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Journal articles on the topic 'Repetitive DNA elements'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

Liehr, Thomas. "Repetitive Elements in Humans." International Journal of Molecular Sciences 22, no. 4 (February 19, 2021): 2072. http://dx.doi.org/10.3390/ijms22042072.

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Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called ‘genetic background’, being able to at least potentially influence disease susceptibilities. Here, the known ‘bad boys’ among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.

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2

Papin, Christophe, Abdulkhaleg Ibrahim, Stéphanie Le Gras, Amandine Velt, Isabelle Stoll, Bernard Jost, Hervé Menoni, Christian Bronner, Stefan Dimitrov, and Ali Hamiche. "Combinatorial DNA methylation codes at repetitive elements." Genome Research 27, no. 6 (March 27, 2017): 934–46. http://dx.doi.org/10.1101/gr.213983.116.

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3

Requena, J. M., M. C. López, and C. Alonso. "Genomic repetitive DNA elements of Trypanosoma cruzi." Parasitology Today 12, no. 7 (July 1996): 279–83. http://dx.doi.org/10.1016/0169-4758(96)10024-7.

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4

Surzycki, Stefan A., and William R. Belknap. "Characterization of Repetitive DNA Elements in Arabidopsis." Journal of Molecular Evolution 48, no. 6 (June 1999): 684–91. http://dx.doi.org/10.1007/pl00006512.

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5

Lower, Sarah E., Anne-Marie Dion-Côté, Andrew G. Clark, and Daniel A. Barbash. "Special Issue: Repetitive DNA Sequences." Genes 10, no. 11 (November 6, 2019): 896. http://dx.doi.org/10.3390/genes10110896.

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Repetitive DNAs are ubiquitous in eukaryotic genomes and, in many species, comprise the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNAs are often ignored in genomic studies due to technical challenges in identifying, assembling, and quantifying them. New technologies and methods are now allowing unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNAs are of particular interest because they can represent distinct modes of genome evolution. Some repetitive DNAs form essential genome structures, such as telomeres and centromeres, that are required for proper chromosome maintenance and segregation, while others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and cause genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. However, even these “neutral” repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.

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6

Serakıncı, N., B. Pedersen, and J. Koch. "Expansion of repetitive DNA into cytogenetically visible elements." Cytogenetic and Genome Research 92, no. 3-4 (2001): 182–85. http://dx.doi.org/10.1159/000056899.

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7

Fried, Claudia, Sonja J. Prohaska, and Peter F. Stadler. "Exclusion of repetitive DNA elements from gnathostomeHox clusters." Journal of Experimental Zoology 302B, no. 2 (2004): 165–73. http://dx.doi.org/10.1002/jez.b.20007.

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8

Deininger, Prescott L., and Gary R. Daniels. "The recent evolution of mammalian repetitive DNA elements." Trends in Genetics 2 (January 1986): 76–80. http://dx.doi.org/10.1016/0168-9525(86)90183-6.

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9

Bollati, V., D. Galimberti, L. Pergoli, E. Dalla Valle, F. Barretta, F. Cortini, E. Scarpini, P. A. Bertazzi, and A. Baccarelli. "DNA methylation in repetitive elements and Alzheimer disease." Brain, Behavior, and Immunity 25, no. 6 (August 2011): 1078–83. http://dx.doi.org/10.1016/j.bbi.2011.01.017.

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10

Lo, Cecilia W. "Novel approach for restriction mapping repetitive DNA elements using DNA transformation." Somatic Cell and Molecular Genetics 11, no. 5 (September 1985): 455–65. http://dx.doi.org/10.1007/bf01534839.

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11

Zhao, Xinping, Rod A. Wing, and Andrew H. Paterson. "Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.)." Genome 38, no. 6 (December 1, 1995): 1177–88. http://dx.doi.org/10.1139/g95-156.

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Repetitive DNA elements representing 60–70% of the total repetitive DNA in tetraploid cotton (Gossypium barbadense L.) and comprising 30–36% of the tetraploid cotton genome were isolated from a genomic library of DNA digested with a mixture of four blunt-end cutting restriction enzymes. A total of 313 clones putatively containing nuclear repetitive sequences were classified into 103 families, based on cross hybridization and Southern blot analysis. The 103 families were characterized in terms of genome organization, methylation pattern, abundance, and DNA variation. As in many other eukaryotic genomes, interspersed repetitive elements are the most abundant class of repetitive DNA in the cotton genome. Paucity of tandem repeat families with high copy numbers (>104) may be a unique feature of the cotton genome as compared with other higher plant genomes. Interspersed repeats tend to be methylated, while tandem repeats seem to be largely unmethylated in the cotton genome. Minimal variation in repertoire and overall copy number of repetitive DNA elements among different tetraploid cotton species is consistent with the hypothesis of a relatively recent origin of tetraploid cottons.Key words: genome analysis, genome evolution, tandemly repetitive DNA sequences, interspersed repetitive DNA sequences, polyploid.

