Tcf21 Regulates the Specification and Maturation of Proepicardial Cells Panna Tandon1,2, Yana V
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Article Genetic Control of Gonadal Sex Determination and Development STEVANT, Isabelle, NEF, Serge Abstract Sex determination is the process by which the bipotential gonads develop as either testes or ovaries. With two distinct potential outcomes, the gonadal primordium offers a unique model for the study of cell fate specification and how distinct cell populations diverge from multipotent progenitors. This review focuses on recent advances in our understanding of the genetic programs and epigenetic mechanisms that regulate gonadal sex determination and the regulation of cell fate commitment in the bipotential gonads. We rely primarily on mouse data to illuminate the complex and dynamic genetic programs controlling cell fate decision and sex-specific cell differentiation during gonadal formation and gonadal sex determination. Reference STEVANT, Isabelle, NEF, Serge. Genetic Control of Gonadal Sex Determination and Development. Trends in Genetics, 2019 PMID : 30902461 DOI : 10.1016/j.tig.2019.02.004 Available at: http://archive-ouverte.unige.ch/unige:115790 Disclaimer: layout of this document may differ from the published version. 1 / 1 Trends in Genetics Genetic control of sex determination and gonad development --Manuscript Draft-- Manuscript Number: TIGS-D-18-00173R1 Article Type: Review Keywords: sex determination; ovary; testis; lineage specification; gene expression; epigenetic regulation Corresponding Author: Serge Nef geneva, SWITZERLAND First Author: Isabelle Stévant Order of Authors: Isabelle Stévant Serge Nef Abstract: Sex determination is the process by which the bipotential gonads develop as either testes or ovaries. With two distinct potential outomes, the gonadal primordium offers a unique model for the study of cell fate specification and how distinct cell populations diverge from multipotent progenitors. -
Epigenetic Regulation of the Tumor Suppressor Gene TCF21 on 6Q23-Q24 in Lung and Head and Neck Cancer
Epigenetic regulation of the tumor suppressor gene TCF21 on 6q23-q24 in lung and head and neck cancer Laura T. Smith*, Mauting Lin*, Romulo M. Brena*, James C. Lang†, David E. Schuller†, Gregory A. Otterson‡, Carl D. Morrison§, Dominic J. Smiraglia¶, and Christoph Plass*ʈ *Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, †Department of Otolaryngology, ‡Division of Hematology͞Oncology, Department of Internal Medicine, and §Department of Pathology and Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210; and ¶Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14250 Communicated by Albert de la Chapelle, Ohio State University, Columbus, OH, November 28, 2005 (received for review August 22, 2005) The identification of tumor suppressor genes has classically depended types, but no tumor suppressor has been identified (16). LOH from on their localization within recurrent regions of loss of heterozygos- the 9.6-Mb region of 6q23-q24 has been described in Ͼ20% of ity. According to Knudson’s two-hit hypothesis, the remaining allele HNSCC and in Ϸ50% of NSCLC, and complete loss of the long is lost, either genetically or, more recently identified, through epige- arm of chromosome 6 is even more common (17–20). The complete netic events. To date, retrospective analyses have determined pro- 6q23-q24 sequence was obtained from the June 2002 BLAT data- moter methylation as a common alternative alteration in cancer cells base. In silico digestion with methylation-sensitive landmark restric- to silence cancer-related genes. Here we report an application of tion enzyme combinations used in RLGS (NotI–EcoRV–HinfI or restriction landmark genomic scanning that allows for DNA methyl- AscI–EcoRV–HinfI) identified sequences migrating in RLGS gels. -
E Proteins and ID Proteins: Helix-Loop-Helix Partners in Development and Disease
