Searching journal content for articles similar to Krassovsky et al. 31 (7): 1187.

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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
...-agnostic MNase-based chromatin profiling method requires high sequencing depth across the to accurately resolve the positioning of nucleosomes and other DNA-binding factors. For this reason, and with the aim of using our sequencing budget to interrogate the broadest possible range of transcriptional regulators...
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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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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
..., Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, et al. 2019. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 570: 385–389. doi:10.1038/s41586-019-1272-6 ↵De Coster W, Weissensteiner MH, Sedlazeck FJ. 2021. Towards population-scale long-read sequencing. Nat Rev Genet 22: 572...
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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
.... Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22: 2497–2506. doi:10.1101/gr.143008.112 ↵Kouzine F, Gupta A, Baranello L, Wojtowicz D, Ben-Aissa K, Liu J, Przytycka TM, Levens D. 2013. Transcription-dependent dynamic supercoiling is a short...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson’s disease Kangli Wang,1 Weikun Xia,1 Yingli Gu,1 Songpeng Zu,1 Qian Yang,2 Maria Luisa Amaral,1 Yaozhi Wang,1 Allen Wang,2 Xiang-Dong Fu,3 William C. Mobley,4 and Bing Ren1...
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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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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
...). Therefore, it is surmised that DNA interaction frequently appears in the regulatory elements. To confirm this hypothesis, Hi-C analysis was conducted to investigate the 3D chromatin structures of BmN cells (Fig. 1C). The chromatin interaction profiles were highly correlated between the two replicate samples...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...-positive genes during diapause of Asian corn borer larvae. (E) Heatmaps showing the dynamics of H3K27me3 (left) and DNA methylation (right) on H3K27me3-positive genes during diapause of Asian corn borer larvae. (F–H) Genome-wide correlation plots depicting the association between H3K9me3 and DNA...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...(median normalized read counts ≥ 10 across all samples) for downstream analysis. Similar to DNA methylation data, we performed a QC of RNA-seq data and excluded a total of 53 samples based on PCA, density plots, and expression profiles using normalized read count of the selected transcripts, retaining...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...; Braaker and Heckel 2009; Martínková et al. 2013; Lischer et al. 2014; Wang et al. 2023). New resequencing was performed for four samples. Sequence data from all samples are available at NCBI BioProject (https://www.ncbi.nlm.nih.gov/bioproject) under accession number PRJNA963218.DNA extraction...

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