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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...sequence that is assigned to the four genomic contexts.Active CREs in tissues and cells are associated with increased chromatin accessibility (Keene et al. 1981; McGhee et al. 1981; Buenrostro et al. 2013). Thus, to study the contribution of TEs to the salmon CRE landscape, we integrated our TE annotation...
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Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...-based techniques such as ATAC-STARR-seq (Wang et al. 2018), ChIP-STARR-seq (Barakat et al. 2018), and FAIRE-STARR-seq (Chaudhri et al. 2020). Using the host cell DNA for these methods enables selection of cell type–specific candidate enhancers, which can then be functionally validated with STARR-seq upon...

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