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12

Bachellier, Sophie, Jean-Marie Clément, and Maurice Hofnung. "Short palindromic repetitive DNA elements in enterobacteria: a survey." Research in Microbiology 150, no. 9-10 (November 1999): 627–39. http://dx.doi.org/10.1016/s0923-2508(99)00128-x.

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13

SIBSON, D. R., S. G. HUGHES, J. A. BRYANT, and P. N. FITCHETT. "Sequence Organization of Simple, Highly Repetitive DNA Elements inBrassicaspecies." Journal of Experimental Botany 42, no. 2 (1991): 243–49. http://dx.doi.org/10.1093/jxb/42.2.243.

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14

Zheng, Yinan, Brian T. Joyce, Lei Liu, Zhou Zhang, Warren A. Kibbe, Wei Zhang, and Lifang Hou. "Prediction of genome-wide DNA methylation in repetitive elements." Nucleic Acids Research 45, no. 15 (July 7, 2017): 8697–711. http://dx.doi.org/10.1093/nar/gkx587.

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15

Huda, Ahsan, Leonardo Mariño-Ramírez, David Landsman, and I. King Jordan. "Repetitive DNA elements, nucleosome binding and human gene expression." Gene 436, no. 1-2 (May 2009): 12–22. http://dx.doi.org/10.1016/j.gene.2009.01.013.

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16

Suyama, Mikita, Warren C. Lathe, and Peer Bork. "Palindromic repetitive DNA elements with coding potential inMethanocaldococcus jannaschii." FEBS Letters 579, no. 24 (September 12, 2005): 5281–86. http://dx.doi.org/10.1016/j.febslet.2005.08.051.

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17

Ahmad, Syed Farhan, Worapong Singchat, Thitipong Panthum, and Kornsorn Srikulnath. "Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution." Cells 10, no. 7 (July 6, 2021): 1707. http://dx.doi.org/10.3390/cells10071707.

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The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

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18

Fabris, Sonia, Valentina Bollati, Laura Mosca, Valeria Pegoraro, Domenica Ronchetti, Gabriella Ciceri, Luca Baldini, et al. "Repetitive DNA Hypomethylation in Multiple Myeloma." Blood 112, no. 11 (November 16, 2008): 2703. http://dx.doi.org/10.1182/blood.v112.11.2703.2703.

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Abstract Multiple myeloma (MM) is a malignant proliferation of bone marrow plasma cells characterized by a wide spectrum of genetic and epigenetic changes. Global hypomethylation of repetitive genomic sequences such as long interspersed nuclear elements-1 (LINE-1) and Alu repetitive elements (approximately 500.000 and 1.4 million in the human genome) has been associated with chromosomal instability. Additionally, satellite alfa DNA (SAT-alpha DNA) hypomethylation has been reported to be associated to karyotypic instability in human cancer, possibly playing a role in centromere function. So far, the LINE-1/Alu and centromeric SAT-alpha DNA methylation patterns have not been investigated in the context of the different clinical and molecular MM subtypes. Global DNA methylation changes were investigated in a panel of 53 newly diagnosed, untreated MMs, 7 plasma cell leukemias (PCL) and 11 healthy subjects as controls. DNA was extracted from purified plasma cells, treated with bisulfite and analyzed by bisulfite-PCR and Pyrosequencing. Methylation of LINE-1 and Alu elements was shown to correlate with total 5mC content and thus used to estimate global DNA methylation. MMs showed a decrease of Alu (21.1%) and LINE-1 (70.0%) methylation average levels compared with controls (25.2% and 79.5% respectively). Lower median methylation levels were also found in centromeric SAT-alpha DNA of MMs (77.95%) compared to controls (89.5%). The median methylation level of PCLs was lower than MMs (16.7% versus 21.1% for Alu; 45.5% versus 70.0% for LINE-1; and 33.3% versus 77.9% for SATalpha DNA). Notably, a statistically significant association between SAT-alpha DNA and LINE-1 methylation (Spearman’s rank correlation, ρ = 0.94; P < 0.001) was found in MM. The comparison between methylation pattern and different molecular MM subgroups by means of non parametric tests, revealed that LINE-1 and SAT-alpha DNA methylation was significantly lower in the nonhyperdiploid versus hyperdiploid (HD) tumors (P = 0.01 and 0.02 respectively). Alu and SAT-alpha were significantly lower in the MMs with t(4;14) (P = 0.02 and 0.004 respectively). Finally, in the context of translocation/cyclin D (TC) classification, a statistically significant differences inside the five different groups were found for SAT-alpha DNA methylation (P = 0.008, Kruskal-Wallis test). These findings may provide insights into the molecular mechanisms of MM pathogenesis and suggest that our approach may contribute toward a more exhaustive stratification of the disease.

