Evx1 and Evx2 Specify Excitatory Neurotransmitter Fates and Suppress Inhibitory Fates Through a Pax2-Independent Mechanism
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Detection of Interacting Transcription Factors in Human Tissues Using
Myšičková and Vingron BMC Genomics 2012, 13(Suppl 1):S2 http://www.biomedcentral.com/1471-2164/13/S1/S2 PROCEEDINGS Open Access Detection of interacting transcription factors in human tissues using predicted DNA binding affinity Alena Myšičková*, Martin Vingron From The Tenth Asia Pacific Bioinformatics Conference (APBC 2012) Melbourne, Australia. 17-19 January 2012 Abstract Background: Tissue-specific gene expression is generally regulated by combinatorial interactions among transcription factors (TFs) which bind to the DNA. Despite this known fact, previous discoveries of the mechanism that controls gene expression usually consider only a single TF. Results: We provide a prediction of interacting TFs in 22 human tissues based on their DNA-binding affinity in promoter regions. We analyze all possible pairs of 130 vertebrate TFs from the JASPAR database. First, all human promoter regions are scanned for single TF-DNA binding affinities with TRAP and for each TF a ranked list of all promoters ordered by the binding affinity is created. We then study the similarity of the ranked lists and detect candidates for TF-TF interaction by applying a partial independence test for multiway contingency tables. Our candidates are validated by both known protein-protein interactions (PPIs) and known gene regulation mechanisms in the selected tissue. We find that the known PPIs are significantly enriched in the groups of our predicted TF-TF interactions (2 and 7 times more common than expected by chance). In addition, the predicted interacting TFs for studied tissues (liver, muscle, hematopoietic stem cell) are supported in literature to be active regulators or to be expressed in the corresponding tissue. -
Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells
Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897 -
CREB3L2-Pparg Fusion Mutation Identifies a Thyroid Signaling Pathway Regulated by Intramembrane Proteolysis
Research Article CREB3L2-PPARg Fusion Mutation Identifies a Thyroid Signaling Pathway Regulated by Intramembrane Proteolysis Weng-Onn Lui,3 Lingchun Zeng,1 Victoria Rehrmann,1 Seema Deshpande,5 Maria Tretiakova,1 Edwin L. Kaplan,2 Ingo Leibiger,3 Barbara Leibiger,3 Ulla Enberg,3 Anders Ho¨o¨g,4 Catharina Larsson,3 and Todd G. Kroll1 Departments of 1Pathology and 2Surgery, University of Chicago Medical Center, Chicago, Illinois; Departments of 3Molecular Medicine and Surgery and 4Oncology-Pathology, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden; and 5Department of Pathology, Emory University School of Medicine, Atlanta, Georgia Abstract cancer in patients; and (c) the implementation of effective molecular-targeted chemotherapies that have relatively few side The discovery of gene fusion mutations, particularly in effects. The discovery of fusion mutations is therefore important, leukemia, has consistently identified new cancer pathways particularly in carcinoma, the most common cancer group in and led to molecular diagnostic assays and molecular-targeted which few gene fusions have been identified (1). The recent chemotherapies for cancer patients. Here, we report our discoveries of ERG (2) and ALK (3) gene fusions in prostate and discovery of a novel CREB3L2-PPARg fusion mutation in lung carcinoma, respectively, increase the prospect that new thyroid carcinoma with t(3;7)(p25;q34), showing that a family diagnostic and therapeutic strategies based on gene fusions will of somatic PPARg fusion mutations exist in thyroid cancer. The be applicable to common epithelial cancers. CREB3L2-PPARg fusion encodes a CREB3L2-PPAR; fusion Families of gene fusions tend to characterize specific cancer protein that is composed of the transactivation domain of types. -
