Searching journal content for articles similar to Helmrich et al. 16 (10): 1222.

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  1. Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
    • Basanta Bista,
    • Laura González-Rodelas,
    • Lucía Álvarez-González,
    • Zhi-qiang Wu,
    • Eugenia E. Montiel,
    • Ling Sze Lee,
    • Daleen B. Badenhorst,
    • Srihari Radhakrishnan,
    • Robert Literman,
    • Beatriz Navarro-Dominguez,
    • John B. Iverson,
    • Simon Orozco-Arias,
    • Josefa González,
    • Aurora Ruiz-Herrera,
    • and Nicole Valenzuela
    Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
    ...are linked to evolutionary innovations in nonmodel vertebrates remains underexplored.Amniote vertebrates shared a last common ancestor ∼325 million years ago (Mya) (Shedlock and Edwards 2009) and are characterized by distinctive chromosome morphology and evolutionary adaptations. Sauropsids (lizards, snakes...
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  2. Research: Large transcription units unify copy number variants and common fragile sites arising under replication stress
    • Thomas E. Wilson,
    • Martin F. Arlt,
    • So Hae Park,
    • Sountharia Rajendran,
    • Michelle Paulsen,
    • Mats Ljungman,
    • and Thomas W. Glover
    Genome Res. February 2015 25: 189-200; Published in Advance November 4, 2014, doi:10.1101/gr.177121.114
    ...Corresponding author: wilsonte@umich.edu Abstract Copy number variants (CNVs) resulting from genomic deletions and duplications and common fragile sites (CFSs) seen as breaks on metaphase chromosomes are distinct forms of structural chromosome instability precipitated by replication inhibition...
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  3. Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
    • Arkarachai Fungtammasan,
    • Erin Walsh,
    • Francesca Chiaromonte,
    • Kristin A. Eckert,
    • and Kateryna D. Makova
    Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
    ...A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome? Arkarachai Fungtammasan 1 , 2 , 3 , Erin Walsh 3 , 4 , Francesca Chiaromonte 3 , 5 , 7 , Kristin A. Eckert 3 , 6 , 7...
  4. Research: Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes
    • Eskeatnaf Mulugeta,
    • Evelyne Wassenaar,
    • Esther Sleddens-Linkels,
    • Wilfred F.J. van IJcken,
    • Edith Heard,
    • J. Anton Grootegoed,
    • Walter Just,
    • Joost Gribnau,
    • and Willy M. Baarends
    Genome Res. September 2016 26: 1202-1210; Published in Advance August 10, 2016, doi:10.1101/gr.201665.115
    ...high percentages of amino acid identity to their mouse orthologs (ZFY1/2: 62%/64%; USP9Y: 77%) (Supplemental Tables S15, S16). It should be noted that we cannot exclude that additional Y-derived genes that were present on the Y Chromosome of the E. lutescens and E. talpinus common ancestor...
  5. Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
    • Christelle Cayrou,
    • Philippe Coulombe,
    • Alice Vigneron,
    • Slavica Stanojcic,
    • Olivier Ganier,
    • Isabelle Peiffer,
    • Eric Rivals,
    • Aurore Puy,
    • Sabine Laurent-Chabalier,
    • Romain Desprat,
    • and Marcel Méchali
    Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
    ...are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating...
  6. Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
    • Marcin von Grotthuss,
    • Michael Ashburner,
    • and José M. Ranz
    Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
    ...patterns of change and conservation across species. The orthologous landmarks more likely to be under constraint exhibit both a remarkable internal functional heterogeneity and a lack of common functional themes with the exception of the presence of highly conserved noncoding elements. Fragile regions...
  7. Research: Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
    • Wouter Meuleman,
    • Daan Peric-Hupkes,
    • Jop Kind,
    • Jean-Bernard Beaudry,
    • Ludo Pagie,
    • Manolis Kellis,
    • Marcel Reinders,
    • Lodewyk Wessels,
    • and Bas van Steensel
    Genome Res. February 2013 23: 270-280; Published in Advance November 2, 2012, doi:10.1101/gr.141028.112
    ..., shown for a 40-Mb region of chromosome 2. (B) Regions common to all cell types are termed cLADs (mustard) and ciLADs (cyan), with dynamic regions termed fLADs (gray). (C )Meanprofile of lamin B1 association in the cell types indicated inA. Colors as in B. The core architecture of constitutive...
  8. Letter: Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
    • Denis M. Larkin,
    • Greg Pape,
    • Ravikiran Donthu,
    • Loretta Auvil,
    • Michael Welge,
    • and Harris A. Lewin
    Genome Res. May 2009 19: 770-777; Published in Advance April 2, 2009, doi:10.1101/gr.086546.108
    ...as a reuse breakpoint (Murphy et al. 2005). A special case is the identification of EBRs specific to the reference . Such EBRs were identified as those common to all s or all s except one species from a different clade (to allow for a small number of possible errors in EBR coordinates) relative...
  9. Dog Special/Letters: Hotspots of mutation and breakage in dog and human chromosomes
    • Caleb Webber and
    • Chris P. Ponting
    Genome Res. December 2005 15: 1787-1797; doi:10.1101/gr.3896805
    ...correlation to be greatest for dog and human orthologs ( Table 2 ); among individual dog chromosomes, the correlation coefficient rises to a value of 0.80 (CFA6 and CFA31). Once more, the correlation is least for mouse and rat orthologs, despite these species sharing a more recent common ancestor. View...
  10. Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
    • Ignacio Maeso,
    • Manuel Irimia,
    • Juan J. Tena,
    • Esther González-Pérez,
    • David Tran,
    • Vydianathan Ravi,
    • Byrappa Venkatesh,
    • Sonsoles Campuzano,
    • José Luis Gómez-Skarmeta,
    • and Jordi Garcia-Fernàndez
    Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
    ...al. 2011), most validated Sowah enhancers were located in a common set of conserved and exceptionally long introns (introns 5–9), suggesting the possibility of an ancestral regulatory system for this GRB in all bilaterians. In addition, these results show that GRBs, as a particular type of functional...
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