Searching journal content for articles similar to Koo et al. 21 (6): 908.

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  1. Perspective: The genetics and epigenetics of satellite centromeres
    • Paul B. Talbert and
    • Steven Henikoff
    Genome Res. April 2022 32: 608-615; Published in Advance March 31, 2022, doi:10.1101/gr.275351.121
    ...reduce the impact of such positional flexibility.An intriguing feature of the DNA methylation patterns in active human centromeres is a hypomethylated region, known as the centromeric dip region, within a hypermethylated HOR that is occupied by CENPA (Gershman et al. 2022). The hypomethylated regions...
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  2. Research: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
    • Jonathan I. Gent,
    • Nathanael A. Ellis,
    • Lin Guo,
    • Alex E. Harkess,
    • Yingyin Yao,
    • Xiaoyu Zhang,
    • and R. Kelly Dawe
    Genome Res. April 2013 23: 628-637; Published in Advance December 26, 2012, doi:10.1101/gr.146985.112
    ...CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize Jonathan I. Gent 1 , Nathanael A. Ellis 1 , Lin Guo 1 , Alex E. Harkess 1 , Yingyin Yao 1 , Xiaoyu Zhang 1 and R. Kelly Dawe 1 , 2 , 3...
  3. LETTER: Differential methylation of genes and repeats in land plants
    • Pablo D. Rabinowicz,
    • Robert Citek,
    • Muhammad A. Budiman,
    • Andrew Nunberg,
    • Joseph A. Bedell,
    • Nathan Lakey,
    • Andrew L. O'Shaughnessy,
    • Lidia U. Nascimento,
    • W. Richard McCombie,
    • and Robert A. Martienssen
    Genome Res. October 2005 15: 1431-1440; doi:10.1101/gr.4100405
    ...is a common DNA modification among eukaryotes, typically in the form of cytosine methylated on carbon-5 (5-methylcytosine, 5mC). Saccharomyces cerevisiae has no 5mC, and in other fungi methylation is targeted to the scarce repeated DNA ( Selker 1990 ; Rossignol and Faugeron 1994 ). The levels and patterns...
  4. LETTER: Sequence, Regulation, and Evolution of the Maize 22-kD α Zein Gene Family
    • Rentao Song,
    • Victor Llaca,
    • Eric Linton,
    • and Joachim Messing
    Genome Res. November 1, 2001 11: 1817-1825; Published in Advance October 15, 2001, doi:10.1101/gr.197301
    .... The twenty-third copy of the gene family is also located on chromosome 4S at a site ∼20 cM closer to the centromere and appears to be the wild-type allele of the floury-2 ( fl2 ) mutation. On the basis of an analysis of maize cDNA databases, only seven of these genes appear to be expressed including the fl2...
  5. Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
    • Rodolphe Dombey,
    • Daniel Buendía-Ávila,
    • Verónica Barragán-Borrero,
    • Laura Diezma-Navas,
    • Arturo Ponce-Mañe,
    • José Mario Vargas-Guerrero,
    • Rana Elias,
    • and Arturo Marí-Ordóñez
    Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
    ...and epigenetic mechanisms are well characterized by molecular and genetic means. Furthermore, the two species display similar size and TE content (Fig. 1A).View larger version: In this window In a new window Figure 1. Spirodela polyrhiza sRNA and DNA methylation patterns. (A) Genome size, number, and genomic...
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  6. REPORT: A Contiguous 66-kb Barley DNA Sequence Provides Evidence for Reversible Genome Expansion
    • Ken Shirasu,
    • Alan H. Schulman,
    • Thomas Lahaye,
    • and Paul Schulze-Lefert
    Genome Res. July 1, 2000 10: 908-915; doi:10.1101/gr.10.7.908
    ..., which represent 30% of the human and 50% of the maize ( SanMiguel et al. 1996 ). To understand the relation of structure and repetitive DNAs to expansion/contraction, analysis of large contiguous genomic sequences is essential. In maize, a plant with a large , “diagnostic sequencing” was taken to study...
  7. Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
    • Alexandra Dallaire,
    • Bethan F. Manley,
    • Maya Wilkens,
    • Iliana Bista,
    • Clement Quan,
    • Edouard Evangelisti,
    • Charles R. Bradshaw,
    • Navin B. Ramakrishna,
    • Sebastian Schornack,
    • Falk Butter,
    • Uta Paszkowski,
    • and Eric A. Miska
    Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
    .... Whole- epigenomic profiling of R. irregularis provides direct evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a model in which TE activity shapes the , while DNA methylation and small RNA–mediated silencing keep their overproliferation in check. We propose...
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  8. Research: Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans
    • Jitendra Thakur and
    • Kaustuv Sanyal
    Genome Res. April 2013 23: 638-652; Published in Advance February 25, 2013, doi:10.1101/gr.141614.112
    .... albicanswhen a native centromere was deleted. However, the process of site selection for CENPA deposition on native or neocentromeres in the absence of defined DNA sequences remains elusive. By systematic deletion of CENPA chromatin-containing regions of variable length of different chromosomes, followed...
  9. Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
    • Ariadna Picart-Picolo,
    • Stefan Grob,
    • Nathalie Picault,
    • Michal Franek,
    • Christel Llauro,
    • Thierry Halter,
    • Tom R. Maier,
    • Edouard Jobet,
    • Julie Descombin,
    • Panpan Zhang,
    • Vijayapalani Paramasivan,
    • Thomas J. Baum,
    • Lionel Navarro,
    • Martina Dvořáčková,
    • Marie Mirouze,
    • and Frédéric Pontvianne
    Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
    ...on 3D organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we...
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  10. Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
    • Xiaofan Jin,
    • Geoff Fudenberg,
    • and Katherine S. Pollard
    Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
    ...interesting patterns related to recombination. Cis/total ratios quantify the fraction of contacts within versus between chromosomes. Low cis/total ratios are associated with increased spatial accessibility (not to be confused with DNA accessibility associated with nucleosome occupancy) (Kalhor et al. 2012...
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