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. -
Self-Organized Amniogenesis by Human Pluripotent Stem Cells in a Biomimetic Implantation-Like Niche
LETTERS PUBLISHED ONLINE: 12 DECEMBER 2016 | DOI: 10.1038/NMAT4829 Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche Yue Shao1†, Kenichiro Taniguchi2†, Katherine Gurdziel3, Ryan F. Townshend2, Xufeng Xue1, Koh Meng Aw Yong1, Jianming Sang1, Jason R. Spence2, Deborah L. Gumucio2* and Jianping Fu1,2,4* Amniogenesis—the development of amnion—is a critical factors seen in the in vivo amniogenic niche: a three-dimensional developmental milestone for early human embryogenesis (3D) extracellular matrix (ECM) that is provided by the basement and successful pregnancy1,2. However, human amniogenesis membrane surrounding the epiblast during implantation11; and a is poorly understood due to limited accessibility to peri- soft tissue bed provided by the uterine wall and trophoblast to implantation embryos and a lack of in vitro models. Here support the developing amnion (Fig. 1a,b). Since amniogenesis ini- we report an ecient biomaterial system to generate human tiates from the expanding pluripotent epiblast, we utilized mTeSR1 amnion-like tissue in vitro through self-organized development medium and basement membrane matrix (Geltrex) to render the of human pluripotent stem cells (hPSCs) in a bioengineered culture permissive for pluripotency maintenance. niche mimicking the in vivo implantation environment. We In this culture system, H9 human embryonic stem cells (hESCs) show that biophysical niche factors act as a switch to toggle were plated as single cells at 30,000 cells cm−2 onto a thick, hPSC self-renewal versus amniogenesis under self-renewal- soft gel bed of Geltrex (with thickness ≥100 µm, bulk Young's permissive biochemical conditions. We identify a unique modulus ∼900 Pa, coated on a glass coverslip), in mTeSR1 medium molecular signature of hPSC-derived amnion-like cells and supplemented with the ROCK inhibitor Y27632 (Fig. -
1714 Gene Comprehensive Cancer Panel Enriched for Clinically Actionable Genes with Additional Biologically Relevant Genes 400-500X Average Coverage on Tumor
xO GENE PANEL 1714 gene comprehensive cancer panel enriched for clinically actionable genes with additional biologically relevant genes 400-500x average coverage on tumor Genes A-C Genes D-F Genes G-I Genes J-L AATK ATAD2B BTG1 CDH7 CREM DACH1 EPHA1 FES G6PC3 HGF IL18RAP JADE1 LMO1 ABCA1 ATF1 BTG2 CDK1 CRHR1 DACH2 EPHA2 FEV G6PD HIF1A IL1R1 JAK1 LMO2 ABCB1 ATM BTG3 CDK10 CRK DAXX EPHA3 FGF1 GAB1 HIF1AN IL1R2 JAK2 LMO7 ABCB11 ATR BTK CDK11A CRKL DBH EPHA4 FGF10 GAB2 HIST1H1E IL1RAP JAK3 LMTK2 ABCB4 ATRX BTRC CDK11B CRLF2 DCC EPHA5 FGF11 GABPA HIST1H3B IL20RA JARID2 LMTK3 ABCC1 AURKA BUB1 CDK12 CRTC1 DCUN1D1 EPHA6 FGF12 GALNT12 HIST1H4E IL20RB JAZF1 LPHN2 ABCC2 AURKB BUB1B CDK13 CRTC2 DCUN1D2 EPHA7 FGF13 GATA1 HLA-A IL21R JMJD1C LPHN3 ABCG1 AURKC BUB3 CDK14 CRTC3 DDB2 EPHA8 FGF14 GATA2 HLA-B IL22RA1 JMJD4 LPP ABCG2 AXIN1 C11orf30 CDK15 CSF1 DDIT3 EPHB1 FGF16 GATA3 HLF IL22RA2 JMJD6 LRP1B ABI1 AXIN2 CACNA1C CDK16 CSF1R DDR1 EPHB2 FGF17 GATA5 HLTF IL23R JMJD7 LRP5 ABL1 AXL CACNA1S CDK17 CSF2RA DDR2 EPHB3 FGF18 GATA6 HMGA1 IL2RA JMJD8 LRP6 ABL2 B2M CACNB2 CDK18 CSF2RB DDX3X EPHB4 FGF19 GDNF HMGA2 IL2RB JUN LRRK2 ACE BABAM1 CADM2 CDK19 CSF3R DDX5 EPHB6 FGF2 GFI1 HMGCR IL2RG JUNB LSM1 ACSL6 BACH1 CALR CDK2 CSK DDX6 EPOR FGF20 GFI1B HNF1A IL3 JUND LTK ACTA2 BACH2 CAMTA1 CDK20 CSNK1D DEK ERBB2 FGF21 GFRA4 HNF1B IL3RA JUP LYL1 ACTC1 BAG4 CAPRIN2 CDK3 CSNK1E DHFR ERBB3 FGF22 GGCX HNRNPA3 IL4R KAT2A LYN ACVR1 BAI3 CARD10 CDK4 CTCF DHH ERBB4 FGF23 GHR HOXA10 IL5RA KAT2B LZTR1 ACVR1B BAP1 CARD11 CDK5 CTCFL DIAPH1 ERCC1 FGF3 GID4 HOXA11 IL6R KAT5 ACVR2A -
