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| Status |
Public on Feb 15, 2019 |
| Title |
Small-molecule-based Human Genome G4 Profiling Reveals Potential Gene Regulation Activity |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
G-quadruplexes (G4s) are a type of secondary structure of nucleic acids, the formation of which depends on the π-π stacking of guanine-rich sequences. Herein, we present a readily accessible strategy, based on small molecule pulldown, for direct genomic G4 profiling of HEK 293T cells. A small molecule was rationally designed, containing PDP on one end and biotin on the other, joined by a 24-unit-long hydrophilic PEG linker. G4s isolation from genomic DNA annealed in potassium chloride buffer beforehand, has identified a total of 51446 PQS, which mainly distribute in introns and intergenic regions. Incubating cells with PDP for 3 h to 72 h resulted in the differential expression of a variety of genes, indicating a potential function of G4s in gene regulation.
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| Overall design |
A small molecule was applied for pull-down of G-quadruplexes in the genome of HEK 293T cells. RNA-Seq was performed to measure gene expression difference upon addition of 1 µM PDP for 3 h, 24 h and 72 h.
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| Contributor(s) |
Zeng W, Wu F, Liu C, Yang Y, Wu Z, Zhou X |
| Citation(s) |
30702101 |
| BioProject |
PRJNA429996 |
| Submission date |
Jan 18, 2018 |
| Last update date |
May 18, 2019 |
| Contact name |
Weiwu Zeng |
| E-mail(s) |
zengweiwu@whu.edu.cn
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| Organization name |
Wuhan University
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| Department |
College of Chemistry and Molecular Sciences
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| Street address |
Bayi Road
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platforms (1) |
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| Samples (12)
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| Relations |
| SRA |
SRP129700 |
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