Searching journal content for articles similar to Wu et al. 11 (3): 389.

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  1. Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
    • Bertille Montibus,
    • James A. Cain,
    • Rocio T. Martinez-Nunez,
    • and Rebecca J. Oakey
    Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
    ...the chromosome's genomic sequence separated by intergenic stretches of DNA which are devoid of genes, in a strand-specific manner. However, in practice, the genomic organization is more complex, and genes can in reality occupy the same genomic space as each other and are considered as overlapping genes...
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  2. Resource: Multiscale network modeling reveals the gene regulatory landscape driving cancer prognosis in 32 cancer types
    • Peng Xu and
    • Bin Zhang
    Genome Res. October 2023 33: 1806-1817; Published in Advance October 31, 2023, doi:10.1101/gr.278063.123
    ...by interactions between gene expression and methylation. Coregulated genes of network modules were enriched in chromosome cytobands and preferentially localized in open chromatin regions. The preserved network modules formed 330 module clusters that resided in chromosome hot spots. The cancer...
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  3. LETTER: Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
    • James P. Noonan,
    • Jane Grimwood,
    • Jeremy Schmutz,
    • Mark Dickson,
    • and Richard M. Myers
    Genome Res. March 2004 14: 354-366; doi:10.1101/gr.2133704
    ...Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity James P. Noonan 1 , Jane Grimwood 2 , Jeremy Schmutz 2 , Mark Dickson 2 , and Richard M. Myers 1 , 2 , 3 1 Department of Genetics, Stanford...
  4. Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
    • Hadi Rahmaninejad,
    • Yao Xiao,
    • Maxime M.C. Tortora,
    • and Geoffrey Fudenberg
    Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
    ...at CTCF binding sites (Nora et al. 2017). Because altered CTCF binding even at individual positions can lead to dysregulated gene expression and disease (Lupiáñez et al. 2015), it is of great interest to understand how binding specifies folding across the .CTCF is thought to exert its influence on folding...
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  5. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...-tuning of differences between cell populations. For instance, we found that in the brain, the astrocyte and oligodendrocyte lineages clearly differ by gene expression, but at the splicing level, oligodendrocyte precursor cells cluster with astrocytes rather than committed and mature oligodendrocytes (Joglekar et al...
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  6. Research: Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
    • Weishi Yu,
    • Carl McIntosh,
    • Ryan Lister,
    • Iris Zhu,
    • Yixing Han,
    • Jianke Ren,
    • David Landsman,
    • Eunice Lee,
    • Victorino Briones,
    • Minoru Terashima,
    • Robert Leighty,
    • Joseph R. Ecker,
    • and Kathrin Muegge
    Genome Res. October 2014 24: 1613-1623; Published in Advance August 28, 2014, doi:10.1101/gr.172015.114
    ...from the murine DNA methylation mutant Hells −/− (helicase, lymphoid specific, also known as LSH ). It has been previously shown that HELLS can influence de novo methylation of retroviral sequences and endogenous genes. Here, we describe that HELLS controls cytosine methylation in a nuclear...
  7. Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
    • Varsha Poondi Krishnan,
    • Barbara Morone,
    • Shir Toubiana,
    • Monika Krzak,
    • Salvatore Fioriniello,
    • Floriana Della Ragione,
    • Maria Strazzullo,
    • Claudia Angelini,
    • Sara Selig,
    • and Maria R. Matarazzo
    Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
    ...DNMT3B protein to reestablish the normal DNA methylation pattern, whereas others are impervious to such a correction.The correlation between H3K4me3 levels and DNA methylation restoration can be exemplified at specific genic regions. The PCDHGA6 gene from the protocadherin gene cluster contains hypo...
  8. Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Bo Zhang,
    • Yan Zhou,
    • Nan Lin,
    • Rebecca F. Lowdon,
    • Chibo Hong,
    • Raman P. Nagarajan,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Michael Stevens,
    • Hyung Joo Lee,
    • Xiaoyun Xing,
    • Jia Zhou,
    • Vasavi Sundaram,
    • GiNell Elliott,
    • Junchen Gu,
    • Taoping Shi,
    • Philippe Gascard,
    • Mahvash Sigaroudinia,
    • Thea D. Tlsty,
    • Theresa Kadlecek,
    • Arthur Weiss,
    • Henriette O’Geen,
    • Peggy J. Farnham,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Pamela A.F. Madden,
    • Angela Tam,
    • Richard Moore,
    • Martin Hirst,
    • Marco A. Marra,
    • Baoxue Zhang,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
    ...imprinting, and tissue-specific gene expression. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA methylomes. This includes one of the most widely applied technologies for measuring DNA methylation: methylated DNA immunoprecipitation followed...
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  9. Research: Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
    • Timothy E. Reddy,
    • Jason Gertz,
    • Florencia Pauli,
    • Katerina S. Kucera,
    • Katherine E. Varley,
    • Kimberly M. Newberry,
    • Georgi K. Marinov,
    • Ali Mortazavi,
    • Brian A. Williams,
    • Lingyun Song,
    • Gregory E. Crawford,
    • Barbara Wold,
    • Huntington F. Willard,
    • and Richard M. Myers
    Genome Res. May 2012 22: 860-869; Published in Advance February 2, 2012, doi:10.1101/gr.131201.111
    ...factor (Fig. 1D). Together, the results reveal the existence of hubs of coordinated differential allelic gene regulation involving multiple TFs throughout the human . Most differential allelic occupancy results from variation outside the DNA binding motif To better understand the mechanisms underlying...
  10. Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
    • Samuel Thudium,
    • Katherine Palozola,
    • Éloïse L'Her,
    • and Erica Korb
    Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
    ...susceptibility genes encode epigenetic regulators (O'Roak et al. 2012; Parikshak et al. 2013; De Rubeis et al. 2014; Iossifov et al. 2014). In particular, many such mutations are found in proteins that regulate chromatin, the complex of DNA and histone proteins that helps to regulate transcription...
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