Research Topics
Genomes and Genes | J JurkaSummaryAffiliation: Genetic Information Research Institute Country: USA Publications
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Publications
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzaeJames E Galagan
The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02142, USA
Nature 438:1105-15. 2005..These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation...- Evolutionary history of 7SL RNA-derived SINEs in SupraprimatesJan Ole Kriegs
Institute of Experimental Pathology, ZMBE, University of Munster, Von Esmarch Str 56, D 48149 Munster, Germany
Trends Genet 23:158-61. 2007..As well as new elements in Tupaia and primates, we also found that the purported ancestral fossil Alu monomer was restricted to Primates, and provide here the first description of a potential chimeric promoter box region in SINEs... 
Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebratesJerzy Jurka
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA, 94043, USA
Biol Direct 7:36. 2012..abstract:..
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansionNatalay Kouprina
Laboratory of Biosystems and Cancer, National Cancer Institute, Bethesda, Maryland, USA
PLoS Biol 2:E126. 2004..Our data suggest that evolutionary selection of specific segments of the ASPM sequence strongly relates to differences in cerebral cortical size...- Analysis of the human Alu Ye lineageAbdel Halim Salem
Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio Modular Multi Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
BMC Evol Biol 5:18. 2005..Alu elements are therefore a rich source of inter- and intra-species primate genomic variation... - VisualRepbase: an interface for the study of occurrences of transposable element familiesSebastien Tempel
Genetic Information Research Institute, 1925 Landings Dr, Mountain View, CA 94043, USA
BMC Bioinformatics 9:345. 2008..Repbase already has software for entering new sequence families and for comparing the user's sequence with the database of consensus sequences... - Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and CensorOleksiy Kohany
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
BMC Bioinformatics 7:474. 2006..Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases... - Origin and diversification of minisatellites derived from human Alu sequencesJerzy Jurka
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
Gene 365:21-6. 2006..Our analysis shows that they can be effectively used in comparative studies of the overall sequence context which may contribute to instability of DNA segments flanked by short direct repeats... - Repetitive sequences in complex genomes: structure and evolutionJerzy Jurka
Genetic Information Research Institute, Mountain View, California 94043, USA
Annu Rev Genomics Hum Genet 8:241-59. 2007..Remnants of TEs appear to be overrepresented in transcription regulatory modules and other regions conserved among distantly related species, which may have implications for our understanding of their impact on speciation... - Duplication, coclustering, and selection of human Alu retrotransposonsJerzy Jurka
Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043 0815, USA
Proc Natl Acad Sci U S A 101:1268-72. 2004..We also propose that long-term Alu accumulation in GC-rich DNA is associated with DNA duplication initiated by elevated recombinogenic activities in Alu clusters... - Evolutionary impact of human Alu repetitive elementsJerzy Jurka
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
Curr Opin Genet Dev 14:603-8. 2004..Studying the Alu family in a human genomic context is likely to have general significance for our understanding of the evolutionary impact of other repetitive elements in diverse eukaryotic genomes... - Conserved eukaryotic transposable elements and the evolution of gene regulationJ Jurka
Genetic Information Research Institute, Mountain View, California, 94043, USA
Cell Mol Life Sci 65:201-4. 2008..Multiple remnants of transposable elements preserved in cis-regulatory modules may represent a record of mutations that were critical to the evolution of gene regulation and speciation... - Clustering, duplication and chromosomal distribution of mouse SINE retrotransposonsJ Jurka
Genetic Information Research Institute, Mountain View, CA 94043, USA
Cytogenet Genome Res 110:117-23. 2005..We propose that the accumulation of mouse SINE elements observed in GC-rich regions may be due to the excess of DNA duplications over deletions in gene-rich regions that tend to be GC rich... - Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposonsWeidong Bao
Genetic Information Research Institute, Mountain View, CA, USA
Mob DNA 1:3. 2010..In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons... - Repbase Update, a database of eukaryotic repetitive elementsJ Jurka
Genetic Information Research Institute, Mountain View, CA 94043, USA
Cytogenet Genome Res 110:462-7. 2005..Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html... - Families of transposable elements, population structure and the origin of speciesJerzy Jurka
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
Biol Direct 6:44. 2011..We present a new hypothesis to explain the observed correlations based on classical concepts of population genetics... - Crypton transposons: identification of new diverse families and ancient domestication eventsKenji K Kojima
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
Mob DNA 2:12. 2011..abstract:.. - Molecular paleontology of transposable elements from Arabidopsis thalianaV V Kapitonov
Genetic Information Research Institute, Sunnyvale, CA 94089, USA
Genetica 107:27-37. 1999..thaliana are relatively young, extremely diverse and much smaller than those from mammalian genomes. We discuss the potential factors determining similarities and differences in the evolution of TEs in mammals and A. thaliana... - New superfamilies of eukaryotic DNA transposons and their internal divisionsWeidong Bao
