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Journal articles on the topic 'Vertebrate DNA'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Ahmad, Hafiz Ishfaq, Gulnaz Afzal, Sehrish Sadia, Ghulam Haider, Shakeel Ahmed, Saba Saeed, and Jinping Chen. "Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates." Oxidative Medicine and Cellular Longevity 2022 (April 4, 2022): 1–20. http://dx.doi.org/10.1155/2022/1144387.

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Oxidative stress is a type of stress that damages DNA and can occur from both endogenous and exogenous sources. Damage to DNA caused by oxidative stress can result in base modifications that promote replication errors and the formation of sites of base loss, which pose unique challenges to the preservation of genomic integrity. However, the adaptive evolution of the DNA repair mechanism is poorly understood in vertebrates. This research aimed to explore the evolutionary relationships, physicochemical characteristics, and comparative genomic analysis of the Nei-like glycosylase gene family involved in DNA base repair in the vertebrates. The genomic sequences of NEIL1, NEIL2, and NEIL3 genes were aligned to observe selection constraints in the genes, which were relatively low conserved across vertebrate species. The positive selection signals were identified in these genes across the vertebrate lineages. We identified that only about 2.7% of codons in these genes were subjected to positive selection. We also revealed that positive selection pressure was increased in the Fapy-DNA-glyco and H2TH domain, which are involved in the base excision repair of DNA that has been damaged by oxidative stress. Gene structure, motif, and conserved domain analysis indicated that the Nei-like glycosylase genes in mammals and avians are evolutionarily low conserved compared to other glycosylase genes in other “vertebrates” species. This study revealed that adaptive selection played a critical role in the evolution of Nei-like glycosylase in vertebrate species. Systematic comparative genome analyses will give key insights to elucidate the links between DNA repair and the development of lifespan in various organisms as more diverse vertebrate genome sequences become accessible.

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2

Carvalho, C. B. V. "DNA Barcoding in Forensic Vertebrate Species Identification." Brazilian Journal of Forensic Sciences, Medical Law and Bioethics 4, no. 1 (2014): 12–23. http://dx.doi.org/10.17063/bjfs4(1)y201412.

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3

Ortega-Recalde, Oscar, and Timothy Alexander Hore. "DNA methylation in the vertebrate germline: balancing memory and erasure." Essays in Biochemistry 63, no. 6 (November 22, 2019): 649–61. http://dx.doi.org/10.1042/ebc20190038.

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Abstract Cytosine methylation is a DNA modification that is critical for vertebrate development and provides a plastic yet stable information module in addition to the DNA code. DNA methylation memory establishment, maintenance and erasure is carefully balanced by molecular machinery highly conserved among vertebrates. In mammals, extensive erasure of epigenetic marks, including 5-methylcytosine (5mC), is a hallmark of early embryo and germline development. Conversely, global cytosine methylation patterns are preserved in at least some non-mammalian vertebrates over comparable developmental windows. The evolutionary mechanisms which drove this divergence are unknown, nevertheless a direct consequence of retaining epigenetic memory in the form of 5mC is the enhanced potential for transgenerational epigenetic inheritance (TEI). Given that DNA methylation dynamics remains underexplored in most vertebrate lineages, the extent of information transferred to offspring by epigenetic modification might be underestimated.

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4

Ross, Samuel E., Allegra Angeloni, Fan-Suo Geng, Alex de Mendoza, and Ozren Bogdanovic. "Developmental remodelling of non-CG methylation at satellite DNA repeats." Nucleic Acids Research 48, no. 22 (December 4, 2020): 12675–88. http://dx.doi.org/10.1093/nar/gkaa1135.

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Abstract In vertebrates, DNA methylation predominantly occurs at CG dinucleotides however, widespread non-CG methylation (mCH) has been reported in mammalian embryonic stem cells and in the brain. In mammals, mCH is found at CAC trinucleotides in the nervous system, where it is associated with transcriptional repression, and at CAG trinucleotides in embryonic stem cells, where it positively correlates with transcription. Moreover, CAC methylation appears to be a conserved feature of adult vertebrate brains. Unlike any of those methylation signatures, here we describe a novel form of mCH that occurs in the TGCT context within zebrafish mosaic satellite repeats. TGCT methylation is inherited from both male and female gametes, remodelled during mid-blastula transition, and re-established during gastrulation in all embryonic layers. Moreover, we identify DNA methyltransferase 3ba (Dnmt3ba) as the primary enzyme responsible for the deposition of this mCH mark. Finally, we observe that TGCT-methylated repeats are specifically associated with H3K9me3-marked heterochromatin suggestive of a functional interplay between these two gene-regulatory marks. Altogether, this work provides insight into a novel form of vertebrate mCH and highlights the substrate diversity of vertebrate DNA methyltransferases.

