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  1. Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
    • Koichi Kitao,
    • Kenji Ichiyanagi,
    • and So Nakagawa
    Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
    ...Corresponding authors: kitao.z7deb13@gmail.com, so@tokai.ac.jpAbstractTransposons, occasionally domesticated as novel host protein-coding genes, are responsible for the lineage-specific functions in vertebrates. LINE-1 (L1) is one of the most active transposons in the vertebrate s. Despite its abundance, few...
  2. Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
    • Vedran Franke,
    • Sravya Ganesh,
    • Rosa Karlic,
    • Radek Malik,
    • Josef Pasulka,
    • Filip Horvat,
    • Maja Kuzman,
    • Helena Fulka,
    • Marketa Cernohorska,
    • Jana Urbanova,
    • Eliska Svobodova,
    • Jun Ma,
    • Yutaka Suzuki,
    • Fugaku Aoki,
    • Richard M. Schultz,
    • Kristian Vlahovicek,
    • and Petr Svoboda
    Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
    ...in red, SINE insertions in green, and a large LINE-1 insert in blue. The conserved 3′ UTR region is framed. (B) CAG trinucleotide density in MTD-driven transcripts in mice, rat, and hamster. Each CAG is represented by a vertical line. The widening depicts the coding sequence; the initiation codon...
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  3. Method: Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing
    • Nara L.M. Sobreira,
    • Veena Gnanakkan,
    • Michael Walsh,
    • Beth Marosy,
    • Elizabeth Wohler,
    • George Thomas,
    • Julie E. Hoover-Fong,
    • Ada Hamosh,
    • Sarah J. Wheelan,
    • and David Valle
    Genome Res. October 2011 21: 1720-1727; Published in Advance September 2, 2011, doi:10.1101/gr.122986.111
    ...,081,810–67,793,011 bp, and chromosome 6 from 45,166,074–45,806,126 bp. These regions totaled 5.6 Mb, but after removing repetitive regions, the total length captured was ;3.5 Mb. The baits were 120 bp long, and the average bait coverage of each base in the target region was 23. We avoided standard repeat masked regions...
  4. Research: Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus
    • Yasuhiro Yamamoto,
    • Toshiaki Watanabe,
    • Yuko Hoki,
    • Kenjiro Shirane,
    • Yufeng Li,
    • Kenji Ichiiyanagi,
    • Satomi Kuramochi-Miyagawa,
    • Atsushi Toyoda,
    • Asao Fujiyama,
    • Masayuki Oginuma,
    • Hitomi Suzuki,
    • Takashi Sado,
    • Toru Nakano,
    • and Hiroyuki Sasaki
    Genome Res. February 2013 23: 292-299; Published in Advance November 6, 2012, doi:10.1101/gr.137224.112
    .... 2006; Girard et al. 2006; Grivna et al. 2006a; Lau et al. 2006; Watanabe et al. 2006), their role in retrotransposon silencing is less clear. A partial deletion of a pachytene piRNA cluster, however, was reported to result in increased expression of LINE-1 ORF1 proteins (Xu et al. 2008). A more recent...
  5. ARTICLE: Shuffling of Genes Within Low-Copy Repeats on 22q11 (LCR22) by Alu-Mediated Recombination Events During Evolution
    • Melanie Babcock,
    • Adam Pavlicek,
    • Elizabeth Spiteri,
    • Catherine D. Kashork,
    • Ilya Ioshikhes,
    • Lisa G. Shaffer,
    • Jerzy Jurka,
    • and Bernice E. Morrow
    Genome Res. December 2003 13: 2519-2532; doi:10.1101/gr.1549503
    ...kinkable DNA sites. Such sites may represent focal points for recombination. Thus, shuffling by Alu -mediated rearrangements has contributed to architecture during primate evolution. Segmental duplications, or low-copy repeats (LCRs) of >95% sequence identity, cluster within different chromosome regions...
  6. ARTICLE: Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27
    • Natalay Kouprina,
    • Adam Pavlicek,
    • Vladimir N. Noskov,
    • Greg Solomon,
    • John Otstot,
    • William Isaacs,
    • John D. Carpten,
    • Jeffrey M. Trent,
    • Joanna Schleutker,
    • J. Carl Barrett,
    • Jerzy Jurka,
    • and Vladimir Larionov
    Genome Res. November 2005 15: 1477-1486; doi:10.1101/gr.4212705
    ...demonstrated a role of interspersed repeats (such as LINE1 and Alu ) in generating SDs (Figs. 2A and 3 ). It is notable that the human SPANX-B gene contains a specific 18-bp insertion in the exon 1 sequence. We found that SPANX-B of African Great Apes lacks a 18-bp insertion ( Fig. 2B ; Supplemental Fig. 6S...
