Centromeric Satellite Dnas: Hidden Sequence Variation in the Human Population
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Discrete-Length Repeated Sequences in Eukaryotic Genomes (DNA Homology/Nuclease SI/Silk Moth/Sea Urchin/Transposable Element) WILLIAM R
Proc. Nati Acad. Sci. USA Vol. 78, No. 7, pp. 4016-4020, July 1981 Biochemistry Discrete-length repeated sequences in eukaryotic genomes (DNA homology/nuclease SI/silk moth/sea urchin/transposable element) WILLIAM R. PEARSON AND JOHN F. MORROW Department of Microbiology, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205 Communicated by James F. Bonner, January 12, 1981 ABSTRACT Two of the four repeated DNA sequences near the 5' end ofthe silk fibroin gene (15) and one in the sea urchin the 5' end of the silk fibroin gene hybridize with discrete-length Strongylocentrotus purpuratus (16, 17). families of repeated DNA. These two families comprise 0.5% of the animal's genome. Arepeated sequencewith aconserved length MATERIALS AND METHODS has also been-found in the short class of moderately repeated se- quences in the sea urchin. The discrete length, interspersion, and DNA was prepared from frozen silk moth pupae or frozen sea sequence fidelityofthese moderately repeated sequences suggests urchin sperm (15). Unsheared DNA [its single strands were that each has been multiplied as a discrete unit. Thus, transpo- >100 kilobases (kb) long] was digested with 2 units ofrestriction sition mechanisms may be responsible for the multiplication and enzyme (Bethesda Research Laboratories, Rockville, MD) per dispersion of a large class of repeated sequences in phylogeneti- ,Ag of DNA (1 unit digests 1 pg of A DNA in 1 hr) for at least cally diverse eukaryotic genomes. The repeat we have studied in 1 hr and then with an additional 2 units for a second hour. most detail differs from previously described eukaryotic trans- Alternatively, silk moth DNA was sheared to 6-10 kb (single- posable elements: it is much shorter (1300 base pairs) and does not stranded length) and sea urchin DNA was sheared to 1.2-2.0 have terminal repetitions detectable by DNAhybridization. -
Bioinformatic and Phylogenetic Analyses of Retroelements in Bacteria
University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2018-11-29 Bioinformatic and phylogenetic analyses of retroelements in bacteria Wu, Li Wu, L. (2018). Bioinformatic and phylogenetic analyses of retroelements in bacteria (Unpublished doctoral thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/34667 http://hdl.handle.net/1880/109215 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Bioinformatic and phylogenetic analyses of retroelements in bacteria by Li Wu A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOLOGICAL SCIENCES CALGARY, ALBERTA NOVEMBER, 2018 © Li Wu 2018 Abstract Retroelements are mobile elements that are capable of transposing into new loci within genomes via an RNA intermediate. Various types of retroelements have been identified from both eukaryotic and prokaryotic organisms. This dissertation includes four individual projects that focus on using bioinformatic tools to analyse retroelements in bacteria, especially group II introns and diversity-generating retroelements (DGRs). The introductory Chapter I gives an overview of several newly identified retroelements in eukaryotes and prokaryotes. In Chapter II, a general search for bacterial RTs from the GenBank DNA sequenced database was performed using automated methods. -
An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial Chromosome
The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 133-151 Article 7 2018 An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial chromosome Robert W. Carter Stephen Lee University of Idaho John C. Sanford Cornell University, Cornell University College of Agriculture and Life Sciences School of Integrative Plant Science,Follow this Plant and Biology additional Section works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y- chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. -
Chromosomal Locations of Highly Repeated Dna
