Searching journal content for articles similar to Zhao et al. 33 (11): 1958.

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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
...enhancers and promoters, revealing allele-specific regulatory interactions that are crucial for understanding gene expression regulation and epigenetic modifications (Gigante et al. 2019). Additionally, this approach facilitates the study of chromatin interactions and the 3D architecture, providing insights...
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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
...in response to these genetic perturbations, allowing us to gain a comprehensive understanding of the chromatin-mediated mechanisms of transcriptional regulation, thereby demonstrating the potential for chromatin profiling to reconstruct and enhance transcriptional regulatory networks (TRNs...
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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
...abundances of accessible ssDNA and accessible DNA). (C) KAS-seq, ATAC-seq, and KAS-ATAC mitochondrial profiles in human GM12878 cells. (D) Fragment length distribution in biotin-ATAC-seq and KAS-ATAC libraries (GM12878 cells). (E) Genome-wide TSS metaprofiles for biotin-ATAC-seq and KAS-ATAC libraries (GM...
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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
...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...). Primarily, we adopted the YOLOv8-nano architecture with fewer parameters and simplified layers, enabling it to efficiently process large Hi-C matrices at high speed.Furthermore, as chromatin loops are rather small targets relative to the contact matrix, it is essential to enhance the model's accuracy...
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Research: MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites
- Yi Xiang See,
- Kaijing Chen,
- and Melissa J. Fullwood
Genome Res. April 2022 32: 629-642; Published in Advance February 3, 2022, doi:10.1101/gr.276313.121
...cells modulated histone acetylation and increased MYC binding at super-enhancers. SIQHiC analysis revealed increased global chromatin contact frequency, particularly at chromatin interactions connecting MYC binding sites at promoters and enhancers. Immunofluorescence staining showed that MYC molecules...
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Research: Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
- Aneta Mikulasova,
- Daniel Kent,
- Marco Trevisan-Herraz,
- Nefeli Karataraki,
- Kent T.M. Fung,
- Cody Ashby,
- Agata Cieslak,
- Shmuel Yaccoby,
- Frits van Rhee,
- Maurizio Zangari,
- Sharmilan Thanendrarajan,
- Carolina Schinke,
- Gareth J. Morgan,
- Vahid Asnafi,
- Salvatore Spicuglia,
- Chris A. Brackley,
- Anne E. Corcoran,
- Sophie Hambleton,
- Brian A. Walker,
- Daniel Rico,
- and Lisa J. Russell
Genome Res. July 2022 32: 1343-1354; Published in Advance December 21, 2021, doi:10.1101/gr.276042.121
.... Polycomb at the CCND1 locus was obtained as regions upstream and overlapping with the promoter.Genome-wide H3K4me3-BD and super-enhancer co-occurrenceWe used an epigenomic consensus approach to test whether H3K4me3-BDs co-occur with super-enhancers at the -wide level in the BLUEPRINT data set (Supplemental...
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
...studies have revealed that the effect of a given enhancer on its target gene depends on the enhancer's own activity, as well as its contact intensity with the gene promoter, a model named ABC (Fulco et al. 2019). The H3K27ac HiChIP assay combines H3K27ac ChIP-seq (enhancer activity) and Hi-C (contact...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...localization of EP300 at promoter regions leads to the higher sensitivity of these peaks to the ratio of antibody to cell number.DiscussionWe presented here spa-ChIP-seq, a single-pot automated protocol for chromatin profiling. We benchmarked spa-ChIP-seq by performing parallel manual ChIP-seq reactions...
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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
...previous findings in vertebrates highlighting the connection between DNA methylation and repressive histone methylations, we have examined changes in the -wide profile of H3K9me3, H3K27me3, and DNA methylation at the nondiapause, prediapause, and diapause stages. Data analysis reveals significant...

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