17Q21.31 Microduplications

Total Page:16

File Type:pdf, Size:1020Kb

17Q21.31 Microduplications 17q21.31 microduplications rarechromo.org Sources and 17q21.31 microduplications references A 17q21.31 microduplication is a rare genetic condition caused by an extra part of one of the body’s 46 chromosomes – The information in this chromosome 17. For healthy development, chromosomes guide is based on should contain just the right amount of genetic material (DNA) medical information – not too much and not too little. Even a tiny piece of extra on a number of material can influence development. individuals. Most information is drawn from the published Background on Chromosomes medical literature. Chromosomes are structures found in the nucleus of the The first-named body’s cells. Every chromosome contains thousands of genes author and publication which may be thought of as individual instruction booklets (or date are given to allow recipes) that contain all the genetic information telling the you to look for the body how to develop, grow and function. Chromosomes (and abstracts or original genes) usually come in pairs with one half of each articles on the chromosome pair being inherited from each parent. Humans internet in PubMed have 23 pairs of chromosomes giving a total of 46 individual (www.ncbi.nlm.nih.gov chromosomes. Of these 46 chromosomes, two are the sex /pubmed/). If you wish, chromosomes that determine gender. Females have two X you can obtain most chromosomes and males have one X chromosome and one Y articles from Unique. chromosome. The remaining 44 chromosomes are grouped in In addition, this leaflet 22 pairs, numbered 1 to 22 approximately from the largest to draws on information the smallest. Each chromosome has a short (p) arm (shown at from the Decipher the top in the diagram on page 3) and a long (q) arm (the database bottom part of the chromosome). (decipher.sanger. ac.uk) and from a Chromosome Duplications survey of members of A sperm cell from the father and an egg cell from the mother Unique conducted in each carry just one copy of each chromosome. When they join 2013, referenced together they form a single cell that now carries two copies of Unique. When this each chromosome. This cell must make many copies of itself guide was written in (and all the chromosomes and genetic material) in order to June 2013 Unique had make all of the many cells that form during human growth and eight member families development. Sometimes during the formation of the egg or with a pure sperm cells or during this complicated copying and replication microduplication of process, parts of the chromosomes can break off or become 17q21.31 (no other arranged differently from usual. People with a 17q21.31 chromosome was microduplication have two intact chromosome 17s, but also an involved) ranging in extra piece from the long arm of chromosome 17. It is believed age from a 3-year-old that at least part of the clinical difficulties are caused by having to an adult. Two three copies (instead of the usual two) of a gene or number of further members had genes from the extra piece of chromosome 17. We are still a 17q21.31 learning about the specific jobs or functions of the genes in this microduplication as region. However, it is likely that other genes, environment well as another factors and your child’s unique personality also help to chromosome deletion determine future development, needs and achievements. or duplication. 2 1Mb Looking at 17q21.31 Chromosomes can been seen using a microscope. After staining, each chromosome has a distinctive pattern of light p arm and dark bands. These bands are depicted in the diagram of of chromosome 17 on the right. Band 17q21.31 contains around 4 million base pairs. Base pairs are the chemicals in DNA that form the ends of the ‘rungs’ of its ladder-like structure. The recurrent 17q21.31 microduplication encompasses a part of band 17q21.31: approximately 500- 600 thousand base pairs. This sounds a lot but it is actually quite small and is only 0.01 per cent of the DNA in each cell 40.9 Mb and only 0.6 per cent of the DNA on chromosome 17. q arm 17q21.31 People who have extra chromosome material are said to have duplication but when the amount is so small that it can’t 44.9 Mb be seen even under a high-powered microscope, it is called a microduplication. The 17q21.31 microduplication can often only be found using molecular or DNA technology, in particular a technique using microarrays (array-CGH), that 81.2Mb shows gains and losses of tiny amounts of DNA throughout the 1 base pair = bp genome and can demonstrate 1,000 base pairs = 1kb whether particular gene(s) are 1,000,000 base pairs = 1Mb present or not. Genetic Report Your geneticist or genetic counsellor will be able to tell you about the changes found in your child’s chromosomes. With a 17q21.31 microduplication, the results are likely to read something like the following example: arr[hg19] 17q21.31 (43,717,703-44,345,038)x3 arr The analysis was by array (arr) comparative genomic hybridisation (cgh) hg19 Human Genome build 19. This is the reference DNA sequence that the base pair numbers refer to. As more information