Genetic Information Research Institute, Mountain View, CA, USA
Mol Biol Evol 26:983-93. 2009..These transposons are named TP36 elements (abbreviated from transposase 36)... - Repeats in genomic DNA: mining and meaningJ Jurka
Genetic Information Research Institute, Sunnyvale, CA 94089, USA
Curr Opin Struct Biol 8:333-7. 1998..Analysis of these sequences, combined with experimental research, reveals a history of complex 'intracellular ecosystems' of transposable elements that are inseparably associated with genomic evolution... - The esterase and PHD domains in CR1-like non-LTR retrotransposonsVladimir V Kapitonov
Genetic Information Research Institute, Mountain View, California, USA
Mol Biol Evol 20:38-46. 2003..Unexpectedly, ES links together non-LTR retrotransposons and single-stranded RNA viruses like influenza C and coronaviruses, which are known to depend on their own ES... - Rolling-circle transposons in eukaryotesV V Kapitonov
Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043, USA
Proc Natl Acad Sci U S A 98:8714-9. 2001..Sequence conservation suggests that Helitrons continue to be transposed... - The long terminal repeat of an endogenous retrovirus induces alternative splicing and encodes an additional carboxy-terminal sequence in the human leptin receptorV V Kapitonov
Genetic Information Research Institute, 1170 Morse Avenue, Sunnyvale, CA 94089, USA
J Mol Evol 48:248-51. 1999..We suggest the possibility of transcriptional and posttranscriptional regulation of OBR expression by steroids that bind the LTR... - Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposonsJ Jurka
Genetic Information Research Institute, Palo Alto, CA 94306, USA
Proc Natl Acad Sci U S A 94:1872-7. 1997..Moran, J. V., Kazazian, H. H. & Boeke, J. D. (1996) Cell 87, 905-916]. A model for integration of mammalian retroposons based on the presented data is discussed... - Mammalian retroposons integrate at kinkable DNA sitesJ Jurka
Genetic Information Research Institute, Palo Alto, CA 94306, USA
J Biomol Struct Dyn 15:717-21. 1998..Nicking at kinkable sites, particularly at TA steps, may also play a role in integration of other insertion elements... - Self-synthesizing DNA transposons in eukaryotesVladimir V Kapitonov
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
Proc Natl Acad Sci U S A 103:4540-5. 2006.... - Helitrons on a roll: eukaryotic rolling-circle transposonsVladimir V Kapitonov
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
Trends Genet 23:521-9. 2007..Helitrons seem to have a major role in the evolution of host genomes. They frequently capture diverse host genes, some of which can evolve into novel host genes or become essential for helitron transposition... - Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequencesVladimir V Kapitonov
Genetic Information Research Institute, 1925 Landings Dr, Mountain View, CA 94041, USA
Gene 448:207-13. 2009..5% accuracy. RT1class1 works either as a stand-alone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1)... - Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1)Weidong Bao
Genetic Information Research Institute, Mountain View, CA 94043, USA
Gene 465:9-16. 2010..The implications of HAL1 for the evolution of L1 elements and the host genomes are discussed... - Molecular paleontology of transposable elements in the Drosophila melanogaster genomeVladimir V Kapitonov
Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 94043, USA
Proc Natl Acad Sci U S A 100:6569-74. 2003..The chromosomal and age distributions of TEs in D. melanogaster are very similar to those in Arabidopsis thaliana. Both genomes contain only relatively young TEs (<20 Myr old), constituting a main component of paracentromeric regions... - A novel class of SINE elements derived from 5S rRNAVladimir V Kapitonov
Genetic Information Research Institute, Mountain View, California, USA
Mol Biol Evol 20:694-702. 2003..Given the common structural features, it is highly likely that the enzymatic machinery encoded by CR1-like elements powers proliferation of SINE3... - Active Alu elements are passed primarily through paternal germlinesJerzy Jurka
Genetic Information Research Institute, Mountain View, California 94043, USA
Theor Popul Biol 61:519-30. 2002..Finally, we propose that the origin of Alu subfamilies in human populations may be related to evolution of chromosome Y... - Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposonsAndrew J Gentles
Genetic Information Research Institute, Mountain View, California, USA
Mol Biol Evol 22:1983-91. 2005..This provides a possible driving force for the continual emergence of new L1 subfamilies which, in turn, may affect selection of L1-dependent SINE subfamilies... - RAG1 core and V(D)J recombination signal sequences were derived from Transib transposonsVladimir V Kapitonov
Genetic Information Research Institute, Mountain View, California, USA
PLoS Biol 3:e181. 2005..We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction... - Harbinger transposons and an ancient HARBI1 gene derived from a transposaseVladimir V Kapitonov
Genetic Information Research Institute, Mountain View, California 94040, USA
DNA Cell Biol 23:311-24. 2004..Based on this observation, we suggest that the hypothetical HARBI1 nucleases are also characterized by a strong DNA-target specificity... - Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predispositionAdam Pavlicek
Genetic Information Research Institute, Mountain View, CA, USA
Hum Mol Genet 13:2737-51. 2004..Finally, on the basis of protein sequence conservation, we identified missense changes that are likely to compromise BRCA1 function... - Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndromeAdam Pavlicek
Genetic Information Research Institute, Mountain View, California 94043, USA