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Egeter, Bastian, Sara Peixoto, José C. Brito, Simon Jarman, Pamela Puppo, and Guillermo Velo-Antón. "Challenges for assessing vertebrate diversity in turbid Saharan water-bodies using environmental DNA." Genome 61, no. 11 (November 2018): 807–14. http://dx.doi.org/10.1139/gen-2018-0071.

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The Sahara desert is the largest warm desert in the world and a poorly explored area. Small water-bodies occur across the desert and are crucial habitats for vertebrate biodiversity. Environmental DNA (eDNA) is a powerful tool for species detection and is being increasingly used to conduct biodiversity assessments. However, there are a number of difficulties with sampling eDNA from such turbid water-bodies and it is often not feasible to rely on electrical tools in remote desert environments. We trialled a manually powered filtering method in Mauritania, using pre-filtration to circumvent problems posed by turbid water in remote arid areas. From nine vertebrate species expected in the water-bodies, four were detected visually, two via metabarcoding, and one via both methods. Difficulties filtering turbid water led to severe constraints, limiting the sampling protocol to only one sampling point per study site, which alone may largely explain why many of the expected vertebrate species were not detected. The amplification of human DNA using general vertebrate primers is also likely to have contributed to the low number of taxa identified. Here we highlight a number of challenges that need to be overcome to successfully conduct metabarcoding eDNA studies for vertebrates in desert environments in Africa.

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6

Varriale, Annalisa. "DNA Methylation, Epigenetics, and Evolution in Vertebrates: Facts and Challenges." International Journal of Evolutionary Biology 2014 (January 16, 2014): 1–7. http://dx.doi.org/10.1155/2014/475981.

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DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved in biological processes such as regulation of gene expression, DNA structure and control of transposable elements. Despite increasing knowledge about DNA methylation, we still lack a complete understanding of its specific functions and correlation with environment and gene expression in diverse organisms. To understand how global DNA methylation levels changed under environmental influence during vertebrate evolution, we analyzed its distribution pattern along the whole genome in mammals, reptiles and fishes showing that it is correlated with temperature, independently on phylogenetic inheritance. Other studies in mammals and plants have evidenced that environmental stimuli can promote epigenetic changes that, in turn, might generate localized changes in DNA sequence resulting in phenotypic effects. All these observations suggest that environment can affect the epigenome of vertebrates by generating hugely different methylation patterns that could, possibly, reflect in phenotypic differences. We are at the first steps towards the understanding of mechanisms that underlie the role of environment in molding the entire genome over evolutionary times. The next challenge will be to map similarities and differences of DNA methylation in vertebrates and to associate them with environmental adaptation and evolution.

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7

Carone, A., S. B. Malladi, M. Attimonelli, and C. Saccone. "Vertebrate MitBASE: a specialised database on vertebrate mitochondrial DNA sequences." Nucleic Acids Research 27, no. 1 (January 1, 1999): 150–52. http://dx.doi.org/10.1093/nar/27.1.150.

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8

Tweedie, S., J. Charlton, V. Clark, and A. Bird. "Methylation of genomes and genes at the invertebrate-vertebrate boundary." Molecular and Cellular Biology 17, no. 3 (March 1997): 1469–75. http://dx.doi.org/10.1128/mcb.17.3.1469.

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Patterns of DNA methylation in animal genomes are known to vary from an apparent absence of modified bases, via methylation of a minor fraction of the genome, to genome-wide methylation. Representative genomes from 10 invertebrate phyla comprise predominantly nonmethylated DNA and (usually but not always) a minor fraction of methylated DNA. In contrast, all 27 vertebrate genomes that have been examined display genome-wide methylation. Our studies of chordate genomes suggest that the transition from fractional to global methylation occurred close to the origin of vertebrates, as amphioxus has a typically invertebrate methylation pattern whereas primitive vertebrates (hagfish and lamprey) have patterns that are typical of vertebrates. Surprisingly, methylation of genes preceded this transition, as many invertebrate genes have turned out to be heavily methylated. Methylation does not preferentially affect genes whose expression is highly regulated, as several housekeeping genes are found in the heavily methylated fraction whereas several genes expressed in a tissue-specific manner are in the nonmethylated fraction.

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9

GRANTHAM, RICHARD. "CG doublet difficulties in vertebrate DNA." Nature 313, no. 6002 (February 1985): 437. http://dx.doi.org/10.1038/313437a0.

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10

MAX, EDWARD E. "CG doublet difficulties in vertebrate DNA." Nature 313, no. 6002 (February 1985): 437–38. http://dx.doi.org/10.1038/313437b0.