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19

Hankeln, Thomas, Angela Rohwedder, Bettina Weich, and Erwin R. Schmidt. "Transposition of minisatellite-like DNA in Chironomus midges." Genome 37, no. 4 (August 1, 1994): 542–49. http://dx.doi.org/10.1139/g94-077.

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Cla elements are a family of tandem repetitive DNA sequences present in the genome of several Chironomus species. Interspersed clusters of Cla elements are widely distributed all over the chromosomes in C. thummi thummi, while they seem to be limited to the centromeric regions in the closely related subspecies C. t. piger. Here we present molecular evidence that this differential distribution is due to a transposition of Cla elements during evolution of the C. t. thummi genome. We have cloned a "filled" integration site (containing a Cla element cluster) from C. t. thummi and the corresponding "empty" genomic site from C. t. piger and other related species. The comparison shows that tandem repetitive elements may be mobilized together with flanking DNA.Key words: minisatellites, transposition, Chironomus.

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20

Surzycki, S. A., and W. R. Belknap. "Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes." Proceedings of the National Academy of Sciences 97, no. 1 (January 4, 2000): 245–49. http://dx.doi.org/10.1073/pnas.97.1.245.

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21

KUBIS, S. "Repetitive DNA Elements as a Major Component of Plant Genomes." Annals of Botany 82 (December 1998): 45–55. http://dx.doi.org/10.1006/anbo.1998.0779.

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22

Choi, Si Ho, Hyang-Min Byun, Jia Yi Jiang, Guillermo Garcia-Manero, and Allen S. Yang. "Changes in DNA Methylation of Repetitive Elements during the Progression of Chronic Myelogenous Leukemia." Blood 108, no. 11 (November 16, 2006): 4302. http://dx.doi.org/10.1182/blood.v108.11.4302.4302.

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Abstract Epigenetic changes are a common finding in cancer, and promoter hypermethylation of tumor suppressor genes leads to aberrant gene silencing. In contrast to gene promoter hypermethylation, global hypomethylation is also a well-described phenomenon in cancer. Measurement of total 5-methylcytosine in the DNA show decreases in cancer despite increases in gene specific methylation. This discrepancy can be accounted for by the decrease of DNA methylation found in DNA repetitive elements, which make up approximately over half of the human genome. Decreases in repetitive element DNA methylation are a sensitive surrogate marker of global methylation, and have been used to measure DNA methylation changes induced by chemotherapy, dietary folate and environmental exposure. Decreases in LINE1 methylation have been described in numerous human cancers. In CML decrease in LINE1 methylation has been associated with progression to blast crisis. We investigated the DNA methylation changes of DNA repetitive elements in CML during the progression of CML from chronic phase to accelerated phase and finally blast crisis. We used a previously described assay (Yang et al. 2004) employing Bisulfite-PCR Pyrosequencing to quantitatively study the DNA methylation changes associated with the LINE1, Alu, D4Z4, and NBL-2 repetitive elements (See table). LINE1 and Alu hypomethylation was significantly associated with the progression of CML. Surprisingly, we found that NBL-2 and D4Z4 hypermethylation significantly increased during the progression of CML. Interestingly, these two repetitive elements were found to be specifically hypomethylated in immunodeficiency, centromeric instability and facial abnormalities (ICF) syndrome which is caused by a germline mutation of DNA methyltransferase 3b (DNMT3b) (Kondo T et al, 2000). This result suggests that DNMT3b may be involved in the progression of CML. DNA methylation (Mean ± S.E.M) Repetitive Elements Normal Chronic Phase Accelerated Phase Blast Crisis LINE1 32.4 ± 1.3 29.3 ± 0.6 27.8 ± 0.8 28.3 ± 0.8 Alu 79.4 ± 1.1 77.9 ± 0.6 77.6 ± 0.9 77.5 ± 0.8 D4Z4 47.9 ± 2.9 49.0 ± 1.1 52.9 ± 1.4 57.5 ± 2.0 NBL-2 71.7 ± 2.2 71.7 ± 0.7 75.9 ± 1.3 77.2 ± 1.6