Hereditjv (1980), 44, 269-276 0018-067X/80/01620269$02.00 1980The Genetical Society of Great Britain CHROMOSOMALLOCATIONS OF HIGHLY REPEATED DNA SEQUENCES IN WHEAT W.LGERLACH and W. J. PEACOCK Division of Plant Industry, Commonwealth ScientificandIndustrial Research Organisation, P.O. Box 1600, Canberra City, ACT 2601, Australia Received17.ix.79 SUMMARY C0t l0 DNA was isolated from hexaploid wheat Tr-iticum aestivum cv. Chinese Spring by hydroxyapatite chromatography (70°C in 0l2 Mphosphatebuffer). The higher Tm of the Cot 10-2 DNA compared with total wheat DNA sug- gested that it was relatively GC rich and contained well matched hybrids. In situ hybridisation using wheat species of different ploidy levels located major sites of the C0t l0— DNA on the B genome chromosomes. More than one particular highly repeated sequence is located in these sites. Other chromo- somal locations could be visualised by heating in situ hybridisation reactions before renaturation. This was attributed to the availability for hybridisation both of chromosomal sequences additional to those normally available after acid denaturation of cytological preparations and to single stranded cRNA molecules which were otherwise present as double stranded structures. 1. INTRODUCTION HIGI-ILY repeated DNA sequences, sometimes detected as rapidly reassociat- ing DNA (Britten and Kohne, 1968), are a characteristic component of eukaryotic genomes. Rapidly renaturing fractions of hexaploid wheat DNA have been isolated (Mitra and Bhatia, 1973; Smith and Flavell, 1974, 1975; Dover, 1975; Flavell and Smith, 1976; Ranjekar et al., 1976), up to 10 per cent of the genome being recovered as duplexes by hydroxy- apatite chromatography after reassociation to C0t values between 8 x l0 and 2 x 10—2 mol sec 1 in 012 M phosphate buffer at 60°C. -
Inverted Repeats in Chloroplast DNA from Higher Plants* (Circular DNA/Electron Microscopy/Denaturation Mapping/Circular Dimers) RICHARD Kolodnert and K
Proc. Natl. Acad. Sci. USA Vol. 76, No. 1, pp. 41-45, January 1979 Biochemistry Inverted repeats in chloroplast DNA from higher plants* (circular DNA/electron microscopy/denaturation mapping/circular dimers) RICHARD KOLODNERt AND K. K. TEWARI Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92717 Communicated by Lawrence Bogorad, May 15, 1978 ABSTRACT The circular chloroplast DNAs from spinach, MATERIALS AND METHODS lettuce, and corn plants have been examined by electron mi- croscopy and shown to contain a large sequence repeated one DNA. Covalently closed circular ctDNA from corn (Zea time in reverse polarity. The inverted sequence in spinach and mays), spinach (Spinacia oleracea), lettuce (Lactuca sativa), lettuce chloroplast DNA has been found to be 24,400 base pairs and pea (Pisum sativum) plants was prepared as previously long. The inverted sequence in the corn chloroplast DNA is described (3). The ctDNAs were treated with y irradiation so 22,500 base pairs long. Denaturation mapping studies have that 50% of the DNA molecules contained approximately one shown that the structure of the inverted sequence is highly single-strand break per molecule (nicked circular DNA) (2, 3, conserved in these three plants. Pea chloroplast DNA does not kX174 DNA and monomers of contain an inverted repeat. All of the circular dimers of pea 6). bacteriophage (OX) open chloroplast DNA are found to be in a head-to-tail conformation. circular replicative form DNA of OX (OX RFII DNA) were Circular dimers of spinach and lettuce were also found to have provided by Robert C. Warner. head-to-tail conformation. -
Chromosomal Localisation of a Y Specific Growth Gene(S) J Med Genet: First Published As 10.1136/Jmg.32.7.572 on 1 July 1995