Genome Res 15:1487-95. 2005..We also found that gaps up to 1.5 kb long can be transferred between LCR22s... - Retroposition of processed pseudogenes: the impact of RNA stability and translational controlAdam Pavlicek
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
Trends Genet 22:69-73. 2006..They are preferentially translated on free cytoplasmic ribosomes and encode soluble proteins. Our results indicate that interactions between mRNAs and L1 proteins seem to occur at free cytoplasmic ribosomes... - Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genesLudivine Sinzelle
Max Delbruck Center for Molecular Medicine, 13092 Berlin, Germany
Proc Natl Acad Sci U S A 105:4715-20. 2008..The Harbinger transposon will serve as a useful experimental system for transposon biology and for investigating the enzymatic functions of domesticated, transposon-derived cellular genes... - A universal classification of eukaryotic transposable elements implemented in RepbaseVladimir V Kapitonov
Nat Rev Genet 9:411-2; author reply 414. 2008 
The amphioxus genome and the evolution of the chordate karyotypeNicholas H Putnam
Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 453:1064-71. 2008..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...- Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolutionMelanie Babcock
Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA
Genome Res 13:2519-32. 2003..Such sites may represent focal points for recombination. Thus, genome shuffling by Alu-mediated rearrangements has contributed to genome architecture during primate evolution... - Comprehensive analysis of two Alu Yd subfamiliesJinchuan Xing
Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
J Mol Evol 57:S76-89. 2003..These Alu subfamilies are a source of genomic fossil relics for the study of primate phylogenetics and human population genetics... - Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organizationNicholas H Putnam
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 317:86-94. 2007..Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor... - Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27Natalay Kouprina
Laboratory of Biosystems and Cancer, National Cancer Institute, Bethesda, Maryland 20892, USA
Genome Res 15:1477-86. 2005..We speculate that the predisposition to prostate cancer in X-linked families is an example of a genomic disease caused by a specific architecture of the SPANX gene cluster... - Identification of sequence motifs at the breakpoint junctions in three t(1;9)(p36.3;q34) and delineation of mechanisms involved in generating balanced translocationsMarzena Gajecka
Health Research and Education Center, Washington State University Spokane, Spokane, WA, 99210-1495, USA
Hum Genet 120:519-26. 2006..We propose a model for balanced translocation formation in humans similar to transposition in bacteria, in which staggered nicks are repaired resulting in duplications and insertions at the translocation breakpoints... - Introduction for the Gene special issue dedicated to the meeting "Genomic impact of eukaryotic transposable elements" at AsilomarMark A Batzer
Gene 390:1-2. 2007 - The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolismE Virginia Armbrust
School of Oceanography, University of Washington, Seattle, WA 98195, USA
Science 306:79-86. 2004.... - SINEs, evolution and genome structure in the opossumWanjun Gu
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
Gene 396:46-58. 2007..Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state... - Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domesticaAndrew J Gentles
Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA
Genome Res 17:992-1004. 2007..Many of these conserved repeats are also present in human, and are highly over-represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals... - Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequencesTarjei S Mikkelsen
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nature 447:167-77. 2007..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation... - Potential for retroposition by old Alu subfamiliesKarla Johanning
Tulane Cancer Center SL-66, Department of Environmental Health Sciences, Tulane University Medical Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA
J Mol Evol 56:658-64. 2003..The presence of few conserved Alu Sx elements and the dynamic expansion/contraction of the A-tail suggests that some of these older subfamilies may still be active at very low levels or in a few individuals... - HERVd: the Human Endogenous RetroViruses Database: updateJan Paces
Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo 2, CZ-16637 Prague, Czech Republic
Nucleic Acids Res 32:D50. 2004..This leads to a more precise identification of members with individual families. The second improvement is better accessibility of the database and connection with human genome annotation... - Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylationYijun Qi
Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
Nature 443:1008-12. 2006..Second, AGO4 catalytic activity can be crucial for the generation of secondary siRNAs that reinforce its repressive effects... - Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22Chingfer Chen
Department of Mathematics, Stanford University, Stanford, CA 94305-2125, USA
Proc Natl Acad Sci U S A 99:2930-5. 2002..Other assessments concern comparisons of intergenic lengths, properties of Psig sequences, and correlations between Alu and Psig sequences... - Tracing genetic history of modern humans using X-chromosome lineagesVania Yotova
Centre de Recherche, Hopital Sainte Justine, CHU Mère Enfant, 3175 Cote Sainte Catherine, Montreal, QC, Canada, H3T 1C5
Hum Genet 122:431-43. 2007..e. before the mitochondrial DNA and well before the Y-chromosome most recent common ancestors...