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Sequence Overlap Between Autosomal and Sex-Linked Probes on the Illumina Humanmethylation27 Microarray
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 97 (2011) 214–222 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Sequence overlap between autosomal and sex-linked probes on the Illumina HumanMethylation27 microarray Yi-an Chen a,b, Sanaa Choufani a, Jose Carlos Ferreira a,b, Daria Grafodatskaya a, Darci T. Butcher a, Rosanna Weksberg a,b,⁎ a Program in Genetics and Genome Biology, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada b Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada article info abstract Article history: The Illumina Infinium HumanMethylation27 BeadChip (Illumina 27k) microarray is a high-throughput Received 12 August 2010 platform capable of interrogating the human DNA methylome. In a search for autosomal sex-specific DNA Accepted 18 December 2010 methylation using this microarray, we discovered autosomal CpG loci showing significant methylation Available online 4 January 2011 differences between the sexes. However, we found that the majority of these probes cross-reacted with sequences from sex chromosomes. Moreover, we determined that 6–10% of the microarray probes are non- Keywords: specific and map to highly homologous genomic sequences. Using probes targeting different CpGs that are Illumina Infinium HumanMethylation 27 BeadChip exact duplicates of each other, we investigated the precision of these repeat measurements and concluded Non-specific cross-reactive probe that the overall precision of this microarray is excellent. In addition, we identified a small number of probes Sex-specific DNA methylation targeting CpGs that include single-nucleotide polymorphisms. -
Radial Glia Reveal Complex Regulation by the Neuropeptide Secretoneurin
Transcriptomic and proteomic characterizations of goldfish (Carassius auratus) radial glia reveal complex regulation by the neuropeptide secretoneurin Dillon Da Fonte Thesis submitted to the Faculty of Graduate and Postdoctoral Studies University of Ottawa in partial fulfillment of the requirements for the Master of Science degree in biology Department of Biology Faculty of Science University of Ottawa © Dillon Da Fonte, Ottawa, Canada, 2016 Acknowledgements Finishing this thesis has been both a challenging and rewarding experience. This accomplishment would not have been possible without the never-ending support of colleagues, friends, family. First, I would like to express my most sincere gratitude to my supervisor and mentor, Dr. Vance Trudeau. Thank you for the opportunities you have given me, this experience has truly solidified my passion for research. I appreciate our many conversations that were enjoyed over a beer – it was truly a memorable experience. I would also like to thank my M.Sc. advisory committee, Dr. Michael Jonz and Dr. Marc Ekker for your time and insightful comments. A special thank you to Dr. Chris Martynuik who taught me the bioinformatics needed to analyze both transcriptomic and proteomic data and for all your help during my time at the University of Florida. I would like to also acknowledge my funding support from University of Ottawa, NSERC, and the Michael Smith Foreign Study Award for supporting my research stay at the University of Florida. To all current and past members of TeamENDO, thank you for the sense of community you all instilled in the lab. Both inside and outside the lab, I have made memories with all of you that I will cherish forever. -
Human and Chimpanzee Chorionic Gonadotropin Beta Genes Pille Hallast1, Janna Saarela2, Aarno Palotie3,4,5 and Maris Laan*1
BMC Evolutionary Biology BioMed Central Research article Open Access High divergence in primate-specific duplicated regions: Human and chimpanzee Chorionic Gonadotropin Beta genes Pille Hallast1, Janna Saarela2, Aarno Palotie3,4,5 and Maris Laan*1 Address: 1Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia, 2Department of Molecular Medicine, National Public Health Institute, Haartmaninkatu 8, 00290 Helsinki, Finland, 3Finnish Genome Center, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland, 4The Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, MA 02142, USA and 5Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK Email: Pille Hallast - [email protected]; Janna Saarela - [email protected]; Aarno Palotie - [email protected]; Maris Laan* - [email protected] * Corresponding author Published: 7 July 2008 Received: 29 August 2007 Accepted: 7 July 2008 BMC Evolutionary Biology 2008, 8:195 doi:10.1186/1471-2148-8-195 This article is available from: http://www.biomedcentral.com/1471-2148/8/195 © 2008 Hallast et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Low nucleotide divergence between human and chimpanzee does not sufficiently explain the species-specific morphological, physiological and behavioral traits. As gene duplication is a major prerequisite for the emergence of new genes and novel biological processes, comparative studies of human and chimpanzee duplicated genes may assist in understanding the mechanisms behind primate evolution. -
WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174282 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ C12Q 1/68 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/0425 19 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 14 June 2012 (14.06.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, English (25) Filing Language: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, Publication Language: English DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, 61/497,895 16 June 201 1 (16.06.201 1) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 61/499,138 20 June 201 1 (20.06.201 1) US OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/501,680 27 June 201 1 (27.06.201 1) u s SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/506,019 8 July 201 1(08.07.201 1) u s TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
The Study of the Expression of CGB1 and CGB2 in Human Cancer Tissues
G C A T T A C G G C A T genes Article The Study of the Expression of CGB1 and CGB2 in Human Cancer Tissues Piotr Białas * , Aleksandra Sliwa´ y , Anna Szczerba y and Anna Jankowska Department of Cell Biology, Poznan University of Medical Sciences, Rokietnicka 5D, 60-806 Pozna´n,Poland; [email protected] (A.S.);´ [email protected] (A.S.); [email protected] (A.J.) * Correspondence: [email protected]; Tel.: +48-6185-4-71-89 These authors contributed equally to this work. y Received: 14 August 2020; Accepted: 15 September 2020; Published: 17 September 2020 Abstract: Human chorionic gonadotropin (hCG) is a well-known hormone produced by the trophoblast during pregnancy as well as by both trophoblastic and non-trophoblastic tumors. hCG is built from two subunits: α (hCGα) and β (hCGβ). The hormone-specific β subunit is encoded by six allelic genes: CGB3, CGB5, CGB6, CGB7, CGB8, and CGB9, mapped to the 19q13.32 locus. This gene cluster also encompasses the CGB1 and CGB2 genes, which were originally considered to be pseudogenes, but as documented by several studies are transcriptionally active. Even though the protein products of these genes have not yet been identified, based on The Cancer Genome Atlas (TCGA) database analysis we showed that the mutual presence of CGB1 and CGB2 transcripts is a characteristic feature of cancers of different origin, including bladder urothelial carcinoma, cervical squamous cell carcinoma, esophageal carcinoma, head and neck squamous cell carcinoma, ovarian serous cystadenocarcinoma, lung squamous cell carcinoma, pancreatic adenocarcinoma, rectum adenocacinoma, testis germ cell tumors, thymoma, uterine corpus endometrial carcinoma and uterine carcinosarcoma. -
WO 2013/022995 A2 14 February 2013 (14.02.2013) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2013/022995 A2 14 February 2013 (14.02.2013) P O P C T (51) International Patent Classification: David [US/US]; 13539 N . 95th Way, Scottsdale, AZ G01N 33/53 (2006.01) 85260 (US). (21) International Application Number: (74) Agent: AKHAVAN, Ramin; Caris Science, Inc., 6655 N . PCT/US20 12/050030 Macarthur Blvd., Irving, TX 75039 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 8 August 2012 (08.08.2012) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, English (25) Filing Language: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (30) Priority Data: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 61/521,333 8 August 201 1 (08.08.201 1) US ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, 61/523,763 15 August 201 1 (15.08.201 1) US NO, NZ, OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, 61/526,623 23 August 201 1 (23.08.201 1) u s SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, 61/529,762 31 August 201 1 (3 1.08.201 1) u s TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, 61/534,352 13 September 201 1 (13.09.201 1) u s ZW. -
A Novel Two-Promoter-One-Gene System of the Chorionic Gonadotropin B Gene Enables Tissue-Specific Expression
285 A novel two-promoter-one-gene system of the chorionic gonadotropin b gene enables tissue-specific expression Christian Adams*, Alexander Henke* and Jo¨ rg Gromoll Institute of Reproductive and Regenerative Biology, Centre of Reproduction and Andrology, University Hospital Mu¨nster, Domagkstrasse 11, 48129 Mu¨nster, Germany (Correspondence should be addressed to J Gromoll; Email: [email protected]) *(C Adams and A Henke contributed equally to this work) (A Henke is now at Medical Research Council, Centre for Reproductive Health, The Queen’s Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, Scotland, UK) Abstract The New World monkey (NWM), Callithrix jacchus, a preferred model in medical research, displays an interesting endocrine regulation of reproduction: LH, the heterodimeric glycoprotein hormone, is functionally replaced by the chorionic gonadotropin (CG), a hormone indispensable for establishment of pregnancy in humans and normally expressed in the