Searching journal content for articles similar to Bhinge et al. 17 (6): 910.

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  1. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...-492 containing genomic regions undergo dynamic histone modifications during antiviral 493 signalling, indicating their functional relevance in gene regulation. This study also expands 494 upon previous research on ISREs in salmonids, focusing on gene families such as mx, 495 rsad2, stat1, stat2...
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  2. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...Bio) and Oxford Nanopore Technologies (ONT) are revolutionizing genomics: They are making chromosome-level assemblies routine, and full diploid, telomere-to-telomere (T2T) assemblies are becoming the standard for human assemblies. LRS employs single-molecule sequencing, avoiding many biases, errors...
  3. Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
    • Jiawei Shen,
    • Siyuan Cheng,
    • Deepak Purushotham,
    • Xiaoyu Zhuo,
    • Alan Y Du,
    • Wenjin Zhang,
    • Daofeng Li,
    • and Ting Wang
    Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
    ...chosen repeat subfamilies can be visualized via the Heatmap View, Consensus View, and Genome View. Profiles of individual repeat copies in the can be visualized in the linked WashU Epi Browser platform. Figure 2. Overview of analysis of MER41B in HeLa-S3 cell line bound by STAT1. (A) The highlighted cell...
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  4. Method: Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
    • Fan Yang,
    • Jiebiao Wang,
    • The GTEx Consortium,
    • Brandon L. Pierce,
    • and Lin S. Chen
    Genome Res. November 2017 27: 1859-1871; Published in Advance October 11, 2017, doi:10.1101/gr.216754.116
    ...on Chromosome 1 (Fig. 4A). IFI44L is a cis-eGene in two GTEx tissues (cerebellar hemisphere and tibial nerve), and the cis-eSNPs associated with IFI44L expression are also associated with expression of multiple genes in trans in both cerebellar and tibial nerve tissue. OAS1 is a trans target of these SNPs...
  5. Perspective: Genomic approaches for understanding the genetics of complex disease
    • William L. Lowe, Jr. and
    • Timothy E. Reddy
    Genome Res. October 2015 25: 1432-1441; doi:10.1101/gr.190603.115
    ...to phenotypes. Genomic regulatory elements are highly enriched in phenotype-associated variants Although eQTLs have demonstrated value in identifying target genes for genetic association studies, they too suffer from the same limitation that the most strongly associated variant may not be causal...
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  6. Research: Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping
    • Pei-Yin Hsu,
    • Hang-Kai Hsu,
    • Gregory A.C. Singer,
    • Pearlly S. Yan,
    • Benjamin A.T. Rodriguez,
    • Joseph C. Liu,
    • Yu-I Weng,
    • Daniel E. Deatherage,
    • Zhong Chen,
    • Julia S. Pereira,
    • Ricardo Lopez,
    • Jose Russo,
    • Qianben Wang,
    • Coral A. Lamartiniere,
    • Kenneth P. Nephew,
    • and Tim H.-M. Huang
    Genome Res. June 2010 20: 733-744; Published in Advance May 4, 2010, doi:10.1101/gr.101923.109
    ...Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping Pei-Yin Hsu 1 , Hang-Kai Hsu 1 , Gregory A.C. Singer 1 , Pearlly S. Yan 1 , Benjamin A.T. Rodriguez 1 , Joseph C. Liu 1 , Yu-I Weng 1...
  7. Research: ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors
    • Stephan R. Starick,
    • Jonas Ibn-Salem,
    • Marcel Jurk,
    • Céline Hernandez,
    • Michael I. Love,
    • Ho-Ryun Chung,
    • Martin Vingron,
    • Morgane Thomas-Chollier,
    • and Sebastiaan H. Meijsing
    Genome Res. June 2015 25: 825-835; Published in Advance February 26, 2015, doi:10.1101/gr.185157.114
    ...and one of the FOX TFs are simultaneously cross-linked (combinatorial mode of binding); and (C) for the STAT1 motif (JASPAR MA0137.3) where GR is tethered to the DNA via STAT proteins. Starick et al. 830 Genome Research www..org reporters containing genomic regions bearing both FOX and GR binding sites...
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  8. Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
    • Liangxi Wang,
    • Tiegh Taylor,
    • Kumaragurubaran Rathnakumar,
    • Nadiya Khyzha,
    • Minggao Liang,
    • Azad Alizada,
    • Laura F. Campitelli,
    • Sara E. Pour,
    • Zain M. Patel,
    • Lina Antounians,
    • Ian C. Tobias,
    • Huayun Hou,
    • Timothy R. Hughes,
    • Sushmita Roy,
    • Jennifer A. Mitchell,
    • Jason E. Fish,
    • and Michael D. Wilson
    Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
    ...cells, we also observed an enrichment of RELA motifs at specific positions in MER41B and MER81. MER41B is a primate LTR subfamily bound by interferon gamma (IFNG)-inducible TFs STAT1 and IRF1 (Chuong et al. 2016). We find that the RELA motif occurs at positions 378 to 387 bp of the consensus sequence...
  9. Research: Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
    • Conor J. Kelly,
    • Carol G. Chitko-McKown,
    • and Edward B. Chuong
    Genome Res. August 2022 32: 1474-1486; Published in Advance August 10, 2022, doi:10.1101/gr.276241.121
    ...of IFNG-stimulated and untreated MDBK cells using ATAC-seq and CUT&RUN with antibodies against H3K27ac, phosphorylated RNA polymerase II subunit A (POLR2A; Entrez gene ID 282312), total STAT1, and phosphorylated STAT1 (Supplemental Tables S3, S4). Successful antibody targeting of bovine STAT1...
  10. Resource: Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    • Jie Wang,
    • Jiali Zhuang,
    • Sowmya Iyer,
    • XinYing Lin,
    • Troy W. Whitfield,
    • Melissa C. Greven,
    • Brian G. Pierce,
    • Xianjun Dong,
    • Anshul Kundaje,
    • Yong Cheng,
    • Oliver J. Rando,
    • Ewan Birney,
    • Richard M. Myers,
    • William S. Noble,
    • Michael Snyder,
    • and Zhiping Weng
    Genome Res. September 2012 22: 1798-1812; doi:10.1101/gr.139105.112
    ...in the human , and the results are summarized in Figure 3A. We confirmed the previously reported enrichment of STAT1, NF-Y, and CTCF binding sites in various repetitive elements (Bourque et al. 2008; Schmid and Bucher 2010), and we uncovered many more TFs whose binding sites are enriched in certain repetitive...
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