Sex Determination: a 'Window' of DAX1 Activity
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Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Rep 467 Morrish & Sinclair
Reproduction (2002) 124, 447–457 Review Vertebrate sex determination: many means to an end Bronwyn C. Morrish and Andrew H. Sinclair* Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Rd, Melbourne, Victoria 3052, Australia The differentiation of a testis or ovary from a bipotential gonadal primordium is a develop- mental process common to mammals, birds and reptiles. Since the discovery of SRY, the Y-linked testis-determining gene in mammals, extensive efforts have failed to find its orthologue in other vertebrates, indicating evolutionary plasticity in the switch that triggers sex determination. Several other genes are known to be important for sex determination in mammals, such as SOX9, AMH, WT1, SF1, DAX1 and DMRT1. Analyses of these genes in humans with gonadal dysgenesis, mouse models and using in vitro cell culture assays have revealed that sex determination results from a complex interplay between the genes in this network. All of these genes are conserved in other vertebrates, such as chickens and alligators, and show gonad-specific expression in these species during the period of sex determination. Intriguingly, the sequence, sex specificity and timing of expression of some of these genes during sex determination differ among species. This finding indicates that the interplay between genes in the regulatory network leading to gonad development differs between vertebrates. However, despite this, the development of a testis or ovary from a bipotential gonad is remarkably similar across vertebrates. The existence of two sexes is nearly universal in the animal and alligators. Ectopic administration of oestrogen or kingdom and although gonadal morphogenesis is remark- inhibitors of oestrogen synthesis during a critical period of ably similar across vertebrates, the sex-determining mecha- gonadogenesis in chickens and alligators can feminize or nism varies considerably. -
Seq2pathway Vignette
seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway. -
Genomic Approaches to Deconstruct Pluripotency
GG12CH08-Daley ARI 26 July 2011 14:10 Genomic Approaches to Deconstruct Pluripotency Yuin-Han Loh,1,2,∗ Lin Yang,1,2,∗ Jimmy Chen Yang,1,2,∗∗ Hu Li,3,4,∗∗ James J. Collins,3,4,5 and George Q. Daley1,2,5,6,7 1Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Children’s Hospital Boston; Dana-Farber Cancer Institute; and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; email: [email protected] 2Harvard Stem Cell Institute, Cambridge, Massachusetts 02115 3Department of Biomedical Engineering and Center for BioDynamics, Boston University, Boston, Massachusetts 02215 4Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115 5Howard Hughes Medical Institute, Boston, Massachusetts 02115 6Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts 02115 7Manton Center for Orphan Disease Research, Boston, Massachusetts 02115 Annu. Rev. Genomics Hum. Genet. 2011. Keywords 12:165–85 transcription regulation, epigenetics, histone modifications, DNA First published online as a Review in Advance on July 25, 2011 methylation, pluripotent stem cells The Annual Review of Genomics and Human Genetics Abstract is online at genom.annualreviews.org Embryonic stem cells (ESCs) first derived from the inner cell mass of by Boston University on 10/07/11. For personal use only. This article’s doi: 10.1146/annurev-genom-082410-101506 blastocyst-stage embryos have the unique capacity of indefinite self- renewal and potential to differentiate into all somatic cell types. Similar Copyright c 2011 by Annual Reviews. All rights reserved developmental potency can be achieved by reprogramming differen- tiated somatic cells into induced pluripotent stem cells (iPSCs). -
Cops5 Safeguards Genomic Stability of Embryonic Stem Cells Through Regulating Cellular Metabolism and DNA Repair