placenta. In the marmoset pituitary, the expression of the b-subunit (CGB) gene is regulated similar to human LH b-subunit, but its placental regulation is unknown. This study intended to decipher the underlying mechanism of tissue-specific expression of CGB in the marmoset placenta. We identified a new placental transcriptional start site, described a new, previously undiscovered exon, and define a novel placental core promoter in the marmoset CGB gene. This promoter contains a TATA box and binding sites for activating protein 2 and selective promoter factor 1, the latter acting synergistically by forming a regulation cassette. Differential first exon usage directed the tissue-specific expression. Methylation analyses revealed a tissue-specific pattern in the placental promoter indicating additional epigenetic regulation of gene expression. -
The Correlation Between CGB Gene Splice Variants in Women with Re- Current Spontaneous Abortions
Psarris A, et al., J Reprod Med Gynecol Obstet 2019, 4: 027 DOI: 10.24966/RMGO-2574/100027 HSOA Journal of Reproductive Medicine, Gynaecology & Obstetrics Original Research variant (627bp) was expressed in all the women of the study (both The Correlation between CGB study group and control group). Gene Splice Variants in Women Keywords: CGB splice variants; HCG genes; Recurrent miscar- with Recurrent Spontaneous riage; Recurrent spontaneous abortions Abortions Introduction Human Chorionic Gonadotrophin (hCG) is a heterodimer glyco- Alexandros Psarris*, Chrisa Lourida, Sofoklis Stavrou, Despi- protein which is mainly produced by the syncytiotrophoblast cells of na Mavrogianni, Dimitris Loutradis and Peter Drakakis the placenta during pregnancy and it is involved in a variety of bio- 1st Department of Obstetrics and Gynecology, “Alexandra” General Hospital, logical procedures [1]. The synthesis of the β-subunit of Human Cho- National and Kapodistrian University of Athens, Athens, Greece rionic Gonadotropin (βhCG) begins shortly after fertilization (βhCG been detected in the 2-cell stage embryo [2]) and it reaches its peak in the maternal blood stream at 9-10 weeks of pregnancy. HCG has many functions during normal pregnancy as it is involved in delaying Abstract the apoptosis of the corpus luteum [3], modulating the implantation Background: Human Chorionic Gonadotrophin (hCG) is a heterod- of the blastocyst [4,5], regulating the placentation and angiogenesis imer glycoprotein which is mainly produced by the syncytiotropho- [6-8] and developing maternal immunotolerance [9]. blast cells of the placenta during pregnancy and it is involved in a variety of biological procedures. The β-subunit of hCG is coded by HCG is composed of two subunits α and β. -
Transcriptomics of Early Human Development
TRANSCRIPTOMICS OF EARLY HUMAN DEVELOPMENT NAHENIWELA HERATH MUDIYANSELAGE WISHVA BANDARA HERATH NATIONAL UNIVERSITY OF SINGAPORE 2011 TRANSCRIPTOMICS OF EARLY HUMAN DEVELOPMENT NAHENIWELA HERATH MUDIYANSELAGE WISHVA BANDARA HERATH BSc. (Hons.), Grad. Chem. A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY NUS GRADUATE SCHOOL FOR INTEGRATIVE SCIENCES AND ENGINEERING NATIONAL UNIVERSITY OF SINGAPORE 2011 Acknowledgement My phD journey was an extremely eventful one. I was trained as a microbiologist and a chemist, then became a biochemist working on proteomics and ended up doing my thesis project as a developmental / molecular biologist on transcriptomics. Without the help of several special people this thesis would not have been possible. I would like to thank... Dr. Paul Robson, my supervisor, for giving me the opportunity to work under him, for his advice, insights and guidance throughout the project and for creating a stress-free environment in the lab which is a pleasure to work in. Prof. Justine Burley, for her kindness and support when I needed it the most. My wife Dulani, for being by my side, through thick and thin. Thank you! The trophoblast differentiation protocol which I use extensively in my thesis was first described by Dr. Luo Wenlong. Dr. Mikael Huss helped me with bioinformatic analysis and helped me learn python programming, Mr. Audi Harsono helped me in validating RNA-Seq data, Ms. Woon Chow Thai ran the microarrays, Ms. Jameelah Sheik Mohamed taught me stem cell culture and Dr. Guo Guoji helped me extract mouse embryo samples. I would also like to acknowledge NUS Graduate School for Integrative Sciences and Engineering (NGS) for my scholarship and the Genome Institute of Singapore (GIS) where I carried out my research. -
Human Chorionic Gonadotropin Beta Subunit Genes CGB1 and CGB2 Are Transcriptionally Active in Ovarian Cancer
