Searching journal content for articles similar to Boyle et al. 21 (3): 456.

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  1. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
    ...-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes -wide, providing a deeper, more mechanistic understanding...
  2. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...methods, provide a guide for considerations that need to be made during study design, and highlight novel approaches that are becoming possible with recent developments in editing as well as high-resolution imaging.To answer which proteins are bound to and directly regulate the transcription of a GOI, we...
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  3. Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
    • Rachel M. Petersen,
    • Christopher M. Vockley,
    • and Amanda J. Lea
    Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
    ...Uncovering methylation-dependent genetic effects on regulatory element function in diverse s Rachel M. Petersen1,2, Christopher M. Vockley3 and Amanda J. Lea1,2,4 1Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA; 2Evolutionary Studies Initiative, Vanderbilt...
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  4. 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
    ...and purification of psoralen-bound DNA fragments.View larger version: In this window In a new window Figure 1. Genome-wide mapping strategy for DNA supercoils reveals negative supercoiling at transcription start sites (TSSs) of embryos. (A,B) Strategy for -wide mapping of DNA supercoils (BP-seq). (A) When...
  5. Method: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
    • Qianru Li,
    • Haiwang Yang,
    • Emily K. Stroup,
    • Hongbin Wang,
    • and Zhe Ji
    Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
    ...we aimed to develop a low-input RNase footprinting approach to rapidly quantify cytosolic and mitochondrial ribosome footprints simultaneously. And we applied our method to characterize the translation landscape in diverse primary tissue samples.ResultsRNase digestion distinguishes RNA fragments...
  6. Resource: Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq
    • Margaret C.W. Ho,
    • Porfirio Quintero-Cadena,
    • and Paul W. Sternberg
    Genome Res. December 2017 27: 2108-2119; Published in Advance October 26, 2017, doi:10.1101/gr.223735.117
    ...–treated chromatin (DNase-seq) allows high-resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1...
  7. Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
    • Tatsunori Hashimoto,
    • Richard I. Sherwood,
    • Daniel D. Kang,
    • Nisha Rajagopal,
    • Amira A. Barkal,
    • Haoyang Zeng,
    • Bart J.M. Emons,
    • Sharanya Srinivasan,
    • Tommi Jaakkola,
    • and David K. Gifford
    Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
    ...A synergistic DNA logic predicts genome-wide chromatin accessibility Tatsunori Hashimoto 1 , 3 , Richard I. Sherwood 2 , 3 , Daniel D. Kang 1 , 3 , Nisha Rajagopal 1 , Amira A. Barkal 1 , 2 , Haoyang Zeng 1 , Bart J...
  8. Method: Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles
    • Su Wang,
    • Chongzhi Zang,
    • Tengfei Xiao,
    • Jingyu Fan,
    • Shenglin Mei,
    • Qian Qin,
    • Qiu Wu,
    • Xujuan Li,
    • Kexin Xu,
    • Housheng Hansen He,
    • Myles Brown,
    • Clifford A. Meyer,
    • and X. Shirley Liu
    Genome Res. October 2016 26: 1417-1429; Published in Advance July 27, 2016, doi:10.1101/gr.201574.115
    ....115 Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles Wang et al. Modeling transcriptional -regulation Modeling cis-regulation with a compendium of -wide histone H3K27ac profiles Su Wang,1,2,8 Chongzhi Zang,3,4,8 Tengfei Xiao,3,4,5 Jingyu Fan,2 Shenglin Mei,2 Qian Qin,2 Qiu Wu,2...
  9. Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
    • Boning Chen,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
    ....1021/bi300129b ↵Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM. 2015. Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly. Genes Dev 29: 212–224. doi:10.1101/gad.247924.114 ↵Böhm V, Hieb AR, Andrews AJ, Gansen A, Rocker A, Tóth...
  10. 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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