Cops5 safeguards genomic stability of embryonic stem cells through regulating cellular metabolism and DNA repair Peng Lia, Lulu Gaoa, Tongxi Cuia, Weiyu Zhanga, Zixin Zhaoa, and Lingyi Chena,1 aState Key Laboratory of Medicinal Chemical Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Collaborative Innovation Center for Biotherapy, Tianjin Key Laboratory of Protein Sciences, National Demonstration Center for Experimental Biology Education and College of Life Sciences, Nankai University, 300071 Tianjin, China Edited by Janet Rossant, Hospital for Sick Children, University of Toronto, Toronto, Canada, and approved December 24, 2019 (received for review August 29, 2019) The highly conserved COP9 signalosome (CSN), composed of 8 transiently expressed in about 5% of ESCs at a given time, subunits (Cops1 to Cops8), has been implicated in pluripotency promotes rapid telomere elongation by telomere recombination maintenance of human embryonic stem cells (ESCs). Yet, the mech- and regulates genomic stability (11). Induced by genotoxic stress, anism for the CSN to regulate pluripotency remains elusive. We Filia stimulates the PARP1 activity and relocates from centro- previously showed that Cops2, independent of the CSN, is essential somes to DNA damage sites and mitochondria to regulate DDR for the pluripotency maintenance of mouse ESCs. In this study, we and apoptosis (12). Sall4, a pluripotency transcription factor, set out to investigate how Cops5 and Cops8 regulate ESC differ- facilitates the ataxia telangiectasia-mutated activation in re- entiation and tried to establish Cops5 and Cops8 knockout (KO) sponse to DSBs (13). To minimize the ROS-induced genomic ESC lines by CRISPR/Cas9. To our surprise, no Cops5 KO ESC clones DNA damage, ESCs produce lower levels of mitochondrial ROS were identified out of 127 clones, while three Cops8 KO ESC lines and express higher levels of antioxidants than differentiated cells were established out of 70 clones. -
Aromatase (Cyp19) Expression Is Up-Regulated by Targeted Disruption of Dax1
Aromatase (Cyp19) expression is up-regulated by targeted disruption of Dax1 Zhen J. Wang*, Baxter Jeffs*, Masafumi Ito*, John C. Achermann*, Richard N. Yu*, Dale B. Hales†, and J. Larry Jameson*‡ *Division of Endocrinology, Metabolism, and Molecular Medicine, Northwestern University Medical School, Chicago, IL 60611; and †University of Illinois, Chicago, IL 60612 Edited by Jean D. Wilson, University of Texas Southwestern Medical Center, Dallas, TX, and approved May 14, 2001 (received for review November 14, 2000) DAX-1 [dosage-sensitive sex reversal, adrenal hypoplasia con- nuclear receptors (6, 7). Consistent with this idea, DAX-1 genita (AHC) critical region on the X chromosome, gene 1] is an interacts directly with SF-1 and inhibits SF-1-mediated transac- orphan nuclear receptor that represses transcription by steroido- tivation (15, 16). genic factor-1 (SF-1), a factor that regulates expression of multiple Testicular Leydig cells express both Dax1 and Sf1 (7, 17) and steroidogenic enzymes and other genes involved in reproduction. constitute the major site of testosterone production in males Mutations in the human DAX1 gene (also known as AHC) cause the (17). Testosterone biosynthesis requires five steroidogenic pro- X-linked syndrome AHC, a disorder that is associated with hypogo- teins: steroidogenic acute regulatory protein (StAR), cholesterol nadotropic hypogonadism also. Characterization of Dax1-deficient side-chain cleavage enzyme (CYP11A), 3-hydroxysteroid de- male mice revealed primary testicular defects that included Leydig hydrogenase (3-HSD type II), 17␣-hydroxylase (CYP17), and cell hyperplasia (LCH) and progressive degeneration of the germi- 17-hydroxysteroid dehydrogenase (17-HSD type III). Testos- nal epithelium, leading to infertility. -
Molecular Basis Governing Primary Sex in Mammals
Jpn J Human Genet 41, 363-379, 1996 Review Article MOLECULAR BASIS GOVERNING PRIMARY SEX IN MAMMALS Kozo NAGAI Department of Biochemistry, Tokyo Medical College, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160, Japan Summary The function of Sry for inducing a male gonad was iden- tified due to a development of a transgenic XX male mouse with testes by introducing a single gene into an embryo. The intronless Sry encodes a putative transcriptional protein harboring an HMG motif. The sequence similarity within the HMG motif has been highly conserved despite less conservation in other domains. Hence, the HMG motif must play a critical role in the transcriptional regulation, leading to the development of a male gonad. However, a non HMG box C terminal domain of Sry protein may also be indispensable for inducing normal testicular develop- ment. Further, several autosomal genes, such as SF1, WT1, SOX and MIS, as well as a unique X chromosomal DAX1 were suggested to be associated with the development of gonadal sex in mammals. Therefore, the significance on the involvement of these genes in the molecular mechanism of mammalian sex determination should be also considered. Key Words sex determining gene, primary sex determination, mam- malian sex Introduction The clarification and understanding of the molecular mechanism responsible for mammalian sex determination is very interesting, because the presences of male and female sexes are not only surprising in its mysterious manifestations and graceful in its conception but also absolute benefits. In a mammalian system, the appearance of gonadal sex in a lineage of sex differentiation is most exciting, yet is still not sufficiently understood. -
