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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
...of SOX9 at the enhancers e1–e4, with the strongest binding observed at e3 (Fig. 6F; Supplemental Fig. S8E). Together, these data identified an oncogenic isoform of the NET1 gene that is transcriptionally activated by SOX9-bound enhancers within a duplication hotspot in gastric cancer...
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Research: Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
- Olivia Corradin,
- Alina Saiakhova,
- Batool Akhtar-Zaidi,
- Lois Myeroff,
- Joseph Willis,
- Richard Cowper-Sal·lari,
- Mathieu Lupien,
- Sanford Markowitz,
- and Peter C. Scacheri
Genome Res. January 2014 24: 1-13; Published in Advance November 6, 2013, doi:10.1101/gr.164079.113
...and Hirchsprung’s disease (Visel et al. 2009). SNPs at the SOX9 locus that confer risk to prostate cancer disrupt transcription factor binding sites at a single enhancer and alter SOX9 transcript levels in prostate cancer cells (Zhang et al. 2012). Moreover, in our studies of enhancer function in colon cancer...
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Research: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...-catenin. Beta-catenin and CTCF colocalize upon pathway activation, and disruption of selected binding sites perturbs target gene regulation. Moreover, Wnt signaling reorganizes the 3D as evidenced by -wide alterations in CTCF-bound loops. This work reveals a previously unexplored role for CTCF in the regulation...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...-range loop was associated with down-regulation of BDNF (twofold), suggesting the emergence of looping with a repressive element or disruption of existing enhancer-promoter interactions at the locus. In short, this locus exemplified how a few SVs can cause altered chromatin organization and deregulation...
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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
...patternswere reported previously for the SOX9 region associated with prostate cancer risk (Zhang et al. 2012). The observation that multiple variants within an LD block can affect regulatory element activity and gene expression argues that testing single variants in isolation will be both an inefficient...
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