Transcriptional Regulation of Tenascin Genes
View metadata, citation and similar papers at core.ac.uk brought to you by CORE REVIEW provided by Bern Open Repository and Information System (BORIS) Cell Adhesion & Migration 9:1-2, 34--47; January–April 2015; © 2015 Taylor & Francis Group, LLC Transcriptional regulation of tenascin genes Francesca Chiovaro1,2, Ruth Chiquet-Ehrismann1,2,*, and Matthias Chiquet3 1Friedrich Miescher Institute for Biomedical Research; Basel, Switzerland; 2Faculty of Science; University of Basel; Basel, Switzerland; 3Department of Orthodontics and Dentofacial Orthopedics; School of Dental Medicine; University of Bern; Bern, Switzerland Keywords: cytokine, cancer, development, extracellular matrix, glucocorticoid, growth factor, gene regulation, gene promoter, homeobox gene, matricellular, mechanical stress, tenascin, transcription factor Abbreviations: AKT, v-akt murine thymoma viral oncogene homolog; ALK, anaplastic lymphoma kinase; ATF, activating transcrip- tion factor; AP-1, activator protein-1; BMP, bone morphogenetic protein; CBP, CREB binding protein; ChIP, chromatin immuno- precipitation; CREB, cAMP response element-binding protein; CREB-RP, CREB-related protein; CYP21A2, cytochrome P450 family 21 subfamily A polypeptide 2; EBS, Ets binding site; ECM, extracellular matrix; EGF, epidermal growth factor; ERK1/2, extracellular signal-regulated kinase 1/2; ETS, E26 transformation-specific; Evx1, even skipped homeobox 1; EWS-ETS, Ewing sar- coma-Ets fusion protein; FGF, fibroblast growth factor; HBS, homeodomain binding sequence; IL, interleukin; ILK, -
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immunohistochemistry stain offerings TRUSTED PATHOLOGISTS. INVALUABLE ANSWERS.™ MARCHMAY 20172021 www.aruplab.com/ap-ihcaruplab.com/ap-ihc InformationInformation in this brochurein this brochure is current is current as of as May of March 2021. 2017. All content All content is subject is subject to tochange. change. Please contactPlease ARUPcontact ClientARUP Services Client Services at 800-522-2787 at (800) 522-2787 with any with questions any questions or concerns.or concerns. ARUP LABORATORIES As a nonprofit, academic institution of the University of Utah and its Department We believe in of Pathology, ARUP believes in collaborating, sharing and contributing to laboratory science in ways that benefit our clients and their patients. collaborating, Our test menu is one of the broadest in the industry, encompassing more sharing and than 3,000 tests, including highly specialized and esoteric assays. We offer comprehensive testing in the areas of genetics, molecular oncology, pediatrics, contributing pain management, and more. to laboratory ARUP’s clients include many of the nation’s university teaching hospitals and children’s hospitals, as well as multihospital groups, major commercial science in ways laboratories, and group purchasing organizations. We believe that healthcare should be delivered as close to the patient as possible, which is why we support that provide our clients’ efforts to be the principal healthcare provider in the communities they serve by offering highly complex assays and accompanying consultative support. the best value Offering analytics, consulting, and decision support services, ARUP provides for the patient. clients with the utilization management tools necessary to prosper in this time of value-based care. -