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11

Sonoda, E., M. Takata, Y. M. Yamashita, C. Morrison, and S. Takeda. "Homologous DNA recombination in vertebrate cells." Proceedings of the National Academy of Sciences 98, no. 15 (July 17, 2001): 8388–94. http://dx.doi.org/10.1073/pnas.111006398.

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12

Miskey, C., Z. Izsvák, K. Kawakami, and Z. Ivics. "DNA transposons in vertebrate functional genomics." Cellular and Molecular Life Sciences 62, no. 6 (March 2005): 629–41. http://dx.doi.org/10.1007/s00018-004-4232-7.

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13

Bernal, Juan A., and Ashok R. Venkitaraman. "A vertebrate N-end rule degron reveals that Orc6 is required in mitosis for daughter cell abscission." Journal of Cell Biology 192, no. 6 (March 21, 2011): 969–78. http://dx.doi.org/10.1083/jcb.201008125.

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Orc6, an evolutionarily conserved component of the origin recognition complex, is essential for deoxyribonucleic acid (DNA) replication initiation from yeast to humans. Whether vertebrate Orc6 has a mitotic function remains unresolved. In vertebrates, but not yeast, its depletion causes centrosome amplification and multinucleate division, but replication stress indirectly causes similar abnormalities. In this paper, we exploit Varshavsky’s N-end rule to create a temperature-sensitive degron form of avian Orc6. Orc6 depletion during the S phase triggers centrosome amplification suppressed by G2 checkpoint inhibition, reflecting an indirect consequence of aberrant DNA replication. However, Orc6 depletion during mitosis suffices to cause asymmetric division and failure in cytokinesis, with a delay in daughter cell abscission revealed by a fluorescence-bleaching assay. A mutant lacking the C-terminal 25 residues cannot rescue these defects. Thus, vertebrate Orc6 is necessary during mitosis for the abscission stage of cytokinesis. Our findings exemplify N-end rule degrons as tools to unravel functions of a single protein during different phases of the vertebrate cell cycle.

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14

Hopken, Matthew W., Limarie J. Reyes-Torres, Nicole Scavo, Antoinette J. Piaggio, Zaid Abdo, Daniel Taylor, James Pierce, and Donald A. Yee. "Temporal and Spatial Blood Feeding Patterns of Urban Mosquitoes in the San Juan Metropolitan Area, Puerto Rico." Insects 12, no. 2 (February 2, 2021): 129. http://dx.doi.org/10.3390/insects12020129.

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Urban ecosystems are a patchwork of habitats that host a broad diversity of animal species. Insects comprise a large portion of urban biodiversity which includes many pest species, including those that transmit pathogens. Mosquitoes (Diptera: Culicidae) inhabit urban environments and rely on sympatric vertebrate species to complete their life cycles, and in this process transmit pathogens to animals and humans. Given that mosquitoes feed upon vertebrates, they can also act as efficient samplers that facilitate detection of vertebrate species that utilize urban ecosystems. In this study, we analyzed DNA extracted from mosquito blood meals collected temporally in multiple neighborhoods of the San Juan Metropolitan Area, Puerto Rico to evaluate the presence of vertebrate fauna. DNA was collected from 604 individual mosquitoes that represented two common urban species, Culex quinquefasciatus (n = 586) and Aedes aegypti (n = 18). Culex quinquefasciatus fed on 17 avian taxa (81.2% of blood meals), seven mammalian taxa (17.9%), and one reptilian taxon (0.85%). Domestic chickens dominated these blood meals both temporally and spatially, and no statistically significant shift from birds to mammals was detected. Aedes aegypti blood meals were from a less diverse group, with two avian taxa (11.1%) and three mammalian taxa (88.9%) identified. The blood meals we identified provided a snapshot of the vertebrate community in the San Juan Metropolitan Area and have potential implications for vector-borne pathogen transmission.

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15

ELMORE, TAMARA, ANTONY RODRIGUEZ, and DEAN P. SMITH. "dRGS7 Encodes a Drosophila Homolog of EGL-10 and Vertebrate RGS7." DNA and Cell Biology 17, no. 11 (November 1998): 983–89. http://dx.doi.org/10.1089/dna.1998.17.983.

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16

Clayton, David A. "Replication and Transcription of Vertebrate Mitochondrial DNA." Annual Review of Cell Biology 7, no. 1 (November 1991): 453–78. http://dx.doi.org/10.1146/annurev.cb.07.110191.002321.

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17

Fisher, D. "Vertebrate HoxB gene expression requires DNA replication." EMBO Journal 22, no. 14 (July 15, 2003): 3737–48. http://dx.doi.org/10.1093/emboj/cdg352.

