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  • 1
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    Construction and analysis of a human-chimpanzee comparative clone map (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-01-05
    Description: The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes us human. Here we present a first-generation human-chimpanzee comparative genome map and its initial analysis. The map was constructed through paired alignment of 77,461 chimpanzee bacterial artificial chromosome end sequences with publicly available human genome sequences. We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fujiyama, Asao -- Watanabe, Hidemi -- Toyoda, Atsushi -- Taylor, Todd D -- Itoh, Takehiko -- Tsai, Shih-Feng -- Park, Hong-Seog -- Yaspo, Marie-Laure -- Lehrach, Hans -- Chen, Zhu -- Fu, Gang -- Saitou, Naruya -- Osoegawa, Kazutoyo -- de Jong, Pieter J -- Suto, Yumiko -- Hattori, Masahira -- Sakaki, Yoshiyuki -- New York, N.Y. -- Science. 2002 Jan 4;295(5552):131-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. afujiyam@gsc.riken.go.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11778049" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Chromosomes, Human, Pair 21/genetics ; Cloning, Molecular ; Contig Mapping ; Female ; Gene Library ; *Genome ; *Genome, Human ; Humans ; Male ; Pan troglodytes/*genetics ; *Physical Chromosome Mapping ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Tagged Sites ; X Chromosome/genetics ; Y Chromosome/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-07-05
    Description: The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We used shotgun sequencing of transcripts to generate randomly distributed reads. Of these, 50% mapped to unique genomic locations, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to nonannotated genomic regions. On the basis of known transcripts, RNA-Seq can detect 25% more genes than can microarrays. A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sultan, Marc -- Schulz, Marcel H -- Richard, Hugues -- Magen, Alon -- Klingenhoff, Andreas -- Scherf, Matthias -- Seifert, Martin -- Borodina, Tatjana -- Soldatov, Aleksey -- Parkhomchuk, Dmitri -- Schmidt, Dominic -- O'Keeffe, Sean -- Haas, Stefan -- Vingron, Martin -- Lehrach, Hans -- Yaspo, Marie-Laure -- New York, N.Y. -- Science. 2008 Aug 15;321(5891):956-60. doi: 10.1126/science.1160342. Epub 2008 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599741" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Cell Line ; Cell Line, Tumor ; Computational Biology ; DNA, Complementary ; DNA, Intergenic ; Exons ; *Gene Expression Profiling ; *Genome, Human ; Humans ; Introns ; Oligonucleotide Array Sequence Analysis ; RNA Polymerase II/metabolism ; *RNA Splice Sites ; RNA, Messenger/*genetics ; *Sequence Analysis, RNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-11-26
    Description: Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Henriet, Simon -- Mungpakdee, Sutada -- Aury, Jean-Marc -- Da Silva, Corinne -- Brinkmann, Henner -- Mikhaleva, Jana -- Olsen, Lisbeth Charlotte -- Jubin, Claire -- Canestro, Cristian -- Bouquet, Jean-Marie -- Danks, Gemma -- Poulain, Julie -- Campsteijn, Coen -- Adamski, Marcin -- Cross, Ismael -- Yadetie, Fekadu -- Muffato, Matthieu -- Louis, Alexandra -- Butcher, Stephen -- Tsagkogeorga, Georgia -- Konrad, Anke -- Singh, Sarabdeep -- Jensen, Marit Flo -- Huynh Cong, Evelyne -- Eikeseth-Otteraa, Helen -- Noel, Benjamin -- Anthouard, Veronique -- Porcel, Betina M -- Kachouri-Lafond, Rym -- Nishino, Atsuo -- Ugolini, Matteo -- Chourrout, Pascal -- Nishida, Hiroki -- Aasland, Rein -- Huzurbazar, Snehalata -- Westhof, Eric -- Delsuc, Frederic -- Lehrach, Hans -- Reinhardt, Richard -- Weissenbach, Jean -- Roy, Scott W -- Artiguenave, Francois -- Postlethwait, John H -- Manak, J Robert -- Thompson, Eric M -- Jaillon, Olivier -- Du Pasquier, Louis -- Boudinot, Pierre -- Liberles, David A -- Volff, Jean-Nicolas -- Philippe, Herve -- Lenhard, Boris -- Roest Crollius, Hugues -- Wincker, Patrick -- Chourrout, Daniel -- Z01 LM000073-12/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Institut de Genomique, Genoscope, Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097902" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA Transposable Elements ; DNA, Intergenic ; Exons ; Gene Order ; Genes, Duplicate ; Genes, Homeobox ; *Genome ; Introns ; Invertebrates/classification/genetics ; Molecular Sequence Data ; Recombination, Genetic ; Spliceosomes/metabolism ; Synteny ; Urochordata/anatomy & histology/classification/*genetics/immunology ; Vertebrates/classification/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
    Location Call Number Expected Availability
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