5727 JMed Genet 1995;32:572-575 Chromosomal localisation of a Y specific growth gene(s) J Med Genet: first published as 10.1136/jmg.32.7.572 on 1 July 1995. Downloaded from Tsutomu Ogata, Keiko Tomita, Akiko Hida, Nobutake Matsuo, Yutaka Nakahori, Yasuo Nakagome Abstract apparently large Yq terminal deletions are in- Although a Y specific growth gene(s) has variably sterile and occasionally have short been postulated in the Yqll region, the stature.24 However, since correlations between precise location has not been determined. genotype and stature have not been properly To localise the growth gene(s), we cor- examined, the precise location ofthe Y specific related genotype with stature in 13 Jap- growth gene(s) has not been determined. anese and four European non-mosaic In this paper, we attempt to localise the Y adult male patients with a partial Yq de- specific growth gene(s) on the basis of geno- letion. Fourteen patients preserving the type-phenotype correlations in patients with region between DYSll and DYS246 did Yq - chromosomes. not have short stature (11 Japanese, 165-180 cm; three Europeans, 165-173 cm) whereas the remaining three patients with Methods SELECTION OF PATIENTS the region deleted had short stature (two The patients analysed in the present study were Japanese, both 159 cm; one European, collected from a large series ofinfertile Japanese 157 cm). The results suggest that the region males ascertained from 1988 to 1993. The defined by DYS1I at interval 5C and by selection criteria used were: (1) measurement DYS246 at interval SD may be the critical of height between 20 and 50 years of age; region for the Y specific growth gene(s). -
Simian Virus 40 Tandem Repeated Sequences As an Element of The
Proc. NatL Acad. Sci. USA Vol. 78, No. 2, pp. 943-947, February 1981 Biochemistry Simian virus 40 tandem repeated sequences as an element of the early promoter (deletion mutants/chromatin/RNA initiation/transcriptional regulation) PETER GRUSS, RAVI DHAR, AND GEORGE KHOURY Laboratory of Molecular Virology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20205 Communicated by Hilary Koprowski, November 17, 1980 ABSTRACT On the late side of the simian virus 40 (SV40) and tsB4 are derived from strain VA-4554. The host cell lines DNA replication origin are several sets of tandem repeated se- were secondary African green monkey kidney (AGMK) cells. quences, the largest of which is 72 base pairs long. The role of Preparation of SV40 DNA Fragments and Cytoplasmic these sequences was examined through construction of deletion mutants of SV40. A mutant from which one of the 72-base-pair RNA. Purified SV40 virion DNA was cleaved with restriction repeated units was removed is viable upon transfection of monkey enzymes (as detailed in figure legends) and separated in either kidney cells with viral DNA. Extension of this deletion into the 1.4% (wt/vol) agarose gels or 4% (wt/vol) polyacrylamide gels second repeated unit, however, leads to nonviability, as recog- (4). 32P-Labeled SV40 DNA (specific activity 2 X 106 cpm/ig) nized by the absence of early transcription and of tumor antigen was obtained as described (5). Restriction enzyme fragments production. These observations indicate that the 72-base-pair re- were separated for nuclease SI analysis in 1.4% alkaline agarose peated sequences form an essential element in the early viral tran- scriptional promoter and explain the inability of such a deleted gels (4). -
Y Chromosome in the Male Drosophila'
THE EFFECT OF TEMPERATURE ON MEIOTIC LOSS OF THE Y CHROMOSOME IN THE MALE DROSOPHILA' S. ZIMMERING Department of Biology, Brown University, Prouidence, Rhode Island Received September 19, 1962 GERSHENSON (1933) and SANDLERand BRAVER(1954) have clearly shown that following nondisjunction of X and Y in the Drosophila mehnogaster male, the frequency of recovery of XY sperm is markedly lower than that of nullo-X-nullo-Y sperm. Their suggestion to account for this discrepancy was to suppose that a chromosome which fails to pair with its homologue may be lost at meiosis. Such loss was found to be most pronounced in cases in which the X chromosome was deficient for a large portion of the basal heterochromatin ordinarily involved in pairing with the Y chromosome. Preliminary data ( ZIMMERING1962 and unpublished) have suggested that (1) from situations in which the homology between X and Y is greatly reduced, the rate of chromosome loss at meiosis can be appreciably decreased