Searching journal content for articles similar to Zachgo et al. 6 (1): 19.

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  1. Research: Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map
    • Rik Kooke,
    • Lionel Morgado,
    • Frank Becker,
    • Henriëtte van Eekelen,
    • Rashmi Hazarika,
    • Qunfeng Zheng,
    • Ric C.H. de Vos,
    • Frank Johannes,
    • and Joost J.B. Keurentjes
    Genome Res. January 2019 29: 96-106; Published in Advance November 30, 2018, doi:10.1101/gr.232371.117
    ...of defense metabolites in Arabidopsis thaliana using -wide association mapping. Genetics 185: 991–1007. doi:10.1534/genetics.109.108522 ↵Chan EK, Rowe HC, Corwin JA, Joseph B, Kliebenstein DJ. 2011. Combining -wide association mapping and transcriptional networks to identify novel genes controlling...
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  2. Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
    • Kyuha Choi,
    • Xiaohui Zhao,
    • Andrew J. Tock,
    • Christophe Lambing,
    • Charles J. Underwood,
    • Thomas J. Hardcastle,
    • Heïdi Serra,
    • Juhyun Kim,
    • Hyun Seob Cho,
    • Jaeil Kim,
    • Piotr A. Ziolkowski,
    • Nataliya E. Yelina,
    • Ildoo Hwang,
    • Robert A. Martienssen,
    • and Ian R. Henderson
    Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
    ..., with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant , we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes...
  3. Resource: A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci
    • Kaitlin U. Laverty,
    • Jake M. Stout,
    • Mitchell J. Sullivan,
    • Hardik Shah,
    • Navdeep Gill,
    • Larry Holbrook,
    • Gintaras Deikus,
    • Robert Sebra,
    • Timothy R. Hughes,
    • Jonathan E. Page,
    • and Harm van Bakel
    Genome Res. January 2019 29: 146-156; Published in Advance November 8, 2018, doi:10.1101/gr.242594.118
    ...embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic...
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  4. Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
    • Ying Huang,
    • Sanchari Sicar,
    • Juan S. Ramirez-Prado,
    • Deborah Manza-Mianza,
    • Javier Antunez-Sanchez,
    • Rim Brik-Chaouche,
    • Natalia Y. Rodriguez-Granados,
    • Jing An,
    • Catherine Bergounioux,
    • Magdy M. Mahfouz,
    • Heribert Hirt,
    • Martin Crespi,
    • Lorenzo Concia,
    • Fredy Barneche,
    • Simon Amiard,
    • Aline V. Probst,
    • Jose Gutierrez-Marcos,
    • Federico Ariel,
    • Cécile Raynaud,
    • David Latrasse,
    • and Moussa Benhamed
    Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
    ...acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics...
  5. Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
    • Charles J. Underwood,
    • Kyuha Choi,
    • Christophe Lambing,
    • Xiaohui Zhao,
    • Heïdi Serra,
    • Filipe Borges,
    • Joe Simorowski,
    • Evan Ernst,
    • Yannick Jacob,
    • Ian R. Henderson,
    • and Robert A. Martienssen
    Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
    ...dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation...
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  6. Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
    • Chang Liu,
    • Congmao Wang,
    • George Wang,
    • Claude Becker,
    • Maricris Zaidem,
    • and Detlef Weigel
    Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
    ..., to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage...
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  7. Research: Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
    • Congmao Wang,
    • Chang Liu,
    • Damian Roqueiro,
    • Dominik Grimm,
    • Rebecca Schwab,
    • Claude Becker,
    • Christa Lanz,
    • and Detlef Weigel
    Genome Res. February 2015 25: 246-256; Published in Advance November 3, 2014, doi:10.1101/gr.170332.113
    ...for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana . We find that local chromatin...
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  8. Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
    • Andrew J. Tock,
    • Daniel M. Holland,
    • Wei Jiang,
    • Kim Osman,
    • Eugenio Sanchez-Moran,
    • James D. Higgins,
    • Keith J. Edwards,
    • Cristobal Uauy,
    • F. Chris H. Franklin,
    • and Ian R. Henderson
    Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
    ...concentrate in distal regions (Saintenac et al. 2009; Choulet et al. 2014). For example, 82% of crossovers on Chromosome 3B occur within 19% of its physical length (Darrier et al. 2017). Bread wheat is an allohexaploid, comprising homoeologous A, B, and D subs of seven chromosomes each (2n = 6x = 42, AABBDD...
  9. Research: Genetic architecture of regulatory variation in Arabidopsis thaliana
    • Xu Zhang,
    • Andrew J. Cal,
    • and Justin O. Borevitz
    Genome Res. May 2011 21: 725-733; Published in Advance April 5, 2011, doi:10.1101/gr.115337.110
    ...Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana , we performed genome-wide association (GWA) mapping of gene expression in an F1 hybrid diversity panel...
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  10. Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    • Sergei A. Filichkin,
    • Henry D. Priest,
    • Scott A. Givan,
    • Rongkun Shen,
    • Douglas W. Bryant,
    • Samuel E. Fox,
    • Weng-Keen Wong,
    • and Todd C. Mockler
    Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
    ...Genome-wide mapping of alternative splicing in Arabidopsis thaliana Sergei A. Filichkin 1 , Henry D. Priest 1 , Scott A. Givan 1 , Rongkun Shen 1 , 3 , Douglas W. Bryant 1 , 2 , Samuel E. Fox 1 , Weng-Keen Wong 2...
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