Dissertations / Theses on the topic 'Repetitive DNA sequence'
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Cai, Zheng. "Repetitive sequence analysis for soybean genome sequences." Diss., Columbia, Mo. : University of Missouri-Columbia, 2005. http://hdl.handle.net/10355/4249.
Full text"May 2005" The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Includes bibliographical references.
Arner, Erik. "Solving repeat problems in shotgun sequencing /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-996-3/.
Full textWang, Xiaofei. "Molecular characterization and cytogenetic analysis of chicken repetitive DNA sequences /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20979393.
Full text王曉飛 and Xiaofei Wang. "Molecular characterization and cytogenetic analysis of chicken repetitive DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31239419.
Full textMadsen, Susan M. "Divergence in repetitive DNA sequences among three sitopsis wheat species /." free to MU campus, to others for purchase, 1998. http://wwwlib.umi.com/cr/mo/fullcit?p9901260.
Full textWang, Suyue. "Characterization of a Human 28S Ribosomal RNA Retropseudogene and Other Repetitive DNA Sequence Elements Isolated from a Human X Chromosome-Specific Library." Thesis, University of North Texas, 1994. https://digital.library.unt.edu/ark:/67531/metadc278083/.
Full textMacDonald, Anna Jayne, and n/a. "Sex chromosome microsatellite markers from an Australian marsupial: development, application and evolution." University of Canberra. n/a, 2008. http://erl.canberra.edu.au./public/adt-AUC20081217.122146.
Full textSindi, Suzanne Soraya. "Describing and modeling repetitive sequences in DNA." College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/3796.
Full textThesis research directed by: Applied Mathematics and Scientific Computation Program. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
Li, Juan, and 李娟. "Molecular characterization of chicken repetitive DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B42577287.
Full textLi, Juan. "Molecular characterization of chicken repetitive DNA sequences." Click to view the E-thesis via HKUTO, 2003. http://sunzi.lib.hku.hk/hkuto/record/B42577287.
Full textMadalena, Christiane Rodriguez Gutierrez. "DNA repetitivo e seu papel na estrutura cromossômica terminal em Rhynchosciara americana (Diptera: Sciaridae)." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-02102008-144225/.
Full textThe chromosomal localization of ribosomal DNA (rDNA) was studied in polytene and diploid tissues of four sciarid species, Trichosia pubescens, Rhynchosciara americana, R. milleri and Schwenkfeldina sp. While hybridization to mitotic chromosomes showed the existence of a single rDNA locus, ribosomal probes hybridized to more than one polytene chromosome region in all the species analyzed as a result of micronucleolar attachment to specific chromosome sites. Micronucleoli are small, round bodies containing transcriptionally active, probably extrachromosomal rDNA. In T. pubescens the rDNA is predominantly localized in chromosome sections X-10 and X-8. In R. americana the rDNA is frequently found associated with centromeric heterochromatin of the chromosomes X, C, B and A, and also with sections X-1 and B-13. Ribosomal probes in R. milleri hybridized with high frequency to pericentric and telomeric regions of its polytene complement. Schwfenkfeldina sp. displays a remarkably unusual distribution of rDNA in polytene nuclei, characterized by the attachment of micronucleoli to many chromosome regions. The results showed that micronucleoli preferentially associate with intercalary or terminal heterochromatin of all sciarid flies analyzed and, depending on the species, are attached to a few (Trichosia), moderate (Rhynchosciara) or a large (Schwenkfeldina sp.) number of polytene chromosome sites. This work also describes the characterization of chromosome end sequences of Rhynchosciara americana, initiated with the screening of a plasmid microlibrary made from a microdissected polytene chromosome end. We report the identification and sequencing of an R. americana satellite displaying base composition, genomic structure and chromosomal localization similar to the complex telomeric repeats of Nematocera that have previously been characterized. However, data obtained in other Rhynchosciara species, as well as distinct chromosomal localization of satellite and reverse transcriptase loci in R. americana, suggest that the repetitive element characterized does not reach the very end of the chromosome. The characterization of chromosome end sequences of Rhynchosciara americana continued with the screening of a phage library made with its genomic DNA. We choose pRaM47.33, a clone whose insert is a repetitive microsatellite characterized in the subtelomeric region of R. americana chromosomes, as a probe for the screening. We analyzed 12kb of a single phage insert, composed of M22 tandem arrays and a new microsatellite which was 16pb long, arranged in tandem (named M16). In situ hybridization showed the presence of M16 repeats in the five telomeric termini of R. americana chromosomes. The M16 repeat was used as a probe in another screen of the same phage library, which allowed us to analyze approximately 50kb of terminal DNA. We find that repetitive sequences, such as the 414pb repeat previously characterized in R. americana and stretches of Ramar1 and RaTART mobile elements, also characterized in R. americana, compose the subtelomeric region of R. americana chromosomes. Additionally, we find sequences that do not match sequences in the GenBank database and do not present repetitive motifs. Our results suggest that the telomeric regions of R. americana chromosomes are composed of more than one type of repetitive sequence.
Murray, Katherine Alice. "Characterisation of repetitive DNA sequences of Onchocerca species." Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.280851.
Full textFarache, Gabriel. "Etudes des regions genomiques delimitant les domaines des genes globine chez le poulet." Paris 7, 1987. http://www.theses.fr/1987PA077009.
Full text何兆康 and Siu-hong Ho. "Isolation and characterization of Panax Ginseng repetitive DNA sequences for DNA fingerprinting." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B31215282.
Full textHo, Siu-hong. "Isolation and characterization of Panax Ginseng repetitive DNA sequences for DNA fingerprinting /." Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19737816.
Full textRong, Ying. "Phylogeny of the genus Gossypium and genome origin of its polyploid species inferred from variation in nuclear repetitive DNA sequences." Texas A&M University, 2004. http://hdl.handle.net/1969.1/3161.
Full textPataskar, Shashank S. "Structure Function Studies Of Biologically Important Simple Repetitive DNA Sequences." Thesis, Indian Institute of Science, 2000. http://hdl.handle.net/2005/261.
Full textJamieson, G. "Constraints on the evolution of repetitive sequences in the genus Allium." Thesis, University of Nottingham, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356026.
Full textPearston, D. H. "Characteristics of transposon-like repetitive genomic DNA sequences in Physarum polycephalum." Thesis, University of Aberdeen, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372623.
