I Rogozin

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Completion of the mapping of transcription start sites for the five-gene block subgenomic RNAs of Beet yellows Closterovirus and identification of putative subgenomic promoters
    Maria V Vitushkina
    Belozersky Institute, Moscow State University, 119992 Moscow, Russia
    Virus Res 128:153-8. 2007
  2. pmc AID/APOBEC cytosine deaminase induces genome-wide kataegis
    Artem G Lada
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
    Biol Direct 7:47; discussion 47. 2012
  3. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
  4. pmc A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
    Diana Chernikova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 6:26. 2011
  5. pmc U12 intron positions are more strongly conserved between animals and plants than U2 intron positions
    Malay Kumar Basu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Biol Direct 3:19. 2008
  6. pmc Accumulation of GC donor splice signals in mammals
    Alexander Churbanov
    Loyola University Medical Center, 2160 S First Ave, Maywood, IL, 60153, USA
    Biol Direct 3:30. 2008
  7. pmc Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors
    Tahir H Tahirov
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198 7696, USA
    Biol Direct 4:11. 2009
  8. pmc Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes
    Vladimir I Mayorov
    Mercer University School of Medicine, Macon, GA 31207, USA
    BMC Immunol 6:10. 2005
  9. pmc Evolution of alternative and constitutive regions of mammalian 5'UTRs
    Alissa M Resch
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Genomics 10:162. 2009
  10. pmc Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    Colin N Dewey
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 7:311. 2006

Detail Information

Publications85

  1. ncbi request reprint Completion of the mapping of transcription start sites for the five-gene block subgenomic RNAs of Beet yellows Closterovirus and identification of putative subgenomic promoters
    Maria V Vitushkina
    Belozersky Institute, Moscow State University, 119992 Moscow, Russia
    Virus Res 128:153-8. 2007
    ..These motifs are conserved in the equivalent positions upstream of three orthologous genes of Citrus tristeza Closterovirus and two orthologous genes of Beet yellow stunt Closterovirus...
  2. pmc AID/APOBEC cytosine deaminase induces genome-wide kataegis
    Artem G Lada
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
    Biol Direct 7:47; discussion 47. 2012
    ..Our data provide evidence that unleashed cytosine deaminase activity is an evolutionary conserved, prominent source of genome-wide kataegis events...
  3. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
    ....
  4. pmc A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
    Diana Chernikova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 6:26. 2011
    ..Estimates of the age of Last Eukaryotic Common Ancestor (LECA) vary approximately twofold, from ~1,100 million years ago (Mya) to ~2,300 Mya...
  5. pmc U12 intron positions are more strongly conserved between animals and plants than U2 intron positions
    Malay Kumar Basu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Biol Direct 3:19. 2008
    ....
  6. pmc Accumulation of GC donor splice signals in mammals
    Alexander Churbanov
    Loyola University Medical Center, 2160 S First Ave, Maywood, IL, 60153, USA
    Biol Direct 3:30. 2008
    ..Thus, there was substantive accumulation of GC donor splice sites during the evolution of mammals. Accumulation of GC sites might have been driven by selection for alternative splicing...
  7. pmc Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors
    Tahir H Tahirov
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198 7696, USA
    Biol Direct 4:11. 2009
    ..However, the details of the evolutionary relationships between DNA polymerases of archaea and eukaryotes remain unresolved...
  8. pmc Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes
    Vladimir I Mayorov
    Mercer University School of Medicine, Macon, GA 31207, USA
    BMC Immunol 6:10. 2005
    ..The DNA sequence context of mutation hotspots at G-C pairs during SHM is DGYW/WRCH (G-C is a hotspot position, R = A/G, Y = T/C, W = A/T, D = A/G/T)...
  9. pmc Evolution of alternative and constitutive regions of mammalian 5'UTRs
    Alissa M Resch
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Genomics 10:162. 2009
    ..By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized...
  10. pmc Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    Colin N Dewey
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 7:311. 2006
    ..We explored the connections between the length of vertebrate introns, the strength of splice sites, exonic splicing signals, and evolution of flanking exons...
  11. pmc Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis
    Vladimir N Babenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
    BMC Cancer 6:36. 2006
    ..This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution...
  12. ncbi request reprint Computational analysis of mutation spectra
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, Bethesda, MD 20894, USA
    Brief Bioinform 4:210-27. 2003
    ..In general, the DNA sequence context of mutation hotspots is a fingerprint of interactions between DNA and DNA repair/replication/modification enzymes, and the analysis of hotspot context provides evidence of such interactions...