  7. Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    • Jonas A. Gustafson,
    • Sophia B. Gibson,
    • Nikhita Damaraju,
    • Miranda P.G. Zalusky,
    • Kendra Hoekzema,
    • David Twesigomwe,
    • Lei Yang,
    • Anthony A. Snead,
    • Phillip A. Richmond,
    • Wouter De Coster,
    • Nathan D. Olson,
    • Andrea Guarracino,
    • Qiuhui Li,
    • Angela L. Miller,
    • Joy Goffena,
    • Zachary B. Anderson,
    • Sophie H.R. Storz,
    • Sydney A. Ward,
    • Maisha Sinha,
    • Claudia Gonzaga-Jauregui,
    • Wayne E. Clarke,
    • Anna O. Basile,
    • André Corvelo,
    • Catherine Reeves,
    • Adrienne Helland,
    • Rajeeva Lochan Musunuri,
    • Mahler Revsine,
    • Karynne E. Patterson,
    • Cate R. Paschal,
    • Christina Zakarian,
    • Sara Goodwin,
    • Tanner D. Jensen,
    • Esther Robb,
    • The 1000 Genomes ONT Sequencing Consortium,
    • University of Washington Center for Rare Disease Research (UW-CRDR),
    • Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
    • William Richard McCombie,
    • Fritz J. Sedlazeck,
    • Justin M. Zook,
    • Stephen B. Montgomery,
    • Erik Garrison,
    • Mikhail Kolmogorov,
    • Michael C. Schatz,
    • Richard N. McLaughlin, Jr.,
    • Harriet Dashnow,
    • Michael C. Zody,
    • Matt Loose,
    • Miten Jain,
    • Evan E. Eichler,
    • and Danny E. Miller
    Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
    ...). Furthermore, there was minimal variation among the 100 assemblies in interspersed repeat content.Among the youngest polymorphic interspersed repeats that are too long to resolve with short reads (Chaisson et al. 2019), LINE-1s (∼6000 bp) are the only types that are actively expanding in the human . We found...
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  8. Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
    • Peter A. Audano and
    • Christine R. Beck
    Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
    ...bp were merged with BEDTools merge (v2.30.0) (Quinlan and Hall 2010), a 200-bp flank was added to all merged regions, and SVs were intersected with both TRF and RMSK. Insertions were marked as TRs if their insertion point was within a padded repeat region. Deletions were marked as TRs if either...
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  9. LETTER: Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
    • Santhosh Girirajan,
    • Lin Chen,
    • Tina Graves,
    • Tomas Marques-Bonet,
    • Mario Ventura,
    • Catrina Fronick,
    • Lucinda Fulton,
    • Mariano Rocchi,
    • Robert S. Fulton,
    • Richard K. Wilson,
    • Elaine R. Mardis,
    • and Evan E. Eichler
    Genome Res. February 2009 19: 178-190; Published in Advance November 24, 2008, doi:10.1101/gr.086041.108
    ...) a “hodgepodge” of repeats, ( vi ) segmental duplications, and ( vii ) LINE-1 elements. The diagram is not to scale. Six breakpoints contained larger insertion sequences ranging from >1 kbp up to 20 kbp in length ( Table 1 ; Supplemental File 1). Three of these corresponded to LINE elements (one case...
  10. RESOURCE: Initial sequence and comparative analysis of the cat genome
    • Joan U. Pontius,
    • James C. Mullikin,
    • Douglas R. Smith,
    • Agencourt Sequencing Team,
    • Kerstin Lindblad-Toh,
    • Sante Gnerre,
    • Michele Clamp,
    • Jean Chang,
    • Robert Stephens,
    • Beena Neelam,
    • Natalia Volfovsky,
    • Alejandro A. Schäffer,
    • Richa Agarwala,
    • Kristina Narfström,
    • William J. Murphy,
    • Urs Giger,
    • Alfred L. Roca,
    • Agostinho Antunes,
    • Marilyn Menotti-Raymond,
    • Naoya Yuhki,
    • Jill Pecon-Slattery,
    • Warren E. Johnson,
    • Guillaume Bourque,
    • Glenn Tesler,
    • NISC Comparative Sequencing Program,
    • and Stephen J. O’Brien
    Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
    ...mitochondrial ( numt ) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs...
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