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Functional validation of a constitutive autonomous silencer element
Heyuan Qi1, Mingdong Liu2, David W Emery3
1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, United States of America.
Plos One
|April 25, 2015
Summary
Researchers validated T39, a human genomic DNA sequence, as a potent silencer element. This constitutive autonomous silencer functions independently and offers a new control for studying gene regulation and regulatory elements.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Gene regulation is crucial, with silencer elements playing a key role.
- Few mammalian silencers are characterized, and fewer tested for autonomous function.
Purpose of the Study:
- To characterize and functionally validate the T39 silencer element from the human genome.
- To compare T39's silencer activity against other putative silencer elements.
Main Methods:
- Functional assays included enhancer-blocking insulator and silencer activity tests.
- Stable transfection in erythroid K562 cells and comparison to a neutral spacer control.
- Analysis of DNase hypersensitivity, CTCF binding, and interactions with distal regulatory elements.
Main Results:
- T39 demonstrated potent silencer activity, outperforming PRE2-S5 and two other elements.
- T39 silenced disparate promoters across multiple cell lines autonomously and independently of topology.
- Only T39 showed constitutive DNase hypersensitivity and CTCF binding, with unique native interactions.
Conclusions:
- T39 is validated as a potent, constitutive, autonomous silencer element.
- T39 serves as a defined control for future studies on regulatory elements like insulators.
- A chromatin profile for T39 provides insights into silencer element function.
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