  13. ncbi request reprint Analysis of evolution of exon-intron structure of eukaryotic genes
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA
    Brief Bioinform 6:118-34. 2005
    ..It was shown that introns indeed predominantly insert into or are fixed in specific protosplice sites which have the consensus sequence (A/C)AG|Gt...
  14. ncbi request reprint Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes
    Igor B Rogozin
    NCBI NLM NIH, 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA
    Brief Bioinform 5:131-49. 2004
    ..In this review, we discuss various computational approaches for identification of conserved gene strings and construction of local alignments of gene orders in prokaryotic genomes...
  15. ncbi request reprint The cytidine deaminase AID exhibits similar functional properties in yeast and mammals
    Igor B Rogozin
    National Center for Biotechnology Information NLM, National Institutes of Health, 8600 Rockville Pike, Bldg 38A room 5N505A, Bethesda, MD 20894, USA
    Mol Immunol 43:1481-4. 2006
    ..In addition, we show that non-uniformity of the mutation hotspot distribution is a factor potentially decreasing the chances of detecting mutations...
  16. ncbi request reprint Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Immunol 172:3382-4. 2004
    ..We also found evidence that a DNA repair enzyme may play a role in modifying the sequence of hypermutation hotspots...
  17. pmc A highly conserved family of inactivated archaeal B family DNA polymerases
    Igor B Rogozin
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD, 20894, USA
    Biol Direct 3:32. 2008
    ..The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication...
  18. pmc Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:7. 2008
    ..However, a non-negligible level of homoplasy was detected...
  19. ncbi request reprint Use of mutation spectra analysis software
    I Rogozin
    Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia
    Hum Mutat 17:83-102. 2001
    ..Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis...
  20. ncbi request reprint Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon
    I B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20804, USA
    Bioinformatics 17:890-900. 2001
    ..To reveal potential connections between the presence of upstream AUGs and other features of 5' UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5' UTR sequences...
  21. ncbi request reprint Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs)
    I B Rogozin
    National Center for Biotechnology Information National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Brief Bioinform 1:260-74. 2000
    ..Repetitive elements should be treated carefully by using special programs and databases. In this paper, various aspects of SINE (short interspersed repetitive element) identification, analysis and evolution are discussed...
  22. ncbi request reprint Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context
    Y I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 11:356-72. 2001
    ....
  23. pmc Cloning of human centromeres by transformation-associated recombination in yeast and generation of functional human artificial chromosomes
    N Kouprina
    Laboratory of Biosystems and Cancer, Center for Cancer Research, National Cancer Institute, NIH, Building 37, Room 5032, Bethesda, MD 20892, USA
    Nucleic Acids Res 31:922-34. 2003
    ..In summary, our results demonstrated that TAR cloning is a useful tool for investigating human centromere organization and the structural requirements for formation of HAC vectors that might have a potential for therapeutic applications...
  24. ncbi request reprint Evolution of eukaryotic gene repertoire and gene structure: discovering the unexpected dynamics of genome evolution
    I B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Cold Spring Harb Symp Quant Biol 68:293-301. 2003
  25. pmc Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins
    I K Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894, USA
    Genome Biol 2:RESEARCH0053. 2001
    ..muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat)...
  26. pmc Genome trees constructed using five different approaches suggest new major bacterial clades
    Y I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 1:8. 2001
    ..Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes...
  27. pmc Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence
    T B Nesterova
    Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia
    Genome Res 11:833-49. 2001
    ..This is also evident from analysis of flanking sequences, which reveals a very high rate of rearrangement and invasion of dispersed repeats. We discuss these results in the context of Xist gene function and evolution...
  28. ncbi request reprint Similarity pattern analysis in mutational distributions
    N N Khromov-Borisov
    Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia
    Mutat Res 430:55-74. 1999
    ..Similarity pattern revealed among genotypic class profiles (GCPs) seems to be also interpretable. When supplemented with descriptive cluster analysis, SPAN appears to be a fruitful methodology in MS analysis...
  29. ncbi request reprint Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix
    G V Glazko
    Institute of Cytology and Genetics, Novosibirsk, Russia
    Biochim Biophys Acta 1517:351-64. 2001
    ..In general, our results suggest that the proportion of missed S/MARs is lower for ChrClass, whereas the proportion of wrong S/MARs is lower for MAR-Finder and MRS...
  30. ncbi request reprint Rapid evolution of a cyclin A inhibitor gene, roughex, in Drosophila
    S N Avedisov
    Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
    Mol Biol Evol 18:2110-8. 2001
    ..These results indicate that even some genes involved in key regulatory processes in eukaryotes evolve at extremely high rates...