Full textPatton, Simon James. "Repetitive DNA sequences and the population genetics of the dog-whelk." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361447.
Full textStaginnus, Christina. "Repetitive DNA-Sequenzen im Genom der Kichererbse (Cicer arietinum L.)." [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=964604442.
Full textSantos, Karla Galvão Bezerra dos. "Isolation, molecular characterisation and chromosomal location of repetitive DNA sequences in Brassica." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=976329433.
Full textTeixeira, Wellcy Gonçalves [UNESP]. "Identificação e caracterização de sequências repetidas de DNA no genoma de peixes ciclídeos do gênero Cichla." Universidade Estadual Paulista (UNESP), 2008. http://hdl.handle.net/11449/100494.
Full textUniversidade Estadual Paulista (UNESP)
O genoma dos organismos eucariotos apresenta-se organizado em seqüências simples e repetidas. As seqüências repetidas de DNA estão presentes em centenas a milhares de cópias dispersas ou agrupadas no genoma e localizam-se preferencialmente em regiões heterocromáticas, desempenhando papel relevante na organização do genoma desses organismos. Nesse sentido, a realização de estudos genéticos básicos sobre a organização genômica dessas seqüências repetidas é fundamental para uma melhor compreensão do seu papel biológico assim como o entendimento de sua dinâmica evolutiva entre os diversos grupos de vertebrados. Os Cichlidae constituem uma das mais especiosas famílias de peixes, com cerca de 3.000 espécies distribuídas pela América Central e do Sul, África, e sudeste da Índia. Este grupo passou por um rápido e extenso processo de radiação adaptativa ao longo dos tempos, constituindo-se em importantes entidades biológicas para a realização de estudos evolutivos. Dentre os Cichlidae, as espécies do gênero Cichla (tucunarés), com distribuição exclusiva na América do Sul, apresentam grande importância ecológica e econômica. No entanto, estudos genéticos envolvendo espécies desse gênero são ainda escassos. Assim, o presente trabalho teve por objetivo isolar e caracterizar seqüências repetidas de DNA no genoma de Cichla kelberi. Elementos repetidos de DNA foram isolados por PCR (elementos Rex1, Rex3, Rex6 e Tc1) e digestão enzimática (elemento Tuc), seqüenciados e mapeados cromossomicamente por FISH para o estudo de seu padrão de distribuição no genoma. O elemento Tuc apresentou elevada similaridade com seqüências do gene da transcriptase reversa de Oryzias melastigma, o que sugere tratar-se de um elemento retrotransponível. Análises comparativas do elemento Tuc a bancos de sequência mostraram alta similaridade...
The genome of eucaryote organisms is organized into single and repetitive sequences. The repetitive DNA sequences are represented by hundreds to thousands of dispersed or tandem-arrayed copies preferentially localized on the heterochromatic regions, having important function on the genome organization of the organisms. Therefore, the development of basic genetic studies about the genome organization of these repetitive sequences are fundamental to a better comprehension of their biologic role and the understanding of their evolutionary dinamics. The Cichlidae are one of the most diverse fish families, having about 3.000 species distributed around Central and South America, Africa and Southeast India. This group underwent a large and rapid process of adaptative radiation, becoming an important biological model. Among the Cichlidae, the species of the genera Cichla (tucunarés), with exclusive distribution in South America, have a significative economic and ecologic importance. However genetic studies on species of this genera are scarce. Therefore, this work had the aim to isolate and characterize repetitive DNA sequences of the genome of Cichla kelberi. Repetitive DNA sequences were isolated using PCR (elements Rex1, Rex3, Rex6 and Tc1) and restriction digestion (element Tuc), sequenced and their genome distribution determined by FISH. The Tuc element showed high similarity to sequences of reverse transcriptase gene of the fish Oryzias melastigma, which suggests that such element correspond to an retrotransposon element. Comparative analysis of the Tuc element to DNA sequence data bank showed high similarity with repetitive sequences in the genome of several vertebrates, including fishes, amphibians and mammals. Results of FISH showed an accumulation of obtained elements preferentially in centromeres of all chromosomes of the complement, and few telomeric blocks in some... (Complete abstract click electronic access below)
Castillejo-López, Casimiro. "Repetitive DNA in search of a function a study of telomeric and centromeric sequences in Chironomus /." Lund : Lund University, 1998. http://catalog.hathitrust.org/api/volumes/oclc/68945096.html.
Full textTuntiwechapikul, Wirote. "Studies of a G-quadruplex-specific cleaving reagent, expansion of long repetitive DNA sequences, and a cytosine-specific alkylating aza-enediyne /." Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3055255.
Full textTeixeira, Wellcy Gonçalves. "Identificação e caracterização de sequências repetidas de DNA no genoma de peixes ciclídeos do gênero Cichla /." Botucatu : [s.n.], 2008. http://hdl.handle.net/11449/100494.
