helix–loop–helix secondary structure as the degree of co-operativity in Ca2+ binding to paired EF-hands. well as the ligands presented by the loop to bind the Ca2+ ion. The Two additional factors can influence the ability of an EF-hand identity of these ligands is semi-conserved in the most common to bind Ca2+: selectivity over Mg2+ (a cation with very similar (the ‘canonical’) EF-hand; however, several non-canonical EF- chemical properties to Ca2+ and with a cytoplasmic concentration hands exist that bind Ca2+ by a different co-ordination mechanism. several orders of magnitude higher) and interaction with a protein EF-hands tend to occur in pairs, which form a discrete domain so target. -
Dimerization of Neuronal Calcium Sensor Proteins
UC Davis UC Davis Previously Published Works Title Dimerization of Neuronal Calcium Sensor Proteins. Permalink https://escholarship.org/uc/item/8426s2jv Author Ames, James B Publication Date 2018 DOI 10.3389/fnmol.2018.00397 Peer reviewed eScholarship.org Powered by the California Digital Library University of California REVIEW published: 02 November 2018 doi: 10.3389/fnmol.2018.00397 Dimerization of Neuronal Calcium Sensor Proteins James B. Ames* Department of Chemistry, University of California, Davis, Davis, CA, United States 2 Neuronal calcium sensor (NCS) proteins are EF-hand containing Ca C binding proteins that regulate sensory signal transduction. Many NCS proteins (recoverin, GCAPs, neurocalcin and visinin-like protein 1 (VILIP1)) form functional dimers under physiological conditions. The dimeric NCS proteins have similar amino acid sequences (50% homology) but each bind to and regulate very different physiological targets. Retinal 2 recoverin binds to rhodopsin kinase and promotes Ca C-dependent desensitization of light-excited rhodopsin during visual phototransduction. The guanylyl cyclase activating proteins (GCAP1–5) each bind and activate retinal guanylyl cyclases (RetGCs) in light- adapted photoreceptors. VILIP1 binds to membrane targets that modulate neuronal secretion. Here, I review atomic-level structures of dimeric forms of recoverin, GCAPs and VILIP1. The distinct dimeric structures in each case suggest that NCS dimerization may play a role in modulating specific target recognition. The dimerization of recoverin 2 2 and VILIP1 is Ca C-dependent and enhances their membrane-targeting Ca C-myristoyl switch function. The dimerization of GCAP1 and GCAP2 facilitate their binding to dimeric 2 RetGCs and may allosterically control the Ca C-dependent activation of RetGCs. -
Identification and Molecular Analysis of DNA in Exosomes
The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 12-2019 Identification And Molecular Analysis Of DNA In Exosomes Jena Tavormina Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons, Diagnosis Commons, Medical Cell Biology Commons, Medical Genetics Commons, Medical Molecular Biology Commons, Nanomedicine Commons, Oncology Commons, and the Therapeutics Commons Recommended Citation Tavormina, Jena, "Identification And Molecular Analysis Of DNA In Exosomes" (2019). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 981. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/981 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. IDENTIFICATION AND MOLECULAR ANALYSIS OF -
1 Program/Abstract # 1 Role of the Core Promoter in the Regulation Of
1 Program/Abstract # 1 Role of the core promoter in the regulation of gene expression Kadonaga, Jim, UC San Diego, United States The RNA polymerase II core promoter comprises the stretch of DNA that directs the initiation of transcription. This basic definition might suggest that core promoters are simple transcriptional elements that function via common mechanism. Current evidence indicates, however, that there is extraordinary diversity in core promoter structure and activity. For instance, there are a variety of sequence-specific DNA elements in core promoters that include the TATA box, Inr, MTE, DPE, BRE, and TCT motifs. These elements do not act universally – the well-known TATA box is present in only about 15% of human promoters. Instead, specific core promoter elements confer distinct transcriptional activities to core promoters. For example, nearly all of the Drosophila Hox genes have DPE-dependent core promoters, and the Caudal protein, a master regulator of the Hox genes, is an enhancer-binding protein that activates transcription specifically through the DPE motif. Hence, the Hox genes are a DPE-based transcriptional network, and Caudal is a DPE-specific activator. In addition, another core promoter element, the TCT motif, is dedicated to the expression of the network of ribosomal protein genes. These and other findings collectively indicate that the core promoter is a diverse transcriptional regulatory element that is employed for the regulation not only of individual genes, but also of gene networks. Moreover, at a more practical level, optimized versions of the core promoter can be used to achieve the desired specificity and level of expression of transgenes. -
Paraneoplastic Neurological and Muscular Syndromes