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23

Foster, E., J. Hattori, P. Zhang, H. Labbé, T. Martin-Heller, J. Li-Pook-Than, T. Ouellet, K. Malik, and B. Miki. "The new RENT family of repetitive elements in Nicotiana species harbors gene regulatory elements related to the tCUP cryptic promoter." Genome 46, no. 1 (February 1, 2003): 146–55. http://dx.doi.org/10.1139/g02-102.

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The tCUP cryptic constitutive promoter was discovered in the tobacco genome by T-DNA (transfer DNA) tagging with a promoterless GUSnos gene. Here, we show that the portion of the tCUP sequence containing a variety of cryptic gene regulatory elements is related to a new family of moderately repetitive sequences (102 copies), the RENT (repetitive element from Nicotiana tabacum) family. The RENT family is found only in certain Nicotiana species. Five RENT elements were cloned and sequenced. The RENT elements are a minimum of 5 kb in length and share 8090% sequence similarity throughout their length. The 5' termini are the same in the isolated RENT family members and are characterized by a conserved border sequence (TGTTGA(T or C)ACCCAATTTT(T or C)). The 3' ends of RENT sequence similarity vary in location and sequence. The tCUP cryptic promoter originated from a unique truncated RENT element that interrupts a phytochelatin synthase-like gene that may have undergone rearrangements prior to or resulting from T-DNA insertion. No evidence was found for expressed coding regions within the RENT elements; however, like the cryptic gene regulatory elements within the tCUP sequence, the isolated RENT elements possess promoter activity and translational enhancer activity.Key words: cryptic promoter, Nicotiana, T-DNA, translational enhancer, repetitive element.

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24

Zwick, Michael S., Robert E. Hanson, M. Nurul Islam-Faridi, David M. Stelly, Rod A. Wing, H. James Price, and Thomas D. McKnight. "A rapid procedure for the isolation of C0t-1 DNA from plants." Genome 40, no. 1 (February 1, 1997): 138–42. http://dx.doi.org/10.1139/g97-020.

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In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

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25

Wickstead, Bill, Klaus Ersfeld, and Keith Gull. "Repetitive Elements in Genomes of Parasitic Protozoa." Microbiology and Molecular Biology Reviews 67, no. 3 (September 2003): 360–75. http://dx.doi.org/10.1128/mmbr.67.3.360-375.2003.

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SUMMARY Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility.

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26

Mossie, Kevin G., Michael W. Young, and Harold E. Varmus. "Extrachromosomal DNA forms of copia-like transposable elements, F elements and middle repetitive DNA sequences in Drosophila melanogaster." Journal of Molecular Biology 182, no. 1 (March 1985): 31–43. http://dx.doi.org/10.1016/0022-2836(85)90025-7.

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27

Tang, Zong-Xiang, Shu-Lan Fu, Zheng-Long Ren, Tao Zhang, Yu-Ting Zou, Zu-Jun Yang, Guang-Rong Li, et al. "Diversity and evolution of four dispersed repetitive DNA sequences in the genus Secale." Genome 54, no. 4 (April 2011): 285–300. http://dx.doi.org/10.1139/g10-118.

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We present the first characterization of 360 sequences in six species of the genus Secale of both cultivated and wild accessions. These include four distinct kinds of dispersed repetitive DNA sequences named pSc20H, pSc119.1, pSaO5411, and pSaD15940 belonging to the Revolver family. During the evolution of the genus Secale from wild to cultivated accessions, the pSaO5411-like sequences became shorter mainly because of the deletion of a trinucleotide tandem repeating unit, the pSc20H-like sequences displayed apparent homogenization in cultivated rye, and the second intron of Revolver became longer. In addition, the pSc20H-, pSc119.1-, and pSaO5411-like sequences cloned from wild rye and cultivated rye could be divided into two large clades. No single case of the four kinds of repetitive elements has been inherited by each Secale accession from a lone ancestor. It is reasonable to consider the vertical transmission of the four repetitive elements during the evolution of the genus Secale. The pSc20H- and pSaO5411-like sequences showed evolutionary elimination at specific chromosomal locations from wild species to cultivated species. These cases imply that different repetitive DNA sequences have played different roles in the chromosome development and genomic evolution of rye. The present study adds important information to the investigations dealing with characterization of dispersed repetitive elements in wild and cultivated rye.