  31. ncbi request reprint [Context organization of mRNA 5'-untranslated regions of higher plants]
    A V Kochetov
    Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, 630090 Russia
    Mol Biol (Mosk) 36:649-56. 2002
    ..A hypothesis is put forward that the efficiency of termination at the uORF stop codon might substantially interfere with the mRNA translation activity...
  32. ncbi request reprint In search of lost introns
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Quebec, Canada
    Bioinformatics 23:i87-96. 2007
    ..The study yields the surprising result that ancestral eukaryotes were fairly intron-rich. For example, the bilaterian ancestor is estimated to have had more than 90% as many introns as vertebrates do now...
  33. pmc Widespread positive selection in synonymous sites of mammalian genes
    Alissa M Resch
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 24:1821-31. 2007
    ..Positive selection at synonymous sites might act through mRNA destabilization affecting mRNA levels and translation...
  34. ncbi request reprint Evolution of the mouse polyubiquitin-C gene
    Andrey A Perelygin
    Department of Biology, Georgia State University, 24 Peachtree Center Avenue, Atlanta, GA 30303, USA
    J Mol Evol 55:202-10. 2002
    ..The sequence divergence of noncoding DNA was used to estimate the frequency of unequal crossing-over events (6.3 x 10(-5) events per generation) in the Ubc gene, as well as to provide evidence of apparent selection in the poly-u gene...
  35. pmc Evolutionarily conserved genes preferentially accumulate introns
    Liran Carmel
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 17:1045-50. 2007
    ..This apparent functional importance of introns is likely to be due, at least in part, to their multiple effects on gene expression...
  36. pmc Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase eta during copying of a mouse immunoglobulin kappa light chain transgene
    Youri I Pavlov
    Laboratories of Molecular Genetics and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 99:9954-9. 2002
    ....
  37. ncbi request reprint Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Nat Immunol 8:647-56. 2007
    ..Vertebrate acquired immunity could have therefore originated from lymphocyte receptor diversification by an ancestral AID-like DNA cytosine deaminase...
  38. ncbi request reprint Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Mol Biol Evol 24:1080-90. 2007
    ..It is expected that RGC_CAM and other RGC-based methods will be crucial for these future, definitive phylogenetic studies...
  39. ncbi request reprint A glimpse of a putative pre-intron phase of eukaryotic evolution
    Alexander V Sverdlov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 23:105-8. 2007
    ....
  40. ncbi request reprint Roles of DNA polymerases in replication, repair, and recombination in eukaryotes
    Youri I Pavlov
    Eppley Institute for Research in Cancer and Allied Diseases, Departments of Biochemistry and Molecular Biology, and Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198 6805, USA
    Int Rev Cytol 255:41-132. 2006
    ..In this review, we discuss the structure, the mechanism, and the evolutionary relationships of DNA polymerases and their possible functions in the replication of intact and damaged chromosomes, DNA damage repair, and recombination...
  41. ncbi request reprint Cross-species conservation of SEL1L, a human pancreas-specific expressing gene
    Ida Biunno
    Institute for Biomedical Technologies CNR, Segrate, Milano, Italy
    OMICS 6:187-98. 2002
    ....
  42. ncbi request reprint Microevolutionary genomics of bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Theor Popul Biol 61:435-47. 2002
    ..This suggests the possibility that nonessential genes are responsible for driving the evolutionary diversification between strains...
  43. ncbi request reprint Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation
    Jie Zheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 24:2583-92. 2007
    ..The developed procedure for the identification and analysis of conserved introns and other characters with minimal or no homoplasy is expected to be useful for resolving many hard phylogenetic problems...
  44. ncbi request reprint Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues
    Malay Kumar Basu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:111-9. 2008
    ..The overall pattern of intron gain and loss in the plastid-derived genes is shaped by this continuing gain and the more general tendency for loss that is characteristic of the recent evolution of plant genes...
  45. pmc A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 380, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:482-96. 2002
    ....
  46. pmc Selection in the evolution of gene duplications
    Fyodor A Kondrashov
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:RESEARCH0008. 2002
    ....
  47. pmc Connected gene neighborhoods in prokaryotic genomes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:2212-23. 2002
    ..Gene neighborhoods appear to evolve via complex rearrangement, with different combinations of genes from a neighborhood fixed in different lineages...
  48. pmc Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Res 12:962-8. 2002
    ..In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales...
  49. pmc A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements
    Eugeny A Elisaphenko
    Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk, Russia
    PLoS ONE 3:e2521. 2008
    ..Additionally we showed that the combination of remnants of protein-coding sequences and mobile elements is not unique to the Xist gene and is found in other XIC genes producing non-coding nuclear RNA...