about the human genome is found, new “builds” of the genome are made and the base pair numbers may be adjusted. At present hg19 is the latest version 17q21.31 The chromosome involved is 17 and part duplicated is in band q21.31 43,717,703-44,345,038 The base pairs between 43,717,703 and 44,345,038 have been duplicated. Take the first long number from the second and you get 627,335 (or 627 kb). This is the number of base pairs that are in the duplication. x3 means there are three copies of these base pairs, not two as you would normally expect 3 17q21.31 microduplications The first published description of a person with a 17q21.31 microduplication was in 2007. There have since been around 8 cases reported in the medical literature worldwide. The duplication occurs equally often in boys and girls (Kirchoff 2007; Grisart 2009; Kitsiou- Tzeli 2012). 17q21.31 microdeletions Many more people have been described with a different disorder known as 17q21.31 microdeletion syndrome or Koolen-De Vries syndrome where the same piece of band 17q21.31 is not extra but is missing. Unique publishes a separate information guide to Koolen-De Vries syndrome. How much do we know? 17q21.31 microduplications have only been recently discovered and therefore the number of people identified is very low. This means it’s rather difficult to draw a clear picture of the features of the microduplication. Comparing different children and adults with 17q21.31 duplications shows that some effects seem to be broadly similar. This information guide tells you what is known about those effects. Comparing your child’s array results with others, both in the medical literature and within Unique, can help to build up a general picture of what to expect. But there will still be differences, sometimes quite marked, between your child and others with an apparently similar array result. It is very important to see your child as an individual and not to make direct comparisons with others with the same chromosome test results. After all, each of us is unique. Most common features Every person with a 17q21.31 microduplication is unique and so each person will have different medical and developmental concerns. Additionally, no one person will have all of the features listed in this information guide. However, a number of common features have emerged: Speech and language delay Behavioural difficulties such as autism spectrum disorder Some children need support with learning Hypotonia (low muscletone or floppiness) in some Otherwise generally healthy Are there people with a 17q21.31 microduplication who are healthy, have no major birth defects and have developed normally? There are several people with the microduplication who had no major birth defects and only discovered they had the microduplication when it was detected in their child (Kitsiou- Tzeli 2012; Decipher; Unique). 4 If one person in a family with the 17q21.31 microduplication is mildly affected, will others in the same family also be mildly affected? Not necessarily. There seems to be a lot of variation between different members of the same family who have the same microduplication. We know that if one person is mildly affected or unaffected, others may be more severely and obviously affected (Kitsiou-Tzeli 2012; Decipher; Unique). What is the outlook? We can’t be certain yet but there appears to be no reason why people who are healthy should not enjoy a normal lifespan and there are a number of adults both at Unique and in the published medical literature (Kitsiou-Tzeli 2012; Decipher; Unique). Pregnancy Many pregnancies were uncomplicated, and babies were born at or near their expected due date Many mothers (7/10) carrying babies with a 17q21.31 microduplication experienced no pregnancy problems, had a normal delivery and only discovered their baby was affected after the birth. However, pregnancy complications in mothers carrying a baby with a 17q21.31 microduplication have been reported. One mother had an amniocentesis and genetic testing after the triple screening test revealed a high risk of a baby with a chromosome disorder. Due to the small size of the microduplication it was not detected. This baby was also shown to have a single umbilical artery (the umbilical cord usually has three blood vessels – two arteries and a vein) and was induced a few days before the due date because of slowed growth.
Recommended publications
  • Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
    Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo
    [Show full text]
  • Transcriptome Analysis of Adipose Tissues from Two Fat-Tailed Sheep
    Li et al. BMC Genomics (2018) 19:338 https://doi.org/10.1186/s12864-018-4747-1 RESEARCHARTICLE Open Access Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition Baojun Li1, Liying Qiao1, Lixia An2, Weiwei Wang1, Jianhua Liu1, Youshe Ren1, Yangyang Pan1, Jiongjie Jing1 and Wenzhong Liu1* Abstract Background: The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed. Results: Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5,andCD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene,and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism.