Notch Signalling Regulates Epibranchial Placode Patterning
Development | Peer review history Notch signalling regulates epibranchial placode patterning and segregation Li Wang, Junjie Xie, Haoran Zhang, Long Hin Tsang, Sze Lan Tsang, Eike-Benjamin Braune, Urban Lendahl and Mai Har Sham DOI: 10.1242/dev.183665 Editor: Francois Guillemot Review timeline Original submission: 16 August 2019 Editorial decision: 11 September 2019 First revision received: 24 December 2019 Accepted: 14 January 2020 Original submission First decision letter MS ID#: DEVELOP/2019/183665 MS TITLE: Notch signaling regulates epibranchial placode patterning, segregation and differentiation AUTHORS: Li Wang, Junjie Xie, Haoran Zhang, Long Hin Tsang, Sze Lan Tsang, Urban Lendahl, and Mai Har Sham I have now received the reports of three referees on your manuscript and I have reached a decision. The reports are appended below and you can access them online: please go to BenchPressand click on the 'Manuscripts with Decisions' queue in the Author Area. As you will see, all the referees express great interest in your work, but they also have some significant criticisms and recommend a substantial revision of your manuscript before we can consider publication. If you are able to revise the manuscript along the lines suggested, which may involve further experiments, I will be happy to receive a revised version of the manuscript. The identification of the Notch targets mentioned by referee 2 would be of course interesting but seems beyond the scope of the study unless you already have some evidence in that direction. The request of referee 3 that you analyse the effect of manipulations of Notch signalling at other stages than E9.5 will also require a significant amount of work without being necessarily informative. -
Prdm13 Mediates the Balance of Inhibitory and Excitatory Neurons in Somatosensory Circuits
Developmental Cell Article Prdm13 Mediates the Balance of Inhibitory and Excitatory Neurons in Somatosensory Circuits Joshua C. Chang,1 David M. Meredith,1 Paul R. Mayer,1 Mark D. Borromeo,1 Helen C. Lai,1 Yi-Hung Ou,2 and Jane E. Johnson1,* 1Department of Neuroscience 2Department of Cell Biology UT Southwestern Medical Center, Dallas, TX 75390, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.devcel.2013.02.015 SUMMARY genesis to generate the correct composition of neurons is critical. Here, we identify a key component of the transcriptional Generating a balanced network of inhibitory and machinery that controls how neurons in the somatosensory cir- excitatory neurons during development requires pre- cuit are generated and how regulated specification of these cise transcriptional control. In the dorsal spinal cord, neurons leads to a correct excitatory/inhibitory balance during Ptf1a, a basic helix-loop-helix (bHLH) transcription development. activator, maintains this delicate balance by inducing Excitatory and inhibitory neurons in the spinal cord arise from homeodomain (HD) transcription factors such as progenitor populations within the ventricular zone of the dorsal neural tube (Gross et al., 2002; Mu¨ ller et al., 2002). These pro- Pax2 to specify the inhibitory lineage while suppress- genitors are competent to give rise to neurons in either class ing HD factors such as Tlx1/3 that specify the excit- depending on the basic helix-loop-helix (bHLH) transcription fac- atory lineage. We uncover the mechanism by which tors that are expressed (Helms and Johnson, 2003; Zhuang and Ptf1a represses excitatory cell fate in the inhibitory Sockanathan, 2006). -
Molecular Mechanism of L-Proline Induced EPL-Cell Formation