Paraneoplastic neurological and muscular syndromes Short compendium Version 4.5, April 2016 By Finn E. Somnier, M.D., D.Sc. (Med.), copyright ® Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark 30/01/2016, Copyright, Finn E. Somnier, MD., D.S. (Med.) Table of contents PARANEOPLASTIC NEUROLOGICAL SYNDROMES .................................................... 4 DEFINITION, SPECIAL FEATURES, IMMUNE MECHANISMS ................................................................ 4 SHORT INTRODUCTION TO THE IMMUNE SYSTEM .................................................. 7 DIAGNOSTIC STRATEGY ..................................................................................................... 12 THERAPEUTIC CONSIDERATIONS .................................................................................. 18 SYNDROMES OF THE CENTRAL NERVOUS SYSTEM ................................................ 22 MORVAN’S FIBRILLARY CHOREA ................................................................................................ 22 PARANEOPLASTIC CEREBELLAR DEGENERATION (PCD) ...................................................... 24 Anti-Hu syndrome .................................................................................................................. 25 Anti-Yo syndrome ................................................................................................................... 26 Anti-CV2 / CRMP5 syndrome ............................................................................................ -
BD Stem Cell Resource Markers of Self-Renewal and Differentiation
BD Stem Cell Resource Markers of Self-Renewal and Differentiation 23-9953-02 Self Renewing Pathway TGF-β/Activin Sperm Liver Thymus Pancreas Thyroid Lung Intestine Wnt BMP-SMad Erk-MAPK Skin and Hair JAK-STAT Wnt TGF-β/Activin BMP4 bFGF LIF LIFR gp130 Egg p p p Jak β-catenin Smads 175 MEK/ERK Stat3 C-myc Sox2 Oct4 Nanog Smads 2/3 Neural Crest Primordial Germ Cell Stem Cell Neural Stem Cell Self Renewal Ectoderm Embryonic Stem Cell or Induced Pluripotent Endoderm Neurons, Glia Stem Cell Smooth Muscle Cardiac Tissue Chondrocytes Glial Restricted Progenitor Osteocytes Neuronal Type 1 Astrocyte Oligodendrocyte Restricted Progenitor Progenitor Mesoderm Mesenchymal Stem Cell Type 2 Astrocyte Endothelium Oligodendrocyte Neuron Heart Skeletal Muscle Kidney Smooth Muscle Myoblast Adipocyte (Fat) Chondrocyte Fibroblast Osteoblast (Bone) Hemangioblast (Cartilage) Myotube (Muscle) Plasmacytoid Dendritic Cell Hematopoietic Stem Cell Committed Lymphoid Progenitor Monoblast Megakaryoblast Proerythroblast Pre-NK Cell Thymocyte Pre B Cell Myeloblast Erythroblast Progranulocyte Monocyte Myeloid Dendrtitic Cell Megakaryocyte NK Lymphoblast T-Lymphoblast B-Lymphoblast Normoblast Neutrophilic Eosinophilic Basophilic Myelocyte Myelocyte Myelocyte NK Cell T Cell B Cell Macrophage Thrombocytes Reticulocyte Neutrophilic Eosinophilic Basophilic (Platelets) Band Cell Band Cell Band Cell Plasma Cell Erythrocyte Neutrophil Eosinophil Basophil (Red Blood Cell) White colored markers are available from BD Biosciences Ectoderm Markers Embryonic Stem Cells Mesoderm Markers -
BARHL2 Transcription Factor Regulates the Ipsilateral/ Contralateral Subtype Divergence in Postmitotic Di1 Neurons of the Developing Spinal Cord
BARHL2 transcription factor regulates the ipsilateral/ contralateral subtype divergence in postmitotic dI1 neurons of the developing spinal cord Qian Dinga,1, Pushkar S. Joshia,1, Zheng-hua Xiea, Mengqing Xiangb, and Lin Gana,c,2 aFlaum Eye Institute and Department of Ophthalmology, University of Rochester, Rochester, NY 14642; cCollege of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China; and bCenter for Advanced Biotechnology and Medicine and Department of Pediatrics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854 Edited* by Constance L. Cepko, Harvard Medical School/Howard Hughes Medical Institute, Boston, MA, and approved December 7, 2011 (received for review July 29, 2011) In the dorsal spinal cord, distinct interneuron classes relay specific regulate the binary diversification of dI1 neurons into dI1i and somatosensory information, such as touch, heat, and pain, from the dI1c subtypes remain unknown. The mammalian Bar class TFs, periphery to higher brain centers via ipsilateral and contralateral BARHL1 and BARHL2, both ATOH1 downstream targets, are axonal pathways. The transcriptional mechanisms by which dorsal potential candidates because their ectopic expression in the dorsal interneurons choose between ipsilateral and contralateral projec- spinal cord specifically induces commissural axonal targeting (12– tion fates are unknown. Here, we show that a single transcription 14). However, the expression of Barhl1 and Barhl2 by both dI1i and factor (TF), BARHL2, regulates this choice in proprioceptive dI1 dI1c neurons provides a significant argument against their role in interneurons by selectively suppressing cardinal dI1contra features subtype divergence (6, 13, 14). Although targeted deletion of in dI1ipsi neurons, despite expression by both subtypes.