Journal ArticleDOI
Mobile elements: drivers of genome evolution.
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Mobile elements within genomes have driven genome evolution in diverse ways and are becoming useful tools for learning more about genome evolution and gene function.Abstract:
Mobile elements within genomes have driven genome evolution in diverse ways. Particularly in plants and mammals, retrotransposons have accumulated to constitute a large fraction of the genome and have shaped both genes and the entire genome. Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function.read more
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Molecular and functional genetics of the proopiomelanocortin gene, food intake regulation and obesity.
TL;DR: Light is shed on the power and limitations of the mammalian central satiety pathways and may contribute to the development of individual and collective strategies to reduce the debilitating effects of the self‐induced obesity pandemia.
Journal ArticleDOI
Characterization of pre-insertion loci of de novo L1 insertions.
Stephen L. Gasior,Graeme Preston,Dale J. Hedges,Nicolas Gilbert,John V. Moran,Prescott L. Deininger +5 more
TL;DR: The analysis of the repetitive element and G+C composition of more than 100 pre-insertion loci derived from de novo L1 insertions in cultured human cancer cells suggests that the initial insertion preference of L1, while A+T-rich in the initial vicinity of the break site, can be influenced by the broader content of the flanking genomic region.
Journal ArticleDOI
Epigenetics: a way to understand the origin and biology of testicular germ cell tumors.
TL;DR: This review summarizes recent research progress in the epigenetics of testicular germ cell tumors in an attempt to explain the abovementioned biological and clinical characteristics oftesticular germcell tumors.
Journal ArticleDOI
Acquisition of Insertion Sequences and the GBSi1 Intron by Streptococcus agalactiae Isolates Correlates with the Evolution of the Species
Geneviève Héry-Arnaud,Guillaume Bruant,Philippe Lanotte,Stella Brun,Agnès Rosenau,Nathalie van der Mee-Marquet,Roland Quentin,Laurent Mereghetti +7 more
TL;DR: The prevalence of insertion sequences IS1548, IS861, IS1381, and ISSa4 and of the group II intron GBSi1 within Streptococcus agalactiae human isolates strongly correlates with the genetic lineages obtained by multilocus sequence typing.
Journal ArticleDOI
Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila
TL;DR: Results show that rates within the genus Drosophila vary substantially between lineages, even within a single species group, and suggest that the phylogenetic relationships in this lineage of the repleta group should be reconsidered.
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Journal ArticleDOI
Initial sequencing and analysis of the human genome.
Eric S. Lander,Lauren Linton,Bruce W. Birren,Chad Nusbaum,Michael C. Zody,Jennifer Baldwin,Keri Devon,Ken Dewar,Michael Doyle,William Fitzhugh,Roel Funke,Diane Gage,Katrina Harris,Andrew Heaford,John Howland,Lisa Kann,Jessica A. Lehoczky,Rosie Levine,Paul A. McEwan,Kevin McKernan,James Meldrim,Jill P. Mesirov,Cher Miranda,William Morris,Jerome Naylor,Christina Raymond,Mark Rosetti,Ralph Santos,Andrew Sheridan,Carrie Sougnez,Nicole Stange-Thomann,Nikola Stojanovic,Aravind Subramanian,Dudley Wyman,Jane Rogers,John Sulston,R