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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
..., oocytes, and embryonic stem cells have shown DNA methylation (DNAm) in non-CG contexts, such as mCHG and mCHH, where H represents A, C, or T (Kinde et al. 2015). These are notably less mitotically active, presumably because such marks are more difficult to maintain with active replication...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...target expression variation and covariation, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells (mESCs) by genetically deleting Drosha, leading to global loss of microRNAs. We apply complementary single...
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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
...classifier for -wide detection. The limitation of the supervised classification framework primarily manifests in its detection speed and relatively small reception fields. Genome-wide detection with a binary classifier can be computationally inefficient as the small window causes scanning to be resource...
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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
...of H3K9me3 and H3K27me3 in the nondiapause (C), prediapause (D), and diapause (E) stages. (F–H) Venn diagram shows the number of genes with H3K9me3 peaks, H3K27me3 peaks, or both at the nondiapause (F), prediapause (G), and diapause (H) stages. (I–K) Genome-wide correlation plots showing correlation...
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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
...and nonrandomly organized in the nucleus. Therefore, the chromatin epigenomic signatures and three-dimensional (3D) architecture are dynamically remodeled during different processes or under different conditions, such as embryonic development (Li et al. 2018; Li et al. 2019), cell differentiation (Vidaurre...
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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
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
...-C, CTCF, RNAPII, and cohesin RAD21 subunit) from embryonic stem (ES) cells, serving as an example of interphase chromatin organization (Nitzsche et al. 2011; Shen et al. 2012; Bonev et al. 2017), allowing the identification of meiosis-specific patterns.PRDM9 sites associated with DSB formation show...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
...plant shoot that orchestrates the balance between stem cell proliferation and organ initiation essential for post-embryonic shoot growth. The SAM provides a perfect context to study miRNA regulation. Cell fates within the growing niche are continuously defined, and the dynamic expression of key fate...
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Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
- Brian S. Roberts,
- E. Christopher Partridge,
- Bryan A. Moyers,
- Vikram Agarwal,
- Kimberly M. Newberry,
- Beth K. Martin,
- Jay Shendure,
- Richard M. Myers,
- and Gregory M. Cooper
Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
...selection favoring efficient transcription. Our results indicate that strand asymmetry is a pervasive and reproducible feature in MPRA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial...
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Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
- Haifen Chen,
- Bo Hu,
- Cynthia Horth,
- Eric Bareke,
- Phillip Rosenbaum,
- Sin Young Kwon,
- Jacinthe Sirois,
- Daniel N. Weinberg,
- Faith M. Robison,
- Benjamin A. Garcia,
- Chao Lu,
- William A. Pastor,
- and Jacek Majewski
Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
...interactions. Here, we use the mouse embryonic stem cell (mESC) model to describe in detail the relationships within the H3K27-H3K36-DNA methylation subnetwork. In particular, we focus on the major epigenetic reorganization caused by deletion of the histone 3 lysine 36 methyltransferase NSD1, which in m...
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