Int. J. Mol. Sci. 2013, 14, 12650-12660; doi:10.3390/ijms140612650 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Human Chorionic Gonadotropin Beta Subunit Genes CGB1 and CGB2 are Transcriptionally Active in Ovarian Cancer Marta Kubiczak 1, Grzegorz P. Walkowiak 1, Ewa Nowak-Markwitz 2 and Anna Jankowska 1,* 1 Department of Cell Biology, Poznan University of Medical Sciences, Rokietnicka 5D, 60-806 Poznan, Poland; E-Mails: [email protected] (M.K.); [email protected] (G.P.W.) 2 Department of Gynecologic Oncology, Poznan University of Medical Sciences, Polna 33, 60-535 Poznan, Poland; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +48-61-8547-190; Fax: +48-61-8547-169. Received: 1 March 2013; in revised form: 28 March 2013 / Accepted: 9 May 2013 / Published: 17 June 2013 Abstract: Human chorionic gonadotropin beta subunit (CGB) is a marker of pregnancy as well as trophoblastic and nontrophoblastic tumors. CGB is encoded by a cluster of six genes, of which type II genes (CGB3/9, 5 and 8) have been shown to be upregulated in relation to type I genes (CGB6/7) in both placentas and tumors. Recent studies revealed that CGB1 and CGB2, originally considered as pseudogenes, might also be active, however, the protein products of these genes have not yet been identified. Our study demonstrates the presence of CGB1 and CGB2 transcripts in ovarian carcinomas. While CGB1 and CGB2 gene activation was not detected in normal ovaries lacking cancerous development, our study demonstrates the presence of CGB1 and CGB2 transcripts in 41% of analyzed ovarian cancer cases. -
Text Mining Gene Selection to Understand Pathological Phenotype Using Biological Big Data
1 Text Mining Gene Selection to Understand Pathological Phenotype Using Biological Big Data Christophe Desterke1,2 • Hans Kristian Lorenzo1,3,4 • Jean-Jacques Candelier1,3 1University Paris-Saclay, UFR Medicine, France; 2INSERM unit UA9, Hospital P. Brousse, France; 3INSERM unit 1197, Hospital P.Brousse, bâtiment Lavoisier, 14 avenue P.V.Couturier, 94800 Villejuif, France; 4Bicêtre Hospital, AP-HP, Department of Nephrology, Le Kremlin-Bicêtre, France Author for correspondence: Jean-Jacques Candelier, Hospital P.Brousse, bâtiment Lavoisier, 14 avenue P.V.Couturier, 94800 Villejuif, France. Email: [email protected] Doi: https://doi.org/10.36255/exonpublications.bioinformatics.2021.ch1 Abstract: Whole transcriptome omics experiments allow for the study of gene regulation at the cellular level. During analysis and interpretation of omics data, false discovery can occur. To minimize false discovery and identify true significant cases, multi-test correction has been introduced to bioinformatics algorithms. The scientific literature offers a huge collection of information that can be parsed using a web Application Programming Interface. Gene selection by text mining can rank information according to its importance while taking into account the most recent updates in scientific literature. The integration of text mining selection in biologi- cal big data, such as transcriptome experiments including single cell transcrip- tome, can achieve an important dimensional reduction of the data without any statistical hypothesis. This avoids false discoveries regarding the molecules of interest. Hydatidiform moles and focal segmental glomerulosclerosis (FSGS) nephropathy are the two examples presented in this chapter, which demonstrate the considerable value of these analytical methods to prove the concept. The best FSGS markers expressed can be displayed by building an interactive online web interface as a web resource based on the glomerular cell transcriptome. -
The Evolution and Genomic Landscape of CGB1 and CGB2 Genes
Molecular and Cellular Endocrinology 260–262 (2007) 2–11 The evolution and genomic landscape of CGB1 and CGB2 genes Pille Hallast a, Kristiina Rull a,b, Maris Laan a,∗ a Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia b Department of Obstetrics and Gynecology, University of Tartu, Estonia Received 12 August 2005; accepted 28 November 2005 Abstract The origin of completely novel proteins is a significant question in evolution. The luteinizing hormone (LHB)/chorionic gonadotropin (CGB) gene cluster in humans contains a candidate example of this process. Two genes in this cluster (CGB1 and CGB2) exhibit nucleotide sequence similarity with the other LHB/CGB genes, but as a result of frameshifting are predicted to encode a completely novel protein. Our analysis of these genes from humans and related primates indicates a recent origin in the lineage specific to humans and African great apes. While the function of these genes is not yet known, they are strongly conserved between human and chimpanzee and exhibit three-fold lower diversity than LHB across human populations with no mutations that would disrupt the coding sequence. The 5-upstream region of CGB1/2 contains most of the promoter sequence of hCG plus a novel region proximal to the putative transcription start site. In silico prediction of putative transcription factor binding sites supports the hypothesis that CGB1 and CGB2 gene products are expressed in, and may contribute to, implantation and placental development. © 2006 Elsevier Ireland Ltd. All rights reserved. Keywords: Chorionic gonadotropin beta 1 and 2; Gene evolution; Polymorphism patterns; Putative promoter region; In silico transcription factor binding site prediction 1.