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28

Kato, S., R. A. Anderson, and R. D. Camerini-Otero. "Foreign DNA introduced by calcium phosphate is integrated into repetitive DNA elements of the mouse L cell genome." Molecular and Cellular Biology 6, no. 5 (May 1986): 1787–95. http://dx.doi.org/10.1128/mcb.6.5.1787.

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We investigated the sites of integration of exogenous DNA fragments introduced by DNA-mediated gene transfer. Mouse Ltk- cells were transformed with the herpes simplex virus thymidine kinase gene and pBR322 DNA by the calcium phosphate precipitation method. Some of the integrated exogenous DNA sequences were recovered from the stable tk+ transformants in the form of plasmids that were capable of propagation in bacteria. Four plasmids derived from two cloned cell lines were analyzed in detail by nucleotide sequencing and hybridization techniques. These plasmids contained a total of seven cellular-exogenous DNA junctions. In all cases, there was no sequence homology between the exogenous and cellular DNA sequences adjacent to the joining sites, and no specific exogenous or cellular sequences occurred at the junctions. Rearrangement or deletion of Ltk- DNA was always associated with the integration of exogenous DNA. All of the assignable cellular sequences at the junctions were repetitive sequences. Two of these sequences were from the MIF-1 repetitive sequence family, and a third consisted of a 40-base pair simple copolymer of alternating deoxyadenosine-deoxythymidine. Our results suggest that repetitive sequences are relatively favorable sites for the integration of exogenous DNA.

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Kato, S., R. A. Anderson, and R. D. Camerini-Otero. "Foreign DNA introduced by calcium phosphate is integrated into repetitive DNA elements of the mouse L cell genome." Molecular and Cellular Biology 6, no. 5 (May 1986): 1787–95. http://dx.doi.org/10.1128/mcb.6.5.1787-1795.1986.

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We investigated the sites of integration of exogenous DNA fragments introduced by DNA-mediated gene transfer. Mouse Ltk- cells were transformed with the herpes simplex virus thymidine kinase gene and pBR322 DNA by the calcium phosphate precipitation method. Some of the integrated exogenous DNA sequences were recovered from the stable tk+ transformants in the form of plasmids that were capable of propagation in bacteria. Four plasmids derived from two cloned cell lines were analyzed in detail by nucleotide sequencing and hybridization techniques. These plasmids contained a total of seven cellular-exogenous DNA junctions. In all cases, there was no sequence homology between the exogenous and cellular DNA sequences adjacent to the joining sites, and no specific exogenous or cellular sequences occurred at the junctions. Rearrangement or deletion of Ltk- DNA was always associated with the integration of exogenous DNA. All of the assignable cellular sequences at the junctions were repetitive sequences. Two of these sequences were from the MIF-1 repetitive sequence family, and a third consisted of a 40-base pair simple copolymer of alternating deoxyadenosine-deoxythymidine. Our results suggest that repetitive sequences are relatively favorable sites for the integration of exogenous DNA.

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30

Gursel, Ihsan, Mayda Gursel, Hiroshi Yamada, Ken J. Ishii, Fumihiko Takeshita, and Dennis M. Klinman. "Repetitive Elements in Mammalian Telomeres Suppress Bacterial DNA-Induced Immune Activation." Journal of Immunology 171, no. 3 (July 21, 2003): 1393–400. http://dx.doi.org/10.4049/jimmunol.171.3.1393.

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31

Liang, Gangning, Matilda F. Chan, Yoshitaka Tomigahara, Yvonne C. Tsai, Felicidad A. Gonzales, En Li, Peter W. Laird, and Peter A. Jones. "Cooperativity between DNA Methyltransferases in the Maintenance Methylation of Repetitive Elements." Molecular and Cellular Biology 22, no. 2 (January 15, 2002): 480–91. http://dx.doi.org/10.1128/mcb.22.2.480-491.2002.