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Developmental Cell Review E Proteins and ID Proteins: Helix-Loop-Helix Partners in Development and Disease Lan-Hsin Wang1 and Nicholas E. Baker1,2,3,* 1Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA 2Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA 3Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.devcel.2015.10.019 The basic Helix-Loop-Helix (bHLH) proteins represent a well-known class of transcriptional regulators. Many bHLH proteins act as heterodimers with members of a class of ubiquitous partners, the E proteins. A widely expressed class of inhibitory heterodimer partners—the Inhibitor of DNA-binding (ID) proteins—also exists. Genetic and molecular analyses in humans and in knockout mice implicate E proteins and ID proteins in a wide variety of diseases, belying the notion that they are non-specific partner proteins. Here, we explore relationships of E proteins and ID proteins to a variety of disease processes and highlight gaps in knowledge of disease mechanisms. E proteins and Inhibitor of DNA-binding (ID) proteins are widely conferring DNA-binding specificity and transcriptional activation expressed transcriptional regulators with very general functions. on heterodimers with the ubiquitous E proteins (Figure 1). They are implicated in diseases by evidence ranging from Another class of pervasive HLH proteins acts in opposition to confirmed Mendelian inheritance, association studies, and E proteins. -
Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol . -
Investigation of KRAS Dependency Bypass and Functional Characterization of All Possible KRAS Missense Variants
Investigation of KRAS Dependency Bypass and Functional Characterization of All Possible KRAS Missense Variants The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:40050098 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Investigation of KRAS Dependency Bypass and Functional Characterization of All Possible KRAS Missense Variants A dissertation presented by Seav Huong Ly to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological and Biomedical Sciences Harvard University Cambridge, Massachusetts April 2018 © 2018 Seav Huong Ly All rights reserved. Dissertation Advisor: William C. Hahn Seav Huong Ly Investigation of KRAS Dependency Bypass and Functional Characterization of All Possible KRAS Missense Variants Abstract The importance of oncogenic KRAS in human cancers have prompted intense efforts to target KRAS and its effectors. To anticipate the development of resistance to these strategies, we previously performed a genome-scale expression screen to identify genes that bypass KRAS oncogenic dependency. Here we test thirty-seven genes that scored over five standard deviations and find that overexpression of LIM homeobox 9 (LHX9), a transcription factor involved in embryonic development, robustly rescues the suppression of KRAS in vitro and xenograft models. Furthermore, LHX9 substantially decreases cell sensitivity to KRASG12C and MEK1/2 inhibitors in KRAS-dependent cells. -
76F0c47cb71e753c0f29618f48ed
International Journal of Molecular Sciences Review Strategies and Challenges to Improve Cellular Programming-Based Approaches for Heart Regeneration Therapy Lin Jiang, Jialiang Liang , Wei Huang, Zhichao Wu, Christian Paul and Yigang Wang * Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267-0529, USA; [email protected] (L.J.); [email protected] (J.L.); [email protected] (W.H.); [email protected] (Z.W.); [email protected] (C.P.) * Correspondence: [email protected]; Tel.: +1-513-558-5798 Received: 30 September 2020; Accepted: 15 October 2020; Published: 16 October 2020 Abstract: Limited adult cardiac cell proliferation after cardiovascular disease, such as heart failure, hampers regeneration, resulting in a major loss of cardiomyocytes (CMs) at the site of injury. Recent studies in cellular reprogramming approaches have provided the opportunity to improve upon previous techniques used to regenerate damaged heart. Using these approaches, new CMs can be regenerated from differentiation of iPSCs (similar to embryonic stem cells), the direct reprogramming of fibroblasts [induced cardiomyocytes (iCMs)], or induced cardiac progenitors. Although these CMs have been shown to functionally repair infarcted heart, advancements in technology are still in the early stages of development in research laboratories. In this review, reprogramming-based approaches for generating CMs are briefly introduced and reviewed, and the challenges (including low efficiency, functional maturity, and safety issues) that hinder further translation of these approaches into a clinical setting are discussed. The creative and combined optimal methods to address these challenges are also summarized, with optimism that further investigation into tissue engineering, cardiac development signaling, and epigenetic mechanisms will help to establish methods that improve cell-reprogramming approaches for heart regeneration. -
