Chimeric Transcript Discovery by Paired-End Transcriptome Sequencing
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Open Dogan Phdthesis Final.Pdf
The Pennsylvania State University The Graduate School Eberly College of Science ELUCIDATING BIOLOGICAL FUNCTION OF GENOMIC DNA WITH ROBUST SIGNALS OF BIOCHEMICAL ACTIVITY: INTEGRATIVE GENOME-WIDE STUDIES OF ENHANCERS A Dissertation in Biochemistry, Microbiology and Molecular Biology by Nergiz Dogan © 2014 Nergiz Dogan Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2014 ii The dissertation of Nergiz Dogan was reviewed and approved* by the following: Ross C. Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology Dissertation Advisor Chair of Committee David S. Gilmour Professor of Molecular and Cell Biology Anton Nekrutenko Professor of Biochemistry and Molecular Biology Robert F. Paulson Professor of Veterinary and Biomedical Sciences Philip Reno Assistant Professor of Antropology Scott B. Selleck Professor and Head of the Department of Biochemistry and Molecular Biology *Signatures are on file in the Graduate School iii ABSTRACT Genome-wide measurements of epigenetic features such as histone modifications, occupancy by transcription factors and coactivators provide the opportunity to understand more globally how genes are regulated. While much effort is being put into integrating the marks from various combinations of features, the contribution of each feature to accuracy of enhancer prediction is not known. We began with predictions of 4,915 candidate erythroid enhancers based on genomic occupancy by TAL1, a key hematopoietic transcription factor that is strongly associated with gene induction in erythroid cells. Seventy of these DNA segments occupied by TAL1 (TAL1 OSs) were tested by transient transfections of cultured hematopoietic cells, and 56% of these were active as enhancers. Sixty-six TAL1 OSs were evaluated in transgenic mouse embryos, and 65% of these were active enhancers in various tissues. -
Research Article Deletion of Herpud1 Enhances Heme Oxygenase-1 Expression in a Mouse Model of Parkinson's Disease
Hindawi Publishing Corporation Parkinson’s Disease Volume 2016, Article ID 6163934, 9 pages http://dx.doi.org/10.1155/2016/6163934 Research Article Deletion of Herpud1 Enhances Heme Oxygenase-1 Expression in a Mouse Model of Parkinson’s Disease Thuong Manh Le,1 Koji Hashida,1 Hieu Minh Ta,1 Mika Takarada-Iemata,1,2 Koichi Kokame,3 Yasuko Kitao,1,2 and Osamu Hori1,2 1 Department of Neuroanatomy, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan 2CREST, JST (Japan Science and Technology), Tokyo 102-8666, Japan 3Department of Molecular Pathogenesis, National Cerebral and Cardiovascular Center, Osaka 565-8565, Japan Correspondence should be addressed to Osamu Hori; [email protected] Received 21 November 2015; Revised 25 January 2016; Accepted 28 January 2016 Academic Editor: Antonio Pisani Copyright © 2016 Thuong Manh Le et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Herp is an endoplasmic reticulum- (ER-) resident membrane protein that plays a role in ER-associated degradation. We studied the expression of Herp and its effect on neurodegeneration in a mouse model of Parkinson’s disease (PD), in which both the oxidative stress and the ER stress are evoked. Eight hours after administering a PD-related neurotoxin, 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine (MPTP), to mice, the expression of Herp increased at both the mRNA and the protein levels. Experiments using +/+ −/− Herpud1 and Herpud1 mice revealed that the status of acute degeneration of nigrostriatal neurons and reactive astrogliosis was comparable between two genotypes after MPTP injection. -
Gene Section Review