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18

Clayton, David A. "Vertebrate Mitochondrial DNA—A Circle of Surprises." Experimental Cell Research 255, no. 1 (February 2000): 4–9. http://dx.doi.org/10.1006/excr.1999.4763.

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19

Drinkwater, Rosie, Joseph Williamson, Elizabeth L. Clare, Arthur Y. C. Chung, Stephen J. Rossiter, and Eleanor Slade. "Dung beetles as samplers of mammals in Malaysian Borneo—a test of high throughput metabarcoding of iDNA." PeerJ 9 (August 13, 2021): e11897. http://dx.doi.org/10.7717/peerj.11897.

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Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a dung beetle digestive tract. We found that the ability to successfully amplify cattle DNA decayed over relatively short time periods, with DNA copy number decreasing by two orders of magnitude in just 6 h. In addition, we sampled communities of dung beetles from a lowland tropical rainforest in Sabah, Malaysia, in order to test whether it is possible to identify vertebrate sequences from dung beetle iDNA. We sequenced both the gut contents from large dung beetle species, as well as whole communities of smaller beetles. We successfully identified six mammalian species from our samples, including the bearded pig (Sus barbatus) and the sambar deer (Rusa unicolor)—both vulnerable species on the IUCN red list. Our results represent the first use of dung beetle iDNA to sample Southeast Asian vertebrate fauna, and highlight the potential for dung beetle iDNA to be used in future biodiversity monitoring surveys.

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20

Nelson, Joseph S. "The next 25 years: vertebrate systematics." Canadian Journal of Zoology 65, no. 4 (April 1, 1987): 779–85. http://dx.doi.org/10.1139/z87-124.

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Systematics, defined here as the study of the evolutionary history of life, plays a vital role in biology. Together with studies of evolutionary mechanisms, it gives special meaning to biology; it is the unifying force in biology. As a result of recent developments in techniques useful to systematics and in philosophical approaches to systematics, it will be possible for vertebrate systematics to make major advances. Comparative morphological studies of extant and extinct species will play the dominant role in our understanding of the overall pattern of vertebrate phylogeny. For extant species, data from immunological, electrophoretic, and amino acid sequence studies will be important, but the major advances will come from studies of mitochondrial DNA and DNA–DNA hybridization. Examples of phylogenetic controversies that should be resolved in the next 25 years concern the following: the ancestral group of jawed vertebrates, the relationships of Latimeria, the ancestral group of tetrapods, the interrelationships of birds and mammals to each other, and the closest living relatives of man. Both cladistic and synthetic classifications will survive; each serves a useful purpose in translating phylogenetic ideas. Systematics, together with evolution, is a fundamental aspect of biology and should be included in the undergraduate program of all biology students; all biology departments should have a research program in systematics involving graduate students and staff. In addition, museums are a vital part of biology departments, in both their teaching and research functions, and their existence within universities must be nourished.

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21

DIGBY, MATTHEW R., WAYNE G. KIMPTON, JENNIFER J. YORK, TERRI E. CONNICK, and JOHN W. LOWENTHAL. "ITA, a Vertebrate Homologue of IAP That Is Expressed in T Lymphocytes." DNA and Cell Biology 15, no. 11 (November 1996): 981–88. http://dx.doi.org/10.1089/dna.1996.15.981.

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22

Vinogradov, Alexander E. "Larger genomes for molluskan land pioneers." Genome 43, no. 1 (February 1, 2000): 211–12. http://dx.doi.org/10.1139/g99-063.

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The terrestrial pulmonate mollusks were found to have the significantly larger genomes than the aquatic pulmonates. Being shown in the independent phylogenetic branch, this phenomenon suggests that the previously observed genome enlargement in the vertebrate land pioneers (amphibians and lungfishes) was not casual. As in the vertebrates, the larger molluskan genomes are also more GC-rich. Key words: genome size, genome evolution, cytoecology, noncoding DNA, genome base composition, flow cytometry.

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23

KRAWETZ, STEPHEN A., WAYNE CONNOR, and GORDON H. DIXON. "Cloning of Bovine P1 Protamine cDNA and the Evolution of Vertebrate P1 Protamines." DNA 6, no. 1 (February 1987): 47–57. http://dx.doi.org/10.1089/dna.1987.6.47.

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24

Semlow, Daniel R., and Johannes C. Walter. "Mechanisms of Vertebrate DNA Interstrand Cross-Link Repair." Annual Review of Biochemistry 90, no. 1 (June 20, 2021): 107–35. http://dx.doi.org/10.1146/annurev-biochem-080320-112510.

