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Series GSE133379 Query DataSets for GSE133379
Status Public on Oct 13, 2020
Title Detection of genomic G-quadruplexes in living cells using a small artificial protein
Organisms Gallus gallus; Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123,000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ~70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
Overall design We engineered a divalent G-quadruplex (G4) probe (G4P) protein that binds to the two terminal G-quartets of a G4 with high affinity and specificity through a synergy of two independent binding activities. G4-ChIP technique was developed by expressing the G4P to capture the formation of G4s in live animal cells to reveal the locations, magnitudes, and sequence identities of G4s genome-wide.
Contributor(s) Zheng K, Zhang J, He Y, Gong J, Wen C, Chen J, Hao Y, Zhao Y, Tan Z
Citation(s) 33045726
Submission date Jun 26, 2019
Last update date May 02, 2023
Contact name Zheng Tan
Organization name Institute of Zoology, Chinese Academy of Sciences
Street address 1 Beichen West Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
Platforms (3)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24517 HiSeq X Ten (Gallus gallus)
Samples (18)
GSM3907012 A549 G4chip rep1
GSM3907013 A549 input rep1
GSM3907014 A549 G4chip rep2
BioProject PRJNA551290
SRA SRP212149

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Supplementary file Size Download File type/resource
GSE133379_293T-G4P-hg19-ratio-rep1.bigWig 321.8 Mb (ftp)(http) BIGWIG
GSE133379_293T-G4P-hg19-ratio-rep2.bigWig 291.9 Mb (ftp)(http) BIGWIG
GSE133379_293T-G4P-hg19-rep1.narrowPeak.gz 993.7 Kb (ftp)(http) NARROWPEAK
GSE133379_293T-G4P-hg19-rep2.narrowPeak.gz 747.1 Kb (ftp)(http) NARROWPEAK
GSE133379_293T-G4P-hg19-subtract-rep1.bigWig 325.4 Mb (ftp)(http) BIGWIG
GSE133379_293T-G4P-hg19-subtract-rep2.bigWig 260.6 Mb (ftp)(http) BIGWIG
GSE133379_3T3-G4P-mm9-ratio-rep1.bigWig 235.5 Mb (ftp)(http) BIGWIG
GSE133379_3T3-G4P-mm9-rep1.narrowPeak.gz 1.0 Mb (ftp)(http) NARROWPEAK
GSE133379_3T3-G4P-mm9-subtract-rep1.bigWig 239.4 Mb (ftp)(http) BIGWIG
GSE133379_A549-G4P-hg19-ratio-rep1.bigWig 265.5 Mb (ftp)(http) BIGWIG
GSE133379_A549-G4P-hg19-ratio-rep2.bigWig 290.3 Mb (ftp)(http) BIGWIG
GSE133379_A549-G4P-hg19-rep1.narrowPeak.gz 2.9 Mb (ftp)(http) NARROWPEAK
GSE133379_A549-G4P-hg19-rep2.narrowPeak.gz 3.7 Mb (ftp)(http) NARROWPEAK
GSE133379_A549-G4P-hg19-subtract-rep1.bigWig 270.1 Mb (ftp)(http) BIGWIG
GSE133379_A549-G4P-hg19-subtract-rep2.bigWig 293.7 Mb (ftp)(http) BIGWIG
GSE133379_DF-1-G4P-gal5-ratio-rep1.bigWig 126.2 Mb (ftp)(http) BIGWIG
GSE133379_DF-1-G4P-gal5-rep1.narrowPeak.gz 824.3 Kb (ftp)(http) NARROWPEAK
GSE133379_DF-1-G4P-gal5-subtract-rep1.bigWig 118.0 Mb (ftp)(http) BIGWIG
GSE133379_H1975-G4P-hg19-ratio-rep1.bigWig 254.1 Mb (ftp)(http) BIGWIG
GSE133379_H1975-G4P-hg19-ratio-rep2.bigWig 267.2 Mb (ftp)(http) BIGWIG
GSE133379_H1975-G4P-hg19-rep1.narrowPeak.gz 3.3 Mb (ftp)(http) NARROWPEAK
GSE133379_H1975-G4P-hg19-rep2.narrowPeak.gz 3.6 Mb (ftp)(http) NARROWPEAK
GSE133379_H1975-G4P-hg19-subtract-rep1.bigWig 232.5 Mb (ftp)(http) BIGWIG
GSE133379_H1975-G4P-hg19-subtract-rep2.bigWig 272.0 Mb (ftp)(http) BIGWIG
GSE133379_HeLa-S3-G4P-hg19-ratio-rep1.bigWig 284.2 Mb (ftp)(http) BIGWIG
GSE133379_HeLa-S3-G4P-hg19-rep1.narrowPeak.gz 475.8 Kb (ftp)(http) NARROWPEAK
GSE133379_HeLa-S3-G4P-hg19-subtract-rep1.bigWig 289.3 Mb (ftp)(http) BIGWIG
GSE133379_PQS-gal5.BigBed 17.7 Mb (ftp)(http) BIGBED
GSE133379_PQS-hg19.BigBed 58.7 Mb (ftp)(http) BIGBED
GSE133379_PQS-mm9.BigBed 57.8 Mb (ftp)(http) BIGBED
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