BMC Genomics Biomed Central
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Screening of a Clinically and Biochemically Diagnosed SOD Patient Using Exome Sequencing: a Case Report with a Mutations/Variations Analysis Approach
The Egyptian Journal of Medical Human Genetics (2016) 17, 131–136 HOSTED BY Ain Shams University The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net www.sciencedirect.com CASE REPORT Screening of a clinically and biochemically diagnosed SOD patient using exome sequencing: A case report with a mutations/variations analysis approach Mohamad-Reza Aghanoori a,b,1, Ghazaleh Mohammadzadeh Shahriary c,2, Mahdi Safarpour d,3, Ahmad Ebrahimi d,* a Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran b Research and Development Division, RoyaBioGene Co., Tehran, Iran c Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran d Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran Received 12 May 2015; accepted 15 June 2015 Available online 22 July 2015 KEYWORDS Abstract Background: Sulfite oxidase deficiency (SOD) is a rare neurometabolic inherited disor- Sulfite oxidase deficiency; der causing severe delay in developmental stages and premature death. The disease follows an auto- Case report; somal recessive pattern of inheritance and causes deficiency in the activity of sulfite oxidase, an Exome sequencing enzyme that normally catalyzes conversion of sulfite to sulfate. Aim of the study: SOD is an underdiagnosed disorder and its diagnosis can be difficult in young infants as early clinical features and neuroimaging changes may imitate some common diseases. Since the prognosis of the disease is poor, using exome sequencing as a powerful and efficient strat- egy for identifying the genes underlying rare mendelian disorders can provide important knowledge about early diagnosis, disease mechanisms, biological pathways, and potential therapeutic targets. -
The Development of the Mammalian Central
Chapter 5: GRIPE is a novel gene that may assume different roles during development and in adulthood Chapter 5: GRIPE is a novel gene that may assume different roles during development and in adulthood 5.1. Characterisation of GRIPE and E12 mRNA expression during development As a first step towards describing the expression of GRIPE and E12 during neurodevelopment, Northern analysis was conducted to acquire a global pattern of mRNA expression. To do this, embryonic and adult tissues were harvested for RNA isolation as described (Section 2.2). Northern hybridisation was then performed using radiolabelled GRIPE and E12 cDNAs as probes, and these results are shown in Fig. 5.1. A single band of approximately 8kb is detected in all samples; this was the only signal detected in all northern hybridisations performed with different GRIPE cDNA and cRNA probes (see Appendix 10.2). It would appear that GRIPE mRNA is abundant in the head and trunk at e11.5, and levels decrease during embryogenesis, and are undetectable by e17.5. In the adult, GRIPE is abundant in the brain, but is undetectable in the placenta and kidney. However, further RT-PCR experiments (see Figs 6.8 and 6.13) indicate that GRIPE is weakly detectable in these tissues, but not in the kidney. Northern analysis of E12 mRNA shows high levels of expression at e11.5, with a gradual decrease during embryogenesis, and is almost undetectable by e17.5. Further, E12 is undetectable in adult brain, placenta and kidney. These observations demonstrate a coincidence in expression of GRIPE and E12 mRNA during embryogenesis, but not in the adult; where E12 mRNA is undetectable. -
Comparative Transcriptome Profiling of the Human and Mouse Dorsal Root Ganglia: an RNA-Seq-Based Resource for Pain and Sensory Neuroscience Research
bioRxiv preprint doi: https://doi.org/10.1101/165431; this version posted October 13, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research Short Title: Human and mouse DRG comparative transcriptomics Pradipta Ray 1, 2 #, Andrew Torck 1 , Lilyana Quigley 1, Andi Wangzhou 1, Matthew Neiman 1, Chandranshu Rao 1, Tiffany Lam 1, Ji-Young Kim 1, Tae Hoon Kim 2, Michael Q. Zhang 2, Gregory Dussor 1 and Theodore J. Price 1, # 1 The University of Texas at Dallas, School of Behavioral and Brain Sciences 2 The University of Texas at Dallas, Department of Biological Sciences # Corresponding authors Theodore J Price Pradipta Ray School of Behavioral and Brain Sciences School of Behavioral and Brain Sciences The University of Texas at Dallas The University of Texas at Dallas BSB 14.102G BSB 10.608 800 W Campbell Rd 800 W Campbell Rd Richardson TX 75080 Richardson TX 75080 972-883-4311 972-883-7262 [email protected] [email protected] Number of pages: 27 Number of figures: 9 Number of tables: 8 Supplementary Figures: 4 Supplementary Files: 6 Word count: Abstract = 219; Introduction = 457; Discussion = 1094 Conflict of interest: The authors declare no conflicts of interest Patient anonymity and informed consent: Informed consent for human tissue sources were obtained by Anabios, Inc. (San Diego, CA). Human studies: This work was approved by The University of Texas at Dallas Institutional Review Board (MR 15-237). -