    [Show full text]
  • Comparative Transcriptome Profiling of Longissimus Muscle Tissues From
    www.nature.com/scientificreports OPEN Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Received: 29 April 2016 Accepted: 31 August 2016 Merino and Small Tail Han sheep Published: 20 September 2016 Limin Sun, Man Bai, Lujie Xiang, Guishan Zhang, Wei Ma & Huaizhi Jiang The Qianhua Mutton Merino (QHMM) is a new sheep (Ovis aries) variety with better meat performance compared with the traditional local variety Small Tail Han (STH) sheep. We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the QHMM and STH. We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH. The results showed that 960 genes were differentially expressed (405 were up- regulated and 555 were down-regulated). Among these, 463 differently expressed genes (DEGs) were probably associated with muscle growth and development and were involved in biological processes such as skeletal muscle tissue development and muscle cell differentiation; molecular functions such as catalytic activity and oxidoreductase activity; cellular components such as mitochondrion and sarcoplasmic reticulum; and pathways such as metabolic pathways and citrate cycle. From the potential genes, a gene-act-network and co-expression-network closely related to muscle growth and development were identified and established. Finally, the expressions of nine genes were validated by real-time PCR. The results suggested that some DEGs, including MRFs, GXP1 and STAC3, play crucial roles in muscle growth and development processes. This genome-wide transcriptome analysis of QHMM and STH muscle is reported for the first time. Sheep (Ovis aries) form a large part of the global animal husbandry industry.
    [Show full text]
  • A Chromosome-Centric Human Proteome Project (C-HPP) To
    computational proteomics Laboratory for Computational Proteomics www.FenyoLab.org E-mail: [email protected] Facebook: NYUMC Computational Proteomics Laboratory Twitter: @CompProteomics Perspective pubs.acs.org/jpr A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17 † ‡ § ∥ ‡ ⊥ Suli Liu, Hogune Im, Amos Bairoch, Massimo Cristofanilli, Rui Chen, Eric W. Deutsch, # ¶ △ ● § † Stephen Dalton, David Fenyo, Susan Fanayan,$ Chris Gates, , Pascale Gaudet, Marina Hincapie, ○ ■ △ ⬡ ‡ ⊥ ⬢ Samir Hanash, Hoguen Kim, Seul-Ki Jeong, Emma Lundberg, George Mias, Rajasree Menon, , ∥ □ △ # ⬡ ▲ † Zhaomei Mu, Edouard Nice, Young-Ki Paik, , Mathias Uhlen, Lance Wells, Shiaw-Lin Wu, † † † ‡ ⊥ ⬢ ⬡ Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Gilbert S. Omenn, , Ronald C. Beavis, † # and William S. Hancock*, ,$, † Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States ‡ Stanford University, Palo Alto, California, United States § Swiss Institute of Bioinformatics (SIB) and University of Geneva, Geneva, Switzerland ∥ Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States ⊥ Institute for System Biology, Seattle, Washington, United States ¶ School of Medicine, New York University, New York, United States $Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia ○ MD Anderson Cancer Center, Houston, Texas, United States ■ Yonsei University College of Medicine, Yonsei University,
    [Show full text]
  • GSGS: a Computational Framework to Reconstruct Signaling Pathways
    GSGS: A Computational Framework to Reconstruct Signaling Pathways from Gene Sets Lipi Acharya§, Thair Judeh∗,†, Zhansheng Duan♭, Michael Rabbat‡ and Dongxiao Zhu∗,†,¶ ∗Department of Computer Science, Wayne State University, 5057 Woodward Avenue, Detroit, MI 48202, USA. §Department of Computer Science, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA. †Research Institute for Children, Children’s Hospital, New Orleans, LA 70118, USA. ♭Center for Information Engineering Science Research, Xi’an Jiaotong University, 28 Xianning West Road, Xi’an, Shaanxi 710049, China. ‡Department of Electrical and Computer Engineering, McGill University, 3480 University Street, Montr´eal, Qu´ebec H3A 2A7, Canada. ¶To whom correspondence should be addressed. abstract We propose a novel two-stage Gene Set Gibbs Sampling (GSGS) framework, to reverse engineer signaling pathways from gene sets inferred from molecular profiling data. We hy- pothesize that signaling pathways are structurally an ensemble of overlapping linear signal transduction events which we encode as Information Flow Gene Sets (IFGS’s). We infer pathways from gene sets corresponding to these events subjected to a random permutation of genes within each set. In Stage I, we use a source separation algorithm to derive un- ordered and overlapping IFGS’s from molecular profiling data, allowing cross talk among IFGS’s. In Stage II, we develop a Gibbs sampling like algorithm, Gene Set Gibbs Sampler, arXiv:1101.3983v3 [q-bio.QM] 13 Oct 2011 to reconstruct signaling pathways from the latent IFGS’s derived in Stage I. The novelty of this framework lies in the seamless integration of the two stages and the hypothesis of IFGS’s as the basic building blocks for signal pathways.