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DNA interstrand cross-links (ICLs) covalently connect the two strands of the double helix and are extremely cytotoxic. Defective ICL repair causes the bone marrow failure and cancer predisposition syndrome, Fanconi anemia, and upregulation of repair causes chemotherapy resistance in cancer. The central event in ICL repair involves resolving the cross-link (unhooking). In this review, we discuss the chemical diversity of ICLs generated by exogenous and endogenous agents. We then describe how proliferating and nonproliferating vertebrate cells unhook ICLs. We emphasize fundamentally new unhooking strategies, dramatic progress in the structural analysis of the Fanconi anemia pathway, and insights into how cells govern the choice between different ICL repair pathways. Throughout, we highlight the many gaps that remain in our knowledge of these fascinating DNA repair pathways.

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25

Lynggaard, Christina, Mads Frost Bertelsen, Casper V. Jensen, Matthew S. Johnson, Tobias Guldberg Frøslev, Morten Tange Olsen, and Kristine Bohmann. "Airborne environmental DNA for terrestrial vertebrate community monitoring." Current Biology 32, no. 3 (February 2022): 701–7. http://dx.doi.org/10.1016/j.cub.2021.12.014.

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26

Pennisi, E. "Frog DNA Yields Clues to Vertebrate Genome Evolution." Science 328, no. 5978 (April 29, 2010): 555. http://dx.doi.org/10.1126/science.328.5978.555.

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27

Parplys, Ann C., Katja Kratz, Michael C. Speed, Stanley G. Leung, David Schild, and Claudia Wiese. "RAD51AP1 -deficiency in vertebrate cells impairs DNA replication." DNA Repair 24 (December 2014): 87–97. http://dx.doi.org/10.1016/j.dnarep.2014.09.007.

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28

Ehrlich, M. "The Controversial Denouement of Vertebrate DNA Methylation Research." Biochemistry (Moscow) 70, no. 5 (May 2005): 568–75. http://dx.doi.org/10.1007/s10541-005-0150-z.

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29

Stinson, Benjamin M., and Joseph J. Loparo. "Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway." Annual Review of Biochemistry 90, no. 1 (June 20, 2021): 137–64. http://dx.doi.org/10.1146/annurev-biochem-080320-110356.

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DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing.

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30

Vander Zanden, Crystal M., Ryan S. Czarny, Ethan N. Ho, Adam B. Robertson, and P. Shing Ho. "Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function." Nucleic Acids Research 48, no. 7 (February 25, 2020): 3962–74. http://dx.doi.org/10.1093/nar/gkaa117.

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Abstract Modified DNA bases functionally distinguish the taxonomic forms of life—5-methylcytosine separates prokaryotes from eukaryotes and 5-hydroxymethylcytosine (5hmC) invertebrates from vertebrates. We demonstrate here that mouse endonuclease G (mEndoG) shows specificity for both 5hmC and Holliday junctions. The enzyme has higher affinity (>50-fold) for junctions over duplex DNAs. A 5hmC-modification shifts the position of the cut site and increases the rate of DNA cleavage in modified versus unmodified junctions. The crystal structure of mEndoG shows that a cysteine (Cys69) is positioned to recognize 5hmC through a thiol-hydroxyl hydrogen bond. Although this Cys is conserved from worms to mammals, a two amino acid deletion in the vertebrate relative to the invertebrate sequence unwinds an α-helix, placing the thiol of Cys69 into the mEndoG active site. Mutations of Cys69 with alanine or serine show 5hmC-specificity that mirrors the hydrogen bonding potential of the side chain (C–H < S–H < O–H). A second orthogonal DNA binding site identified in the mEndoG structure accommodates a second arm of a junction. Thus, the specificity of mEndoG for 5hmC and junctions derives from structural adaptations that distinguish the vertebrate from the invertebrate enzyme, thereby thereby supporting a role for 5hmC in recombination processes.

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Myler, Logan R., Charles G. Kinzig, Nanda K. Sasi, George Zakusilo, Sarah W. Cai, and Titia de Lange. "The evolution of metazoan shelterin." Genes & Development 35, no. 23-24 (November 11, 2021): 1625–41. http://dx.doi.org/10.1101/gad.348835.121.

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The mammalian telomeric shelterin complex—comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1—blocks the DNA damage response at chromosome ends and interacts with telomerase and the CST complex to regulate telomere length. The evolutionary origins of shelterin are unclear, partly because unicellular organisms have distinct telomeric proteins. Here, we describe the evolution of metazoan shelterin, showing that TRF1 emerged in vertebrates upon duplication of a TRF2-like ancestor. TRF1 and TRF2 diverged rapidly during vertebrate evolution through the acquisition of new domains and interacting factors. Vertebrate shelterin is also distinguished by the presence of an HJRL domain in the split C-terminal OB fold of POT1, whereas invertebrate POT1s carry inserts of variable nature. Importantly, the data reveal that, apart from the primate and rodent POT1 orthologs, all metazoan POT1s are predicted to have a fourth OB fold at their N termini. Therefore, we propose that POT1 arose from a four-OB-fold ancestor, most likely an RPA70-like protein. This analysis provides insights into the biology of shelterin and its evolution from ancestral telomeric DNA-binding proteins.

