Searching journal content for articles similar to Wang et al. 22 (10): 1855.

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  1. 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
    ...). In early mouse embryos, imprinted XCI (iXCI), which always inactivates the paternal X Chromosome, takes place at the four-cell stage. It is followed by XCR, in the inner cell mass (ICM) of the blastocyst (Mak et al. 2004; Okamoto et al. 2004; Borensztein et al. 2017a, b). Then, random XCI (rXCI) of one...
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  2. Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
    • Sena A. Gocuk,
    • James Lancaster,
    • Shian Su,
    • Jasleen K. Jolly,
    • Thomas L. Edwards,
    • Doron G. Hickey,
    • Matthew E. Ritchie,
    • Marnie E. Blewitt,
    • Lauren N. Ayton,
    • and Quentin Gouil
    Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
    ...or one. In the case of perfectly balanced X inactivation, haplotype blocks should return skews of 0.5. Folding is done around the x = 0.5 axis, to account for the random assignment of haplotype 1/2 labels to the two alleles in each block. Folding would not be necessary if we could assign haplotype 1...
  3. Research: Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica
    • Xu Wang,
    • Kory C. Douglas,
    • John L. VandeBerg,
    • Andrew G. Clark,
    • and Paul B. Samollow
    Genome Res. January 2014 24: 70-83; Published in Advance September 24, 2013, doi:10.1101/gr.161919.113
    ...somatic cells throughout life (Straub and Becker 2007; Payer and Lee 2008). XCI occurs in two distinct patterns in eutherian mammals: random XCI (rXCI) and paternally imprinted XCI (pXCI). In rXCI, the choice of X chromosome to be inactivated in any given cell is more or less random with regard...
  4. Resource: Exploration of fine-scale recombination rate variation in the domestic horse
    • Samantha K. Beeson,
    • James R. Mickelson,
    • and Molly E. McCue
    Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
    ...485 total horses. Genotypes were phased with Beagle version 4.0 (Browning and Browning 2007) to fill in missing genotypes and predict haplotypes.Recombination rate estimation and hotspot detectionOne hundred random samples of 40 chromosomes from the data set described above were generated to estimate...
  5. Research: Pervasive polymorphic imprinted methylation in the human placenta
    • Courtney W. Hanna,
    • Maria S. Peñaherrera,
    • Heba Saadeh,
    • Simon Andrews,
    • Deborah E. McFadden,
    • Gavin Kelsey,
    • and Wendy P. Robinson
    Genome Res. June 2016 26: 756-767; Published in Advance January 14, 2016, doi:10.1101/gr.196139.115
    ..., and their function in development is unknown. In this study, we developed a -wide approach to identify novel imprinted DMRs in the human placenta and investigated the dynamics of these imprinted DMRs during development in somatic and extraembryonic tissues. DNA methylation was evaluated using the Illumina Human...
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  6. Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
    • Sachin Pundhir,
    • Jinyu Su,
    • Marta Tapia,
    • Anne Meldgaard Hansen,
    • James Seymour Haile,
    • Klaus Hansen,
    • and Bo Torben Porse
    Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
    ...directional RNA preparation kit (New England Biolabs E7760S) following the manufacturer's instructions. Briefly, nascent RNA was fragmentated into an average of 200 nt and reverse-transcribed into stranded DNA using random primers, which was followed by addition of sequencing bar-code during PCR amplification...
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  7. Method: Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases
    • Renan Sauteraud,
    • Jill M. Stahl,
    • Jesica James,
    • Marisa Englebright,
    • Fang Chen,
    • Xiaowei Zhan,
    • Laura Carrel,
    • and Dajiang J. Liu
    Genome Res. September 2021 31: 1629-1637; Published in Advance August 23, 2021, doi:10.1101/gr.275677.121
    ...consequences of XCI escape, a critical first step is to identify genes that escape XCI in a particular tissue or disease state. The chromosome-wide analysis is complicated by the random nature of XCI in early development, as the determination of Xa and Xi Chromosomes differs from cell to cell (cellular...
  8. Method: True single-molecule DNA sequencing of a pleistocene horse bone
    • Ludovic Orlando,
    • Aurelien Ginolhac,
    • Maanasa Raghavan,
    • Julia Vilstrup,
    • Morten Rasmussen,
    • Kim Magnussen,
    • Kathleen E. Steinmann,
    • Philipp Kapranov,
    • John F. Thompson,
    • Grant Zazula,
    • Duane Froese,
    • Ida Moltke,
    • Beth Shapiro,
    • Michael Hofreiter,
    • Khaled A.S. Al-Rasheid,
    • M. Thomas P. Gilbert,
    • and Eske Willerslev
    Genome Res. October 2011 21: 1705-1719; Published in Advance July 29, 2011, doi:10.1101/gr.122747.111
    ...True single-molecule DNA sequencing of a pleistocene horse bone Ludovic Orlando 1 , 9 , Aurelien Ginolhac 1 , Maanasa Raghavan 1 , Julia Vilstrup 1 , Morten Rasmussen 1 , Kim Magnussen 1 , Kathleen E. Steinmann 2...
  9. Research: Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation
    • Geng Chen,
    • John Paul Schell,
    • Julio Aguila Benitez,
    • Sophie Petropoulos,
    • Marlene Yilmaz,
    • Björn Reinius,
    • Zhanna Alekseenko,
    • Leming Shi,
    • Eva Hedlund,
    • Fredrik Lanner,
    • Rickard Sandberg,
    • and Qiaolin Deng
    Genome Res. October 2016 26: 1342-1354; Published in Advance August 2, 2016, doi:10.1101/gr.201954.115
    .... In contrast to mESCs, mouse EpiStem cells (mEpiSCs) represent a primed developmental state of pluripotency, defined by their propensity for differentiation and random XCI, representing a suitable model for post-implantation development (Brons et al. 2007; Tesar et al. 2007). Random XCI is a crucial event...
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  10. Research: Random replication of the inactive X chromosome
    • Amnon Koren and
    • Steven A. McCarroll
    Genome Res. January 2014 24: 64-69; Published in Advance September 24, 2013, doi:10.1101/gr.161828.113
    ...be required for the regulation of gene activity. However, random replication has not been observed in mammals or outside the context of embryonic development. In mammals, developmentally regulated, chromosome-wide transcriptional silencing occurs in the process of X chromosome inactivation (XCI). XCI...
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