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Review MIRN21 (microRNA 21) Sadan Duygu Selcuklu, Mustafa Cengiz Yakicier, Ayse Elif Erson Biology Department, Room: 141, Middle East Technical University, Ankara 06531, Turkey Published in Atlas Database: March 2007 Online updated version: http://AtlasGeneticsOncology.org/Genes/MIRN21ID44019ch17q23.html DOI: 10.4267/2042/38450 This work is licensed under a Creative Commons Attribution-Non-commercial-No Derivative Works 2.0 France Licence. © 2007 Atlas of Genetics and Cytogenetics in Oncology and Haematology sequences of MIRN21 showed enrichment for Pol II Identity but not Pol III. Hugo: MIRN21 MIRN21 gene was shown to harbor a 5' promoter Other names: hsa-mir-21; miR-21 element. 1008 bp DNA fragment for MIRN21 gene Location: 17q23.1 was cloned (-959 to +49 relative to T1 transcription Location base pair: MIRN21 is located on chr17: site, see Figure 1; A). Analysis of the sequence showed 55273409-55273480 (+). a candidate 'CCAAT' box transcription control element Local order: Based on Mapviewer, genes flanking located approximately about 200 nt upstream of the T1 MIRN21 oriented from centromere to telomere on site. T1 transcription site was found to be located in a 17q23 are: sequence similar to 'TATA' box - TMEM49, transmembrane protein 49, 17q23.1. (ATAAACCAAGGCTCTTACCATAGCTG). To test - MIRN21, microRNA 21, 17q23.1. the activity of the element, about 1kb DNA fragment - TUBD1, tubulin, delta 1, 17q23.1. was inserted into the 5' end of firefly luciferase - LOC729565, similar to NADH dehydrogenase indicator gene and transfected into 293T cells. The (ubiquinone) 1 beta subcomplex, 8, 19 kDa, 17q23.1. -
Clinical Validation of the Tempus Xt Next-Generation Targeted Oncology Sequencing Assay
www.oncotarget.com Oncotarget, 2019, Vol. 10, (No. 24), pp: 2384-2396 Research Paper Clinical validation of the tempus xT next-generation targeted oncology sequencing assay Nike Beaubier1, Robert Tell1, Denise Lau1, Jerod R. Parsons1, Stephen Bush1, Jason Perera1, Shelly Sorrells1, Timothy Baker1, Alan Chang1, Jackson Michuda1, Catherine Iguartua1, Shelley MacNeil1, Kaanan Shah1, Philip Ellis1, Kimberly Yeatts1, Brett Mahon1, Timothy Taxter1, Martin Bontrager1, Aly Khan1, Robert Huether1, Eric Lefkofsky1 and Kevin P. White1 1Tempus Labs Inc., Chicago, IL 60654, USA Correspondence to: Nike Beaubier, email: [email protected] Kevin P. White, email: [email protected] Keywords: tumor profiling, next-generation sequencing assay validation Received: August 03, 2018 Accepted: February 03, 2019 Published: March 22, 2019 Copyright: Beaubier et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT We developed and clinically validated a hybrid capture next generation sequencing assay to detect somatic alterations and microsatellite instability in solid tumors and hematologic malignancies. This targeted oncology assay utilizes tumor- normal matched samples for highly accurate somatic alteration calling and whole transcriptome RNA sequencing for unbiased identification of gene fusion events. The assay was validated with a combination of clinical specimens and cell lines, and recorded a sensitivity of 99.1% for single nucleotide variants, 98.1% for indels, 99.9% for gene rearrangements, 98.4% for copy number variations, and 99.9% for microsatellite instability detection. This assay presents a wide array of data for clinical management and clinical trial enrollment while conserving limited tissue. -
Fusion Transcripts and Transcribed Retrotransposed Loci Discovered Through Comprehensive Transcriptome Analysis Using Paired-End Ditags (Pets)
Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs) Yijun Ruan,1,6 Hong Sain Ooi,2 Siew Woh Choo,2 Kuo Ping Chiu,2 Xiao Dong Zhao,1 K.G. Srinivasan,1 Fei Yao,1 Chiou Yu Choo,1 Jun Liu,1 Pramila Ariyaratne,2 Wilson G.W. Bin,2 Vladimir A. Kuznetsov,2 Atif Shahab,3 Wing-Kin Sung,2,4 Guillaume Bourque,2 Nallasivam Palanisamy,5 and Chia-Lin Wei1,6 1Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore; 2Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore; 3Bioinformatics Institute, Singapore 138671, Singapore; 4School of Computing, National University of Singapore, Singapore 117543, Singapore; 5Cancer Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
Wo 2010/081001 A2
(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 15 July 2010 (15.07.2010) WO 2010/081001 A2 (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/68 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (21) International Application Number: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, PCT/US20 10/020501 DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, ! January 2010 (08.01 .2010) KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (25) Filing Language: English NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (26) Publication Language: English SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 61/143,598 9 January 2009 (09.01 .2009) US (84) Designated States (unless otherwise indicated, for every 61/187,776 17 June 2009 (17.06.2009) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, (71) Applicant (for all designated States except US): THE ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, REGENTS OF THE UNIVERSITY OF MICHIGAN TM), European (AT, BE, BG, CH, CY, CZ, DE, DK, EE, [US/US]; 1214 South University, 2nd Floor, Ann Arbor, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, Michigan 48104 (US). -
