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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...active ICRs or together with H3K27me3 at transcriptionally inactive ones (Sanz et al. 2008; Henckel et al. 2009; Maupetit-Méhouas et al. 2016).When the maintenance of gamete-derived methylation asymmetry is temporary: the transient gDMRsAlong with ubiquitous gDMRs/ICRs, other regions that exhibit...
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Research: Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition
- Jiawei Xu,
- Yimin Shu,
- Guidong Yao,
- Yu Zhang,
- Wenbin Niu,
- Yile Zhang,
- Xueshan Ma,
- Haixia Jin,
- Fuli Zhang,
- Senlin Shi,
- Yang Wang,
- Wenyan Song,
- Shanjun Dai,
- Luyao Cheng,
- Xiangyang Zhang,
- Wei Xie,
- Aaron J. Hsueh,
- and Yingpu Sun
Genome Res. September 2021 31: 1519-1530; Published in Advance July 30, 2021, doi:10.1101/gr.273318.120
...reproductive technology, and the Human Sperm Bank and the Helsinki Declaration. Our research followed the guiding principles of the human embryonic stem cell ethics issued by the MOST and MOH of China and was regularly reviewed by the medical ethics committee of The First Affiliated Hospital of Zhengzhou...
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Research: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations
- Stefan F. Pinter,
- Ruslan I. Sadreyev,
- Eda Yildirim,
- Yesu Jeon,
- Toshiro K. Ohsumi,
- Mark Borowsky,
- and Jeannie T. Lee
Genome Res. October 2012 22: 1864-1876; Published in Advance September 4, 2012, doi:10.1101/gr.133751.111
...levels reflect a graded concentration originating from strong sites. This suggests that PRC2 and H3K27 methylation spread along a gradient unique to XCI. We propose that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis . Footnotes ↵ 4...
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Research: Chromatin architecture transitions from zebrafish sperm through early embryogenesis
- Candice L. Wike,
- Yixuan Guo,
- Mengyao Tan,
- Ryohei Nakamura,
- Dana Klatt Shaw,
- Noelia Díaz,
- Aneasha F. Whittaker-Tademy,
- Neva C. Durand,
- Erez Lieberman Aiden,
- Juan M. Vaquerizas,
- David Grunwald,
- Hiroyuki Takeda,
- and Bradley R. Cairns
Genome Res. June 2021 31: 981-994; Published in Advance May 18, 2021, doi:10.1101/gr.269860.120
...and developmental promoters and enhancers in zebrafish sperm lack DNA methylation and contain H3K4me3, H2A.Z/FV, H3K27ac, and (at developmental genes) H3K27me3 (Wu et al. 2011; Murphy et al. 2018; Zhang et al. 2018). Additionally, histone chromatin marks and DNA methylation are reprogrammed during pre-ZGA zebrafish...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...3 signal are weak domains in young cells, and genes that show a loss of H3K27me3 signal are strong domains in young cells. (G,H) Genome browser tracks of genes that are differentially methylated in enterocytes, showing a loss (G) and gain (H) in H3K27me3 signal with age.To map age-dependent changes...
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Research: Characterization and dynamics of pericentromere-associated domains in mice
- Patrick J. Wijchers,
- Geert Geeven,
- Michael Eyres,
- Atze J. Bergsma,
- Mark Janssen,
- Marjon Verstegen,
- Yun Zhu,
- Yori Schell,
- Carlo Vermeulen,
- Elzo de Wit,
- and Wouter de Laat
Genome Res. July 2015 25: 958-969; Published in Advance April 16, 2015, doi:10.1101/gr.186643.114
...) DNase I H3K4me1 H3K4me3 H3K27me3 SINEs LINEs rep timing (late > early) Hi-C PC1 (B > A) H3K9me2 CpG methylation (%) H3K9me3 H4K20me3 PAD nPAD 100 Figure 2. Pericentromeric association segregates repressed chromatin from active chromatin. (A) Sat4C profile of Chromosome 17 with designated PADs (red...
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Research: Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming
- Adrian Janiszewski,
- Irene Talon,
- Joel Chappell,
- Samuel Collombet,
- Juan Song,
- Natalie De Geest,
- San Kit To,
- Greet Bervoets,
- Oskar Marin-Bejar,
- Caterina Provenzano,
- Lotte Vanheer,
- Jean-Christophe Marine,
- Florian Rambow,
- and Vincent Pasque
Genome Res. October 2019 29: 1659-1672; Published in Advance September 12, 2019, doi:10.1101/gr.249706.119
...(Supplemental Fig. S4D). Thus, although H3K27me3 may restrict the activation of silenced genes on the Xi, it is not sufficient to explain the delay in reactivation of late genes. Additionally, on the Xi, H3K36me3 and H3K4me3 were depleted on all classes of genes. DNA methylation (Milagre et al. 2017) was also...
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Method: Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
- Maxwell W. Libbrecht,
- Ferhat Ay,
- Michael M. Hoffman,
- David M. Gilbert,
- Jeffrey A. Bilmes,
- and William Stafford Noble
Genome Res. April 2015 25: 544-557; Published in Advance February 12, 2015, doi:10.1101/gr.184341.114
...is independent of compartment-driven repression (Fig. 3F). However, FAC domains are almost completely absent from the annotation of the embryonic stem cell line H1-hESC, consistent with previous observations that H3K27me3 does not form domains in embryonic stem cells but rather occurs only at so-called poised...
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Research: Genome-wide depletion of replication initiation events in highly transcribed regions
- Melvenia M. Martin,
- Michael Ryan,
- RyangGuk Kim,
- Anna L. Zakas,
- Haiqing Fu,
- Chii Mei Lin,
- William C. Reinhold,
- Sean R. Davis,
- Sven Bilke,
- Hongfang Liu,
- James H. Doroshow,
- Mark A. Reimers,
- Manuel S. Valenzuela,
- Yves Pommier,
- Paul S. Meltzer,
- and Mirit I. Aladjem
Genome Res. November 2011 21: 1822-1832; Published in Advance August 3, 2011, doi:10.1101/gr.124644.111
...factor (Cadoret et al. 2008), but this enrichment was minimal. Histone modifications such as methylation of H3K4 or acetylation of H3K9 and H3K27 exhibited minor but statistically significant enrichment in replication initiation. CpG methylation, replication, and gene expression To further explore...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
..., such as H3K4 mono- and trimethylation and H3K36 trimethylation, with little or no signal for the repressive modifications H3K27 trimethylation or H3K9 trimethylation (Fig. 4). This analysis was conducted for TAL1 OSs in G1E cells, ER4 cells, Ter119+ erythroblasts, and megakaryocytes, for which the histone...
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