by tempera- ture treatment, and furthermore, that (2) such a decrease in the rate of loss need not necessarily involve an increase in the frequency of X-Y synapsis prior to anaphase I separation. A detailed account of these and subsequent experi- ments is presented below. MATERIALS AND METHODS Males possessing a modified X chromosome, Zns(1)y sc4-sc8, and the sc8.Y of MULLER( 1948) were employed in the initial temperature experiments. Zn(1)y scb, a long inversion of the X chromosome marked distally with the mutant y (yellow body), leaves most of the basal heterochromatin including bb+ and Block A at the proximal region, while Zn(l)sc8, also a long inversion of the X chromosome, transposes most of the basal heterochromatin including bb+ and Block A distally. -
Genome of an Acetabularia Mediterranea Strain (Southern Blot/Molecular Cloning/Dasycladaceae/Evolution) MARTIN J
Proc. Natl. Acad. Sci. USA Vol. 82, pp. 1706-1710, March 1985 Cell Biology Tandemly repeated nonribosomal DNA sequences in the chloroplast genome of an Acetabularia mediterranea strain (Southern blot/molecular cloning/Dasycladaceae/evolution) MARTIN J. TYMMS AND HANS-GEORG SCHWEIGER Max-Planck-Institut fur Zellbiologie, D-6802 Ladenburg, Federal Republic of Germany Communicated by Philip Siekevitz, October 29, 1984 ABSTRACT A purified chloroplast fraction was prepared the life cycle and that are not homologous to heterologous from caps of the giant unicellular green alga Acetabularia probes for ribosomal RNA genes. mediterranea (strain 17). High molecular weight DNA obtained from these chloroplasts contains at least five copies of a MATERIALS AND METHODS 10-kilobase-pair (kbp) sequence tandemly arranged. This Preparation of Chloroplasts. A. mediterranea was grown in unique sequence is present in DNA from chloroplasts of all Muller's medium as described (for references, see ref. 9). stages of the life cycle examined. A chloroplast rDNA clone Cells of three different stages, 1 cm long, 3.5 cm long (i.e., from mustard hybridized with some restriction fragments just prior to cap formation), and fully developed caps (9) from Acetabularia chloroplast DNA but not with the repeated were studied. sequence. An 8-kbp EcoRI-.Pst I fragment of the repeated Caps from A. mediterranea cells were harvested prior to sequence was cloned into pBR322 and used as a hybridization the formation of secondary nuclei. Five-thousand caps probe. No homology was found between the cloned 8-kbp ('100 g) were homogenized in a blender fitted with razor sequence and chloroplast DNA from related species blades on a vertical shaft in 1 liter of ice-cold buffer A Acetabularia crenulata or chloroplast DNA from spinach. -
Molecular Evolution of a Y Chromosome to Autosome Gene Duplication in Drosophila Research Article
Molecular Evolution of a Y Chromosome to Autosome Gene Duplication in Drosophila Kelly A. Dyer,*,1 Brooke E. White,1 Michael J. Bray,1 Daniel G. Pique´,1 and Andrea J. Betancourt* ,2 1Department of Genetics, University of Georgia 2Institute of Evolutionary Biology, University of Edinburgh, Ashworth Labs, Edinburgh, United Kingdom Present address: Institute for Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria *Corresponding author: [email protected], [email protected]. Associate editor: Jody Hey Abstract In contrast to the rest of the genome, the Y chromosome is restricted to males and lacks recombination. As a result, Research article Y chromosomes are unable to respond efficiently to selection, and newly formed Y chromosomes degenerate until few genes remain. The rapid loss of genes from newly formed Y chromosomes has been well studied, but gene loss from highly degenerate Y chromosomes has only recently received attention. Here, we identify and characterize a Y to autosome duplication of the male fertility gene kl-5 that occurred during the evolution of the testacea group species of Drosophila. The duplication was likely DNA based, as other Y-linked genes remain on the Y chromosome, the locations of introns are conserved, and expression analyses suggest that regulatory elements remain linked. Genetic mapping reveals that the autosomal copy of kl-5 resides on the dot chromosome, a tiny autosome with strongly suppressed recombination. Molecular evolutionary analyses show that autosomal copies of kl-5 have reduced polymorphism and little recombination. Importantly, the rate of protein evolution of kl-5 has increased significantly in lineages where it is on the dot versus Y linked. -
