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Research: Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer
- Sven Bilke,
- Raphaela Schwentner,
- Fan Yang,
- Maximilian Kauer,
- Gunhild Jug,
- Robert L. Walker,
- Sean Davis,
- Yuelin J. Zhu,
- Marbin Pineda,
- Paul S. Meltzer,
- and Heinrich Kovar
Genome Res. November 2013 23: 1797-1809; Published in Advance August 12, 2013, doi:10.1101/gr.151340.112
...), and there is ample functional evidence for its decisive role in malignant transformation and tumorigenesis (Kovar 2010). However, ;10% of ES are characterized by alternative EWSR1 fusion partners from the ETS family (ERG, ETV1, ETV4, FEV ), and the oncogenic role of EWSR1/ERG, the second most frequent ES gene fusion...
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Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
- Zhizhuo Zhang,
- Kern Rei Chng,
- Shreyas Lingadahalli,
- Zikai Chen,
- Mei Hui Liu,
- Huy Hoang Do,
- Shaojiang Cai,
- Nicola Rinaldi,
- Huay Mei Poh,
- Guoliang Li,
- Ying Ying Sung,
- Charlie L. Heng,
- Leighton J. Core,
- Si Kee Tan,
- Xiaoan Ruan,
- John T. Lis,
- Manolis Kellis,
- Yijun Ruan,
- Wing-Kin Sung,
- and Edwin Cheung
Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
...interactions (Fig. 3D, right panel). We found EZH2, a subunit of the Polycomb repressive complex 2 (PRC2), specifically targeting enhancer hubs driven by AR and ERG binding (Supplemental Fig. S14), suggesting that PRC2 regulates those interaction hub regions, which is consistent with the previous model...
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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
...-specific enhancer within the rs1859962 risk LD block that establishes a 1-Mb chromatin loop with the SOX9 gene. The rs8072254 and rs1859961 SNPs mapping to this enhancer impose allele-specific gene expression. The variant allele of rs8072254 facilitates androgen receptor (AR) binding driving increased enhancer...
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
...Chips. SA-DNAm changes are highly reproducible and they are enriched in intergenic and nonpromoter regions of developmental genes. Furthermore, SA-hypomethylation in particular appears to be associated with H3K9me3, H3K27me3, and Polycomb-group 2 target genes. We demonstrate that ionizing irradiation...
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Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
..., and are commonly paired with promoters that are repressed by the Polycomb repressive complex in order to facilitate cellular reprogramming by master regulatory factors (Taberlay et al. 2011). In contrast, we found that cancer cells are rendered resistant to cellular reprogramming if the cognate enhancer...
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Method: ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
- Piotr J. Balwierz,
- Mikhail Pachkov,
- Phil Arnold,
- Andreas J. Gruber,
- Mihaela Zavolan,
- and Erik van Nimwegen
Genome Res. May 2014 24: 869-884; Published in Advance February 10, 2014, doi:10.1101/gr.169508.113
...occurrence of TFBSs. Indeed, in recent work (Arnold et al. 2012b) we applied the MARA approach to ChIP-seq data mapping the dynamics of trimethylation at lysine 27 of histone 3 (H3K27me3) and identified TFs involved in recruiting this epigenetic mark that is set by the Polycomb system. In ISMARA...
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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
...bp of one another. Indeed, Roder et al. showed that NF-Yand SP1 proteins bind to each other and that they cobind to the same promoter (Roder et al. 1999). In another example, YY1was shown to interactwithMYC, and cooperatively, the two TFs regulate the expression of the ITGA3 gene of the a3b1integrin...
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