    [Show full text]
  • Biopython Tutorial and Cookbook
    Biopython Tutorial and Cookbook Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock Last Update – September 2008 Contents 1 Introduction 5 1.1 What is Biopython? ......................................... 5 1.1.1 What can I find in the Biopython package ......................... 5 1.2 Installing Biopython ......................................... 6 1.3 FAQ .................................................. 6 2 Quick Start – What can you do with Biopython? 8 2.1 General overview of what Biopython provides ........................... 8 2.2 Working with sequences ....................................... 8 2.3 A usage example ........................................... 9 2.4 Parsing sequence file formats .................................... 10 2.4.1 Simple FASTA parsing example ............................... 10 2.4.2 Simple GenBank parsing example ............................. 11 2.4.3 I love parsing – please don’t stop talking about it! .................... 11 2.5 Connecting with biological databases ................................ 11 2.6 What to do next ........................................... 12 3 Sequence objects 13 3.1 Sequences and Alphabets ...................................... 13 3.2 Sequences act like strings ...................................... 14 3.3 Slicing a sequence .......................................... 15 3.4 Turning Seq objects into strings ................................... 15 3.5 Concatenating or adding sequences ................................. 16 3.6 Nucleotide sequences and
    [Show full text]
  • Jputs;Sth;Gy;Fiyf;Fofk; Common Admission Test for M.Phil/Ph.D
    jpUts;Sth; gy;fiyf;fofk; THIRUVALLUVAR UNIVERSITY Vellore – 632 115 Tamil Nadu, India Common Admission Test for M.Phil/Ph.D. BIOTECHNOLOGY Syllabus UNIT 1: BIOCHEMISTRY:Units of measurements of solutesin solution. Biomolecules: Definitions,nomenclature, classification, structure, chemistry and properties of carbohydrates, amino acids,proteins, lipids and Nucleic acids. Metabolism: Metabolism of Carbohydrates - EMP, TCA, HMP. Amino Acids, Lipids and Nucleic Acids-Their Biosynthesis. Mechanism of Oxidative Phosphorylation and its Inhibitors, Photophosphorylation.Enzymology: Enzyme – classificationandstructure,allosteric mechanism, regulatory and active sites,activationenergy,iso- enzymes, enzyme kinetics(MM, LB plot, Km) and hormones. Clinical biochemistry: Blood sugar level-factors controlling blood sugar level – hypo, hyper glycemia, diabetes mellitus & its types. GTT, Metabolism of bilirubin, jaundicetypes& differential diagnosis and liver function tests. Renal functional test and gastric function test. CELL AND MOLECULAR BIOLOGY:Structure and function of cells in prokaryotes and eukaryotes, Structure and organization of Membrane - Membrane Model, active and passive, transport channels and pumps, Structure & Biogenesis of Mitochondria and Chloroplast. Structure of Endoplasmic reticulum, Golgi complex, lysosomes.Celldivision:Mitosis, Meiosis, regulation of cell cycle; factors regulating cell cycle. Nucleic acid structure,Genome Organization. DNA replication: Enzymes and mechanisms of DNA replication in prokaryotes and eukaryotes, Telomeres,
    [Show full text]
  • Molecular Cloning of the B4GALNT2 Gene and Its Single Nucleotide Polymorphisms Association with Litter Size in Small Tail Han Sheep
    animals Article Molecular Cloning of the B4GALNT2 Gene and Its Single Nucleotide Polymorphisms Association with Litter Size in Small Tail Han Sheep Xiaofei Guo 1,2,† , Xiangyu Wang 1,†, Benmeng Liang 1, Ran Di 1, Qiuyue Liu 1, Wenping Hu 1, Xiaoyun He 1, Jinlong Zhang 2, Xiaosheng Zhang 2 and Mingxing Chu 1,* 1 Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] (X.G.); [email protected] (X.W.); [email protected] (B.L.); [email protected] (R.D.); [email protected] (Q.L.); [email protected] (W.H.); [email protected] (X.H.) 2 Tianjin Institute of Animal Sciences, Tianjin 300381, China; [email protected] (J.Z.); [email protected] (X.Z.) * Correspondence: [email protected]; Tel.: +86-01-062-819-850 † These authors contributed equally to this study. Received: 1 August 2018; Accepted: 15 September 2018; Published: 20 September 2018 Simple Summary: In French Lacaune sheep, the B4GALNT2 (beta-1, 4-N-acetyl-galactosaminyl transferase 2) gene was considered as the potential gene for a FecL (mutation), which regulates the ovine ovulation rate. Three specific mutation sites linked with the FecL mutation have not been previously found in 11 sheep breeds. However, two mutations of g.36946470C > T and g.36933082C > T in the exon of B4GALNT2 were found to have had a significant effect on the litter size in the first parity for Small Tail Han (STH) Sheep (p < 0.05). B4GALNT2, which is mainly expressed in ovine ovary, also plays an important role in sheep reproduction.
