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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
...IP-seq, DNase-seq, and ATAC-seq (Krogan et al. 2006; Johnson et al. 2007; Shivaswamy et al. 2008; Lenstra et al. 2011; Weiner et al. 2012; Toenhake et al. 2018) to supplement GRNs (Zhong et al. 2016; Miraldi et al. 2019; Li et al. 2022). Despite these efforts, these methods do not have the capability...
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Research: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
- Deborah R. Winter,
- Lingyun Song,
- Sayan Mukherjee,
- Terrence S. Furey,
- and Gregory E. Crawford
Genome Res. July 2013 23: 1118-1129; Published in Advance May 8, 2013, doi:10.1101/gr.150482.112
...in LCL DNase-seq reads overlapping non-LCL DNase I hypersensitive (DHS) sites but not in LCL-specific DHS sites. Genome Research 1119 www..org DNase-seq predicts nucleosome positioning tribution of distances between pairs of reads in the combined data set exhibited the expected spacing on both...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...et al. 2019a), and methods like DNase-seq or ATAC-seq exaggerate accessibility differences, which was explained recently (Chereji et al. 2019b). Our absolute occupancy measurements clarify this method-driven misconception. Nonetheless, anecdotal reports of nucleosome depletion over highly transcribed...
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Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
- Hamish W. King,
- Nadezda A. Fursova,
- Neil P. Blackledge,
- and Robert J. Klose
Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
..., and FAIRE-seq signal at PcG-occupied (n = 4020) or PcG-free (n = 10,251) CGI promoters, centered on TSSs. Input for ATAC-seq and DNase-seq represents digestion of naked genomic DNA by Tn5 or DNase I, respectively. (E) A metaplot analysis at CGI intervals (±20%) for CGI-positive TSSs with (PcG) or without...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
...transcription. Although a -wide allele-specific chromatin accessibility map had recently been generated using DNase-seq and ATAC-seq in mammal (Lu et al. 2016; Wu et al. 2016), a global pattern of allele-specific nucleosome occupancy has not been reported in any other high eukaryotic species. Here, we reported...
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Research: Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns
- Elisheva Javasky,
- Inbal Shamir,
- Shashi Gandhi,
- Shawn Egri,
- Oded Sandler,
- Scott B. Rothbart,
- Noam Kaplan,
- Jacob D. Jaffe,
- Alon Goren,
- and Itamar Simon
Genome Res. October 2018 28: 1455-1466; Published in Advance August 30, 2018, doi:10.1101/gr.230300.117
...on the chromosomes during mitosis (Black et al. 2016; Teves et al. 2016; Liu et al. 2017b). Second, a -wide DNase-seq experiment revealed that accessibility is widely preserved and only locally modulated during mitosis (Hsiung et al. 2015). Finally, a recent study utilized 5-EU labeling to demonstrate that many...
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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 around nucleosomes. (A) ATAC-seq (green) insertion track for S. cerevisiae shows enrichment of insertions at accessible chromatin regions, similar to DNase-seq cut density (orange). Both tracks were smoothed by 150 bp and scaled so that the maximum density in the region is 1. (B) Fragment...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., modeling 3D chromatin organization, and predicting gene expression (Thibodeau et al. 2021; Karbalayghareh et al. 2022; Tan et al. 2023; Zhang et al. 2023; Grover et al. 2024). Although experimental assays such as FAIRE-seq (Giresi et al. 2007), DNase-seq (Song and Crawford 2010), and ATAC-seq (Buenrostro...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...model. (G) Visualization of m6A calls in the HMBS locus that are unique to fibertools (purple), unique to the subread GMM model (red), or shared by both (gray). Reads are sorted by the number of CCS passes (low to high). DNase-seq (ENCODE July 2012 Freeze) and CAGE signals are shown above...
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Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
..., such as DNase-seq or FAIRE-seq. We observed that phasing occurs in all cell types, although it remains unclear what is dictating the precise organization that is evident at NDRs and even at absent NDRs (f NDRs). The first possibility is a sequence-based propensity for DNA to be associated with nucleosome...
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