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ABSTRACT We used mouse embryonic stem (ES) cells with systematic gene knockouts for DNA methyltransferases to delineate the roles of DNA methyltransferase 1 (Dnmt1) and Dnmt3a and -3b in maintaining methylation patterns in the mouse genome. Dnmt1 alone was able to maintain methylation of most CpG-poor regions analyzed. In contrast, both Dnmt1 and Dnmt3a and/or Dnmt3b were required for methylation of a select class of sequences which included abundant murine LINE-1 promoters. We used a novel hemimethylation assay to show that even in wild-type cells these sequences contain high levels of hemimethylated DNA, suggestive of poor maintenance methylation. We showed that Dnmt3a and/or -3b could restore methylation of these sequences to pretreatment levels following transient exposure of cells to 5-aza-CdR, whereas Dnmt1 by itself could not. We conclude that ongoing de novo methylation by Dnmt3a and/or Dnmt3b compensates for inefficient maintenance methylation by Dnmt1 of these endogenous repetitive sequences. Our results reveal a previously unrecognized degree of cooperativity among mammalian DNA methyltransferases in ES cells.

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32

Vilahur, Nadia, Hyang-Min Byun, Mariona Bustamante, Marina Vafeiadi, Raquel Garcia, Xavier Estivill, Mariana F. Fernandez, Andrea A. Baccarelli, and Jordi Sunyer. "Prenatal exposure to xenoestrogens and placental DNA methylation of repetitive elements." ISEE Conference Abstracts 2013, no. 1 (September 19, 2013): 5293. http://dx.doi.org/10.1289/isee.2013.p-2-13-17.

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Ferreira, Alda Maria T., SÃ©rgio Suzart, Odilon Vidotto, Don P. Knowles, and Marilda C. Vidotto. "Use of repetitive DNA elements to define genetic relationships amongAnaplasma marginaleisolates." FEMS Microbiology Letters 197, no. 2 (April 2001): 139–43. http://dx.doi.org/10.1111/j.1574-6968.2001.tb10595.x.

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34

Fatyol, K., K. Illies, A. A. Szalay, D. C. Diamond, and C. Janish. "Mer22-related sequence elements form pericentric repetitive DNA families in primates." Molecular and General Genetics MGG 262, no. 6 (January 2000): 931–39. http://dx.doi.org/10.1007/pl00008661.

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35

Taboada, Xoana, Magalí Rey, Carmen Bouza, and Ana Viñas. "Cytogenomic analysis of several repetitive DNA elements in turbot ( Scophthalmus maximus )." Gene 644 (February 2018): 4–12. http://dx.doi.org/10.1016/j.gene.2017.12.013.

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36

Black, William C., and Karamjit S. Rai. "Genome evolution in mosquitoes: intraspecific and interspecific variation in repetitive DNA amounts and organization." Genetical Research 51, no. 3 (June 1988): 185–96. http://dx.doi.org/10.1017/s0016672300024289.

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SummaryDNA reassociation kinetics were used to determine the amounts and organization of repetitive and unique DNA in four mosquito species: Anopheles quadrimaculatus (Say), Culex pipiens (L.), Aedes albopictus (Skuse) and Ae. triseriatus (Say). Intraspecific variation in repetitive DNA amounts was examined in two geographic strains of Ae. albopictus fom Calcutta, India and the island of Mauritius. Repetitive and unique sequences in An. quadrimaculatus were distributed in a pattern of long period interspersion. Repetitive DNA in all other mosquito species exhibited a pattern of short period interspersion. The amounts of fold-back, middle repetitive, and highly repetitive sequences increased with genome size. The amount of foldback DNA increased at a much slower rate than the middle and highly repetitive sequences. Intraspecific variation in genome size in Ae. albopictus was due primarily to the amounts of highly repetitive DNA. S1 nuclease digestion of repetitive DNA in all species revealed a positive correlation between genome size and the proportion of the repetitive DNA consisting of short repeats. The amounts of long and short repeats increased with genome size but short repeats increased at a higher rate. The repetitive DNA of the Mauritius strain contained approximately 15% more short repeats than the Calcutta strain. These findings suggest that genome evolution in mosquitoes has resulted from changes in both the amounts and organization of repetitive elements.

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Grebenstein, Bärbel, Oliver Grebenstein, Wilhelm Sauer, and Vera Hemleben. "Distribution and complex organization of satellite DNA sequences in Aveneae species." Genome 39, no. 6 (December 1, 1996): 1045–50. http://dx.doi.org/10.1139/g96-131.

