Searching journal content for articles similar to Rossi et al. 28 (4): 497.

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  1. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ...Cas9 and Cas9 specificity using ssDNA mapping. Genome Biol 24: 85. doi:10.1186/s13059-023-02930-z ↵Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. 2023b. Genome-wide mapping of active regulatory elements using ATAC-seq. Methods Mol Biol 2611: 3–19. doi:10.1007/978-1-0716-2899-7_1 ↵McGhee JD, Wood WI...
  2. Research: Genome-wide oscillations in G + C density and sequence conservation
    • Zarmik Moqtaderi,
    • Susan Brown,
    • and Welcome Bender
    Genome Res. November 2021 31: 2050-2057; Published in Advance October 14, 2021, doi:10.1101/gr.274332.120
    ...(short wavelengths); this sort of “background noise” might be expected as a baseline for all DNA sequences. Specific sequences may have patterns unrelated to G + C content that generate oscillation power. An appropriate comparison for the G + C oscillations might be a magnitude graph for G + A or G + T...
  3. Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
    • Shudi Zhao,
    • Yuedong Li,
    • Guanping Chen,
    • Xingyang Wang,
    • Nan Chen,
    • and Xiaofeng Wu
    Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
    ....The regulatory activity of enhancers and the correspondence with certain promoters are closely related to the chromatin accessibility, histone modification, and DNA interaction frequency (The ENCODE Project Consortium 2012; Shibata et al. 2012; Whalen et al. 2016). In eukaryotic cells, the is dynamic...
  4. Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
    • Jordan John,
    • Javaid Jabbar,
    • Nitika Badjatia,
    • Matthew J. Rossi,
    • William K.M. Lai,
    • and B. Franklin Pugh
    Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
    ...of their discovery, NAPs were thought to compact DNA by seemingly nonspecific binding and bending (Finkel and Johnson 1992; Feldman-Cohen et al. 2006). However, it is now known that both Fis and IHF bind somewhat degenerate, but sequence-specific sites (Rice et al. 1996; Cho et al. 2008; Stella et al. 2010...
  5. Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
    • Etienne Routhier,
    • Edgard Pierre,
    • Ghazaleh Khodabandelou,
    • and Julien Mozziconacci
    Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
    ...Flow: large-scale machine learning on heterogeneous systems. arXiv:1603.04467 [cs.DC]. ↵Alipanahi B, Delong A, Weirauch MT, Frey BJ. 2015. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nat Biotechnol 33: 831–838. doi:10.1038/nbt.3300 ↵Anderson J, Widom J. 2001. Poly...
  6. Method: A systematic genome-wide account of binding sites for the model transcription factor Gcn4
    • Christopher T. Coey and
    • David J. Clark
    Genome Res. February 2022 32: 367-377; Published in Advance December 16, 2021, doi:10.1101/gr.276080.121
    ...Corresponding author: clarkda@mail.nih.govAbstractSequence-specific DNA-binding transcription factors are central to gene regulation. They are often associated with consensus binding sites that predict far more genomic sites than are bound in vivo. One explanation is that most sites are blocked by nucleosomes...
  7. 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
    ..., such as DNA-repair proteins, resides on the axis (Blat et al. 2002; Grey et al. 2018; Tock and Henderson 2018; Slotman et al. 2020). This “tethered-loop/axis complex” model of recombination suggests that 3D folding could place constraints on the recombination process. Here we apply computational analyses...
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  8. Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
    • Kristina Krassovsky,
    • Rajarshi P. Ghosh,
    • and Barbara J. Meyer
    Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
    ...overwind or underwind DNA, creating DNA supercoils (Kouzine and Levens 2007). Supercoils can, in turn, induce formation of single-stranded DNA (ssDNA, hereafter SS DNA) or other non-B DNA structures.Genome-wide mapping of alternative DNA structures in cell lines and computational predictions in s suggested...
  9. Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
    • Brian S. Roberts,
    • E. Christopher Partridge,
    • Bryan A. Moyers,
    • Vikram Agarwal,
    • Kimberly M. Newberry,
    • Beth K. Martin,
    • Jay Shendure,
    • Richard M. Myers,
    • and Gregory M. Cooper
    Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
    ...the development of “massively parallel reporter assays” (MPRAs), in which numerous sequence fragments are assayed in a single experiment for their ability to alter transcript levels. MPRAs take a variety of forms but typically include the cloning of a diverse collection of short (∼200-bp to ∼1.5-kb) DNA elements...
  10. Method: Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
    • Ruben Boers,
    • Joachim Boers,
    • Bas de Hoon,
    • Christel Kockx,
    • Zeliha Ozgur,
    • Anco Molijn,
    • Wilfred van IJcken,
    • Joop Laven,
    • and Joost Gribnau
    Genome Res. January 2018 28: 88-99; Published in Advance December 8, 2017, doi:10.1101/gr.222885.117
    ...for determining the DNA methylome.ResultsWhole- DNA methylation analysis using LpnPI, MspJI, and FspEIThe MspJI family of Mrr-like modification-dependent restriction endonucleases cleave DNA after recognition of modified cytosines in a sequence-specific manner (Zheng et al. 2010; Cohen-Karni et al. 2011...
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