Comparative Transcriptomics of Primary Cells in Vertebrates
Edinburgh Research Explorer Comparative transcriptomics of primary cells in vertebrates Citation for published version: Alam, T, Agrawal, S, Severin, J, Young, R, Andersson, R, Amer, E, Hasegawa, A, Lizio, M, Ramilowski, J, Abugessaisa, I, Ishizu, Y, Noma, S, Tarui, H, Taylor, MS, Lassmann, T, Itoh, M, Kasukawa, T, Kawaji, H, Marchionni, L, Sheng, G, Forrest, ARR, Khachigian, LM, Hayashizaki, Y, Carninci, P & De Hoon, M 2020, 'Comparative transcriptomics of primary cells in vertebrates', Genome Research. https://doi.org/10.1101/gr.255679.119 Digital Object Identifier (DOI): 10.1101/gr.255679.119 Link: Link to publication record in Edinburgh Research Explorer Document Version: Peer reviewed version Published In: Genome Research Publisher Rights Statement: is article, published inGenome Research, is avail-able under a Creative Commons License (Attribution 4.0 Internatio General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 30. Sep. 2021 1 1 Comparative transcriptomics of primary cells in vertebrates 2 Tanvir Alam1, Saumya Agrawal2, Jessica Severin2, Robert S. Young3,4, Robin Andersson5, Erik 3 Arner2, Akira Hasegawa2, Marina Lizio2, Jordan Ramilowski2, Imad Abugessaisa2, Yuri Ishizu6, 4 Shohei Noma2, Hiroshi Tarui7, Martin S. -
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 -
Homotypic Clusters of Transcription Factor Binding Sites Are a Key Component of Human Promoters and Enhancers
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Research Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers Valer Gotea,1 Axel Visel,2,3 John M. Westlund,4 Marcelo A. Nobrega,4 Len A. Pennacchio,2,3 and Ivan Ovcharenko1,5 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA; 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 3United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; 4Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA Clustering of multiple transcription factor binding sites (TFBSs) for the same transcription factor (TF) is a common feature of cis-regulatory modules in invertebrate animals, but the occurrence of such homotypic clusters of TFBSs (HCTs) in the human genome has remained largely unknown. To explore whether HCTs are also common in human and other verte- brates, we used known binding motifs for vertebrate TFs and a hidden Markov model–based approach to detect HCTs in the human, mouse, chicken, and fugu genomes, and examined their association with cis-regulatory modules. We found that evolutionarily conserved HCTs occupy nearly 2% of the human genome, with experimental evidence for individual TFs supporting their binding to predicted HCTs. More than half of the promoters of human genes contain HCTs, with a dis- tribution around the transcription start site in agreement with the experimental data from the ENCODE project. In addition, almost half of the 487 experimentally validated developmental enhancers contain them as well—a number more than 25-fold larger than expected by chance. -
Epi)Genomics Data in the 3T9mycer, Eµ-Myc and Tet-MYC
PhD degree in Molecular Medicine (curriculum in Computational Biology) European School of Molecular Medicine (SEMM), University of Milan and University of Naples “Federico II” An integrative approach to identify binding partners of Myc using (epi)genomics data in the 3T9MycER, Eµ-myc and tet-MYC systems Pranami Bora Center for Genomic Science of IIT@SEMM, Milan Matricola n. R10337 Supervisor: Dr. Bruno Amati Center for Genomic Science of IIT@SEMM, Milan Added Supervisor: Dr. Marco Morelli Center for Genomic Science of IIT@SEMM, Milan Anno accademico 2016-2017 Table of Contents List of abbreviations ...................................................................................................... 4 Figures index ................................................................................................................. 5 Abstract ........................................................................................................................ 8 Chapter 1 ..................................................................................................................... 10 Introduction ................................................................................................................. 10 1.1 Epigenetics ............................................................................................................... 10 1.1.1 Acetylation and methylation ..................................................................................... 10 1.1.2 Transcription factors ................................................................................................. -
