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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
...revealed a roughly periodic pattern of CPD deamination, particularly at distal positions (i.e., −73 to −20 and +20 to +73) in the nucleosome DNA (Supplemental Fig. S9, top). In general, normalized dCPD levels were lower at minor-out rotational settings (Supplemental Fig. S9, dashed lines) and higher...
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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
...factors bind directly to the DNA to activate or repress transcription (Marr et al. 2021; Minnoye et al. 2021). Recent advances in sequencing technology have enabled the characterization of chromatin remodelers, nucleosome positioning, and chromatin accessibility using high-throughput assays like Ch...
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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...with shorter 2- to 11-min lifetimes (Nakahashi et al. 2013; Hansen et al. 2017, 2020; Kieffer-Kwon et al. 2017; Oomen et al. 2019; Soochit et al. 2021; Narducci and Hansen 2025). SPT for CTCF indicated a slightly more rapid 1-min lifetime (Hansen et al. 2017). Tracking DNA, often via integrated arrays...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...DNA regions (such as gene spacer regions) to achieve spatiotemporal-specific epigenetic encoding (Suzuki and Bird 2008). Furthermore, k-mers frequently found in eukaryotic negative samples (e.g., “CCC,” “GGG,” “GCC,” etc.) potentially act as an “antimethylation” signal, analogous to the methylation...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...). Genome-wide maps of nucleosome positions are usually obtained by digesting linker DNA with nucleases, such as MNase, followed by sequencing the DNA associated with the histone octamer core (Teif and Clarkson 2019; Shtumpf et al. 2022). Most previous studies of this kind investigated cell lines...
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Research: Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites
- Patrick D. Wilson,
- Xinyang Yu,
- Christopher R. Handelmann,
- and Michael J. Buck
Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
...affinity to its DNA-binding sites at all possible positions within the nucleosome core particle. Using Pioneer-seq, we analyzed the binding affinities of TP53, TP63, and TP73 to 10 TP53 family binding sites across the nucleosome core particle. We find that the affinities of TP53, TP63, and TP73...
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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...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...IP-seq enrichment patterns, genomic DNA coverage, and gene annotations across defined centromeric regions. In Dt7DS and Dt7DL, centromere structure and CENH3 positioning remain stable, consistent with the CS reference. In Dt6BL, a contraction of the CENH3-enriched domain is observed, indicating centromere shrinkage...
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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
...-strandedness, which is most pronounced at transcript end sites, is dependent on high AT content and symmetrically positioned nucleosomes. We propose that sharp transitions in sequence composition at functional genomic elements constitute a common regulatory code and that DNA structure and propagation of torsional...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...are incubated with BrdU, followed by nuclei isolation. GFP-positive nuclei are then sorted by DNA content, separating into one of four S-phase fractions: early, early-mid, late-mid, or late replicating. Next, the BrdU-containing DNA is immunoprecipitated and prepared for sequencing to identify genomic locations...
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