  50. pmc Low-fidelity DNA synthesis by human DNA polymerase theta
    Mercedes E Arana
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 36:3847-56. 2008
    ..Thus, pol is an exception among family A polymerases, and its low fidelity is consistent with its proposed roles in TLS and SHM...
  51. ncbi request reprint Purifying and directional selection in overlapping prokaryotic genes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 18:228-32. 2002
    ..This could be a general evolutionary mode for genes emerging from noncoding sequences, in which the protein sequence has not been subject to selection...
  52. pmc 129-derived strains of mice are deficient in DNA polymerase iota and have normal immunoglobulin hypermutation
    John P McDonald
    Laboratory of Genomic Integrity, Building 6, Room 1A13, NICHD, NIH, 9000 Rockville Pike, Bethesda, MD 20892 2725, USA
    J Exp Med 198:635-43. 2003
    ..Thus, either poliota does not participate in hypermutation, or its role is nonessential and can be readily assumed by another low-fidelity polymerase...
  53. doi request reprint Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach
    Miklos Csuros
    Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 25:903-11. 2008
    ..It is suggested that, at early stages of evolution, chromalveolates went through major population bottlenecks that were accompanied by intron invasion...
  54. pmc Evolution of protein domain promiscuity in eukaryotes
    Malay Kumar Basu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 18:449-61. 2008
    ..Thus, a limited repertoire of promiscuous domains makes a major contribution to the diversity and evolvability of eukaryotic proteomes and signaling networks...
  55. ncbi request reprint Identification of murine B cell lines that undergo somatic hypermutation focused to A:T and G:C residues
    Palash Bhattacharya
    Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL 60612 7344, USA
    Eur J Immunol 38:227-39. 2008
    ....
  56. pmc Three distinct modes of intron dynamics in the evolution of eukaryotes
    Liran Carmel
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 17:1034-44. 2007
    ..Intron dynamics could depend on multiple mechanisms, and in the balanced mode, gain and loss of introns might share common mechanistic features...
  57. ncbi request reprint APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis
    Igor B Rogozin
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 4:1281-5. 2005
    ..In mammals, APOBEC4 is expressed primarily in testis which suggests the possibility that it is an editing enzyme for mRNAs involved in spermatogenesis...
  58. ncbi request reprint Genome trees and the tree of life
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 18:472-9. 2002
    ..However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution...
  59. pmc A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 5:R7. 2004
    ....
  60. ncbi request reprint Context of deletions and insertions in human coding sequences
    Alexey S Kondrashov
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Hum Mutat 23:177-85. 2004
    ..Two-thirds of deletions remove a repeat, and over 80% of insertions create a repeat, i.e., they are duplications...
  61. pmc Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 14:29-36. 2004
    ..All of these approaches supported the coelomate clade and showed concordance between evolution of protein sequences and higher-level evolutionary events, such as domain fusion or gene loss...
  62. ncbi request reprint Evidence of splice signal migration from exon to intron during intron evolution
    Alexander V Sverdlov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Biol 13:2170-4. 2003
    ..Accumulation of information inside the intron during evolution suggests that new introns largely emerge de novo rather than through propagation and migration of old introns...
  63. pmc The rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R19. 2003
    ....
  64. pmc Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    Dmitri M Krylov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 13:2229-35. 2003
    ..Thus, propensity of a gene to be lost during evolution seems to be a direct reflection of its biological importance...
  65. ncbi request reprint Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Biol 13:1512-7. 2003
    ..In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent...
  66. pmc Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
    Marina V Omelchenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R55. 2003
    ....
  67. pmc Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation
    Yongqing Liu
    Environmental Sciences and Life Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Proc Natl Acad Sci U S A 100:4191-6. 2003
    ..Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals...
  68. pmc Getting positive about selection
    Eugene V Koonin
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:331. 2003
    ..A report on the 68th Symposium on Quantitative Biology, The Genome of Homo Sapiens', Cold Spring Harbor, USA, 28 May-2 June 2003...
  69. ncbi request reprint Theoretical analysis of mutation hotspots and their DNA sequence context specificity
    Igor B Rogozin
    Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia
    Mutat Res 544:65-85. 2003
    ..The nucleotide sequence context of mutational hotspots is a fingerprint of interactions between DNA and DNA repair, replication, and modification enzymes, and the analysis of hotspot context provides evidence of such interactions...
  70. ncbi request reprint Unique error signature of the four-subunit yeast DNA polymerase epsilon
    Polina V Shcherbakova
    Laboratory of Molecular Genetics, NIEHS, National Institutes of Health, North Carolina 27709, USA
    J Biol Chem 278:43770-80. 2003
    ..We discuss the implications of these findings for the role of Pol epsilon polymerase activity in DNA replication...