Full textBanca: Luciana Bolsoni
Banca: Maeli Del Paiva
Resumo: O genoma dos organismos eucariotos apresenta-se organizado em seqüências simples e repetidas. As seqüências repetidas de DNA estão presentes em centenas a milhares de cópias dispersas ou agrupadas no genoma e localizam-se preferencialmente em regiões heterocromáticas, desempenhando papel relevante na organização do genoma desses organismos. Nesse sentido, a realização de estudos genéticos básicos sobre a organização genômica dessas seqüências repetidas é fundamental para uma melhor compreensão do seu papel biológico assim como o entendimento de sua dinâmica evolutiva entre os diversos grupos de vertebrados. Os Cichlidae constituem uma das mais especiosas famílias de peixes, com cerca de 3.000 espécies distribuídas pela América Central e do Sul, África, e sudeste da Índia. Este grupo passou por um rápido e extenso processo de radiação adaptativa ao longo dos tempos, constituindo-se em importantes entidades biológicas para a realização de estudos evolutivos. Dentre os Cichlidae, as espécies do gênero Cichla (tucunarés), com distribuição exclusiva na América do Sul, apresentam grande importância ecológica e econômica. No entanto, estudos genéticos envolvendo espécies desse gênero são ainda escassos. Assim, o presente trabalho teve por objetivo isolar e caracterizar seqüências repetidas de DNA no genoma de Cichla kelberi. Elementos repetidos de DNA foram isolados por PCR (elementos Rex1, Rex3, Rex6 e Tc1) e digestão enzimática (elemento Tuc), seqüenciados e mapeados cromossomicamente por FISH para o estudo de seu padrão de distribuição no genoma. O elemento Tuc apresentou elevada similaridade com seqüências do gene da transcriptase reversa de Oryzias melastigma, o que sugere tratar-se de um elemento retrotransponível. Análises comparativas do elemento Tuc a bancos de sequência mostraram alta similaridade... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: The genome of eucaryote organisms is organized into single and repetitive sequences. The repetitive DNA sequences are represented by hundreds to thousands of dispersed or tandem-arrayed copies preferentially localized on the heterochromatic regions, having important function on the genome organization of the organisms. Therefore, the development of basic genetic studies about the genome organization of these repetitive sequences are fundamental to a better comprehension of their biologic role and the understanding of their evolutionary dinamics. The Cichlidae are one of the most diverse fish families, having about 3.000 species distributed around Central and South America, Africa and Southeast India. This group underwent a large and rapid process of adaptative radiation, becoming an important biological model. Among the Cichlidae, the species of the genera Cichla (tucunarés), with exclusive distribution in South America, have a significative economic and ecologic importance. However genetic studies on species of this genera are scarce. Therefore, this work had the aim to isolate and characterize repetitive DNA sequences of the genome of Cichla kelberi. Repetitive DNA sequences were isolated using PCR (elements Rex1, Rex3, Rex6 and Tc1) and restriction digestion (element Tuc), sequenced and their genome distribution determined by FISH. The Tuc element showed high similarity to sequences of reverse transcriptase gene of the fish Oryzias melastigma, which suggests that such element correspond to an retrotransposon element. Comparative analysis of the Tuc element to DNA sequence data bank showed high similarity with repetitive sequences in the genome of several vertebrates, including fishes, amphibians and mammals. Results of FISH showed an accumulation of obtained elements preferentially in centromeres of all chromosomes of the complement, and few telomeric blocks in some... (Complete abstract click electronic access below)
Mestre
Dechyeva, Daryna. "Molecular-cytogenetic analysis of repetitive sequences in genomes of Beta species and hybrids." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2006. http://nbn-resolving.de/urn:nbn:de:swb:14-1153318263914-87397.
Full text陳美娥 and May-ngor Chan. "Isolation and characterization of repetitive DNA sequences and their use in DNA fingerprinting and the population genetics of Perna viridis(L.) (Bivalvia : Mytilidae)." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1997. http://hub.hku.hk/bib/B31214964.
Full textChan, May-ngor. "Isolation and characterization of repetitive DNA sequences and their use in DNA fingerprinting and the population genetics of Perna viridis (L.) (Bivalvia : Mytilidae) /." Hong Kong : University of Hong Kong, 1997. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19470423.
Full textMoore, Catherine Samantha. "The use of repetitive DNA sequences, in particular retrotransposons, in the genetic analysis of oil palm (Elaeis guineensis)." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340012.
Full textSilva, Keteryne Rodrigues da [UNESP]. "Isolamento de sequências repetitivas do genoma de espécies do gênero Ancistrus (Siluriformes: Loricariidae)." Universidade Estadual Paulista (UNESP), 2016. http://hdl.handle.net/11449/137992.
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O DNA pode estar organizado no genoma em sequências de cópias únicas e em sequências que se repetem várias vezes, denominadas sequências repetitivas. Estas sequências são constituídas basicamente por repetições em tandem (satélites, minissatélites e microssatélites) ou dispersas (transposons ou retrotransposons), e parecem estar envolvidas em diversos eventos celulares importantes, como por exemplo nos processos de replicação do DNA, de recombinação, de expressão gênica e de evolução dos cromossomos, auxiliando na manutenção e propagação do material genético celular. Em nível cromossômico parecem ser responsáveis por proporções significativas das variações cariotípicas observadas em diversos grupos. O gênero Ancistrus (Siluriformes, Loricariidae) apresenta atualmente 68 espécies nominais, e uma enorme quantidade de espécies ainda não identificadas. Alguns trabalhos vêm utilizando sequências repetitivas também em análises citogenéticas e moleculares para identificação de cromossomos homólogos e marcadores cariotípicos interessantes que podem auxiliar os trabalhos de identificação de espécies. Apesar de serem amplamente estudadas em diversos organismos, há ainda muito a ser entendido sobre essas sequências e sua organização no genoma. Este trabalho teve como objetivo isolar sequências repetitivas no genoma de espécies de Ancistrus, afim de encontrar possíveis marcadores para o gênero, que pudessem contribuir para o entendimento da taxonomia deste grupo, bem como auxiliar no entendimento do processo de evolução dos cromossomos sexuais dessas espécies. Dentre as sequências isoladas está um transposon da família TC1/mariner que se mostrou presente em todos os cromossomos das espécies analisadas e dois DNAs satélites que se apresentam acumulados em regiões centroméricas de alguns cromossomos. Sendo assim, este estudo resultou em dados que poderão contribuir com o entendimento da evolução cariotípica do gênero Ancistrus bem como fornecer mais informações sobre características e evolução dos cromossomos sexuais em peixes.
DNA may be organized in the genome as single copy sequences and as sequences that are repeated several times, called repetitive sequences. These sequences are basically constituted by tandem repeats (satellites, minisatellites and microsatellites) or scattered (transposons and retrotransposons), and seem to be involved in important cellular events such as, DNA replication process, recombination, gene expression and chromosome evolution, assisting in maintenance and spread the genetic material of cells. At chromosome level, seems to be significant proportions of karyotypic variations observed in several groups. The genus Ancistrus (Siluriformes, Loricariidae) has, actually, 68 nominal species and several species not identified yet. Repetitive sequences have been used in molecular cytogenetic analysis for identification of homologous chromosomes and interesting karyotypic markers that can assist in species identification works. Despite being widely studied in several organisms, there is still much to be understood about these sequences and their organization in the genome. This study aimed to isolate repetitive sequences in the genome of Ancistrusspecies in order to find possible markers for the genus, which could contribute to the understanding of the taxonomy of this group and to the understanding of the process of evolution of sex chromosomes of these species. Among the isolated sequences, there is a family of TC1/mariner transposon that showed to be present in all the chromosomes of the analyzed species, and two satellites DNAs that have accumulated in centromeric regions. Thus, this study resulted in data that could be contribute to understanding the karyotype evolution of Ancistrus genus as well as providing more information on the characteristics and evolution of sex chromosomes in fish.
