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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...—the locations and modifications of retained histones, most notably—may also play a role in programming early gene expression in the preimplantation embryo and may thereby influence later phenotypes in offspring (Siklenka et al. 2015; Lesch et al. 2019).In the mouse system, sperm are typically...
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Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
...if any transcriptional and translational activity (for review, see Steger 1999), contain little cytoplasm, develop “tail” structures that enable the cells to swim, and have small nuclei. The formation of small nuclei is thought to facilitate sperm swimming (for review, see Balhorn 2007) and require...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...accompanied by the dispersal of the Xist cloud. Notably, we find the loss of enrichment of repressive marks such as H3K27me3, H4K20me1, and MacroH2A, except that of H2AK119ub, in dispersed Xist nuclei. However, X-linked genes remain silent despite Xist dispersal and loss of enrichment of repressive marks...
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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...an enrichment of MHBs in open chromatin. We observed a lower level of GCH methylation in the centers of MHBs in sperm, which could be explained by a higher degree of chromatin packing at the global scale, including within the regions around transcription start sites (TSSs) (Supplemental Fig. 14C).Next, we...
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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
...in flares, but they are not significantly used for early embryo gene expression (ZGA TSS), suggesting that flares in sperm are not pre-marking early embryonic expression (Supplemental Fig. S8D,E). Last, we analyzed available -wide chromatin immunoprecipitation sequencing (ChIP-seq) data, derived from sperm...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...Supplemental Methods), we retained 505 (171 from control, 334 from treated) high-quality single-cell transcriptomes from 18 embryos, with an average of 26,051 expressed genes (reads per kilobase of transcript, per million mapped reads [RPKM] ≥ 1; average Spearman's ρ = 0.73) (Fig. 1A,B; Supplemental Fig. S1C...
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Research: Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos
- Guowei Bu,
- Wei Zhu,
- Xin Liu,
- Jingjing Zhang,
- Longtao Yu,
- Kai Zhou,
- Shangke Wang,
- Zhekun Li,
- Zhengang Fan,
- Tingting Wang,
- Taotao Hu,
- Ruifeng Hu,
- Zhiting Liu,
- Tao Wang,
- Linhui Wu,
- Xia Zhang,
- Shuhong Zhao,
- and Yi-Liang Miao
Genome Res. August 2022 32: 1487-1501; Published in Advance July 22, 2022, doi:10.1101/gr.276207.121
...if the establishment of broad H3K4me3 domains was related to the loss of DNA methylation during early development. We found that DNA methylation (Ivanova et al. 2020) maintained comparably low levels at gene promoters in porcine sperm, oocytes, and embryos, whether for all genes or for only genes in Cluster 2a...
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Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
- Pauliina Paloviita,
- Christel Hydén-Granskog,
- Dawit A. Yohannes,
- Priit Paluoja,
- Juha Kere,
- Juha S. Tapanainen,
- Kaarel Krjutškov,
- Timo Tuuri,
- Urmo Võsa,
- and Sanna Vuoristo
Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
...infertility treatments at Helsinki University Hospital Reproduction Medicine Unit. The samples were donated with an informed consent, and patients understood that donating oocytes, zygotes, or embryos is voluntary.Collection of human oocytes and embryosImmature oocytes from intracytoplasmic sperm injection...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...of specific plant cell types, showing that as in animals, gamete, zygote, and differentiated cells present striking differences in their nuclear 3D chromatin configuration. By integrating single-cell 3C and Hi-C approaches, Zhou and collaborators analyzed the 3D s of rice sperm, egg, unicellular zygote...
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Research: Single-cell RNA-sequencing reveals the existence of naive and primed pluripotency in pre-implantation rhesus monkey embryos
- Denghui Liu,
- Xinyi Wang,
- Dajian He,
- Chunli Sun,
- Xiechao He,
- Lanzhen Yan,
- Yizhou Li,
- Jing-Dong J. Han,
- and Ping Zheng
Genome Res. October 2018 28: 1481-1493; Published in Advance August 28, 2018, doi:10.1101/gr.233437.117
.... After 32–35 h of rhCG administration, mature oocytes were collected by laparoscopic follicular aspiration (Niu et al. 2010). Oocytes were removed of cumulus cells and those with extrusion of the first polar body (metaphase II stage) were collected for downstream experiments. Semen collection, sperm...

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