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  1. 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
    ...Project Consortium. 2015. A global reference for human genetic variation. Nature 526: 68–74. doi:10.1038/nature15393 ↵Accounting for sex in the . 2017. Nat Med 23: 1243. doi:10.1038/nm.4445 ↵Amos-Landgraf JM, Cottle A, Plenge RM, Friez M, Schwartz CE, Longshore J, Willard HF. 2006. X chromosome-inactivation...
  2. Research: Copy number variation alters local and global mutational tolerance
    • Grace Avecilla,
    • Pieter Spealman,
    • Julia Matthews,
    • Elodie Caudal,
    • Joseph Schacherer,
    • and David Gresham
    Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
    ...in novel genetic interactions with unlinked genes. We validated a novel genetic interaction between different CNVs and BMH1 that was common to multiple strains. We also analyzed global gene expression and found that transcriptional dosage compensation does not affect most genes amplified by CNVs, although...
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  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
    ...constructed at Global Biologics, LLC (Columbia, MO). After sequencing, raw reads were quality filtered, trimmed, and aligned using Bowtie in the Galaxy suite (Giardine et al. 2005; Blankenberg et al. 2010; Goecks et al. 2010). Aligned reads were visualized on the UCSC Genome Browser and IGV (Robinson et al...
  4. Research: Random X inactivation in the mule and horse placenta
    • Xu Wang,
    • Donald C. Miller,
    • Andrew G. Clark,
    • and Douglas F. Antczak
    Genome Res. October 2012 22: 1855-1863; Published in Advance May 29, 2012, doi:10.1101/gr.138487.112
    ...inactivation in the equid placenta The vast majority of studies of X inactivation have analyzed human or mouse samples; investigations of X inactivation in other mammals are rare and limited in scope, relying on a single or a fewX-linked gene(s). This study represents the first systematic analysis of global X...
  5. 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
    ...Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations Stefan F. Pinter 1 , 2 , 3 , Ruslan I. Sadreyev 1 , 2 , 3 , Eda Yildirim 1 , 2 , 3 , Yesu Jeon 1 , 2 , 3 , Toshiro K. Ohsumi 2 , 3...
  6. Research: Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus
    • Julie E. Horvath,
    • Christina B. Sheedy,
    • Stephanie L. Merrett,
    • Abdoulaye Banire Diallo,
    • David L. Swofford,
    • NISC Comparative Sequencing Program,
    • Eric D. Green,
    • and Huntington F. Willard
    Genome Res. June 2011 21: 850-862; Published in Advance April 25, 2011, doi:10.1101/gr.111849.110
    ...there are no data indicating that these are genes in the nonhuman primates, dog, or cow. Previous directed studies identified conservation of Tsx (Chureau et al. 2002) sequences between human and mouse. Our global alignment across the candidate XIC shows sequence alignment across some Tsx exons in humans...
  7. Research: Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features
    • Lisa Barros de Andrade e Sousa,
    • Iris Jonkers,
    • Laurène Syx,
    • Ilona Dunkel,
    • Julie Chaumeil,
    • Christel Picard,
    • Benjamin Foret,
    • Chong-Jian Chen,
    • John T. Lis,
    • Edith Heard,
    • Edda G. Schulz,
    • and Annalisa Marsico
    Genome Res. July 2019 29: 1087-1099; Published in Advance June 7, 2019, doi:10.1101/gr.245027.118
    ...transcriptome by allele-specific PRO-seq (Kwak et al. 2013) at different time points up to 24 h of Dox treatment (Fig. 1A). Xist started to be up-regulated from the B6 chromosome about 1 h after Dox treatment and reached a plateau after 4 h (Fig. 1B,C; Supplemental Fig. S1), whereas global expression of the B6...
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  8. Research: Emergence of male-biased genes on the chicken Z-chromosome: Sex-chromosome contrasts between male and female heterogametic systems
    • Hans Ellegren
    Genome Res. December 2011 21: 2082-2086; Published in Advance August 25, 2011, doi:10.1101/gr.119065.110
    ...of therian sex chromosomes. PLoS Biol 6: e80. doi: 10.1371/journal.pbio.0060080. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, et al. 2000. A global profile of germline gene expression in C. elegans. Mol Cell 6: 605–616. Rice WR. 1984. Sex chromosomes...
  9. Research: Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X
    • Di Kim Nguyen,
    • Fan Yang,
    • Rajinder Kaul,
    • Can Alkan,
    • Anthony Antonellis,
    • Karen F. Friery,
    • Baoli Zhu,
    • Pieter J. de Jong,
    • and Christine M. Disteche
    Genome Res. March 2011 21: 402-409; Published in Advance January 31, 2011, doi:10.1101/gr.108563.110
    ..., Willard HF, Mukherjee S, Furey TS. 2006. Evidence of influence of genomic DNA sequence on human X chromosome inactivation. PLoS Comput Biol 2: e113. doi: 10.1371/journal.pcbi.0020113. Yang F, Babak T, Shendure J, Disteche CM. 2010. Global survey of escape from X inactivation by RNA-sequencing in mouse...
  10. Research: Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
    • Sahin Naqvi,
    • Daniel W. Bellott,
    • Kathy S. Lin,
    • and David C. Page
    Genome Res. April 2018 28: 474-483; Published in Advance February 15, 2018, doi:10.1101/gr.230433.117
    .... 2013. Haploinsufficiency of KDM6A is associated with severe psychomotor retardation, global growth restriction, seizures and cleft palate. Hum Genet 132: 537–552. ↵Mank JE, Ellegren H...
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