Oliveira, Maria Lígia Marques de. "Mapeamento físico de sequênias repetitivas de DNA no genoma de espécies do gênero Trichomycterus (Siluriformes, Trichomycteridae) /." Botucatu, 2015. http://hdl.handle.net/11449/128102.
Full textCoorientador: José Carlos Pansonato Alves
Banca: Diogo Teruo Hashimoto
Banca: Vanessa Paes da Cruz
Resumo: No presente estudo, foram analisadas citogeneticamente cinco espécies de peixes pertencentes ao gênero Trichomycterus: T. diabolus, T. iheringi, T. zonatus, Trichomycterus cf. mimonha e Trichomycterus sp., provenientes de diferentes bacias hidrográficas brasileiras. Foram utilizadas as técnicas de citogenética clássica (coloração com Giemsa, localização das RONs pela marcação com nitrato de Prata e bandamento C) e cito-moleculares (Hibridação Fluorescente in situ - FISH com sondas de DNAr 5S e 18S e o snDNA U2). Todas as espécies apresentaram número diploide de 2n=54 cromossomos com variações em sua fórmula cariotípica. Trichomycterus diabolus, T. iheringi, T. zonatus e Trichomycterus cf. mimonha apresentaram seu cariótipo com 34m + 12sm + 8st e Trichomycterus sp. apresentou 36m + 10sm + 8st, além da ocorrência de cromossomos supranumerários. As espécies também revelaram diferenças em relação ao tamanho dos dois primeiros pares cromossômicos do cariótipo, onde Trichomycterus sp. e T. diabolus apresentaram o primeiro e segundo metacêntrico de tamanho semelhante e maiores em relação aos demais cromossomos, enquanto em T. zonatus, Trichomycterus cf. mimonha e T. iheringi apenas o primeiro metacêntrico foi considerado o maior par. O bandamento C evidenciou blocos heterocromáticos instersticiais nos pares 2, 3, 7, 8, 19 e 23 de T. iheringi e no par 18 de T. diabolus, sendo que as demais espécies apresentaram blocos centroméricos de diferentes tamanhos espalhados por quase todo o cariótipo. As RONs foram identificadas em apenas um par cromossômico e foram coincidentes com a hibridação fluorescente in situ realizada com a sonda para DNAr 18S, com exceção de T. zonatus e Trichomycterus sp. que apresentaram marcações centroméricas no primeiro par e em um pequeno metacêntrico, respectivamente. A hibridação com a sonda para DNAr 5S revelou resultados mais diversos, sendo detectado um par para...
Abstract: In the present study five species of fish from the genus Trichomycterus were analyzed cytogenetically, including T. diabolus, T. iheringi, T. zonatus, Trichomycterus cf. mimonha and Trichomycterus sp., collected at different Brazilian basins. The analyses involved classical (Giemsa conventional staining, localization of NORs for silver nitrate marking and C-banding) and molecular cytogenetic techniques (fluorescent in situ hybridization with ribosomal 5S and 18S, and U2 snDNA probes). All species showed diploid number of 2n = 54 chromosomes with variations in karyotype formula. Trichomycterus diabolus, T. iheringi, T. zonatus and Trichomycterus cf. mimonha presented their karyotype with 34m + 12sm + 8st and Trichomycterus sp. presented 36m + 10sm + 8st, besides the occurrence of supernumerary chromosomes. The species also reveals differences in relation to the size of the first two chromosome pairs of the karyotype, where Trichomycterus sp. and T. diabolus presented the first and second metacentric with similar size and larger than the other chromosomes, while in T. zonatus, Trichomycterus cf. mimonha and T. iheringi only the first metacentric was considered the largest pair. The constitutive heterochromatin showed interstitial blocks in pairs 2, 3, 7, 8, 19 and 23 in T. iheringi and the par 18 in T. diabolus and the other species presented centromeric blocks with different sizes spread throughout the greater part of the karyotype. NORs were identified in only one chromosome pair and were coincident with the fluorescent in situ hybridization using probes of 18S rDNA, except for T. zonatus and Trichomycterus sp. that showed additional centromeric signals on the first pair and other small metacentric, respectively. FISH using the probes of 5S rDNA was differentially distributed in the different species, with one chromosome pairs detected in T. diabolus, two pairs in T. iheringi, T. zonatus and three ...
Mestre
Oliveira, Maria Lígia Marques de [UNESP]. "Mapeamento físico de sequênias repetitivas de DNA no genoma de espécies do gênero Trichomycterus (Siluriformes, Trichomycteridae)." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/128102.
Full textCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
No presente estudo, foram analisadas citogeneticamente cinco espécies de peixes pertencentes ao gênero Trichomycterus: T. diabolus, T. iheringi, T. zonatus, Trichomycterus cf. mimonha e Trichomycterus sp., provenientes de diferentes bacias hidrográficas brasileiras. Foram utilizadas as técnicas de citogenética clássica (coloração com Giemsa, localização das RONs pela marcação com nitrato de Prata e bandamento C) e cito-moleculares (Hibridação Fluorescente in situ - FISH com sondas de DNAr 5S e 18S e o snDNA U2). Todas as espécies apresentaram número diploide de 2n=54 cromossomos com variações em sua fórmula cariotípica. Trichomycterus diabolus, T. iheringi, T. zonatus e Trichomycterus cf. mimonha apresentaram seu cariótipo com 34m + 12sm + 8st e Trichomycterus sp. apresentou 36m + 10sm + 8st, além da ocorrência de cromossomos supranumerários. As espécies também revelaram diferenças em relação ao tamanho dos dois primeiros pares cromossômicos do cariótipo, onde Trichomycterus sp. e T. diabolus apresentaram o primeiro e segundo metacêntrico de tamanho semelhante e maiores em relação aos demais cromossomos, enquanto em T. zonatus, Trichomycterus cf. mimonha e T. iheringi apenas o primeiro metacêntrico foi considerado o maior par. O bandamento C evidenciou blocos heterocromáticos instersticiais nos pares 2, 3, 7, 8, 19 e 23 de T. iheringi e no par 18 de T. diabolus, sendo que as demais espécies apresentaram blocos centroméricos de diferentes tamanhos espalhados por quase todo o cariótipo. As RONs foram identificadas em apenas um par cromossômico e foram coincidentes com a hibridação fluorescente in situ realizada com a sonda para DNAr 18S, com exceção de T. zonatus e Trichomycterus sp. que apresentaram marcações centroméricas no primeiro par e em um pequeno metacêntrico, respectivamente. A hibridação com a sonda para DNAr 5S revelou resultados mais diversos, sendo detectado um par para...
