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Resource: Charting the regulatory landscape of TP53 on transposable elements in cancer
- Xuan Qu,
- Yonghao Liang,
- Colin McCornack,
- Xiaoyun Xing,
- Heather Schmidt,
- Chad Tomlinson,
- Catrina Fronick,
- Edward A. Belter, Jr.,
- Juan F. Macias-Velasco,
- and Ting Wang
Genome Res. June 2025 35: 1456-1471; Published in Advance May 13, 2025, doi:10.1101/gr.279398.124
...but repressed by the treatment of doxorubicin, making inference of the mechanism of their activity non-trivial (Fig. 4G). The fourth set of TE-derived transcripts is repressed by TP53 regardless of doxorubicin-activation, driven by LTR10F and AluSx copies (Fig. 4H). The last set of transcripts were those...
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Research: Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
...data and characterized genomic and epigenetic signatures associated with their transcription profile and potential function as cell-type–specific enhancers.ResultsIdentification of primary Alu transcripts using RAMPAGE dataRAMPAGE uses several strategies to enrich for TSSs (Batut and Gingeras 2013...
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Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Roman Spektor,
- Nathaniel D. Tippens,
- Claudia A. Mimoso,
- and Paul D. Soloway
Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
.... 2009. Global analysis of DNA methylation and transcription of human repetitive sequences. Epigenetics 4: 339–350. doi:10.4161/epi.4.5.9284 ↵Jordà M, Díez-Villanueva A, Mallona I, Martín B, Lois S, Barrera V, Esteller M, Vavouri T, Peinado MA. 2017. The epigenetic landscape of Alu repeats delineates...
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LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
- Aileen M. Smith,
- Maria-Jose Sanchez,
- George A. Follows,
- Sarah Kinston,
- Ian J. Donaldson,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
...recent, primate-specific Alu family of repeats. However, a role for more ancient repeats in gene regulation is also now emerging with the discovery of two neuronal enhancers that are derived from ancient short interspersed nucleotide elements (SINE) retroposons ( Bejerano et al. 2006 ; Santangelo et al...
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March 2026, 36 (3)

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