Searching journal content for articles similar to Wang et al. 25 (2): 246.

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  1. 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
    ...Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution Chang Liu 1 , 2 , Congmao Wang 1 , 3 , George Wang 1 , Claude Becker 1 , Maricris Zaidem 1 and Detlef Weigel 1 1...
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  2. 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
    ...- and B-compartment loops may remain comparable owing to the relaxed linear packing density in A-compartment. (C) Concurrently during leptonema, PRDM9 binds across both A- and B-compartment regions, causing local increases in chromatin activity and spatial accessibility. Schematic depicts hypothetical...
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  3. 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...
  4. Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
    • Joana Sequeira-Mendes,
    • Zaida Vergara,
    • Ramon Peiró,
    • Jordi Morata,
    • Irene Aragüez,
    • Celina Costas,
    • Raul Mendez-Giraldez,
    • Josep M. Casacuberta,
    • Ugo Bastolla,
    • and Crisanto Gutierrez
    Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
    ...in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have identified a set of ORIs of Arabidopsis thaliana and their chromatin landscape at two stages of post-embryonic development. ORIs associate with multiple chromatin signatures including transcription...
  5. Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
    • Juncheng Lin,
    • Fu-Yu Hung,
    • Congting Ye,
    • Liwei Hong,
    • Yuan-Hsin Shih,
    • Keqiang Wu,
    • and Qingshun Q. Li
    Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
    ...mechanism in plants that is not yet understood.Nucleosomes are formed when histone proteins are wrapped with DNA. These nucleosomes are then packed into highly condensed chromatins in the eukaryotic nucleus. It was reported that the nucleosome position affects the usage of proximal or distal poly(A) sites...
  6. Method: Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling
    • Florian A. Steiner,
    • Paul B. Talbert,
    • Sivakanthan Kasinathan,
    • Roger B. Deal,
    • and Steven Henikoff
    Genome Res. April 2012 22: 766-777; Published in Advance January 4, 2012, doi:10.1101/gr.131748.111
    ...Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling Florian A. Steiner 1 , Paul B. Talbert 1 , Sivakanthan Kasinathan 1 , Roger B. Deal 1 and Steven Henikoff 1 , 2 , 3...
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  7. Research: Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
    • Pingli Lu,
    • Xinwei Han,
    • Ji Qi,
    • Jiange Yang,
    • Asela J. Wijeratne,
    • Tao Li,
    • and Hong Ma
    Genome Res. March 2012 22: 508-518; Published in Advance November 21, 2011, doi:10.1101/gr.127522.111
    ...Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis Pingli Lu 1 , 7 , Xinwei Han 1 , 2 , 7 , Ji Qi 3 , 4 , 7 , Jiange Yang...
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  8. Research: Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery
    • Xiuli Bi,
    • Ying-Juan Cheng,
    • Bo Hu,
    • Xiaoli Ma,
    • Rui Wu,
    • Jia-Wei Wang,
    • and Chang Liu
    Genome Res. July 2017 27: 1162-1173; Published in Advance April 6, 2017, doi:10.1101/gr.215186.116
    ...comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme–mediated chromatin immunoprecipitation, we present -wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10...
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  9. RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    • Vardhman K. Rakyan,
    • Thomas A. Down,
    • Natalie P. Thorne,
    • Paul Flicek,
    • Eugene Kulesha,
    • Stefan Gräf,
    • Eleni M. Tomazou,
    • Liselotte Bäckdahl,
    • Nathan Johnson,
    • Marlis Herberth,
    • Kevin L. Howe,
    • David K. Jackson,
    • Marcos M. Miretti,
    • Heike Fiegler,
    • John C. Marioni,
    • Ewan Birney,
    • Tim J.P. Hubbard,
    • Nigel P. Carter,
    • Simon Tavaré,
    • and Stephan Beck
    Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
    ...An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) Vardhman K. Rakyan 1 , 9 , 10 , Thomas A. Down 2 , 9 , Natalie P. Thorne 3 , 9 , Paul Flicek 4 , 9...
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  10. LETTER: A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
    • Ligeng Ma,
    • Chen Chen,
    • Xigang Liu,
    • Yuling Jiao,
    • Ning Su,
    • Lin Li,
    • Xiangfeng Wang,
    • Mengliang Cao,
    • Ning Sun,
    • Xiuqing Zhang,
    • Jingyue Bao,
    • Jian Li,
    • Soren Pedersen,
    • Lars Bolund,
    • Hongyu Zhao,
    • Longping Yuan,
    • Gane Ka-Shu Wong,
    • Jun Wang,
    • Xing Wang Deng,
    • and Jian Wang
    Genome Res. September 2005 15: 1274-1283; doi:10.1101/gr.3657405
    ...gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar...
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