Searching journal content for articles similar to Chen et al. 26 (10): 1342.

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  1. 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
    ...methylation, and small RNAs. These findings highlight the need for prospective analyses of embryo cell health and a quantitative measure to assess the impact of specific additives and adjuvants. Given the rapid advances in technology, particularly the single-cell genomics...
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  2. Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
    • Qiao Rui Xing,
    • Chadi A El Farran,
    • Ying Ying Zeng,
    • Yao Yi,
    • Tushar Warrier,
    • Pradeep Gautam,
    • James J. Collins,
    • Jian Xu,
    • Peter Dröge,
    • Cheng-Gee Koh,
    • Hu Li,
    • Li-Feng Zhang,
    • and Yuin-Han Loh
    Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
    ...to this work. Corresponding authors: yhloh@imcb.a-star.edu.sg, Li.Hu@mayo.eduAbstractJoint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different...
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  3. 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
    ..., editing by CRISPR/Cas9 or TALEN has achieved success in monkeys (Liu et al. 2014; Niu et al. 2014). These works highlight the importance of studying cell lineage segregation as well as pluripotency dynamics in monkeys. Herein, we collected single cells from rhesus monkey early embryos encompassing...
  4. 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
    ...successfully (Schwarz et al. 2018). Moreover, single-cell analyses confirmed that different groups of X-linked genes are activated at different times. Furthermore, additional single-cell analyses might allow to pinpoint the most upstream events of XCR.A subset of X-linked genes reactivates before pluripotency...
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  5. Method: Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing
    • Hongshan Guo,
    • Ping Zhu,
    • Xinglong Wu,
    • Xianlong Li,
    • Lu Wen,
    • and Fuchou Tang
    Genome Res. December 2013 23: 2126-2135; Published in Advance October 31, 2013, doi:10.1101/gr.161679.113
    ...analyses separately for both the male Figure 2. The sensitivity and reproducibility of the single-cell RRBS technique. (A) The number and proportion of CpG sites detected in the merged single mESC RRBS data set overlapped with those from the RRBS of the bulk mESCs. (B) Pearson correlation heatmap among...
  6. Research: CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning
    • Marlies E. Oomen,
    • Anders S. Hansen,
    • Yu Liu,
    • Xavier Darzacq,
    • and Job Dekker
    Genome Res. February 2019 29: 236-249; Published in Advance January 17, 2019, doi:10.1101/gr.241547.118
    ...chromosomes during most phases of mitosis (e.g., telophase), CTCF localization appeared to be diffuse during prometaphase. Second, to quantify CTCF binding dynamics, we used FRAP. As for the genomics experiments, we used nocodazole to arrest cells in prometaphase. As we observed with time-lapse microscopy...
  7. Research: Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments
    • Michael I. Robson,
    • Jose I. de las Heras,
    • Rafal Czapiewski,
    • Aishwarya Sivakumar,
    • Alastair R.W. Kerr,
    • and Eric C. Schirmer
    Genome Res. July 2017 27: 1126-1138; Published in Advance April 19, 2017, doi:10.1101/gr.212308.116
    ...multiple analyses testing the spatial independence of domains along chromosomes (Favorov et al. 2012), confirmed this correspondence betweenCDs and LADswhich displayed a uniformdistance separation and an increased overlap frequency compared to chance (Supplemental Fig. S5B). To determine if CD structure...
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  8. 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
    ...trypsinized and made into single cell suspensions before being spundown at 200g for 4min. Themediawas aspirated and the cells taken up in 5 mL PBS and spun again at 200g for 4 min. Cells were aspirated again and taken up in 90 µLnucleofection buffer (90mM sodium phosphate buffer pH 7.2, 5 mM KCL, 10 mM MgCl2...
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  9. Article: Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis
    • Ichiro Hiratani,
    • Tyrone Ryba,
    • Mari Itoh,
    • Joy Rathjen,
    • Michael Kulik,
    • Bernadett Papp,
    • Eden Fussner,
    • David P. Bazett-Jones,
    • Kathrin Plath,
    • Stephen Dalton,
    • Peter D. Rathjen,
    • and David M. Gilbert
    Genome Res. February 2010 20: 155-169; Published in Advance December 1, 2009, doi:10.1101/gr.099796.109
    ...of partially reprogrammed induced pluripotent stem cells (piPSCs) failed to re-establish ESC-specific replication-timing and transcription programs. These regions were enriched for lineage-independent early-to-late changes, which in female cells included the inactive X chromosome. Together, these results...
  10. Resource: Epigenomics of embryogenesis in turbot
    • Oscar Aramburu,
    • Belen G Pardo,
    • Ada Jimenez-Gonzalez,
    • Andrés Blanco-Hortas,
    • Daniel Macqueen,
    • Carmen Bouza,
    • and Paulino Martinez
    Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
    ...developmental stage transitions, highlighting the dynamic regulation 525 associated with the specification and differentiation of diverse cell types 526 comprising the turbot body plan. Chromatin state analyses provided further 527 insights into changes in chromatin state and CRE activity after ZGA is 528...
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