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Distribution, organization, and molecular analysis of four unrelated satellite DNA components in Aveneae species are described. Highly repeated DNA elements were cloned from Helictotrichon convolutum (CON1 and CON2) and Helictotrichon compression (COM1 and COM2). The lengths of the repeat monomers are 365 bp (CON1), 562 bp (CON2), 346 bp (COM1), and 476 bp (COM2). Similar repeats were detected by dot blots, Southern blots, and by DNA sequencing in other species of the genus Helictotrichon, in Aveneae species, and in species of the tribes Andropogoneae and Oryzeae. All four satellite DNAs are differently distributed in the taxonomic groups mentioned above. Remarkably, the longer elements are built up in a complex pattern of either shorter subrepeats arranged in tandem (COM2) or by duplications inserted into an original 369-bp element (CON2). Shorter representatives, 190 bp, similar to CON1 elements occur in Holcus species. In Koeleria species, COM1-related repeats are only 180 bp in length. No similarity was found among the sequences CON2, COM1, and COM2 or with sequences of other repetitive DNA elements of the grasses, but CON1 shows sequence similarity to an A genome specific repetitive DNA of Oryza (rice). Key words : genome evolution, grasses, Poaceae, repetitive DNA, wild oats.

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38

Izsvák, Zsuzsanna, Zoltan Ivics, and Perry B. Hackett. "Repetitive elements and their genetic applications in zebrafish." Biochemistry and Cell Biology 75, no. 5 (October 1, 1997): 507–23. http://dx.doi.org/10.1139/o97-045.

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Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.

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39

da Silva, Marcelo J., Raquel Fogarin Destro, Thiago Gazoni, Hideki Narimatsu, Paulo S. Pereira dos Santos, Célio F. B. Haddad, and Patricia P. Parise-Maltempi. "Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing." Cytogenetic and Genome Research 160, no. 3 (2020): 141–47. http://dx.doi.org/10.1159/000506531.

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Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.

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40

Francastel, Claire, and Frédérique Magdinier. "DNA methylation in satellite repeats disorders." Essays in Biochemistry 63, no. 6 (August 6, 2019): 757–71. http://dx.doi.org/10.1042/ebc20190028.

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Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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Matrajt, Mariana, Sergio O. Angel, Viviana Pszenny, Eduardo Guarnera, David S. Roos, and Juan C. Garberi. "Arrays of repetitive DNA elements in the largest chromosomes of Toxoplasma gondii." Genome 42, no. 2 (April 1, 1999): 265–69. http://dx.doi.org/10.1139/g98-120.

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A novel tandemly repeated DNA structure of Toxoplasma gondii that meets the requirements assigned for satellital DNA was characterized. A DNA fragment of 1002 bp contains two different elements of repetitive DNA families named ABGTg7 and ABGTg8.2. Both repeats are members of a more complex tandem structure where ABGTg7-like monomers can be arranged either as direct tandems or flanked by other related or non-related repeats. Pulse-field gel electrophoresis analysis showed that these repeats hybridize with the largest T. gondii chromosomes. Bal31 sensitivity assays indicated that these elements are located near the telomeres and along other regions too. Five genomic lambda phages were isolated and two different completed clusters of the repeated structure were analyzed.Key words: Toxoplasma gondii, tandem repeat, satellite DNA, molecular karyotype, telomere.

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Hartley, Gabrielle, and Rachel O’Neill. "Centromere Repeats: Hidden Gems of the Genome." Genes 10, no. 3 (March 16, 2019): 223. http://dx.doi.org/10.3390/genes10030223.

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Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.

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43

McKinnon, Christian, and Guy Drouin. "Chromatin diminution in the copepod Mesocyclops edax: elimination of both highly repetitive and nonhighly repetitive DNA." Genome 56, no. 1 (January 2013): 1–8. http://dx.doi.org/10.1139/gen-2012-0097.

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Chromatin diminution, a developmentally regulated process of DNA elimination, is found in numerous eukaryotic species. In the copepod Mesocyclops edax, some 90% of its genomic DNA is eliminated during the differentiation of embryonic cells into somatic cells. Previous studies have shown that the eliminated DNA contains highly repetitive sequences. Here, we sequenced DNA fragments from pre- and postdiminution cells to determine whether nonhighly repetitive sequences are also eliminated during the process of chromatin diminution. Comparative analyses of these sequences, as well as the sequences eliminated from the genome of the copepod Cyclops kolensis, show that they all share similar abundances of tandem repeats, dispersed repeats, transposable elements, and various coding and noncoding sequences. This suggests that, in the chromatin diminution observed in M. edax, both highly repetitive and nonhighly repetitive sequences are eliminated and that there is no bias in the type of nonhighly repetitive DNA being eliminated.