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32

Chen, Xin-Xin, Wei-Chen Wu, and Mang Shi. "Discovery and Characterization of Actively Replicating DNA and Retro-Transcribing Viruses in Lower Vertebrate Hosts Based on RNA Sequencing." Viruses 13, no. 6 (May 31, 2021): 1042. http://dx.doi.org/10.3390/v13061042.

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In a previous study, a metatranscriptomics survey of RNA viruses in several important lower vertebrate host groups revealed huge viral diversity, transforming the understanding of the evolution of vertebrate-associated RNA virus groups. However, the diversity of the DNA and retro-transcribing viruses in these host groups was left uncharacterized. Given that RNA sequencing is capable of revealing viruses undergoing active transcription and replication, we collected previously generated datasets associated with lower vertebrate hosts, and searched them for DNA and retro-transcribing viruses. Our results revealed the complete genome, or “core gene sets”, of 18 vertebrate-associated DNA and retro-transcribing viruses in cartilaginous fishes, ray-finned fishes, and amphibians, many of which had high abundance levels, and some of which showed systemic infections in multiple organs, suggesting active transcription or acute infection within the host. Furthermore, these new findings recharacterized the evolutionary history in the families Hepadnaviridae, Papillomaviridae, and Alloherpesviridae, confirming long-term virus–host codivergence relationships for these virus groups. Collectively, our results revealed reliable and sufficient information within metatranscriptomics sequencing to characterize not only RNA viruses, but also DNA and retro-transcribing viruses, and therefore established a key methodology that will help us to understand the composition and evolution of the total “infectome” within a diverse range of vertebrate hosts.

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Takenaka, Katsuya, Tomoo Ogi, Takashi Okada, Eiichiro Sonoda, Caixia Guo, Errol C. Friedberg, and Shunichi Takeda. "Involvement of Vertebrate Polκ in Translesion DNA Synthesis across DNA Monoalkylation Damage." Journal of Biological Chemistry 281, no. 4 (November 23, 2005): 2000–2004. http://dx.doi.org/10.1074/jbc.m506153200.

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34

Feehery, George R., Erbay Yigit, Samuel O. Oyola, Bradley W. Langhorst, Victor T. Schmidt, Fiona J. Stewart, Eileen T. Dimalanta, et al. "A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA." PLoS ONE 8, no. 10 (October 28, 2013): e76096. http://dx.doi.org/10.1371/journal.pone.0076096.

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35

Zhang, Jing, Liam J. Hawkins, and Kenneth B. Storey. "DNA methylation and regulation of DNA methyltransferases in a freeze-tolerant vertebrate." Biochemistry and Cell Biology 98, no. 2 (April 2020): 145–53. http://dx.doi.org/10.1139/bcb-2019-0091.

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The wood frog is one of the few freeze-tolerance vertebrates. This is accomplished in part by the accumulation of cryoprotectant glucose, metabolic rate depression, and stress response activation. These may be achieved by mechanisms such as DNA methylation, which is typically associated with transcriptional repression. Hyperglycemia is also associated with modifications to epigenetic profiles, indicating an additional role that the high levels of glucose play in freeze tolerance. We sought to determine whether DNA methylation is affected during freezing exposure, and whether this is due to the wood frog’s response to hyperglycemia. We examined global DNA methylation and DNA methyltransferases (DNMTs) in the liver and muscle of frozen and glucose-loaded wood frogs. The results showed that levels of 5-methylcytosine (5mC) increased in the muscle, suggesting elevated DNA methylation during freezing. DNMT activities also decreased in muscle during thawing, glucose loading, and in vitro glucose experiments. Liver DNMT activities were similar to muscle; however, a varied response to DNMT levels and a decrease in 5mC highlight the metabolic role the liver plays during freezing. Glucose was also shown to decrease DNMT activity levels in the wood frog, in vitro, elucidating a potentially novel regulatory mechanism. Together these results suggest an interplay between freeze tolerance and hyperglycemic regulation of DNA methylation.

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36

Rus Hoelzel, A. "Evolution by DNA turnover in the control region of vertebrate mitochondrial DNA." Current Opinion in Genetics & Development 3, no. 6 (January 1993): 891–95. http://dx.doi.org/10.1016/0959-437x(93)90010-m.