Ainscough,Stephan Beck,David Bentley,John Burton,C M Clee,Nigel P. Carter,Alan Coulson,Rebecca Deadman,Panos Deloukas,Andrew Dunham,Ian Dunham,Richard Durbin,Lisa French,Darren Grafham,Simon G. Gregory,Tim Hubbard,Sean Humphray,Adrienne Hunt,Matthew Jones,Christine Lloyd,Amanda McMurray,Lucy Matthews,Simon Mercer,Sarah Milne,James C. Mullikin,Andrew J. Mungall,Robert W. Plumb,Mark T. Ross,Ratna Shownkeen,Sarah Sims,Robert H. Waterston,Richard K. Wilson,LaDeana W. Hillier,John Douglas Mcpherson,Marco A. Marra,Elaine R. Mardis,Lucinda Fulton,Asif T. Chinwalla,Kymberlie H. Pepin,Warren Gish,Stephanie L. Chissoe,Michael C. Wendl,Kim D. Delehaunty,Tracie L. Miner,Andrew Delehaunty,Jason B. Kramer,Lisa Cook,Robert S. Fulton,Douglas L. Johnson,Patrick Minx,Sandra W. Clifton,Trevor Hawkins,Elbert Branscomb,Paul Predki,Paul G. Richardson,Sarah Wenning,Tom Slezak,Norman A. Doggett,Jan Fang Cheng,Anne S. Olsen,Susan Lucas,Christopher J. Elkin,Edward Uberbacher,Marvin Frazier,Richard A. Gibbs,Donna M. Muzny,Steven E. Scherer,John Bouck,Erica Sodergren,Kim C. Worley,Catherine M. Rives,James H. Gorrell,Michael L. Metzker,Susan L. Naylor,Raju Kucherlapati,David L. Nelson,George M. Weinstock,Yoshiyuki Sakaki,Asao Fujiyama,Masahira Hattori,Tetsushi Yada,Atsushi Toyoda,Takehiko Itoh,Chiharu Kawagoe,Hidemi Watanabe,Yasushi Totoki,Todd D. Taylor,Jean Weissenbach,Roland Heilig,William Saurin,François Artiguenave,Philippe Brottier,Thomas Brüls,Eric Pelletier,Catherine Robert,Patrick Wincker,André Rosenthal,Matthias Platzer,Gerald Nyakatura,Stefan Taudien,Andreas Rump,Douglas R. Smith,Lynn Doucette-Stamm,Marc Rubenfield,Keith Weinstock,Mei Lee Hong,Joann Dubois,Huanming Yang,Jun Yu,Jian Wang,Guyang Huang,Jun Gu,Leroy Hood,Lee Rowen,Anup Madan,Shizen Qin,Ronald W. Davis,Nancy A. Federspiel,A. Pia Abola,Michael Proctor,Bruce A. Roe,Feng Chen,Huaqin Pan,Juliane Ramser,Hans Lehrach,Richard Reinhardt,W. Richard McCombie,Melissa De La Bastide,Neilay Dedhia,H. Blöcker,K. Hornischer,Gabriele Nordsiek,Richa Agarwala,L. Aravind,Jeffrey A. Bailey,Alex Bateman,Serafim Batzoglou,Ewan Birney,Peer Bork,Daniel G. Brown,Christopher B. Burge,Lorenzo Cerutti,Hsiu Chuan Chen,Deanna M. Church,Michele Clamp,Richard R. Copley,Tobias Doerks,Sean R. Eddy,Evan E. Eichler,Terrence S. Furey,James E. Galagan,James G. R. Gilbert,Cyrus L. Harmon,Yoshihide Hayashizaki,David Haussler,Henning Hermjakob,Karsten Hokamp,Wonhee Jang,L. Steven Johnson,Thomas A. Jones,Simon Kasif,Arek Kaspryzk,Scot Kennedy,W. James Kent,Paul Kitts,Eugene V. Koonin,Ian F Korf,David Kulp,Doron Lancet,Todd M. Lowe,Aoife McLysaght,Tarjei S. Mikkelsen,John V. Moran,Nicola Mulder,Victor J. Pollara,Chris P. Ponting,Greg Schuler,Jörg Schultz,Guy Slater,Arian F.A. Smit,Elia Stupka,Joseph Szustakowki,Danielle Thierry-Mieg,Jean Thierry-Mieg,Lukas Wagner,John W. Wallis,Raymond Wheeler,Alan Williams,Yuri I. Wolf,Kenneth H. Wolfe,Shiaw Pyng Yang,Ru Fang Yeh,Francis S. Collins,Mark S. Guyer,Jane Peterson,Adam Felsenfeld,Kris A. Wetterstrand,Richard M. Myers,Jeremy Schmutz,Mark Dickson,Jane Grimwood,David R. Cox,Maynard V. Olson,Rajinder Kaul,Christopher K. Raymond,Nobuyoshi Shimizu,Kazuhiko Kawasaki,Shinsei Minoshima,Glen A. Evans,Maria Athanasiou,Roger A. Schultz,Aristides Patrinos,Michael J. Morgan +248 more
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI
Initial sequencing and comparative analysis of the mouse genome.