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44

Yang, A. S. "A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements." Nucleic Acids Research 32, no. 3 (February 13, 2004): 38e—38. http://dx.doi.org/10.1093/nar/gnh032.

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45

Neale, Rachel E., Paul J. Clark, Jonathan Fawcett, Lin Fritschi, Belinda N. Nagler, Harvey A. Risch, Rhiannon J. Walters, et al. "Association between hypermethylation of DNA repetitive elements in white blood cell DNA and pancreatic cancer." Cancer Epidemiology 38, no. 5 (October 2014): 576–82. http://dx.doi.org/10.1016/j.canep.2014.08.006.

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46

Smith, Cory J., Oscar Castanon, Khaled Said, Verena Volf, Parastoo Khoshakhlagh, Amanda Hornick, Raphael Ferreira, et al. "Enabling large-scale genome editing at repetitive elements by reducing DNA nicking." Nucleic Acids Research 48, no. 9 (April 21, 2020): 5183–95. http://dx.doi.org/10.1093/nar/gkaa239.

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Abstract To extend the frontier of genome editing and enable editing of repetitive elements of mammalian genomes, we made use of a set of dead-Cas9 base editor (dBE) variants that allow editing at tens of thousands of loci per cell by overcoming the cell death associated with DNA double-strand breaks and single-strand breaks. We used a set of gRNAs targeting repetitive elements—ranging in target copy number from about 32 to 161 000 per cell. dBEs enabled survival after large-scale base editing, allowing targeted mutations at up to ∼13 200 and ∼12 200 loci in 293T and human induced pluripotent stem cells (hiPSCs), respectively, three orders of magnitude greater than previously recorded. These dBEs can overcome current on-target mutation and toxicity barriers that prevent cell survival after large-scale genome engineering.

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47

Retterath, M. A., and J. J. Pasternak. "Genomic arrangement of repeated PS700 elements in the nematode Panagrellus silusiae." Genome 33, no. 2 (April 1, 1990): 164–69. http://dx.doi.org/10.1139/g90-027.

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When genomic DNA from the free-living nematode Panagrellus silusiae is digested with the restriction endonuclease BamHI and separated by electrophoresis, a band in the 700 base pair size range is evident after ethidium bromide staining. One of the 0.7-kilobase fragments (PS700-1) was characterized and found to be a member of a moderately repetitive DNA family (T. Warren and J.J. Pasternak. 1988. Nucleic Acids Res. 16: 10 833 – 10 847). In the current study, DNA sequence analyses of three independently isolated copies of the PS700 DNA family showed the same nucleotide sequence and >98% similarity to PS700-1. Four EMBL-4 bacteriophage clones were isolated from a Panagrellus genomic DNA library with PS700-1 as the probe and were analyzed by restriction endonuclease site mapping and Southern blot DNA hybridization. These clones contain 31 copies of the PS700 DNA family. In each case, the units are arranged in head-to-tail arrays. One of the EMBL-4 clones contains copies of a novel variant of the PS700 elements. The maintenance of both nucleotide sequence and restriction endonuclease restriction site homogeneity among members of the dispersed PS700 DNA family may denote a functional role for these sequences.Key words: nematode, Panagrellus, repetitive DNA organization, nucleotide sequence variation.

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48

Morton, Elizabeth A., Ashley N. Hall, Elizabeth Kwan, Calvin Mok, Konstantin Queitsch, Vivek Nandakumar, John Stamatoyannopoulos, Bonita J. Brewer, Robert Waterston, and Christine Queitsch. "Challenges and Approaches to Genotyping Repetitive DNA." G3: Genes|Genomes|Genetics 10, no. 1 (November 22, 2019): 417–30. http://dx.doi.org/10.1534/g3.119.400771.

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Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.

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Wöstemeyer, Johannes, and Anne Kreibich. "Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution." Current Genetics 41, no. 4 (July 1, 2002): 189–98. http://dx.doi.org/10.1007/s00294-002-0306-y.

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Walker, Jerilyn A., David A. Hughes, Dale J. Hedges, Bridget A. Anders, Meredith E. Laborde, Jaiprakash Shewale, Sudhir K. Sinha, and Mark A. Batzer. "Quantitative PCR for DNA identification based on genome-specific interspersed repetitive elements." Genomics 83, no. 3 (March 2004): 518–27. http://dx.doi.org/10.1016/j.ygeno.2003.09.003.

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