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37

Spieth, J., Y. H. Shim, K. Lea, R. Conrad, and T. Blumenthal. "elt-1, an embryonically expressed Caenorhabditis elegans gene homologous to the GATA transcription factor family." Molecular and Cellular Biology 11, no. 9 (September 1991): 4651–59. http://dx.doi.org/10.1128/mcb.11.9.4651-4659.1991.

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The short, asymmetrical DNA sequence to which the vertebrate GATA family of transcription factors binds is present in some Caenorhabditis elegans gene regulatory regions: it is required for activation of the vitellogenin genes and is also found just 5' of the TATA boxes of tra-2 and the msp genes. In vertebrates GATA-1 is specific to erythroid lineages, whereas GATA-2 and GATA-3 are present in multiple tissues. In an effort to identify the trans-acting factors that may recognize this sequence element in C. elegans, we used a degenerate oligonucleotide to clone a C. elegans homolog to this gene. We call this gene elt-1 (erythrocytelike transcription factor). It is single copy and specifies a 1.75-kb mRNA that is present predominantly, if not exclusively, in embryos. The region of elt-1 encoding two zinc fingers is remarkably similar to the DNA-binding domain of the vertebrate GATA-binding proteins. However, outside of the DNA-binding domains the amino acid sequences are quite divergent. Nevertheless, introns are located at identical or nearly identical positions in elt-1 and the mouse GATA-1 gene. In addition, elt-1 mRNA is trans-spliced to the 22-base untranslated leader, SL1. The DNA upstream of the elt-1 TATA box contains eight copies of the GATA recognition sequence within the first 300 bp, suggesting that elt-1 may be autogenously regulated. Our results suggest that the specialized role of GATA-1 in erythroid gene expression was derived after separation of the nematodes and the line that led to the vertebrates, since C. elegans lacks an erythroid lineage.

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38

Spieth, J., Y. H. Shim, K. Lea, R. Conrad, and T. Blumenthal. "elt-1, an embryonically expressed Caenorhabditis elegans gene homologous to the GATA transcription factor family." Molecular and Cellular Biology 11, no. 9 (September 1991): 4651–59. http://dx.doi.org/10.1128/mcb.11.9.4651.

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Abstract:

The short, asymmetrical DNA sequence to which the vertebrate GATA family of transcription factors binds is present in some Caenorhabditis elegans gene regulatory regions: it is required for activation of the vitellogenin genes and is also found just 5' of the TATA boxes of tra-2 and the msp genes. In vertebrates GATA-1 is specific to erythroid lineages, whereas GATA-2 and GATA-3 are present in multiple tissues. In an effort to identify the trans-acting factors that may recognize this sequence element in C. elegans, we used a degenerate oligonucleotide to clone a C. elegans homolog to this gene. We call this gene elt-1 (erythrocytelike transcription factor). It is single copy and specifies a 1.75-kb mRNA that is present predominantly, if not exclusively, in embryos. The region of elt-1 encoding two zinc fingers is remarkably similar to the DNA-binding domain of the vertebrate GATA-binding proteins. However, outside of the DNA-binding domains the amino acid sequences are quite divergent. Nevertheless, introns are located at identical or nearly identical positions in elt-1 and the mouse GATA-1 gene. In addition, elt-1 mRNA is trans-spliced to the 22-base untranslated leader, SL1. The DNA upstream of the elt-1 TATA box contains eight copies of the GATA recognition sequence within the first 300 bp, suggesting that elt-1 may be autogenously regulated. Our results suggest that the specialized role of GATA-1 in erythroid gene expression was derived after separation of the nematodes and the line that led to the vertebrates, since C. elegans lacks an erythroid lineage.

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39

Angeloni, Allegra, and Ozren Bogdanovic. "Sequence determinants, function, and evolution of CpG islands." Biochemical Society Transactions 49, no. 3 (June 22, 2021): 1109–19. http://dx.doi.org/10.1042/bst20200695.

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In vertebrates, cytosine-guanine (CpG) dinucleotides are predominantly methylated, with ∼80% of all CpG sites containing 5-methylcytosine (5mC), a repressive mark associated with long-term gene silencing. The exceptions to such a globally hypermethylated state are CpG-rich DNA sequences called CpG islands (CGIs), which are mostly hypomethylated relative to the bulk genome. CGIs overlap promoters from the earliest vertebrates to humans, indicating a concerted evolutionary drive compatible with CGI retention. CGIs are characterised by DNA sequence features that include DNA hypomethylation, elevated CpG and GC content and the presence of transcription factor binding sites. These sequence characteristics are congruous with the recruitment of transcription factors and chromatin modifying enzymes, and transcriptional activation in general. CGIs colocalize with sites of transcriptional initiation in hypermethylated vertebrate genomes, however, a growing body of evidence indicates that CGIs might exert their gene regulatory function in other genomic contexts. In this review, we discuss the diverse regulatory features of CGIs, their functional readout, and the evolutionary implications associated with CGI retention in vertebrates and possibly in invertebrates.