    [Show full text]
  • An Evolutionary Roadmap to the Microtubule-Associated Protein MAP Tau Frederik Sündermann1, Maria-Pilar Fernandez2 and Reginald O
    Sündermann et al. BMC Genomics (2016) 17:264 DOI 10.1186/s12864-016-2590-9 RESEARCH ARTICLE Open Access An evolutionary roadmap to the microtubule-associated protein MAP Tau Frederik Sündermann1, Maria-Pilar Fernandez2 and Reginald O. Morgan2* Abstract Background: The microtubule associated protein Tau (MAPT) promotes assembly and interaction of microtubules with the cytoskeleton, impinging on axonal transport and synaptic plasticity. Its neuronal expression and intrinsic disorder implicate it in some 30 tauopathies such as Alzheimer’s disease and frontotemporal dementia. These pathophysiological studies have yet to be complemented by computational analyses of its molecular evolution and structural models of all its functional domains to explain the molecular basis for its conservation profile, its site-specific interactions and the propensity to conformational disorder and aggregate formation. Results: We systematically annotated public sequence data to reconstruct unspliced MAPT, MAP2 and MAP4 transcripts spanning all represented genomes. Bayesian and maximum likelihood phylogenetic analyses, genetic linkage maps and domain architectures distinguished a nonvertebrate outgroup from the emergence of MAP4 and its subsequent ancestral duplication to MAP2 and MAPT. These events were coupled to other linked genes such as KANSL1L and KANSL and may thus be consequent to large-scale chromosomal duplications originating in the extant vertebrate genomes of hagfish and lamprey. Profile hidden Markov models (pHMMs), clustered subalignments and 3D structural predictions defined potential interaction motifs and specificity determining sites to reveal distinct signatures between the four homologous microtubule binding domains and independent divergence of the amino terminus. Conclusion: These analyses clarified ambiguities of MAPT nomenclature, defined the order, timing and pattern of its molecular evolution and identified key residues and motifs relevant to its protein interaction properties and pathogenic role.
    [Show full text]
  • Integrative RNA-Seq Analysis of Capsicum Annuum L.- Phytophthora Capsici L
    bioRxiv preprint doi: https://doi.org/10.1101/2021.04.03.438323; this version posted April 4, 2021. 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. Integrative RNA-Seq analysis of Capsicum annuum L.- Phytophthora capsici L. pathosystem reveals molecular cross-talk and activation of host defence response Tilahun Rabuma 1, 3*, Om Prakash Gupta 2, Manju Yadav1, Vinod Chhokar1 1Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India 2Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal-132001, Haryana, INDIA 3Department of Biotechnology, College of Natural and Computational Science, Wolkite University, Wolkite, Ethiopia *Corresponding author E-mail: [email protected] or [email protected] Mobile phone: +251913458760 Abstract Background: Chili pepper (Capsicum annuum L.) being one of an important member of the Solanaceae family, and its productivity is highly affected by the fungal pathogen Phytophthora capsici L. Other to CM-344, the unavailability of resistant landraces to all possible strains of P. capsici imposes a serious threat to its global production. This is because of our current understanding of the molecular mechanisms associated with the defence response in C. annuum-P. capsici pathosystem is limited. Therefore, the current study used RNA-seq technology to dissect the genes associated with defence response against P. capsici infection in two contrasting landraces, i.e. GojamMecha_9086 (Resistant) and Dabat_80045 (susceptible) exposed to P. capsici infection. Results: The transcriptomes from 4 leaf samples (RC, RI, SC and SI) of chili pepper resulted in a total of 1,18, 879 assembled transcripts (with a mean TL of 813.23bp and N50 of 1,277bp) along with 52,384 pooled unigenes with (mean UL of 1029.36 bp and N50 of 1,403bp).
