Searching journal content for articles similar to Alkan et al. 21 (1): 137.

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  1. Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
    • Yang Liu,
    • Qian Liu,
    • Handong Su,
    • Kunpeng Liu,
    • Xue Xiao,
    • Wei Li,
    • Qianwen Sun,
    • James A. Birchler,
    • and Fangpu Han
    Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
    ...of CENH3, a variant of histone H3, which is also known as CENPA in animals (Henikoff et al. 2001; Dhatchinamoorthy et al. 2018). In animals, centromeric DNA is comprised of megabases of tandemly repeated “satellite” sequences (Manuelidis 1978), whereas in plants, multiple retrotransposons are interspersed...
  2. Method: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
    • Arshad H. Khan,
    • Andy Lin,
    • Richard T. Wang,
    • Joshua S. Bloom,
    • Kenneth Lange,
    • and Desmond J. Smith
    Genome Res. October 2020 30: 1458-1467; Published in Advance September 2, 2020, doi:10.1101/gr.262204.120
    ...and Y centromeres have been characterized in their entirety using long-read sequencing, with the α-satellite repeats necessary for centromere function extending over 2.8 Mb and 365 kb, respectively (Jain et al. 2018; Miga et al. 2020). The long reads were placed using landmark patterns of specific...
  3. Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
    • Franck Court,
    • Chiharu Tayama,
    • Valeria Romanelli,
    • Alex Martin-Trujillo,
    • Isabel Iglesias-Platas,
    • Kohji Okamura,
    • Naoko Sugahara,
    • Carlos Simón,
    • Harry Moore,
    • Julie V. Harness,
    • Hans Keirstead,
    • Jose Vicente Sanchez-Mut,
    • Eisuke Kaneki,
    • Pablo Lapunzina,
    • Hidenobu Soejima,
    • Norio Wake,
    • Manel Esteller,
    • Tsutomu Ogata,
    • Kenichiro Hata,
    • Kazuhiko Nakabayashi,
    • and David Monk
    Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
    ...the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted methylation in a substantial range of normal human tissues, reciprocal genome-wide uniparental...
  4. Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
    • Jianghan Qu,
    • Emily Hodges,
    • Antoine Molaro,
    • Pascal Gagneux,
    • Matthew D. Dean,
    • Gregory J. Hannon,
    • and Andrew D. Smith
    Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
    ...the evolution of regulatory systems in different species.Existing comparative analyses of mammalian methylomes have increased our understanding of DNA methylation divergence. Methylation states across multiple primate species recapitulate their phylogenetic relationship (Martin et al. 2011), and greater...
  5. Research: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    • Aaron R. Quinlan,
    • Royden A. Clark,
    • Svetlana Sokolova,
    • Mitchell L. Leibowitz,
    • Yujun Zhang,
    • Matthew E. Hurles,
    • Joshua C. Mell,
    • and Ira M. Hall
    Genome Res. May 2010 20: 623-635; Published in Advance March 22, 2010, doi:10.1101/gr.102970.109
    ...Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome Aaron R. Quinlan 1 , Royden A. Clark 1 , Svetlana Sokolova 1 , Mitchell L. Leibowitz 1 , Yujun Zhang 2 , Matthew E. Hurles 2 , Joshua C...
  6. Research: Characterization and dynamics of pericentromere-associated domains in mice
    • Patrick J. Wijchers,
    • Geert Geeven,
    • Michael Eyres,
    • Atze J. Bergsma,
    • Mark Janssen,
    • Marjon Verstegen,
    • Yun Zhu,
    • Yori Schell,
    • Carlo Vermeulen,
    • Elzo de Wit,
    • and Wouter de Laat
    Genome Res. July 2015 25: 958-969; Published in Advance April 16, 2015, doi:10.1101/gr.186643.114
    ...) suggested that the identified PADs replicate late in S phase (Fig. 2C), similar to pericentromeric satellite repeats themselves. Genome-wide association maps of mammalian s have revealed that active and inactive regions are tightly segregated into an “A” and “B” compartment, with regions from either...
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  7. Method: Reconstructing complex regions of genomes using long-read sequencing technology
    • John Huddleston,
    • Swati Ranade,
    • Maika Malig,
    • Francesca Antonacci,
    • Mark Chaisson,
    • Lawrence Hon,
    • Peter H. Sudmant,
    • Tina A. Graves,
    • Can Alkan,
    • Megan Y. Dennis,
    • Richard K. Wilson,
    • Stephen W. Turner,
    • Jonas Korlach,
    • and Evan E. Eichler
    Genome Res. April 2014 24: 688-696; Published in Advance January 13, 2014, doi:10.1101/gr.168450.113
    ...characterization of centromeric satellites from multiple mammalian s. Genome Res 21: 137–145. Alkan C, Sajjadian S, Eichler EE. 2011b. Limitations of next-generation sequence assembly. Nat Methods 8: 61–65. Au KF, Underwood JG, Lee L, WongWH. 2012. Improving PacBio long read accuracy by short read alignment. PLo...
  8. Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
    • Cristian Groza,
    • Bing Ge,
    • Warren A. Cheung,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
    ...from the CHM13v2 reference (SV-CpGs), thus expanding their number by 43.6%. Using 435 methylomes, we genotyped 4.06 million SV-CpGs, of which 3.93 million (96.8%) are methylated at least once. Nonrepeat sequences contribute 1.59 × 106 novel SV-CpGs, followed by centromeric satellites (6.57 × 105...
  9. REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
    • Laura Elnitski,
    • Victor X. Jin,
    • Peggy J. Farnham,
    • and Steven J.M. Jones
    Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
    ...Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques Laura Elnitski 1 , 4 , Victor X. Jin 2 , Peggy J. Farnham 2 , and Steven J.M. Jones 3 1 Genomic Functional Analysis Section...
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  10. Review: The structure, function, and evolution of plant centromeres
    • Matthew Naish and
    • Ian R. Henderson
    Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
    ..., and indirect evidence for this exists in multiple species, including humans and maize (Chatterjee and Lo 1989; Mahtani and Willard 1990; Nijman and Lenstra 2001; Rudd et al. 2006; Shi et al. 2010; Wolfgruber et al. 2016). Centromeric satellite recombination could occur during meiosis, in which either a homolog...
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