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Xu, Xiaocui, Guoqiang Li, Congru Li, Jing Zhang, Qiang Wang, David K. Simmons, Xuepeng Chen, et al. "Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis." National Science Review 6, no. 5 (May 24, 2019): 993–1003. http://dx.doi.org/10.1093/nsr/nwz064.

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ABSTRACT Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.

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41

Che Lah, Ernieenor Faraliana, Amartuvshin Tsolmon, and Mariana Ahamad. "MOLECULAR IDENTIFICATION OF LOCAL VERTEBRATE SPECIES USING CYTOCHROME OXIDASE SUBUNIT I (COI) GENE." JOURNAL OF ADVANCES IN BIOTECHNOLOGY 5, no. 1 (January 30, 2015): 570–77. http://dx.doi.org/10.24297/jbt.v5i1.1594.

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The aim of this study is to determine a molecular tool for identification of local vertebrate species using mtDNA COI gene. Polymerase Chain Reaction (PCR) using universal primers complementary to the conserved region of the mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) gene fragment, was performed on DNA of blood samples of 30 local animals in Malaysia. DNA of hosts was amplified by PCR and the products were visualized on gel electrophoresis. Twenty two sequences (73.3%) were obtained and compared with sequences registered in GenBank and BOLD Systems databases. The BLAST results for fifteen samples (68%) showed sequences were in congruence with morphological identification at 92% to 100% accuracy while seven sequences had no significant similarity. These results suggest that COI-based PCR is a reliable identification tool for vertebrates and can be applied for epidemiological studies on blood meal analysis of arthropod in Malaysia.

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42

Krizman, David B., and Susan M. Berget. "Efficient selection of 3′-terminal exons from vertebrate DNA." Nucleic Acids Research 21, no. 22 (1993): 5198–202. http://dx.doi.org/10.1093/nar/21.22.5198.

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43

Lachish-Zalait, Aurelie, Corine K. Lau, Boris Fichtman, Ella Zimmerman, Amnon Harel, Michelle R. Gaylord, Douglass J. Forbes, and Michael Elbaum. "Transportin Mediates Nuclear Entry of DNA in Vertebrate Systems." Traffic 10, no. 10 (October 2009): 1414–28. http://dx.doi.org/10.1111/j.1600-0854.2009.00968.x.

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44

Hung, M. S., N. Karthikeyan, B. Huang, H. C. Koo, J. Kiger, and C. K. J. Shen. "Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases." Proceedings of the National Academy of Sciences 96, no. 21 (October 12, 1999): 11940–45. http://dx.doi.org/10.1073/pnas.96.21.11940.

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45

Fukagawa, Tatsuo. "Centromere DNA, proteins and kinetochore assembly in vertebrate cells." Chromosome Research 12, no. 6 (2004): 557–67. http://dx.doi.org/10.1023/b:chro.0000036590.96208.83.

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46

Ronzhina, N. L., T. P. Kravetskaya, and V. M. Krutyakov. "DNA Polymerase-associated and autonomous vertebrate 3′→5′ exonuleases." Journal of Evolutionary Biochemistry and Physiology 36, no. 3 (July 2000): 262–66. http://dx.doi.org/10.1007/bf02737041.

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47

Meehan, Richard, Joe D. Lewis, and Adrian P. Bird. "Characterization of MeCP2, a vertebrate DNA binding protein with affinity for methylated DNA." Nucleic Acids Research 20, no. 19 (1992): 5085–92. http://dx.doi.org/10.1093/nar/20.19.5085.

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48

Murphy, Mark W., David Zarkower, and Vivian J. Bardwell. "Vertebrate DM domain proteins bind similar DNA sequences and can heterodimerize on DNA." BMC Molecular Biology 8, no. 1 (2007): 58. http://dx.doi.org/10.1186/1471-2199-8-58.

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49

FILIPSKI, JAN, JULIO SALINAS, and FRANCIS RODIER. "Two Distinct Compositional Classes of Vertebrate Gene-Bearing DNA Stretches, Their Structures and Possible Evolutionary Origin." DNA 6, no. 2 (April 1987): 109–18. http://dx.doi.org/10.1089/dna.1987.6.109.

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50

Adachi, Noritaka, Susumu Iiizumi, and Hideki Koyama. "Evidence for a Role of Vertebrate Rad52 in the Repair of Topoisomerase II–Mediated DNA Damage." DNA and Cell Biology 24, no. 6 (June 2005): 388–93. http://dx.doi.org/10.1089/dna.2005.24.388.

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