Robert H. Waterston,Kerstin Lindblad-Toh,Ewan Birney,Jane Rogers,Josep F. Abril,Pankaj K. Agarwal,Richa Agarwala,Rachel Ainscough,Marina Alexandersson,Peter An,Stylianos E. Antonarakis,John Attwood,Robert Baertsch,J Bailey,K F Barlow,Stephan Beck,Eric Berry,Bruce W. Birren,Toby Bloom,Peer Bork,Marc Botcherby,Nicolas Bray,Michael R. Brent,Daniel G. Brown,Daniel G. Brown,Stephen D. Brown,Carol J. Bult,John Burton,Jonathan Butler,R. D. Campbell,Piero Carninci,Simon Cawley,Francesca Chiaromonte,Asif T. Chinwalla,Deanna M. Church,Michele Clamp,C M Clee,Francis S. Collins,Lisa Cook,Richard R. Copley,Alan Coulson,Olivier Couronne,James Cuff,Val Curwen,Tim Cutts,Mark J. Daly,Robert David,Joy Davies,Kimberly D. Delehaunty,Justin Deri,Emmanouil T. Dermitzakis,Colin N. Dewey,Nicholas J. Dickens,Mark Diekhans,Sheila Dodge,Inna Dubchak,Diane M. Dunn,Sean R. Eddy,Laura Elnitski,Richard D. Emes,Pallavi Eswara,Eduardo Eyras,Adam Felsenfeld,Ginger A. Fewell,Paul Flicek,Karen Foley,Wayne N. Frankel,Lucinda Fulton,Robert S. Fulton,Terrence S. Furey,Diane Gage,Richard A. Gibbs,Gustavo Glusman,Sante Gnerre,Nick Goldman,Leo Goodstadt,Darren Grafham,Tina Graves,Eric D. Green,Simon G. Gregory,Roderic Guigó,Mark S. Guyer,Ross C. Hardison,David Haussler,Yoshihide Hayashizaki,Deana W. LaHillier,Angela S. Hinrichs,Wratko Hlavina,Timothy Holzer,Fan Hsu,Axin Hua,Tim Hubbard,Adrienne Hunt,Ian J. Jackson,David B. Jaffe,L. Steven Johnson,Matthew Jones,Thomas A. Jones,A Joy,Michael Kamal,Elinor K. Karlsson,Donna Karolchik,Arkadiusz Kasprzyk,Jun Kawai,Evan Keibler,Cristyn Kells,W. James Kent,Andrew Kirby,Diana L. Kolbe,Ian F Korf,Raju Kucherlapati,Edward J. Kulbokas,David Kulp,Tom Landers,J. P. Leger,Steven Leonard,Ivica Letunic,Rosie Levine,Jia Li,Ming Li,Christine Lloyd,Susan Lucas,Bin Ma,Donna Maglott,Elaine R. Mardis,Lucy Matthews,Evan Mauceli,John Mayer,Megan McCarthy,W. Richard McCombie,Stuart McLaren,Kirsten McLay,John Douglas Mcpherson,James Meldrim,Beverley Meredith,Jill P. Mesirov,Webb Miller,Tracie L. Miner,Emmanuel Mongin,Kate Montgomery,Michael J. Morgan,Richard Mott,James C. Mullikin,Donna M. Muzny,William E. Nash,Joanne O. Nelson,Michael N. Nhan,Robert Nicol,Zemin Ning,Chad Nusbaum,Michael J. O’Connor,Yasushi Okazaki,Karen Oliver,Emma Overton-Larty,Lior Pachter,Genís Parra,Kymberlie H. Pepin,Jane Peterson,Pavel A. Pevzner,Robert W. Plumb,Craig Pohl,Alex Poliakov,Tracy C. Ponce,Chris P. Ponting,Simon C. Potter,Michael A. Quail,Alexandre Reymond,Bruce A. Roe,Krishna M. Roskin,Edward M. Rubin,Alistair G. Rust,Ralph Santos,Victor Sapojnikov,Brian Schultz,Jörg Schultz,Matthias S. Schwartz,Scott Schwartz,Carol Scott,Steven Seaman,Steve Searle,Ted Sharpe,Andrew Sheridan,Ratna Shownkeen,Sarah Sims,Jonathan