Regulation of Early Lung Morphogenesis: Questions, Facts and Controversies
REVIEW 1611 Development 133, 1611-1624 (2006) doi:10.1242/dev.02310 Regulation of early lung morphogenesis: questions, facts and controversies Wellington V. Cardoso* and Jining Lü During early respiratory system development, the foregut endodermal specification, lung primordium formation, and the endoderm gives rise to the tracheal and lung cell progenitors. regulation of the initial stages of branching morphogenesis and Through branching morphogenesis, and in coordination with differentiation in the embryonic lung. We address questions such as vascular development, a tree-like structure of epithelial ‘when and how is respiratory cell fate established?’, ‘how do lung tubules forms and differentiates to produce the airways and buds form?’, ‘how are stereotypical patterns of airway branching and alveoli. Recent studies have implicated the fibroblast growth cellular diversity generated in the developing lung?’ and ‘which factor, sonic hedgehog, bone morphogenetic protein, retinoic pathways and targets are key to these processes?’. Most of what is acid and Wnt signaling pathways, and various transcription described refers to mouse lung development because of the genetic factors in regulating the initial stages of lung development. data available (Table 1). Lung vascular development and later events, However, the precise roles of these molecules and how they such as sacculation and alveoli formation, are not discussed in this interact in the developing lung is subject to debate. Here, we review (for reviews, see Pauling and Vu, 2004; Williams, -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
Fusion of the NH2-Terminal Domain of the Basic Helix-Loop-Helix Protein TCF12 to TEC in Extraskeletal Myxoid Chondrosarcoma with Translocation T(9;15)(Q22;Q21)1
[CANCER RESEARCH 60, 6832–6835, December 15, 2000] Advances in Brief Fusion of the NH2-Terminal Domain of the Basic Helix-Loop-Helix Protein TCF12 to TEC in Extraskeletal Myxoid Chondrosarcoma with Translocation t(9;15)(q22;q21)1 Helene Sjo¨gren, Barbro Wedell, Jeanne M. Meis Kindblom, Lars-Gunnar Kindblom, and Go¨ran Stenman2 Lundberg Laboratory for Cancer Research, Department of Pathology, Go¨teborg University, SE-413 45 Go¨teborg, Sweden Abstract domain of TLS/FUS is linked to the entire coding region of the transcription factor CHOP as a result of a t(12;16)(q13;p11) (reviewed Extraskeletal myxoid chondrosarcomas (EMCs) are characterized by in Ref. 9). Thus, the NH -terminal transactivation domains of the recurrent t(9;22) or t(9;17) translocations resulting in fusions of the 2 EWS family of RNA binding proteins are regularly fusion partners of NH2-terminal transactivation domains of EWS or TAF2N to the entire TEC protein. We report here an EMC with a novel translocation t(9; various transcription factors in sarcomas, suggesting that they might 15)(q22;q21) and a third type of TEC-containing fusion gene. The chi- have important oncogenic properties. Indeed, it has been shown that meric transcript encodes a protein in which the first 108 amino acids of EWS-FLI1, TAF2N-FLI1, TLS-CHOP, and EWS-CHOP can trans- the NH2-terminus of the basic helix-loop-helix (bHLH) protein TCF12 is form 3T3 cells and that the transforming activity is dependent on linked to the entire TEC protein. The translocation separates the NH2- the presence of the NH2-terminal parts of EWS, TAF2N, and TLS terminal domain of TCF12 from the bHLH domain as well as from a (10–12). -
Down-Regulation Networks in Acute Strenuous Exercise
Transcriptional profile in rat muscle: down-regulation networks in acute strenuous exercise Stela Mirla da Silva Felipe1,*, Raquel Martins de Freitas1, Emanuel Diego dos Santos Penha1, Christina Pacheco1, Danilo Lopes Martins2, Juliana Osório Alves1, Paula Matias Soares1, Adriano César Carneiro Loureiro1, Tanes Lima3, Leonardo R. Silveira3, Alex Soares Marreiros Ferraz1, Jorge Estefano Santana de Souza2, Jose Henrique Leal-Cardoso1, Denise P. Carvalho4 and Vania Marilande Ceccatto1,* 1 Superior Institute of Biomedic Sciences, Universidade Estadual do Ceará, Fortaleza, Ceará, Brazil 2 Digital Metropolis Institute, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil 3 Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil 4 Carlos Chagas Filho Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil * These authors contributed equally to this work. ABSTRACT Background. Physical exercise is a health promotion