In the present study five species of fish from the genus Trichomycterus were analyzed cytogenetically, including T. diabolus, T. iheringi, T. zonatus, Trichomycterus cf. mimonha and Trichomycterus sp., collected at different Brazilian basins. The analyses involved classical (Giemsa conventional staining, localization of NORs for silver nitrate marking and C-banding) and molecular cytogenetic techniques (fluorescent in situ hybridization with ribosomal 5S and 18S, and U2 snDNA probes). All species showed diploid number of 2n = 54 chromosomes with variations in karyotype formula. Trichomycterus diabolus, T. iheringi, T. zonatus and Trichomycterus cf. mimonha presented their karyotype with 34m + 12sm + 8st and Trichomycterus sp. presented 36m + 10sm + 8st, besides the occurrence of supernumerary chromosomes. The species also reveals differences in relation to the size of the first two chromosome pairs of the karyotype, where Trichomycterus sp. and T. diabolus presented the first and second metacentric with similar size and larger than the other chromosomes, while in T. zonatus, Trichomycterus cf. mimonha and T. iheringi only the first metacentric was considered the largest pair. The constitutive heterochromatin showed interstitial blocks in pairs 2, 3, 7, 8, 19 and 23 in T. iheringi and the par 18 in T. diabolus and the other species presented centromeric blocks with different sizes spread throughout the greater part of the karyotype. NORs were identified in only one chromosome pair and were coincident with the fluorescent in situ hybridization using probes of 18S rDNA, except for T. zonatus and Trichomycterus sp. that showed additional centromeric signals on the first pair and other small metacentric, respectively. FISH using the probes of 5S rDNA was differentially distributed in the different species, with one chromosome pairs detected in T. diabolus, two pairs in T. iheringi, T. zonatus and three ...
Päsold, Susanne. "Entwicklung eines FISH-Referenzkaryotyps der Zuckerrübe (Beta vulgaris) für die Integration genetischer Kopplungskarten und die Analyse der chromosomalen Verteilung von repetitiven Sequenzen." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-131410.
Full textThe correlation of genetic, physical and cytological data is crucial for interdisciplinary genome and chromosome analyses. Beta vulgaris (2n = 18) is an important crop and an object of basic research. Although it is an intensely analysed species, its genetic linkage groups (LG) have not been assigned to chromosomes. Additionally, sugar beet chromosomes lack distinct morphological features and could therefore not be identified and classified individually. Consequently, results generated by cytogenetic methods can not be readily applied to genetic and physical maps. Cytogenetic approaches enable analysing structural chromosomal changes, identifying and localizing repetitive DNA, and mapping of markers which are difficult to place within linkage maps. Therefore, the main objective of this work has been the development of a FISH (fluorescence in situ hybridization) procedure that correlates LGs with chromosomes of sugar beet and that allows the microscopic identification of individual chromosome arms. In this work a FISH reference karyotype for sugar beet has been established. A set of 18 BACs (bacterial artificial chromosome) allows the unequivocal identification of each sugar beet chromosome and assigns them to the southern and northern ends of LGs. Hence, the chromosomes are numbered in accordance with the genetic map. The arm-specific BACs and the satellite DNA families pBV and pBV VI or pEV and pAv34 have been hybridized simultaneously to assign the distribution patterns of the highly abundant sequence families to chromosomes. Simultaneous hybridization of the four repetitive probes revealed a chromosome-specific pattern of subtelomeric, intercalary and centromeric signals. Thus, each of the sugar beet chromosomes can be identified in a single FISH experiment. Furthermore, chromosomes with a high content of repetitive DNA have been identified and chromosomal regions that may hinder the correct sequence assembly have been localized. The BAC set as well as the pooled satellite DNA probes discriminate the somatic chromosomes for the first time independently from trisomic lines. Since the chromosomes are differentially labelled with the satellite DNA probes their physical distances could be determined and correlated with genetic distances of the corresponding LGs. A LG-specific recombination frequency from 0.73 to 1.14 Mb/cM has been disclosed. BACs and subtelomeric or telomeric sequences have been hybridized simultaneously on pachytene chromosomes to estimate distances between BACs plus the markers they contain and the physical chromosome ends. Five BACs showed substantial distances to the physical chromosome ends; the corresponding LGs could thus be extended by additional markers. Furthermore, three BACs showing only minor distances to chromosome ends have been investigated in detail by fiber-FISH. One of these BACs was localized closely adjacent to the telomere. For this chromosome end (Chr 2N) it is unlikely that the LG could be extended distally by additional markers and is therefore considered to be closed. The BACs for the chromosome ends Chr 4S and Chr 9S have been too distant from the terminal probe to be bridged by fiber-FISH. For them it is likely that further markers can be placed distally. Furthermore, the B. vulgaris genomic sequence RefBeet 1.0 has been investigated. Scaffolds containing terminal genetic markers have been identified bioinformatically and analysed for the content of subtelomeric and telomeric sequences. The occurrence of terminal sequences confirms the terminal localization of in silico chromosome segments. Three scaffolds with an initially unknown position could thus be allocated to in silico chromosomes and to the northern or southern position on the chromosome. The strand orientation of 16 scaffolds has been determined based on the localization of terminal sequences in relation to the genetic marker considering the results of FISH on pachytene chromosomes. The distance between markers and terminal sequences has been determined for 14 scaffolds. The median is 196 kb. It is likely that further markers can be placed distally from all LG ends except for the north of LG 2 and LG 4. Satellite DNA is usually homogenous within one species; however, it can form chromosome-specific variants. Southern hybridization revealed that the BAC marker for Chr 2N contains the subtelomeric sequence family pAv34. The BAC has been subcloned and the pAv34 content of the subclones has been analysed by Southern hybridization. Positive clones have been sequenced. Thereby, four pAv34-2N monomeres have been detected. Compared to full-length pAv34 motives derived from the RefBeet 1.0 and from unassembled sequence data of the RefBeet 0.2 the pAv34-2N units form a subfamily together with pAv34 copies assigned to different in silico chromosomes and contigs. The subclone sequences have been assembled to two subclone contigs, which have been positioned within the in silico chromosome segment of Chr 2N (Bvchr2.un.sca001). Thereby, regions of unknown sequence have been decoded and probable misassemblies in repetitive regions within the RefBeet 1.0 have been disclosed. The results obtained in this work enable the identification of all sugar beet chromosomes independently from their stage of cell division and in accordance with genetic information. Cytogenetic data are integrated with molecular data and can be used for identifying the chromosome-specific distribution of repeats and chromosome-specific repeat variants. They enable determining physical distances between markers and investigating the terminal coverage of LGs. The results support the correct mapping of markers and unassigned contigs, uncover reasons for gaps within maps and sequence assemblies, and thus contribute to assembling data into a continuous high quality genome sequence of sugar beet. Moreover, the cytogenetic data represent the basis for future investigations of structural chromosomal changes that took place during evolution
Tran, Anh-Nhi. "A Genetic Survey of the Pathogenic Parasite Trypanosoma cruzi." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3425.