Tandem Repeats Dispersed Repeats
The Origin of Repeated Sequences in Genomes and (parenthetically) What is Life? Jeff Elhai Center for the Study of Biological Complexity A great deal of attention has been lavished on the two billion nucleotides that make up the sequence of the human genome, but almost all that attention has focused on the 2% of the genome that encodes protein. The remaining 98% consists mostly of repeated DNA sequences, either dispersed repeats or tandem repeats. Dispersed repeats are segments of DNA that occur multiple times at more or less random positions in the genome. They are typically transposable elements, large segments that encode a protein responsible for the moving of the segment from one site to another. Most tandem repeats are small segments of DNA repeated one after another. For example, the trinucleotide CAG repeated hundreds of times is responsible for active Huntington Disease in humans. transposon CAGCAGCAGCAGCAGCAGCAGCAGCAGCAG... Dispersed repeats Tandem repeats Bacteria, on the other hand have much smaller (0.6 to 11 million nt) and gene-dense genomes, with generally 70 to 80% of the genome devoted to protein-encoding genes. Many still possess transposons or other smaller dispersed repeats (typically 100 nt), but tandem repeats are rare. Recently a third type of repeated sequence has been discovered, called CRISPRs (for Clustered Regularly Interspaced Short Palindromic Repeats), consisting of short repeated regions (22 to 39 nt) separated by non-repetitive spacer regions of equal length. The mechanism by which they are CRISPRs formed is unknown. My colleagues and I have been examining the genome of the cyanobacterium Nostoc punctiforme, which is remarkable in many respects. -
Male with 45,X/46,X(R)Y Mosaicism Due to a Ring Y Chromosome: a Case Report
Case Report JOJ Case Stud Volume 6 Issue 2 - March 2018 Copyright © All rights are reserved by Soumya Nagaraja DOI: 10.19080/JOJCS.2018.06.555685 Male with 45,X/46,X(r)Y Mosaicism due to a Ring Y Chromosome: A Case Report Soumya Nagaraja*, Mariano S Castro Magana and Robert L Levine Department of Pediatric Endocrinology, NYU Winthrop Hospital, USA Submission: February 24, 2018; Published: March 05, 2018 *Corresponding author: Soumya Nagaraja, Department of Pediatric Endocrinology, NYU Winthrop Hospital, 101 Mineola Blvd, 2nd New York, USA, Email: floor, NY11501, Abstract chromosome mosaicism diagnosed by amniocentesis performed due to advanced maternal age. He was treated for short stature and growth failureThe with clinical, growth molecular, hormone andtherapy. cytogenetic He was transferredfindings in toa ourboy carewith at 45,X/46,X(r)Y 12 years of age. mosaicism On presentation, are described he had ahere. normal He malehas historyphenotype, of ring short Y stature, palpable testes and delayed sexual development. A post-natal karyotype and chromosomal SNP microarray revealed deletions of both terminal regions of the Y chromosome, consistent with the prenatal diagnosis of the ring Y chromosome. On karyotype, the presumptive ring Y chromosome was present in 29% of the cells and a single X chromosome was present in the other 71% of cells. FISH analysis demonstrated the presence of a ring Y chromosome in 37.1% of the cells. SHOX gene analysis revealed a complete gene deletion and is the likely cause of his short stature. He continued treatment with growth hormone and an aromatase inhibitor was added to delay growth plate fusion and to ring Y chromosome and depending upon on the presence or absence of the SRY gene can result in a wide spectrum of manifestations ranging frompotentially females increase with a hisTurner final syndrome-likeadult height.