factor regulating gene expression and causing changes in phenotype, varying according to exercise type and intensity. Acute strenuous exercise in sedentary individuals appears to induce different transcrip- tional networks in response to stress caused by exercise. The objective of this research was to investigate the transcriptional profile of strenuous experimental exercise. Methodology. RNA-Seq was performed with Rattus norvegicus soleus muscle, submit- ted to strenuous physical exercise on a treadmill with an initial velocity of 0.5 km/h and increments of 0.2 km/h at every 3 min until animal exhaustion. Twenty four hours post-physical exercise, RNA-seq protocols were performed with coverage of 30 million reads per sample, 100 pb read length, paired-end, with a list of counts totaling 12816 Submitted 26 May 2020 genes. -
Basic Helix-Loop-Helix Transcription Factor TCF21 Is a Downstream Target of the Male Sex Determining Gene SRY
Basic Helix-Loop-Helix Transcription Factor TCF21 Is a Downstream Target of the Male Sex Determining Gene SRY Ramji K. Bhandari, Ingrid Sadler-Riggleman, Tracy M. Clement, Michael K. Skinner* Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America Abstract The cascade of molecular events involved in mammalian sex determination has been shown to involve the SRY gene, but specific downstream events have eluded researchers for decades. The current study identifies one of the first direct downstream targets of the male sex determining factor SRY as the basic-helix-loop-helix (bHLH) transcription factor TCF21. SRY was found to bind to the Tcf21 promoter and activate gene expression. Mutagenesis of SRY/SOX9 response elements in the Tcf21 promoter eliminated the actions of SRY. SRY was found to directly associate with the Tcf21 promoter SRY/SOX9 response elements in vivo during fetal rat testis development. TCF21 was found to promote an in vitro sex reversal of embryonic ovarian cells to induce precursor Sertoli cell differentiation. TCF21 and SRY had similar effects on the in vitro sex reversal gonadal cell transcriptomes. Therefore, SRY acts directly on the Tcf21 promoter to in part initiate a cascade of events associated with Sertoli cell differentiation and embryonic testis development. Citation: Bhandari RK, Sadler-Riggleman I, Clement TM, Skinner MK (2011) Basic Helix-Loop-Helix Transcription Factor TCF21 Is a Downstream Target of the Male Sex Determining Gene SRY. PLoS ONE 6(5): e19935. doi:10.1371/journal.pone.0019935 Editor: Ferenc Mueller, University of Birmingham, United Kingdom Received December 13, 2010; Accepted April 22, 2011; Published May 17, 2011 Copyright: ß 2011 Bhandari et al. -
KIF14 Is a Candidate Oncogene in the 1Q Minimal Region of Genomic Gain in Multiple Cancers
Oncogene (2005) 24, 4741–4753 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc ORIGINAL PAPERS KIF14 is a candidate oncogene in the 1q minimal region of genomic gain in multiple cancers Timothy W Corson1,2, Annie Huang3, Ming-Sound Tsao4,5,6 and Brenda L Gallie*,1,2,5,7 1Division of Cancer Informatics, Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, ON, Canada M5G 2M9; 2Department of Molecular & Medical Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; 3Labatt Brain Tumour Research Centre, Cancer Research Program, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8; 4Division of Cellular & Molecular Biology, Ontario Cancer Institute/Princess Margaret Hospital, University Health Network, Toronto, ON, Canada M5G 2M9; 5Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9; 6Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5G 1L5; 7Department of Ophthalmology, University of Toronto, Toronto, ON, Canada M5G 1X5 Gain of chromosome 1q31–1q32is seen in >50% of in retinoblastoma development is the loss of function of retinoblastoma and is common in other tumors. To define both alleles of the prototypic tumor suppressor gene, the minimal 1q region of gain, we determined genomic RB1, which encodes a key cell-cycle negative regulatory copy number by quantitative multiplex PCR of 14 transcription factor, pRB (Classon and Harlow, 2002). sequence tagged sites (STSs) spanning 1q25.3–1q41. The These initiating ‘M1’ and ‘M2’ mutations of Knudson’s most frequently gained STS at 1q32.1 (71%; 39 of 55 classic two-hit model for oncogenesis (Knudson, 1971) retinoblastoma) defined a 3.06 Mbp minimal region of are necessary for retinoblastoma initiation, but not gain between flanking markers, containing 14 genes.