Understanding the Genetics of Coronary Artery Disease Through Novel Statistical Approaches
Fakultät für Medizin Deutsches Herzzentrum München - Klinik an der Technischen Universität München Understanding the genetics of coronary artery disease through novel statistical approaches Lingyao Zeng Vollständiger Abdruck der von der Fakultät für Medizin der Technischen Universität München zur Erlangung des akademischen Grades eines Doctor of Philosophy (Ph.D.) genehmigten Dissertation. Vorsitzende/r: Prof. Dr. Dr. Stefan Engelhardt Betreuer/in: Prof. Dr. Adnan Kastrati Prüfer der Dissertation: 1. Prof. Dr. Heribert Schunkert 2. Prof. Dr. Dr. Fabian Theis Die Dissertation wurde am 29.07.2016 bei der Fakultät für Medizin der Technischen Universität München eingereicht und durch die Fakultät für Medizin am 14.09.2016 angenommen. Acknowledgement First of all, I would like to express my sincere gratitude and thanks to my advisor Prof. Heribert Schunkert. It is my honor to join his research group. He has been actively interested in my work and offered tremendous support and guidance at all levels of my PhD research over the last few years. I greatly appreciate all his knowledge, kindness, enthusiasm, and encouragement. I would like to thank the other members of my committee, Prof. Adnan Kastrati and Prof. Fabian Theis. I thank Prof. Adnan Kastrati, who as my supervisor has given me the opportunity to pursue my PhD research at the Deutsches Herzzentrum München and Technische Universität München. I also thank him for the generosity and patience offering the clinical data and descriptions. I thank Prof. Fabian Theis for all his valuable comments and encouragement at both the committee meetings and e:AtheroSysMed project conferences. I am grateful to Prof. Bertram Müller-Myhsok from the Department of Statistical Genetics, Max Planck Institute of Psychiatry, and his team member Dr. -
LHCGR (Luteinizing Hormone/Choriogonadotropin Receptor); LPHN2 (Latrophilin 2) (1P31.1)
Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 8, Number 1, Jan-Mar 2004 Previous Issue / Next Issue Genes ATBF1 (AT-binding transcription factor 1) (16q22.3-q23.1). Nadine Van Roy, Frank Speleman. Atlas Genet Cytogenet Oncol Haematol 2004; 8 (1): 1-7. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/ATBF1ID357.html DIRC2 (3q21). Anita Bonné, Danièlle Bodmer, Marc Eleveld, Eric Schoenmakers, Ad Geurts van Kessel.. Atlas Genet Cytogenet Oncol Haematol 2004; 8 (1): 8-11. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/DIRC2ID497.html DIRC3 (2q35). Anita Bonné, Danièlle Bodmer, Marc Eleveld, Eric Schoenmakers, Ad Geurts van Kessel.. Atlas Genet Cytogenet Oncol Haematol 2004; 8 (1): 12-14. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/DIRC3ID498..html RAP1GDS1 (4q22.3). Franck Viguié. Atlas Genet Cytogenet Oncol Haematol 2004; 8 (1): 15-18. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/RAP1GDS1ID400.html RET (REarranged during Transfection) (10q11.2). Patricia Niccoli-Sire. Atlas Genet Cytogenet Oncol Haematol 2004; 8 (1): 19-25. [Full Text] [PDF] URL : http://AtlasGeneticsOncology.org/Genes/RETID76.html LHCGR (luteinizing hormone/choriogonadotropin receptor); LPHN2 (latrophilin 2) (1p31.1). Jim Heighway. Atlas Genet Cytogenet Oncol Haematol 2004; 8 (1): 26-36. -
Systematic Evaluation of the Causal Relationship Between DNA Methylation and C-Reactive