Full textWong, Kit-man. "Part I : Isolation and characterization of the highly repetitive sequences from Escherichia coli and their uses in DNA fingerprinting ; Part II :Molecular characterization and initial development of a DNA vaccine against the HOG cholera virus /." Hong Kong : University of Hong Kong, 2000. http://sunzi.lib.hku.hk/hkuto/record.jsp?B22053864.
Full textBenediktsson, Elís Ingi. "Detection and analysis of megasatellites in the human genome using in silico methods." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-961.
Full textMegasatellites are polymorphic tandem repetitive sequences with repeat-units longer than or equal to 1000 base pairs. The novel algorithm Megasatfinder predicts megasatellites in the human genome. A structured method of analysing the algorithm is developed and conducted. The analysis method consists of six test scenarios. Scripts are created, which execute the algorithm using various parameter settings. Three nucleotide sequences are applied; a real sequence extracted from the human genome and two random sequences, generated using different base probabilities. Usability and accuracy are investigated, providing the user with confidence in the algorithm and its output. The results indicate that Megasatfinder is an excellent tool for the detection of megasatellites and that the generated results are highly reliable. The results of the complete analysis suggest alterations in the default parameter settings, presented as user guidelines, and state that artificially generated sequences are not applicable as models for real DNA in computational simulations.
Bakalara, Norbert. "Caracterisation dans le genome d'un annelide polychete : owenia fusiformis, d'une region comprenant la repetition du triplet nucleotidique ccx." Aix-Marseille 2, 1987. http://www.theses.fr/1987AIX22121.
Full textWong, Kit-man, and 黃潔文. "Part I: Isolation and characterization of thehighly repetitive sequences from Escherichia coli and their uses inDNA fingerprinting ; Part II :Molecular characterization and initialdevelopment of a DNA vaccine against the HOG cholera virus." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2000. http://hub.hku.hk/bib/B31223643.
Full textHeessen, Stijn. "Regulation of the ubiquitin-proteasome system : characterization of viral and cellular stabilization signals /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-600-6/.
Full textGalvao, Bezerra dos Santos Karla. "Isolation, molecular characterisation and chromosomal location of repetitive DNA sequences in Brassica." Doctoral thesis, 2004. http://hdl.handle.net/11858/00-1735-0000-0006-AB64-B.
Full textWANG, CHUNG-JU, and 王中茹. "Karyotype of Nicotiana plumbaginifolia based on distribution of a repetitive DNA sequence and mapping of 5S and 26S rRNA genes." Thesis, 1998. http://ndltd.ncl.edu.tw/handle/20573507996583438280.
Full text國立臺灣大學
植物學系研究所
86
Nicotiana plumbaginifolia has 10 pairs of acrocentric or telocentricchromosome s, which could not be distinguished from each other by conventional cytologica l techniques. The somatic karyotype of this species was constructed based on f luorescence in situ hybridization (FISH) to a 165 bp tandemly repeated sequenc e, NP3R. Variation in the spatial and quantitative distribution of this repeat allowed the identification of each of the 10 pairs of N. plumbaginifolia chr omosomes. Two-step FISH and multi-color FISH, showed that 5S rDNA was clustere d in a proximal region in the long arm of chromosome 2, and that 26S rDNA was clustered in the terminal regions of chromosomes 9 and 10.
Wang, Tzu-Han, and 王慈涵. "The study of inter-molecular interaction between polyQ strands that promote polyQ-containing proteins co-aggregation and the role of Bem2p plays in the DNA stability of repetitive sequence that encodes polyQ." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/21984963689018542246.
Full text國立陽明大學
生化暨分子生物研究所
97
1.Huntington’s disease (HD) is an autosomal dominant neurodegenerative disorder and is caused by the expansion of CAG repeats, encoding polyglutamines (polyQ), within exon 1 of the huntingtin (htt) gene. The length of polyQ track is a main determinant for the onset of HD and the disease occurs only when the critical length of ~36 glutamines is exceeded. A peculiar feature of mutant htt proteins with abnormal length of polyQ is that they spontaneously self-assemble into aggregates, a pathological hallmark of this disorder found in the brain of affected individuals. Several studies have demonstrated that proteins with normal length of polyQ track can also interact with and recruit into these aggregates, which are initiated by polyQ-expanded proteins. In order to further investigate this inter-molecular interaction between heterogeneous polyQ strands and to find a potential dominant negative mutant that can interfere with the formation of polyQ aggregates in cells, we have established a phenotypic assay system that can reveal the presence of co-aggregation and costructed a library of amino acid substitution within the polyQ track for examining their effect on polyQ aggregation. After three rounds of screening, we find that co-expression of truncated polyQ peptides can partially reduce the aggregation levels of 97Q protein. However, this effect may result from decreased 97Q expression. 2.The BEM2 gene is required for normal polarized cell growth in the budding yeast Saccharomyces cerevisiae. In the carboxyl-terminus, Bem2p contains a GAP domain, which is commoly found in GTPase activating proteins (GAPs) that regulate rho-GTPase activity. In yeast, genes encoding GTPases (CDC42, RHO1, RHO2, RHO3, and RHO4) have been proposed to regulate cellular morphogenesis such as actin cytoskeleton and bud emergence. Using the Snyder’s knock out library, we find that bem2△ mutations confer DNA repetitive sequence instability and enhance contraction of CAA/CAG repeats through homologous recombination, suggesting Bem2p has a role in regulating DNA stability. We also demonstrate the DNA instability is attributed to the defective function of Bem2p in morphogenesis checkpoint. Furthermore, swe1, a△ morphogenesis checkpoint deficient cell, shows an elevated DNA contraction rate. Thus, our study reveals a novel link between morphogenesis checkpoint and repetitive sequence stability in yeast cells.