Obesity-Induced Excess of 17-Hydroxyprogesterone Promotes Hyperglycemia Through Activation of Glucocorticoid Receptor
The Journal of Clinical Investigation RESEARCH ARTICLE Obesity-induced excess of 17-hydroxyprogesterone promotes hyperglycemia through activation of glucocorticoid receptor Yan Lu,1 E Wang,1 Ying Chen,1 Bing Zhou,1 Jiejie Zhao,1 Liping Xiang,1 Yiling Qian,1 Jingjing Jiang,1 Lin Zhao,1 Xuelian Xiong,1 Zhiqiang Lu,1 Duojiao Wu,2 Bin Liu,1,3 Jing Yan,4 Rong Zhang,4,5 Huijie Zhang,6 Cheng Hu,4,5,7 and Xiaoying Li1 1Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Endocrinology and Metabolism, and 2Institute of Clinical Science, Shanghai Institute of Clinical Bioinformatics, Zhongshan Hospital, Fudan University, Shanghai, China. 3Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China. 4Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, and 5Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Center for Diabetes, Shanghai, China. 6Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China. 7Institute for Metabolic Disease, Fengxian Central Hospital, Southern Medical University, Shanghai, China. Type 2 diabetes mellitus (T2DM) has become an expanding global public health problem. Although the glucocorticoid receptor (GR) is an important regulator of glucose metabolism, the relationship between circulating glucocorticoids (GCs) and the features of T2DM remains controversial. Here, we show that 17-hydroxyprogesterone (17-OHP), an intermediate steroid in the biosynthetic pathway that converts cholesterol to cortisol, binds to and stimulates the transcriptional activity of GR. Hepatic 17-OHP concentrations are increased in diabetic mice and patients due to aberrantly increased expression of Cyp17A1. -
Characterization of Transcription Factor Complexes Involved in Globin Gene Regulation
Characterization of Transcription Factor Complexes involved in Globin Gene Regulation Katarzyna Ewa Kołodziej 26th March 2008 Cover: Rodota The work presented in this thesis was performed at the Department of Cell Biology at the Erasmus Univer- sity Medical Center Rotterdam. This department is member of the Medisch Genetisch Centrum Zuid-West Nederland. The research was partially supported by the Netherlandse Organizatie voor Wetenschappelijk Onderzoek (NWO) and by EU. Characterization of Transcription Factor Complexes involved in Globin Gene Regulation Karakterizering van transcriptie factor complexen betrokken bij de regulatie van globine genen PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Erasmus Universiteit Rotterdam op gezag van de Rector Magnificus Prof.dr. S.W.J. Lamberts en volgens besluit van het College voor Promoties. De openbare verdediging zal plaatsvinden op woensdag 26 maart 2008 om 15.45 uur. door Katarzyna Ewa Kołodziej geboren te Wrocław, Polen Promotiecommissie Promotor: Prof.dr. F.G. Grosveld Overige laden: Prof.dr. J.N.J. Philipsen Prof.dr. J.D. Engel Dr.ir. D.N. Meijer Copromotor: Dr. J. Strouboulis Moim rodzicom & for Luc TABLE OF CONTENTS Chapter 1 : Introduction 9 Chapter 2 : Isolation of transcription factor complexes by in vivo biotinylation tagging and direct binding to streptavidin beads (Patrick Rodriguez, Harald Braun, Katarzyna E. Kolodziej, Ernie de Boer, Jennifer Campbel, Edgar Bonte, Sjaak Philipsen and John Strouboulis Methods Mol Bio. 2006; 338: 305-23 ) 33 Chapter 3 : GATA-1 forms distinct activating and repressive complexes in erythroid cells (Patrick Rodriguez, Edgar Bonte, Jeroen Krijgsveld, Katarzyna E. Kolodziej, Boris Guyot, Albert Heck, Paresh Vyas, Ernie de Boer, Frank Grosveld and John Strouboulis, EMBO J. -
Steroid Receptor Coactivator-1-Deficient Mice Exhibit Altered Hypothalamic-Pituitary-Adrenal Axis Function