    [Show full text]
  • Title Analysis of the Genome Architecture of The
    Analysis of the genome architecture of the hyperthermopholic Title archaeon Thermococcus kodakarensis( Dissertation_全文 ) Author(s) Maruyama, Hugo Citation Kyoto University (京都大学) Issue Date 2011-03-23 URL http://dx.doi.org/10.14989/doctor.k16233 Right Type Thesis or Dissertation Textversion author Kyoto University Analysis of the genome architecture of the hyperthermophilic archaeon Thermococcus kodakarensis Hugo Maruyama 要旨 ゲノム DNA は細胞内で高度に折りたたまれ、この染色体高次構造は転写・複製・染色体分 配といった機構と密接に結びついている。染色体の主要な構成タンパク質は真核生物では ヒストン、バクテリアでは HU と全く異なるが、一様な基本構造を基にゲノム DNA が階層 的に折りたたまれている点で両者の染色体構造は共通している。アーキアは真核生物・バ クテリアと並ぶ生命の第三のドメインであり、遺伝情報の発現(複製・転写・翻訳)の機 構は真核生物に、代謝経路はバクテリアに近い。アーキアには染色体を構成するタンパク 質として真核生物のヒストンに相同なもの、バクテリアの HU に相同なもの、アーキア特有 の Alba と呼ばれるタンパク質などが存在し、種によってゲノムがコードするタンパク質の 組合せが異なる。様々なアーキアのゲノムがどのような高次構造を形成しているかを明ら かにすることで、三つのドメインにわたるゲノム構造の共通性あるいは多様性を明らかに できる。本研究ではその第一歩としてヒストンを持つ超好熱性アーキア Thermococcus kodakarensis の染色体構造を解析した。 T. kodakarensis の染色体に含まれるタンパク質を質量分析により同定した結果、ヒ ストン、Alba、TK0471(TrmBL2)、 RNA ポリメラーゼ等の DNA 結合タンパク質が含まれ ることが分かった。TK0471 は転写因子 TrmB と相同な機能未知の DNA 結合タンパク質で あった。次に、染色体をミクロコッカルヌクレアーゼで部分消化した後、5%-20%のショ糖 密度勾配遠心により構成タンパク質の異なる染色体断片が分離された。原子間力顕微鏡に よる解析から、ヒストンは DNA 上に beads-on-a-string 構造を、TK0471 は線維状の構造を形 成することが示された。また大腸菌で発現させた組換えタンパク質(ヒストンおよび TK0471)を用いて同様の構造が DNA 上に再構成された。ショ糖密度勾配で分離されたそ れぞれの染色体断片に含まれる DNA 配列を超並列シークエンサーで同定した結果、ヒスト ンおよび TK0471 はゲノム上のプロモーター領域にもコーディング領域にも偏りなく存在 するが、両者の存在する領域は重複しない傾向があった。以上の結果から、T. kodakarensis の染色体上には、構成タンパク質および構造の異なる領域が存在することが明らかとなっ た。相同組換えにより TK0471 遺伝子を破壊すると染色体の DNA 消化酵素に対する感受性 が高まった。また、約 100 個の遺伝子の転写産物量が増加した。TK0471
    [Show full text]
  • Koolen-De Vries Syndrome
    Koolen-de Vries syndrome May also be known as: KANSL1 haploinsufficiency syndrome or: KANSL1-related intellectual disability syndrome Previously known as 17q21.31 microdeletion syndrome rarechromo.org Koolen-de Vries syndrome Koolen-de Vries syndrome [you pronounce Vries as ‘freeze’] is a rare genetic condition caused by the loss of part of chromosome 17 (17q21.31 microdeletion) including the gene called KANSL1, or by a change in the KANSL1 gene (Zollino 2012; Koolen 2012). These genetic changes cause developmental delay, learning difficulties and possibly some health issues but the degree to which individuals are affected varies. The KANSL1 gene is found on the long arm of chromosome 17. Chromosomes are the structures in the nucleus of the body’s cells that carry genetic information, telling the body how to develop and function. They come in pairs, one from each parent, and are numbered 1 to 22 approximately from largest to smallest. The 23rd pair are the sex chromosomes: XX for females and XY for males. Each chromosome has a short (p) arm and a long (q) arm. KANSL1 is found at a place on the long arm of chromosome 17 called 17q21.31. Until 2012 Koolen-de Vries syndrome was called 17q21.31 microdeletion syndrome. Chromosome 17q and genetic testing You can’t see chromosomes with the naked eye, but if you stain them and magnify them under a microscope, short you can see that each one has a distinctive pattern of base pairs p arm light and dark bands. Each band contains millions of base pairs of DNA. Base pairs are the chemicals in DNA that form the ends of the ‘rungs’ of its ladder-like structure and make up genes.
    [Show full text]