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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...with deleterious coding variants. We also investigate the contribution of SHROOM3 to phenotypic variability in CFM by utilizing quantitative assessments in mouse models.ResultsPutative deleterious rare coding variants in SHROOM3We conducted whole- sequencing on 2009 Chinese CFM patients and enrolled, as controls...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
..., H3K27me3 can spread into regions previously marked by H3K9 methylation, forming new Polycomb domains and contributing to heterochromatin maintenance following the loss of H3K9 methylation (Fukuda et al. 2023). Such epigenomic reorganization is observed not only in developmental processes...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...Suv39h-catalyzed H3K9me3 is critical for euchromatic organization and the maintenance of gene transcription Christine R. Keenan1,2,4,6, Hannah D. Coughlan1,2,4, Nadia Iannarella1, Andres Tapia del Fierro1,2, Andrew Keniry1,2, Timothy M. Johanson1,2, Wing Fuk Chan1,2,7, Alexandra L. Garnham1...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
..., 75005 France; 2Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France; 3Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France ↵4 These authors contributed equally to this work. ↵Present addresses: 5IGBMC–CNRS UMR 7104...
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Research: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
...Epigenetic maintenance of topological domains in the highly rearranged gibbon Nathan H. Lazar1, Kimberly A. Nevonen2, Brendan O'Connell3, Christine McCann4,5, Rachel J. O'Neill4,5, Richard E. Green3, Thomas J. Meyer1, Mariam Okhovat2 and Lucia Carbone1,2,6,7 1Bioinformatics and Computational...
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Research: The organization of genome duplication is a critical determinant of the landscape of genome maintenance
- Blanca Gómez-Escoda and
- Pei-Yun Jenny Wu
Genome Res. August 2018 28: 1179-1192; Published in Advance June 22, 2018, doi:10.1101/gr.224527.117
...whether and how the organization of DNA replication along the chromosomes may contribute to integrity. Potential evidence for such an interplay derives from genetic analyses that have correlated mutation frequency with replication timing on Chromosome VI in budding yeast (Lang and Murray 2011...
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Research: Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma
- Pádraic Corcoran,
- Jennifer L. Anderson,
- David J. Jacobson,
- Yu Sun,
- Peixiang Ni,
- Martin Lascoux,
- and Hanna Johannesson
Genome Res. April 2016 26: 486-498; Published in Advance February 18, 2016, doi:10.1101/gr.197244.115
...Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma Pádraic Corcoran 1 , 2 , Jennifer L. Anderson 1 , David J. Jacobson 1 , Yu Sun 3 , Peixiang Ni 4 , Martin...
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Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
- Andrew Ying-Fei Chang and
- Ben-Yang Liao
Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
..., multiple histone modifications were found to assist mRNA dosage maintenance following gene duplication events and the possible involvement of adenine DNA methylation in this process was excluded. Furthermore, the histone marks and acting regions that mediated the reduction in duplicated gene expression...
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Research: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
- Te-Lun Mai and
- Trees-Juen Chuang
Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
...unclear. Here, we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating and transcriptome sequencing data from 447 human lymphoblastoid cell lines, we show that nonsynonymous editing activities (prevalence/level) are negatively correlated...
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Research: The clustering of functionally related genes contributes to CNV-mediated disease
- Tallulah Andrews,
- Frantisek Honti,
- Rolph Pfundt,
- Nicole de Leeuw,
- Jayne Hehir-Kwa,
- Anneke Vulto-van Silfhout,
- Bert de Vries,
- and Caleb Webber
Genome Res. June 2015 25: 802-813; Published in Advance April 17, 2015, doi:10.1101/gr.184325.114
...present in each source of functional information, we have identified significantly unusual clustering within those regions of the that are affected by pathogenic CNVs. To minimize the contribution of false positives without sacrificing coverage of functional information, we used an integrative approach...

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