Searching journal content for articles similar to González et al. 26 (11): 1532.

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  1. Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
    • Marian F. Laughery,
    • Bastian Stark,
    • Benjamin Morledge-Hampton,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
    ...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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  2. Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
    • Stefano Gnan,
    • Mélody Matelot,
    • Marion Weiman,
    • Olivier Arnaiz,
    • Frédéric Guérin,
    • Linda Sperling,
    • Mireille Bétermier,
    • Claude Thermes,
    • Chun-Long Chen,
    • and Sandra Duharcourt
    Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
    ...with high splicing efficiency. Our data reveal a complex link between GC content, nucleosome positioning, and intron evolution in Paramecium.In eukaryotes, genomic DNA is compacted by histones into chromatin. The basic unit of chromatin is the nucleosome, which comprises a histone octamer made of the four...
  3. Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
    • Benjamin Morledge-Hampton,
    • Kathiresan Selvam,
    • Manish Chauhan,
    • Alan G. Goodman,
    • and John J. Wyrick
    Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
    ...and TC), as expected (Fig. 1B; Brash 2015; Mao et al. 2016). In contrast, no enrichment at dipyrimidine sequences was observed in the unexposed (no UV) control (Fig. 1B). Cellular CPD counts occurring at lesion-forming dipyrimidine sequences were then mapped to nucleosome positions called using...
  4. Research: Allele-specific control of replication timing and genome organization during development
    • Juan Carlos Rivera-Mulia,
    • Andrew Dimond,
    • Daniel Vera,
    • Claudia Trevilla-Garcia,
    • Takayo Sasaki,
    • Jared Zimmerman,
    • Catherine Dupont,
    • Joost Gribnau,
    • Peter Fraser,
    • and David M. Gilbert
    Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
    ...genomic regions with replication asynchrony and classified them into RT signatures (Fig. 2F,G) as previously described (Rivera-Mulia et al. 2015). As expected, the clustering analysis showed that alleles from the V6.5 cell line clustered together and with all other alleles from M. musculus musculus s...
  5. Perspective: What does our genome encode?
    • John A. Stamatoyannopoulos
    Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
    ...with specific functional features or processes (Jacob and Monod 1961). A cornerstone of ENCODE has been the use of biochemical signatures to identify functional elements specified by the genomic sequence. In part, this represents a departure from the widely accepted reductionist approach to function, in which...
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  6. Method: Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control
    • Grzegorz M. Burzynski,
    • Xylena Reed,
    • Leila Taher,
    • Zachary E. Stine,
    • Takeshi Matsui,
    • Ivan Ovcharenko,
    • and Andrew S. McCallion
    Genome Res. November 2012 22: 2278-2289; Published in Advance July 3, 2012, doi:10.1101/gr.139717.112
    ...positive rate (TPR) of at least 47% at a false positive rate (FPR) of 5% (Fig. 1A). Hindbrain enhancers harbor putative binding sites for transcriptional regulators of cell identity Our Hb classifiers rely on sequence motifs representing TFBSs that facilitate distinction of Hb enhancers from random genomic...
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  7. Methods: Genome-wide discovery of human heart enhancers
    • Leelavati Narlikar,
    • Noboru J. Sakabe,
    • Alexander A. Blanski,
    • Fabio E. Arimura,
    • John M. Westlund,
    • Marcelo A. Nobrega,
    • and Ivan Ovcharenko
    Genome Res. March 2010 20: 381-392; Published in Advance January 14, 2010, doi:10.1101/gr.098657.109
    ...the genomic coordinates of functional noncoding sequences that, if mutated, might lead to abnormal gene expression and result in CHDs. Therefore, strategies to map cis-regulatory modules (CRMs) of genes involved in heart development and dissecting their components has become the focus ofmajor efforts...
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  8. Method: SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
    • Zhengqing Ouyang,
    • Michael P. Snyder,
    • and Howard Y. Chang
    Genome Res. February 2013 23: 377-387; Published in Advance October 11, 2012, doi:10.1101/gr.138545.112
    ...SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data Zhengqing Ouyang 1 , 2 , 3 , Michael P. Snyder 2 and Howard Y. Chang 1 , 3 1 Howard Hughes Medical Institute and Program...
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  9. Research: Principles of nucleation of H3K27 methylation during embryonic development
    • Simon J. van Heeringen,
    • Robert C. Akkers,
    • Ila van Kruijsbergen,
    • M. Asif Arif,
    • Lars L.P. Hanssen,
    • Nilofar Sharifi,
    • and Gert Jan C. Veenstra
    Genome Res. March 2014 24: 401-410; Published in Advance December 11, 2013, doi:10.1101/gr.159608.113
    ...absence of DNA methylation is the major determinant of H3K27 methylation when not opposed by transcriptional activation. The sequence and motif signatures reveal the hierarchical and genetically inheritable features of epigenetic cross-talk that impose constraints on Polycomb regulation and guide H3K27...
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  10. Research: Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer
    • Peng Mao,
    • Michael J. Smerdon,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. January 2020 30: 12-21; Published in Advance December 23, 2019, doi:10.1101/gr.253146.119
    ..., but not in NER-deficient cancers, indicating that asymmetric repair of nucleosomal DNA imposes a strand polarity on UV mutagenesis. Somatic mutations are enriched on the relatively slow-repairing 3′ side of the nucleosomal DNA, particularly at positions where the DNA minor groove faces away from the histone...
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