0013-7227/06/$15.00/0 Endocrinology 147(3):1322–1332 Printed in U.S.A. Copyright © 2006 by The Endocrine Society doi: 10.1210/en.2005-0751 Steroid Receptor Coactivator-1-Deficient Mice Exhibit Altered Hypothalamic-Pituitary-Adrenal Axis Function Jonathon N. Winnay, Jianming Xu, Bert W. O’Malley, and Gary D. Hammer Departments of Molecular and Integrative Physiology (H.N.W., G.D.H.) and Internal Medicine (G.D.H.), Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor, Michigan 48109-0678; and Department of Molecular and Cellular Biology, Baylor College of Medicine (J.X., B.W.O.), Houston, Texas 77030 Downloaded from https://academic.oup.com/endo/article/147/3/1322/2501069 by guest on 28 September 2021 Steroidogenic factor-1 (SF-1), has emerged as a critical nu- as well as a concomitant defect in glucocorticoid-mediated clear receptor regulating development and differentiation at feedback inhibition of the HPA axis. An examination of po- several levels of the hypothalamic-pituitary-steroidogenic tential compensatory mechanism(s) revealed an increase in axis. Although many coregulatory factors have been shown to adrenal weight, selective elevation of melanocortin 2 receptor physically and functionally interact with SF-1, the relative mRNA, and a coincident increase in SRC-2 and SRC-3 expres- importance of these interactions in SF-1 target tissues has not sion in SRC-1؊/؊ adrenals. A reduction in blood glucose was been thoroughly established. In this study we assessed roles observed in SRC-1؊/؊ mice after chronic stress, consistent of steroid receptor coactivator-1 (SRC-1) in hypothalamic-pi- with a generalized state of glucocorticoid resistance. -
Regulatory Mechanisms Underlying Sepsis Progression in Patients with Tumor Necrosis Factor‑Α Genetic Variations
EXPERIMENTAL AND THERAPEUTIC MEDICINE 12: 323-328, 2016 Regulatory mechanisms underlying sepsis progression in patients with tumor necrosis factor‑α genetic variations * * YANGZHOU LIU , NING HAN , QINCHUAN LI and ZENGCHUN LI Emergency Trauma Department, Shanghai East Hospital, Shanghai 200120, P.R. China Received November 4, 2014; Accepted November 18, 2015 DOI: 10.3892/etm.2016.3308 Abstract. The present study aimed to investigate the regula- and ubiquitination of the FUS protein. Furthermore, COPS2 tory mechanisms underlying sepsis progression in patients with and CUL3 may be novel targets of miR-15. tumor necrosis factor (TNF)-α genetic variations. The GSE5760 expression profile data, which was downloaded from the Gene Introduction Expression Omnibus database, contained 30 wild-type (WT) and 28 mutation (MUT) samples. Differentially expressed Multiple trauma, which is commonly associated with severe inju- genes (DEGs) between the two types of samples were identified ries and multiple organ failure, may lead to various complications, using the Student's t-test, and the corresponding microRNAs including sepsis and septic shock, which are major healthcare (miRNAs) were screened using WebGestalt software. An problems worldwide (1-3). There are 400,000-500,000 cases of integrated miRNA-DEG network was constructed using the sepsis in the United States annually (4). Antimicrobial therapy Cytoscape software, based on the interactions between the may be applied for the management of sepsis; however, the DEGs, as identified using the Search Tool for the Retrieval mortality rate associated with sepsis has increased, and was of Interacting Genes/Proteins database, and the correlation reported to be as high as 40% in 2003 (5). -
COPS2 Antibody Cat
COPS2 Antibody Cat. No.: 28-027 COPS2 Antibody Antibody used in WB on Human, Mouse at 1:200. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Dog, Drosophila, Human, Mouse, Rat, Zebrafish Antibody produced in rabbits immunized with a synthetic peptide corresponding a region IMMUNOGEN: of human COPS2. TESTED APPLICATIONS: ELISA, WB COPS2 antibody can be used for detection of COPS2 by ELISA at 1:312500. COPS2 APPLICATIONS: antibody can be used for detection of COPS2 by western blot at 1.25 μg/mL, and HRP conjugated secondary antibody should be diluted 1:50,000 - 100,000. POSITIVE CONTROL: 1) Cat. No. XBL-10409 - Fetal Liver Tissue Lysate PREDICTED MOLECULAR 52 kDa WEIGHT: September 27, 2021 1 https://www.prosci-inc.com/cops2-antibody-28-027.html Properties PURIFICATION: Antibody is purified by protein A chromatography method. CLONALITY: Polyclonal CONJUGATE: Unconjugated PHYSICAL STATE: Liquid Purified antibody supplied in 1x PBS buffer with 0.09% (w/v) sodium azide and 2% BUFFER: sucrose. CONCENTRATION: batch dependent For short periods of storage (days) store at 4˚C. For longer periods of storage, store STORAGE CONDITIONS: COPS2 antibody at -20˚C. As with any antibody avoid repeat freeze-thaw cycles. Additional Info OFFICIAL SYMBOL: COPS2 ALTERNATE NAMES: COPS2, CSN2, SGN2, ALIEN, TRIP15 ACCESSION NO.: NP_004227 PROTEIN GI NO.: 4759264 GENE ID: 9318 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References COPS2 is an essential component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the BACKGROUND: deneddylation of the cullin subunits of SCF-type E3 ligase complexes.