Searching journal content for articles similar to Koren and McCarroll 24 (1): 64.

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  1. Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
    • Lakshana Sruthi Sadu Murari,
    • Quinn Dickinson,
    • Silvia Meyer-Nava,
    • and Juan Carlos Rivera-Mulia
    Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
    ...2016a; Rhind 2022; Vouzas and Gilbert 2023; Hyrien et al. 2025). This replication timing (RT) program partitions the into functional units that segregate to distinct nuclear compartments (Rivera-Mulia and Gilbert 2016b; Liu et al. 2025). In fact, RT alignswith the 3D organization measured by chromosome...
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  2. 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
    ...inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. Although XCI has long been studied, providing important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing...
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  3. Research: Delayed DNA replication in haploid human embryonic stem cells
    • Matthew M. Edwards,
    • Michael V. Zuccaro,
    • Ido Sagi,
    • Qiliang Ding,
    • Dan Vershkov,
    • Nissim Benvenisty,
    • Dieter Egli,
    • and Amnon Koren
    Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
    ...correlated on the X Chromosome of female samples (mean r = 0.83) (Supplemental Fig. S7A), as expected due to the random replication of the inactive X Chromosome (Koren and McCarroll 2014) (similar patterns were observed when comparing haploid and diploid cells) (see Supplemental Fig. S2B). However, we...
  4. Research: The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer
    • Ronan Chaligné,
    • Tatiana Popova,
    • Marco-Antonio Mendoza-Parra,
    • Mohamed-Ashick M. Saleem,
    • David Gentien,
    • Kristen Ban,
    • Tristan Piolot,
    • Olivier Leroy,
    • Odette Mariani,
    • Hinrich Gronemeyer,
    • Anne Vincent-Salomon,
    • Marc-Henri Stern,
    • and Edith Heard
    Genome Res. April 2015 25: 488-503; Published in Advance February 4, 2015, doi:10.1101/gr.185926.114
    ...The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer Ronan Chaligné 1 , 2 , 3 , 4 , Tatiana Popova 1 , 5 , Marco-Antonio Mendoza-Parra 6 , Mohamed-Ashick M. Saleem 6 , David Gentien 1 , 7...
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  5. Method: NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
    • Zhengyu Luo,
    • Ran Zhang,
    • Tengfei Hu,
    • Yuting Zhu,
    • Yueming Wu,
    • Wenfei Li,
    • Zhi Zhang,
    • Xuebiao Yao,
    • Haiyi Liang,
    • and Xiaoyuan Song
    Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
    ..., but they either require large amounts of starting materials and are costly, or provide a relative low resolution in chromatin contact maps. Here, we present nicking enzyme-assisted open chromatin interaction capture (NicE-C), a method that leverages nicking enzyme–mediated open chromatin profiling and chromosome...
  6. Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
    • Maude Strobino,
    • Joanna M. Wenda,
    • Laura Padayachy,
    • and Florian A. Steiner
    Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
    ...chromosomes display distinct overall replication timing patterns. Domains of early replication are enriched on Chromosomes I, II, and III, whereas domains of late replication are more prevalent on Chromosomes IV, V, and X (Fig. 1C; Supplemental Fig. S1B). Following the hypothesis that H3.3 has a role in DNA...
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  7. Research: DNA methylation profiles of human active and inactive X chromosomes
    • Andrew J. Sharp,
    • Elisavet Stathaki,
    • Eugenia Migliavacca,
    • Manisha Brahmachary,
    • Stephen B. Montgomery,
    • Yann Dupre,
    • and Stylianos E. Antonarakis
    Genome Res. October 2011 21: 1592-1600; Published in Advance August 23, 2011, doi:10.1101/gr.112680.110
    .... Gene body-specific methylation on the active X chromosome. Science 315: 1141–1143. Jablonka E, Goitein R, Marcus M, Cedar H. 1985. DNA hypomethylation causes an increase in DNase-I sensitivity and an advance in the time of replication of the entire inactive X chromosome. Chromosoma 93: 152...
  8. 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
    ...and random X inactivation. (A) Schematic representing the linear arrangement of genes across the Xist and Tsix TADs. (B) Diagrammatic representation of hybrid XEN cells derived from a cross between Mus musculus (Mus) and Mus molossinus (Mol) mice. The X Chromosome derived from Mus is the inactive X. (C...
  9. Research: Allele-specific control of replication timing and genome organization during development
    • Juan Carlos Rivera-Mulia,
    • Andrew Dimond,
    • Daniel Vera,
    • Claudia Trevilla-Garcia,
    • Takayo Sasaki,
    • Jared Zimmerman,
    • Catherine Dupont,
    • Joost Gribnau,
    • Peter Fraser,
    • and David M. Gilbert
    Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
    ...et al. 2009; Farago et al. 2012). X Chromosome inactivation in female cells is the most impressive example of RT asynchrony linked to large-scale chromosome organization, with the inactive chromosome X (Xi) densely packed into the Barr body at the nuclear periphery and replicating later than...
  10. Research: DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation
    • Joseph C. Siefert,
    • Constantin Georgescu,
    • Jonathan D. Wren,
    • Amnon Koren,
    • and Christopher L. Sansam
    Genome Res. August 2017 27: 1406-1416; Published in Advance May 16, 2017, doi:10.1101/gr.218602.116
    ...et al. 2011). In human cells, the late-replicating inactive X Chromosome (Xi) lacks a defined spatial pattern of replication (Koren and McCarroll 2014). To determine whether this was also true for Chr 4q, the autocorrelation of replication timing along Chr 4q was compared to the autocorrelation...
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