Searching journal content for articles similar to Henikoff et al. 19 (3): 460.

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  1. Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
    • Maria Grazia Mendoza-Ferri,
    • Gwendoline Lozachmeur,
    • Maximilien Duvina,
    • Laetitia Perret,
    • Didier Merciris,
    • Anne Gigout,
    • and Marco Antonio Mendoza-Parra
    Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
    ....Overall, this study covers both the development of a cost-efficient strategy for generating spatial epigenomic maps on tissue sections and a bioinformatics strategy for a pioneer integrative effort in spatial chromatin-state profiling, essential for the field of “spatial omics,” anticipating the need for this type...
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  2. Method: Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes
    • Aylin Cakiroglu,
    • Cedric R. Clapier,
    • Andreas H. Ehrensberger,
    • Elodie Darbo,
    • Bradley R. Cairns,
    • Nicholas M. Luscombe,
    • and Jesper Q. Svejstrup
    Genome Res. June 2019 29: 988-998; Published in Advance May 16, 2019, doi:10.1101/gr.243139.118
    ...and the comprehensive understanding of its deposition mechanism, relatively little is known about the function of H2AZ on the promoters on which it resides.Nucleosome occupancies are determined not only by chromatin remodeling enzymes but also by the intrinsic physical stability of nucleosomes. Features such as high AT...
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  3. 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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  4. Research: Genome-wide analysis of long noncoding RNA stability
    • Michael B. Clark,
    • Rebecca L. Johnston,
    • Mario Inostroza-Ponta,
    • Archa H. Fox,
    • Ellen Fortini,
    • Pablo Moscato,
    • Marcel E. Dinger,
    • and John S. Mattick
    Genome Res. May 2012 22: 885-898; Published in Advance March 9, 2012, doi:10.1101/gr.131037.111
    ...://stability.matticklab.com/. Genome-wide analysis of lncRNA stability Genome Research 889 www..org sense transcripts were also more stable than head-to-head bidirectional transcripts (P < 0.05). Hierarchical clustering of lncRNA stability profiles supported this result. The most stable classes (intergenic, cis-antisense, tail...
  5. Method: High-salt–recovered sequences are associated with the active chromosomal compartment and with large ribonucleoprotein complexes including nuclear bodies
    • Marie-Odile Baudement,
    • Axel Cournac,
    • Franck Court,
    • Marie Seveno,
    • Hugues Parrinello,
    • Christelle Reynes,
    • Robert Sabatier,
    • Tristan Bouschet,
    • Zhou Yi,
    • Sephora Sallis,
    • Mathilde Tancelin,
    • Cosette Rebouissou,
    • Guy Cathala,
    • Annick Lesne,
    • Julien Mozziconacci,
    • Laurent Journot,
    • and Thierry Forné
    Genome Res. November 2018 28: 1733-1746; Published in Advance October 4, 2018, doi:10.1101/gr.237073.118
    ...of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the high-salt–recovered sequences-sequencing (HRS-seq) method, a straightforward -wide approach whereby we...
  6. Research: Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
    • Răzvan V. Chereji,
    • Peter R. Eriksson,
    • Josefina Ocampo,
    • Hemant K. Prajapati,
    • and David J. Clark
    Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119
    ...importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei...
  7. LETTER: Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
    • A. Gordon Robertson,
    • Mikhail Bilenky,
    • Angela Tam,
    • Yongjun Zhao,
    • Thomas Zeng,
    • Nina Thiessen,
    • Timothee Cezard,
    • Anthony P. Fejes,
    • Elizabeth D. Wederell,
    • Rebecca Cullum,
    • Ghia Euskirchen,
    • Martin Krzywinski,
    • Inanc Birol,
    • Michael Snyder,
    • Pamela A. Hoodless,
    • Martin Hirst,
    • Marco A. Marra,
    • and Steven J.M. Jones
    Genome Res. December 2008 18: 1906-1917; Published in Advance September 11, 2008, doi:10.1101/gr.078519.108
    ...Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding A. Gordon Robertson 1 , 4 , Mikhail Bilenky 1 , 4 , Angela Tam 1 , Yongjun Zhao 1 , Thomas Zeng 1 , Nina Thiessen 1...
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  8. Method: Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
    • Alicia N. Schep,
    • Jason D. Buenrostro,
    • Sarah K. Denny,
    • Katja Schwartz,
    • Gavin Sherlock,
    • and William J. Greenleaf
    Genome Res. November 2015 25: 1757-1770; Published in Advance August 27, 2015, doi:10.1101/gr.192294.115
    ...Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions Alicia N. Schep 1 , Jason D. Buenrostro 1 , Sarah K. Denny 2 , Katja Schwartz 1 , Gavin Sherlock 1 and William J...
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  9. Research: Chromatin signatures of the Drosophila replication program
    • Matthew L. Eaton,
    • Joseph A. Prinz,
    • Heather K. MacAlpine,
    • George Tretyakov,
    • Peter V. Kharchenko,
    • and David M. MacAlpine
    Genome Res. February 2011 21: 164-174; Published in Advance December 22, 2010, doi:10.1101/gr.116038.110
    ...and modifications in regulating the DNA replication program. Genome-wide replication timing and early origins of replication are correlated with a variety of activating chromatin marks. Similarly, we find that ORC-binding sites are enriched for a subset of these chromatin marks as well as additional DNA...
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  10. Resource: High-resolution mapping of open chromatin in the rice genome
    • Wenli Zhang,
    • Yufeng Wu,
    • James C. Schnable,
    • Zixian Zeng,
    • Michael Freeling,
    • Gregory E. Crawford,
    • and Jiming Jiang
    Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
    ...associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice ( Oryza sativa ). Approximately 25% of the DH sites from both tissues were found in putative...
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