Application of Genomic Technologies to Study Infertility Nicholas Rui Yuan Ho Washington University in St
Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Spring 5-15-2016 Application of Genomic Technologies to Study Infertility Nicholas Rui Yuan Ho Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Bioinformatics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Yuan Ho, Nicholas Rui, "Application of Genomic Technologies to Study Infertility" (2016). Arts & Sciences Electronic Theses and Dissertations. 786. https://openscholarship.wustl.edu/art_sci_etds/786 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Computational and Systems Biology Dissertation Examination Committee: Donald Conrad, Chair Barak Cohen Joseph Dougherty John Edwards Liang Ma Application of Genomic Technologies to Study Infertility by Nicholas Rui Yuan Ho A dissertation presented to the Graduate School of Arts & Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2016 St. Louis, Missouri © 2016, Nicholas Rui Yuan Ho Table of -
Screening of a Clinically and Biochemically Diagnosed SOD Patient Using Exome Sequencing: a Case Report with a Mutations/Variations Analysis Approach
The Egyptian Journal of Medical Human Genetics (2016) 17, 131–136 HOSTED BY Ain Shams University The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net www.sciencedirect.com CASE REPORT Screening of a clinically and biochemically diagnosed SOD patient using exome sequencing: A case report with a mutations/variations analysis approach Mohamad-Reza Aghanoori a,b,1, Ghazaleh Mohammadzadeh Shahriary c,2, Mahdi Safarpour d,3, Ahmad Ebrahimi d,* a Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran b Research and Development Division, RoyaBioGene Co., Tehran, Iran c Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran d Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran Received 12 May 2015; accepted 15 June 2015 Available online 22 July 2015 KEYWORDS Abstract Background: Sulfite oxidase deficiency (SOD) is a rare neurometabolic inherited disor- Sulfite oxidase deficiency; der causing severe delay in developmental stages and premature death. The disease follows an auto- Case report; somal recessive pattern of inheritance and causes deficiency in the activity of sulfite oxidase, an Exome sequencing enzyme that normally catalyzes conversion of sulfite to sulfate. Aim of the study: SOD is an underdiagnosed disorder and its diagnosis can be difficult in young infants as early clinical features and neuroimaging changes may imitate some common diseases. Since the prognosis of the disease is poor, using exome sequencing as a powerful and efficient strat- egy for identifying the genes underlying rare mendelian disorders can provide important knowledge about early diagnosis, disease mechanisms, biological pathways, and potential therapeutic targets. -
Novel Genes Upregulated When NOTCH Signalling Is Disrupted During Hypothalamic Development Ratié Et Al
Novel genes upregulated when NOTCH signalling is disrupted during hypothalamic development Ratié et al. Ratié et al. Neural Development 2013, 8:25 http://www.neuraldevelopment.com/content/8/1/25 Ratié et al. Neural Development 2013, 8:25 http://www.neuraldevelopment.com/content/8/1/25 RESEARCH ARTICLE Open Access Novel genes upregulated when NOTCH signalling is disrupted during hypothalamic development Leslie Ratié1, Michelle Ware1, Frédérique Barloy-Hubler1,2, Hélène Romé1, Isabelle Gicquel1, Christèle Dubourg1,3, Véronique David1,3 and Valérie Dupé1* Abstract Background: The generation of diverse neuronal types and subtypes from multipotent progenitors during development is crucial for assembling functional neural circuits in the adult central nervous system. It is well known that the Notch signalling pathway through the inhibition of proneural genes is a key regulator of neurogenesis in the vertebrate central nervous system. However, the role of Notch during hypothalamus formation along with its downstream effectors remains poorly defined. Results: Here, we have transiently blocked Notch activity in chick embryos