Huang, Zhao-Wei, and 黃昭維. "Transcription-coupled R-loops mediated DNA instability in repetitive sequences." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/00429939959537414656.
Full text國立陽明大學
生化暨分子生物研究所
102
RNA:DNA hybrids, known as R-loops, are peculiar nucleic acid structures that are generated under transcriptional process; in particular, for these genes with highly repetitive or GC rich sequences. R-loops can be dynamically resolved by a variety of cellular proteins and the persistence of RNA:DNA hybrids has been proposed as a negative factor to influence genome integrity. Recently, R-loops were detected on CAG trinucleotide repeats (TNR) and contributed DNA instability as a consequence of contraction of repetitive sequences. Here, using yeast cells as a model system, we analyzed the integrity of repetitive sequences and found CAG repeat instability is promoted by transcription per se and is dependent on the length of repetitive sequence. This DNA instability is ameliorated by ectopic expression of multiple proteins that bear the enzymatic activity to resolve R-loops. Additionally, we discovered the extent of DNA instability is influenced by the composition of nucleotide sequences. Furthermore, we found a differential effect of transcription elongation factors on the DNA instability of CAG repeats. Our collected results demonstrated the causal effect of R-loops on TNR instability, and also revealed the contribution of transcription elongation factors and TNR nucleotide sequences to this transcription-induced DNA instability.
CHEN, QING=REN, and 陳慶任. "Studies on the repetitive sequences of holstein cattle genomic DNA." Thesis, 1992. http://ndltd.ncl.edu.tw/handle/78021743576368953355.
Full text國立中興大學
畜牧研究所
80
DNA 重複序列遍存於真核生物基因組中,已有研究者以重複序列DNA 為探針,應用 於DNA 指紋分析。本研究之目的在於探討乳牛基因組DNA 重複序列之性質,並探討 其應用於DNA 指紋法分析之可行性。同時也以商品化之人33.15 探針與荷蘭牛、豬 、雞及小鼠之基因組DNA 雜交,進行DNA 指紋分析,供對照之用。 試驗分三部分進行。第一部分,取荷蘭牛基因組DNA ,以Pst Ⅰ切割,經膠體電泳 後,在膠片上形成7條明顯的DNA環帶,並回收其第6條環帶(0.7kb) DNA,架構入 pUC18 內,利用X-gal 及碎裂法快速偵測出重組質體,然後進行DNA 序列分析,再 將之與限制切割之荷蘭牛、豬、雞及小鼠之基因組DNA 進行初步雜交試驗,以探 討其重複序列及其應用於DNA 指紋法分析之可行性。第二部分,取本研究室篩選到 並已接在pUC18 內之牛、豬、雞及小鼠之基因組DNA 片段進行初步雜交試驗,若有 多態性產生,則再進一步分析其DNA 重複序列及其應用於DNA 指紋法分析之可行性 。本試驗也應用人33.15 探針,與經限制切割、電泳及轉漬之荷蘭牛、豬、雞及 小鼠之基因組DNA 雜交,進行DNA 指紋分析法,並將牛α s1-酪蛋白基因之DNA 片 段與之作點雜交,以探討牛α s1-酪蛋白基因之DNA 片段是否與人33.15 探針具有 同源性關係。 試驗結果顯示,牛基因組DNA經PstⅠ處理,回收之第6條環帶之重組質體DNA 探針 ,與經不同濃度之PstⅠ限制切割之荷蘭牛基因組DNA雜交,在X-光片上呈現不同 濃度之梯狀分佈之雜交環帶,顯示該部分之DNA 是由聚合態(polymer) 分解成單一 態(monomer) ,且散佈在基因組中。經分析其DNA 序列,發現其為A+T-rich且其重 複序列大都屬於短核酸序列形態存在。在牛αs1-酪蛋白DNA重複序列之研究中, 發現5'端之0.9 kb之DNA 片段序列中,有4段重複序列,每段長為74-103 bp ,其 氮鹼基組成G+C 佔大部分。利用人33.15 探針與荷蘭牛、豬、雞及小鼠等經限制 切割後之基因組DNA 雜交,結果,發現部份有多態性出現。以人33.15 探針與牛α s1-酪蛋白基因17個分殖DNA片段雜交的結果,發現其中有6個極強之訊息,顯示其 中部份序列與人33.15 探針DNA 序列具有一致之相似性。
Hsin-Yi, Hu, and 胡欣怡. "Isolation and characterization of repetitive DNA sequences in Phalaenopsis orchids." Thesis, 2001. http://ndltd.ncl.edu.tw/handle/60503393325791691495.
Full text國立臺灣大學
植物學研究所
89
Two clones containing repetitive DNA sequences, pvr1-96 and pvr1-57, were isolated from Phalaenopsis violacea and characterized. The insert of pvr1-96 (3838 bp) consists of (ATAAGTC)432 central core flanking by 636 bp and 171 bp nonrepetitive sequence at the 5' and 3' ends, respectively. The insert of pvr1-57 is 4175 bp long which shows high homology to part of the polyprotein (pol) gene of Ty3/gypsy type retrotransposon from other species. Using a 205-bp fragment in the 5' region of pvr1-57 as a probe, a clone pvr283 was isolated. Combining the insert sequences of pvr283 and pvr1-57 gives a 7571-bp sequence, named PVRE1. PVRE1 shares 52 % identity to the pol gene of the Ty3/gypsy type retrotransposon from Oryza sativa. However, several stop codons are present in the major open reading frame (ORF) of PVRE1 and there are no long terminal repeats (LTRs) flanking this sequence, suggesting that PVRE1 is inactive. Southern analysis revealed that PVRE1 is present in all eight Phalaenopsis species studied. Chromosome localization by fluorescence in situ hybridization revealed that PVRE1 is dispersed throughout the genome of P. aphrodite, P. lueddemanniana, P. venosa and P. violacea, with signals being stronger in AT-rich heterochromatic region of the large chromosomes of the later two species. PVRE1 is the first retrotransposon isolated from Phalaenopsis species.