  71. pmc The SPANX gene family of cancer/testis-specific antigens: rapid evolution and amplification in African great apes and hominids
    Natalay Kouprina
    Laboratory of Biosystems and Cancer, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 101:3077-82. 2004
    ..Thus, evolution of the SPANX family appears to have involved positive selection that affected not only the protein sequence but also the synonymous sites in the coding sequence...
  72. ncbi request reprint A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions
    Galina V Glazko
    Institute of Molecular Evolutionary Genetics and Dept of Biology, Pennsylvania State University, 328 Mueller Lab, University Park, PA 16802, USA
    Trends Genet 19:119-24. 2003
    ..An excess of conserved predicted MARs is seen in intergenic regions preceding 5' ends of genes, suggesting that these MARs are primarily involved in transcriptional control...
  73. pmc Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:4264-71. 2002
    ..In contrast, the gene set is optimized for the particular environmental niche of the given microbe, which results in the lack of correlation between the gene number and the characteristics of non-coding regions...
  74. ncbi request reprint DNA polymerase eta contributes to strand bias of mutations of A versus T in immunoglobulin genes
    Vladimir I Mayorov
    Department of Basic Medical Sciences, Mercer University School of Medicine, Macon, GA 31207, USA
    J Immunol 174:7781-6. 2005
    ..Because polymerase eta inserts more mutations opposite template T than template A, it would generate more substitutions of A on the newly synthesized strand...
  75. ncbi request reprint p53 gain-of-function: tumor biology and bioinformatics come together
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 4:686-8. 2005
    ..The latter observation suggests an unexpected level of complexity of p53 evolution in tumors, with distinct novel function gained in different tumors...
  76. pmc Conservation versus parallel gains in intron evolution
    Alexander V Sverdlov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:1741-8. 2005
    ..Thus, the presence of numerous introns in the same positions in orthologous genes from distant eukaryotes, such as animals, fungi and plants, appears to reflect mostly bona fide evolutionary conservation...
  77. ncbi request reprint ESTMAP: a system for expressed sequence tags mapping on genomic sequences
    Luciano Milanesi
    CNR ITB, Via Frotelli Corni, 93, Segrate, MI 20090, Italy
    IEEE Trans Nanobioscience 2:75-8. 2003
    ..ESTMAP is implemented as a part of the WebGene system (http://www.cnr.it/webgene)...
  78. ncbi request reprint Origin of a substantial fraction of human regulatory sequences from transposable elements
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A Room N511M, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Trends Genet 19:68-72. 2003
    ..Thus, TEs have probably contributed substantially to the evolution of both gene-specific and global patterns of human gene regulation...
  79. ncbi request reprint Reconstruction of ancestral protosplice sites
    Alexander V Sverdlov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Biol 14:1505-8. 2004
    ..We show that introns are either predominantly inserted into specific protosplice sites, which have the consensus sequence (A/C)AG/Gt, or that they are inserted randomly but are preferentially fixed at such sites...
  80. ncbi request reprint Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion
    Alexander V Sverdlov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    Gene 338:85-91. 2004
    ..This mechanism could involve duplication of a portion of the coding region during reverse transcription followed by homologous recombination and subsequent rapid sequence divergence in the copy that becomes a new intron...
  81. ncbi request reprint Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection
    Galina V Glazko
    Stowers Institute for Medical Research, Kansas City, MO 64110, USA
    Biochim Biophys Acta 1679:95-106. 2004
    ..These results are compatible with the gain-of-function concept of the role of p53 in tumorigenesis...
  82. ncbi request reprint Differential action of natural selection on the N and C-terminal domains of 2'-5' oligoadenylate synthetases and the potential nuclease function of the C-terminal domain
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 326:1449-61. 2003
    ....
  83. pmc Prevalence of intron gain over intron loss in the evolution of paralogous gene families
    Vladimir N Babenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:3724-33. 2004
    ..These results are generally compatible with the emerging notion of intensive insertion and loss of introns during transitional epochs in contrast to the relative quiet of the intervening evolutionary spans...
  84. pmc Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 32:1774-82. 2004
    ....
  85. ncbi request reprint Yeast POL5 is an evolutionarily conserved regulator of rDNA transcription unrelated to any known DNA polymerases
    Wei Yang
    National Center for Biotechnology Inforamtion, National Library of Medicine, National Institutes of Health Bethesda, Maryland 20894, USA
    Cell Cycle 2:120-2. 2003
    ..These proteins are confidently predicted to have an entirely a-helical structure and are unrelated to the B class DNA polymerases, as claimed for yeast POL5, or any other known polymerases...