MOLECULAR MECHANISM OF L.PROLINE INDUCED EPL.CELL FORMATION A thesis submitted to the,University of Adelaide for the Degree of Doctor of PhilosoPhY By Ana Lonic, Bachelor of Science (Honours) Department of Biochem istrY School of Molecular and Biomedical Science University of Adelaide Adelaide, South Australia December, 2006 TABLE OF GONTENTS Summary Statement....,. Acknowledgements GHAPTER 1: GENERAL INTRODUCTION 11 1.1 MOUSE EMBRYOLOGY 11 1.1.1 Pre-implantation development .......... ....... 11 1.1.2 Peri-and Post-implantationdevelopment.......... ........14 1 .1 .2.1 Blastocyst implantation .......... 14 1.1.2.2 Cavitation and primitive ectoderm formation..................... 15 1.1.2.3 Signalling involved in pluripotent cell progression in vivo . 17 1.1.2.4 Role of visceral endoderm in induction of primitive ectoderm t9 1 1 2 s ,,,",,*"i",,;,;, ,;;: ,: :r,;r:",,",;;'*io, o, the primitive ectoderm. 20 1.1.2.6 Gastrulation of the mouse embryo 21 1.1.2.7 Establishment of polarity during mouse development....... 23 1.2 EMBRYONIC STEM CELLS AND THE]R DERIVATIVES ....25 1.2.1 Mouse ES-cell derivation and properties........ .........25 1.2.2 Human ES cells .............27 1.2.3 ln vitro differentiation of mES cells .........28 1.2.4 ln vitro model of early embryogenesis - Homogeneous formation of early primitive ectoderm-like cells from ES cells .. 32 1.2.4.1 EPL-cell morphology....... '.. 33 I 1.2.4.2 EPL-cell gene expression.............. ... 34 1.2.4.3 EPL-cell differentiation potential ........... ............ 35 1.2.4.4 Cytokine responsiveness of EPL cells .............. 38 1.2.5 ldentification of MEDII derived factors involved in EPL-cell formation ........39 1.2.6 Remodelling of basement membranes - a potential source of t- proline/short t--proline-containing peptides ........42 1.3 SIGNALLING PATHWAYS INVOLVED IN ES-CELL SELF-RENEWAL, PLURIPOTENCE AND DIFFERENTIATION ..............43 1.3.1 Signalling mechanisms involved in self-renewal and differentiation of ES cells .........43 1 .3.1 .1 STAT3 signalling,n ES cells........ -
The Tumor Suppressor HHEX Inhibits Axon Growth When Prematurely Expressed in Developing Central Nervous System Neurons
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by epublications@Marquette Marquette University e-Publications@Marquette Biological Sciences Faculty Research and Biological Sciences, Department of Publications 9-1-2015 The umorT Suppressor HHEX Inhibits Axon Growth when Prematurely Expressed in Developing Central Nervous System Neurons Matthew .T Simpson Marquette University Ishwariya Venkatesh Marquette University Ben L. Callif Marquette University Laura K. Thiel Marquette University Denise M. Coley Marquette University See next page for additional authors Accepted version. Molecular and Cellular Neuroscience, Vol 68 )September 2015): 272-283. DOI. © 2015 Elsevier Inc. Used with permission. NOTICE: this is the author’s version of a work that was accepted for publication in Molecular and Cellular Neuroscience. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Molecular and Cellular Neuroscience, Vol 68 )September 2015): 272-283. DOI. Authors Matthew T. Simpson, Ishwariya Venkatesh, Ben L. Callif, Laura K. Thiel, Denise M. Coley, Kristen N. Winsor, Zimei Wang, Audra A. Kramer, Jessica K. Lerch, and Murray G. Blackmore This article is available at e-Publications@Marquette: https://epublications.marquette.edu/bio_fac/515 NOT THE PUBLISHED VERSION; this is the author’s final, peer-reviewed manuscript. The published version may be accessed by following the link in the citation at the bottom of the page. The Tumor Suppressor HHEX Inhibits Axon Growth When Prematurely Expressed in Developing Central Nervous System Neurons Matthew T.