and used global gene expression analysis to provide evidence that Notch signalling modulates the generation of neurons in the early developing hypothalamus by lateral inhibition. Most importantly, we have taken advantage of this model to identify novel targets of Notch signalling, such as Tagln3 and Chga, which were expressed in hypothalamic neuronal nuclei. Conclusions: These data give essential advances into the early generation of neurons in the hypothalamus. We demonstrate that inhibition of Notch signalling during early development of the hypothalamus enhances expression of several new markers. These genes must be considered as important new targets of the Notch/proneural network. -
Bioinformatics Analysis of Hereditary Disease Gene Set to Identify Key Modulators of Myocardial Remodeling During Heart Regeneration in Zebrafish
EPiC Series in Computing Volume 70, 2020, Pages 226{237 Proceedings of the 12th International Conference on Bioinformatics and Computational Biology Bioinformatics analysis of hereditary disease gene set to identify key modulators of myocardial remodeling during heart regeneration in zebrafish Lawrence Yu-Min Liu1,2, Zih-Yin Lai1, Min-Hsuan Lin1, Yu Shih3 and Yung-Jen Chuang1 1 Department of Medical Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan 2 Division of Cardiology, Department of Internal Medicine, Hsinchu Mackay Memorial Hospital, Hsinchu, 30071, Taiwan 3 Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan [email protected], [email protected], [email protected], [email protected], [email protected] Abstract Unlike mammals, adult zebrafish hearts retain a remarkable capacity to regenerate after injury. Since regeneration shares many common molecular pathways with embryonic development, we investigated myocardial remodeling genes and pathways by performing a comparative transcriptomic analysis of zebrafish heart regeneration using a set of known human hereditary heart disease genes related to myocardial hypertrophy during development. We cross-matched human hypertrophic cardiomyopathy-associated genes with a time-course microarray dataset of adult zebrafish heart regeneration. Genes in the expression profiles that were highly elevated in the early phases of myocardial repair and remodeling after injury in zebrafish were identified. These genes were further analyzed with web-based bioinformatics tools to construct a regulatory network revealing potential transcription factors and their upstream receptors. In silico functional analysis of these genes showed that they are involved in cardiomyocyte proliferation and differentiation, angiogenesis, and inflammation-related pathways. -
Positional Specificity of Different Transcription Factor Classes Within Enhancers
Positional specificity of different transcription factor classes within enhancers Sharon R. Grossmana,b,c, Jesse Engreitza, John P. Raya, Tung H. Nguyena, Nir Hacohena,d, and Eric S. Landera,b,e,1 aBroad Institute of MIT and Harvard, Cambridge, MA 02142; bDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; cProgram in Health Sciences and Technology, Harvard Medical School, Boston, MA 02215; dCancer Research, Massachusetts General Hospital, Boston, MA 02114; and eDepartment of Systems Biology, Harvard Medical School, Boston, MA 02215 Contributed by Eric S. Lander, June 19, 2018 (sent for review March 26, 2018; reviewed by Gioacchino Natoli and Alexander Stark) Gene expression is controlled by sequence-specific transcription type-restricted enhancers (active in <50% of the cell types) and factors (TFs), which bind to regulatory sequences in DNA. TF ubiquitous enhancers (active in >90% of the cell types) (SI Ap- binding occurs in nucleosome-depleted regions of DNA (NDRs), pendix, Fig. S1C). which generally encompass regions with lengths similar to those We next sought to infer functional TF-binding sites within the protected by nucleosomes. However, less is known about where active regulatory elements. In a recent study (5), we found that within these regions specific TFs tend to be found. Here, we char- TF binding is strongly correlated with the quantitative DNA acterize the positional bias of inferred binding sites for 103 TFs accessibility of a region. Furthermore, the TF motifs associated within ∼500,000 NDRs across 47 cell types. We find that distinct with enhancer activity in reporter assays in a cell type corre- classes of TFs display different binding preferences: Some tend to sponded closely to those that are most enriched in the genomic have binding sites toward the edges, some toward the center, and sequences of active regulatory elements in that cell type (5).