Singer,Guy Slater,Arian F.A. Smit,Douglas Smith,Brian Spencer,Arne Stabenau,Nicole Stange-Thomann,Charles W. Sugnet,Mikita Suyama,Glenn Tesler,Johanna Thompson,David Torrents,Evanne Trevaskis,John Tromp,Catherine Ucla,Abel Ureta-Vidal,Jade P. Vinson,Andrew von Niederhausern,Claire M. Wade,Melanie M. Wall,R. J. Weber,Robert B. Weiss,Michael C. Wendl,Anthony P. West,Kris A. Wetterstrand,Raymond Wheeler,Simon Whelan,Jamey Wierzbowski,David Willey,Sophie Williams,Richard K. Wilson,Eitan E. Winter,Kim C. Worley,Dudley Wyman,Shan Yang,Shiaw Pyng Yang,Evgeny M. Zdobnov,Michael C. Zody,Eric S. Lander +222 more
TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Journal ArticleDOI
LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1.
Salima Hacein-Bey-Abina,C von Kalle,C von Kalle,Manfred Schmidt,Matthew P. McCormack,NM Wulffraat,Philippe Leboulch,Annick Lim,Cameron S. Osborne,R. Pawliuk,Estelle Morillon,R. Sorensen,A. Forster,Peter Fraser,Jeffrey I. Cohen,G de Saint Basile,Ian E. Alexander,Uwe Wintergerst,Thierry Frebourg,Alain Aurias,Dominique Stoppa-Lyonnet,Serge Romana,I. Radford-Weiss,Fabian Gross,Françoise Valensi,Eric Delabesse,Elizabeth Macintyre,F. Sigaux,Jean Soulier,L. E. Leiva,Manuela Wissler,Claudia Prinz,Terence H. Rabbitts,F. Le Deist,Alain Fischer,Marina Cavazzana-Calvo +35 more
TL;DR: Retrovirus vector insertion can trigger deregulated premalignant cell proliferation with unexpected frequency, most likely driven by retrovirus enhancer activity on the LMO2 gene promoter.
Journal ArticleDOI
hEST2, the Putative Human Telomerase Catalytic Subunit Gene, Is Up-Regulated in Tumor Cells and during Immortalization
Matthew Meyerson,Christopher M. Counter,Elinor Ng Eaton,Leif W. Ellisen,Philipp Steiner,Stephanie Dickinson Caddle,Liuda Ziaugra,Roderick L. Beijersbergen,Michael J. Davidoff,Qingyun Liu,Silvia Bacchetti,Daniel A. Haber,Robert A. Weinberg +12 more
TL;DR: The cloning of a human gene, hEST2, that shares significant sequence similarity with the telomerase catalytic subunit genes of lower eukaryotes is reported, suggesting that the induction of hEST 2 mRNA expression is required for the telomersase activation that occurs during cellular immortalization and tumor progression.
Journal ArticleDOI
HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots
Astrid R. W Schroder,Paul Shinn,Huaming Chen,Charles C. Berry,Joseph R. Ecker,Frederic D. Bushman +5 more
TL;DR: Global analysis of cellular transcription indicated that active genes were preferential integration targets, particularly genes that were activated in cells after infection by HIV-1, and this data suggests how selective targeting promotes aggressive HIV replication.
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