bioRxiv preprint doi: https://doi.org/10.1101/397836; this version posted August 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. CRP_epiMR Walton et al. Systematic evaluation of the causal relationship between DNA methylation and C-reactive protein Esther Walton1, Gibran Hemani1, Abbas Dehghan2, Caroline Relton1, George Davey Smith1 1 MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, BS8 2BN, United Kingdom; 2 Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, W2 1PG, United Kingdom Corresponding author: Esther Walton; Senior Research Associate in Genetic Epidemiology; MRC Integrative Epidemiology Unit; Bristol Medical School; University of Bristol; Oakfield House; Bristol BS8 2BN; [email protected]; phone: +44 (0) 117 3314026; fax: +44 (0) 117 3314052. Keywords: CRP, Mendelian randomization, epigenetics, ALSPAC, inflammation 1 bioRxiv preprint doi: https://doi.org/10.1101/397836; this version posted August 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. CRP_epiMR Walton et al. Abstract Elevated C-reactive protein (CRP) levels are an indicator of chronic low-grade inflammation. Epigenetic modifications, including DNA methylation, have been linked to CRP, but systematic investigations into potential underlying causal relationships have not yet been performed. -
Supplementary Table S3
TABLE S3: Genes overexpressed in decitabine treated HMCLs. Five HMCLs were cultured with or without 0.5 µM decitabine for 7 days and gene expression was profiled with Affymetrix U133 plus 2.0. Genes significantly differentially expressed between control and decitabine treated cells were identified using SAM supervised paired analysis with a 5% false discovery rate. When a gene was interrogated by several probe sets, we used the probe set yielding to a maximum variance across control and decitabine treated cells. Probeset Gene Ratio Banding Affymetrix description Intercellular communication and membrane proteins 209122_at ADFP 3.70 9p22.1 adipose differentiation-related protein 211990_at HLA-DPA1 1.70 6p21.3 major histocompatibility complex; class II; DP alpha 1 205718_at ITGB7 2.11 12q13.13 integrin; beta 7 1569003_at TMEM49 2.33 17q23.2 transmembrane protein 49 205483_s_at G1P2 2.77 1p36.33 interferon; alpha-inducible protein (clone IFI-15K) 200696_s_at GSN 3.97 9q33 gelsolin (amyloidosis; Finnish type) Signal transduction 203964_at NMI 1.86 2p24.3-q21.3 N-myc (and STAT) interactor 205552_s_at OAS1 1.65 12q24.1 2prime;5prime-oligoadenylate synthetase 1; 40/46kDa 209969_s_at STAT1 2.55 2q32.2 signal transducer and activator of transcription 1; 91kDa 202693_s_at STK17A 2.52 7p12-p14 serine/threonine kinase 17a (apoptosis-inducing) Cytoskeleton 223129_x_at MYLIP 2.00 6p23-p22.3 myosin regulatory light chain interacting protein 209083_at CORO1A 2.38 16p11.2 coronin; actin binding protein; 1A 216323_x_at H2-ALPHA 2.56 2q21.1 alpha-tubulin -
Roles of Xbp1s in Transcriptional Regulation of Target Genes
biomedicines Review Roles of XBP1s in Transcriptional Regulation of Target Genes Sung-Min Park , Tae-Il Kang and Jae-Seon So * Department of Medical Biotechnology, Dongguk University, Gyeongju 38066, Gyeongbuk, Korea; [email protected] (S.-M.P.); [email protected] (T.-I.K.) * Correspondence: [email protected] Abstract: The spliced form of X-box binding protein 1 (XBP1s) is an active transcription factor that plays a vital role in the unfolded protein response (UPR). Under endoplasmic reticulum (ER) stress, unspliced Xbp1 mRNA is cleaved by the activated stress sensor IRE1α and converted to the mature form encoding spliced XBP1 (XBP1s). Translated XBP1s migrates to the nucleus and regulates the transcriptional programs of UPR target genes encoding ER molecular chaperones, folding enzymes, and ER-associated protein degradation (ERAD) components to decrease ER stress. Moreover, studies have shown that XBP1s regulates the transcription of diverse genes that are involved in lipid and glucose metabolism and immune responses. Therefore, XBP1s has been considered an important therapeutic target in studying various diseases, including cancer, diabetes, and autoimmune and inflammatory diseases. XBP1s is involved in several unique mechanisms to regulate the transcription of different target genes by interacting with other proteins to modulate their activity. Although recent studies discovered numerous target genes of XBP1s via genome-wide analyses, how XBP1s regulates their transcription remains unclear. This review discusses the roles of XBP1s in target genes transcriptional regulation. More in-depth knowledge of XBP1s target genes and transcriptional regulatory mechanisms in the future will help develop new therapeutic targets for each disease. Citation: Park, S.-M.; Kang, T.-I.; Keywords: XBP1s; IRE1; ATF6; ER stress; unfolded protein response; UPR; RIDD So, J.-S.