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Research: Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus
- Xiaoyang Zhang,
- Richard Cowper-Sal·lari,
- Swneke D. Bailey,
- Jason H. Moore,
- and Mathieu Lupien
Genome Res. August 2012 22: 1437-1446; Published in Advance June 4, 2012, doi:10.1101/gr.135665.111
...of FOXA1 but increases the binding of AP-1. This latter increases enhancer activity. This E1 enhancer establishes a loop with the SOX9 genes in prostate cancer cells. Zhang et al. 1442 Genome Research www..org Risk variants mapping to noncoding regions may also directly impact unannotated transcripts...
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Research: Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition
- Dan E. Webster,
- Brook Barajas,
- Rose T. Bussat,
- Karen J. Yan,
- Poornima H. Neela,
- Ross J. Flockhart,
- Joanna Kovalski,
- Ashley Zehnder,
- and Paul A. Khavari
Genome Res. May 2014 24: 751-760; Published in Advance January 17, 2014, doi:10.1101/gr.166231.113
..., Leunissen JAM. 2007. Primer3Plus, an enhancedweb interface to Primer3.Nucleic Acids Res 35: W71–W74. Wasserman NF, Aneas I, Nobrega MA. 2010. An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Genome Res 20: 1191–1197. Wellbrock C, Rana...
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Method: Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
- Nicola H. Dryden,
- Laura R. Broome,
- Frank Dudbridge,
- Nichola Johnson,
- Nick Orr,
- Stefan Schoenfelder,
- Takashi Nagano,
- Simon Andrews,
- Steven Wingett,
- Iwanka Kozarewa,
- Ioannis Assiotis,
- Kerry Fenwick,
- Sarah L. Maguire,
- James Campbell,
- Rachael Natrajan,
- Maryou Lambros,
- Eleni Perrakis,
- Alan Ashworth,
- Peter Fraser,
- and Olivia Fletcher
Genome Res. November 2014 24: 1854-1868; Published in Advance August 13, 2014, doi:10.1101/gr.175034.114
....01). Interactions with a false discovery corrected P-value of >0.01 are not shown. Dryden et al. 1860 Genome Research www..org as targets of the 2q35, 9q31.2, and 8q24.21 risk loci. For the protein-coding genes IGFBP5,KLF4, andMYC, therewas some evidence that the tissue specificity of the interaction peaks...
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Research: CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer
- Hui Ling,
- Riccardo Spizzo,
- Yaser Atlasi,
- Milena Nicoloso,
- Masayoshi Shimizu,
- Roxana S. Redis,
- Naohiro Nishida,
- Roberta Gafà,
- Jian Song,
- Zhiyi Guo,
- Cristina Ivan,
- Elisa Barbarotto,
- Ingrid De Vries,
- Xinna Zhang,
- Manuela Ferracin,
- Mike Churchman,
- Janneke F. van Galen,
- Berna H. Beverloo,
- Maryam Shariati,
- Franziska Haderk,
- Marcos R. Estecio,
- Guillermo Garcia-Manero,
- Gijs A. Patijn,
- David C. Gotley,
- Vikas Bhardwaj,
- Imad Shureiqi,
- Subrata Sen,
- Asha S. Multani,
- James Welsh,
- Ken Yamamoto,
- Itsuki Taniguchi,
- Min-Ae Song,
- Steven Gallinger,
- Graham Casey,
- Stephen N. Thibodeau,
- Loïc Le Marchand,
- Maarit Tiirikainen,
- Sendurai A. Mani,
- Wei Zhang,
- Ramana V. Davuluri,
- Koshi Mimori,
- Masaki Mori,
- Anieta M. Sieuwerts,
- John W.M. Martens,
- Ian Tomlinson,
- Massimo Negrini,
- Ioana Berindan-Neagoe,
- John A. Foekens,
- Stanley R. Hamilton,
- Giovanni Lanza,
- Scott Kopetz,
- Riccardo Fodde,
- and George A. Calin
Genome Res. September 2013 23: 1446-1461; Published in Advance June 24, 2013, doi:10.1101/gr.152942.112
...more CCAT2 transcript. Our results support a new mechanism of MYC and WNT regulation by the novel lncRNA CCAT2 in colorectal cancer pathogenesis, and provide an alternative explanation of the SNP-conferred cancer risk. [Supplemental material is available for this article.] Notwithstanding...
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Research: Alterations in TCF7L2 expression define its role as a key regulator of glucose metabolism
- Daniel Savic,
- Honggang Ye,
- Ivy Aneas,
- Soo-Young Park,
- Graeme I. Bell,
- and Marcelo A. Nobrega
Genome Res. September 2011 21: 1417-1425; Published in Advance June 14, 2011, doi:10.1101/gr.123745.111
...differential in vivo activity to a MYC enhancer...
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Research: Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations
- Maitri Y. Shah,
- Manuela Ferracin,
- Valentina Pileczki,
- Baoqing Chen,
- Roxana Redis,
- Linda Fabris,
- Xinna Zhang,
- Cristina Ivan,
- Masayoshi Shimizu,
- Cristian Rodriguez-Aguayo,
- Mihnea Dragomir,
- Katrien Van Roosbroeck,
- Maria Ines Almeida,
- Maria Ciccone,
- Daniela Nedelcu,
- Maria Angelica Cortez,
- Taghi Manshouri,
- Steliana Calin,
- Muharrem Muftuoglu,
- Pinaki P. Banerjee,
- Mustafa H. Badiwi,
- Jan Parker-Thornburg,
- Asha Multani,
- James William Welsh,
- Marcos Roberto Estecio,
- Hui Ling,
- Ciprian Tomuleasa,
- Delia Dima,
- Hui Yang,
- Hector Alvarez,
- M. James You,
- Milan Radovich,
- Elizabeth Shpall,
- Muller Fabbri,
- Katy Rezvani,
- Leonard Girnita,
- Ioana Berindan-Neagoe,
- Anirban Maitra,
- Srdan Verstovsek,
- Riccardo Fodde,
- Carlos Bueso-Ramos,
- Mihai Gagea,
- Guillermo Garcia Manero,
- and George A. Calin
Genome Res. April 2018 28: 432-447; Published in Advance March 22, 2018, doi:10.1101/gr.225128.117
...and non-small cell lung adenocarcinomas (Ling et al. 2013; Redis et al. 2013; Qiu et al. 2014; Cai et al. 2015; Wang et al. 2015a,b; Zhang et al. 2015) and was shown to induce chromosomal instability and metastases in colon cancer by increasing MYC expression (Ling et al. 2013). Although these studies...

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