Huang, Chien-Hao, and 黃建豪. "Isolation and characterization of two repetitive DNA sequences in Phalaenopsis orchids." Thesis, 1999. http://ndltd.ncl.edu.tw/handle/07985466772107743512.
Full text國立臺灣大學
植物學研究所
87
Two repetitive DNA sequences, PvrⅠand PvrⅡ, were isolated from Phalaenopsis violacea and characterized. The PvrⅠfamily consists of AT-rich regions at 5'' and 3'' ends and 7 bp direct subrepeats (GTAAGCC)13-22. Southern analysis and fluorescence in situ hybridization (FISH) revealed that PvrⅠ is present in P. mannii, P. amboinensis, P. venosa, P. violacea and Doritis pulcherrima and mostly located in the AT-rich subtelomeric heterochromatin of large chromosomes. The PvrⅡ family is present in all eight Phalaenopsis species studied. FISH using one clone (Pvr-95) as a probe showed that PvrⅡis dispersed on all chromosomes of P. venosa.
趙培錡. "Thermodynamic Studies of Human Centromere Repetitive DNA Sequences Containing Unusual Shearing Base Pairs." Thesis, 1998. http://ndltd.ncl.edu.tw/handle/57778653732923532948.
Full textHsu, Fu-Chen, and 許富誠. "Molecular structures of TR-1 repetitive DNA sequences in maize and its relatives." Thesis, 2001. http://ndltd.ncl.edu.tw/handle/19533119534341576890.
Full text國立臺灣大學
植物學研究所
89
Heterochromatic knobs are enlarged and deeply stained regions in prophase chromosomes of maize. The main genetic effects of knobs are (1) neocentromere activity and (2) chromatin elimination. Two classes of tandemly repeated sequences associated with knobs have been isolated from the maize genome, the 180-bp repeat and TR-1 element (350-bp). Two segments (12 bp and 31 bp) in these repeats show homology of more than 60%, and the 180-bp repeat has a 72% similarity to a 90-bp stretch of the maize B chromosome centromere sequence. It has been suggested that the 180-bp repeat may be responsible for neocentromere activity. The 180-bp repeat has been extensively studied in maize and its relatives, but the molecular structure of the TR-1 element is not clear. In this study, we isolated TR-1 elements from various lines of maize and its relatives and analysed their structures. Our results demonstrates that TR-1 element is composed of A, B/B’, C repeats, and the unit length is 180 bp but not 350 bp as previously reported. There are some homology between segments of B/B’ and the 180-bp repeat, so we presume that 180-bp repeat is the ancestor of B/B’. The following reasons suggest that C+A may be actually a class of repetitive sequence with a unit length of 180 bp: (1) A and C show high homology in nucleotide sequences; (2) C is always before A in the clones analysed; (3) A and C have the same percentage (approximately 70%) of A+T. The role of TR-1 in neocentromere activity and the mechanism of the formation of TR-1 are discussed.
Ying-FanChen and 陳盈帆. "Study of the impact of genomic repetitive sequences and DNA methylation on gene expression." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/26940216560895395915.
Full text國立成功大學
基礎醫學研究所
98
Human genome contains more than 50% proportion of repetitive DNA sequences, mostly involved chromosome structural diversity. The objective of this dissertation is to study of the impact of genomic repetitive sequences and DNA methylation on gene expression. Low copy repeat (LCR) is a new class of repetitive DNA element and has been implicated in many human disorders through non-allelic homologous recombination mechanism. In order to dissect and refine region-specific LCRs, we downloaded and analyzed the publicly available human genome sequences using computational approaches. We further took the common deletion region in chromosome 22q11.2 as an example to illustrate the use of real-time quantitative PCR assay to detect micro deletion in this region. The assay was validated in 122 patients with suspected DiGeorge/velocardiofacial (DGS/VCFS) syndromes. Our results indicated that the developed assay is reliable for clinical diagnosis. In addition, global hypomethylation of repetitive genomic sequences such as long interspersed nuclear element 1 (LINE-1), SINE-Alu and alpha-satellite (?-satellite) sequences has been associated with chromosomal instability in cancers. In addition, it has been reported that Epstein-Barr virus (EBV) promotes genomic instability in Burkitt's lymphoma and nasopharyngeal carcinoma (NPC). Thus, we investigated the methylation status of high repetitive genomic sequences under the expressions of different EBV proteins, and the impact on gene expression. EBV alternates between latency and lytic replication, and the lytic cycle is initiated when epigenetic silencing is reversed by Zta protein. We first examined methylation levels in a Zta-expression model to determine the genomic methylation of NPC cells upon EBV reactivation. Our data suggest that alteration of NPC cellular gene expression following EBV reactivation reflects methylation-independent Zta-mediated gene activation and not epigenetic modification of the host genome. Next, we analyzed the whole genome methylation profile in EBV-encoded oncoprotein latent membrane protein (LMP1)-expressing BJAB cells. By using methylation-sensitive NotI restriction enzyme, we studied promoter methylation pattern of individual genes at genomic scale. Although the overall methylation content was not changed dramatically, it reshuffled methylation marks of individual genes and specific regions including overmethylation of LINE-1, hypomethylation of ?-satellite, and unbalanced X chromosome inactivation. Overall, these data consist with the result that LMP1 increases DNMT3b expression. Furthermore, our data demonstrated the genes where expression level was significantly altered in BJAB-LMP1 cells are highly associated with cell cycle regulation and the biological markers of lymphoma. Finally, our data suggested that alteration of gene expression observed in BJAB-LMP1 cells is not through the change in promoter methylation. Rather, LMP1-mediated signaling may play significant role in eliciting host gene expression during EBV infection.