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Series GSE270033 Query DataSets for GSE270033
Status Public on Jun 20, 2024
Title DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [ATAC-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary G-quadruplex structures (G4s) have been identified in genomes of multiple organisms and proven to play important epigenetic regulatory roles in various cellular functions. However, the G4 formation mechanism remains largely unknown. Here, we found a negative correlation between DNA 5mC methylation and G4 abundance. The abundance of genomic G4s significantly increased when the whole-genome methylation level was reduced in DNMT1-knockout cells. This increase was then suppressed by DNMT1 over-expression. And more G4s were detected in the hypomethylated cancer cell line HepG2 and rectal cancer tissues. Besides, 5mC modification significantly inhibited G4 formation of the potential G-quadruplex sequences (PQSs). The transcription of genes with 5mC modification sites in their promoter PQSs was affected after treatment with G4 stabilizer pyridostatin or methylation inhibitor 5-aza-dC. The global reduction of genomic methylation elevates gene transcription levels through increased G4s. Taken together, DNA 5mC methylation prevents PQSs from folding into G4s in genomes.
 
Overall design Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC) for 293T cells and DNMT1-KO 293T cells
 
Contributor(s) Niu K, Xiang L, Xiang H
Citation https://doi.org/10.1101/2023.02.16.528796
Submission date Jun 17, 2024
Last update date Sep 27, 2024
Contact name Lijun Xiang
E-mail(s) xiang-lijun@m.scnu.edu.cn
Phone +86-15626099434
Organization name South China Normal University
Department Guangzhou Key Laboratory of Insect Development Regulation and Application Research
Lab Qili Feng lab
Street address No.55, West of Zhongshan Avenue
City Guangzhou
State/province Guangdong
ZIP/Postal code 510631
Country China
 
Platforms (2)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL34281 Illumina NovaSeq X (Homo sapiens)
Samples (6)
GSM8333110 293T_WT_ATAC
GSM8333111 293T_DNMT1_KO_ATAC
GSM8543452 293T_WT_ATAC_rep2
This SubSeries is part of SuperSeries:
GSE221437 DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures
Relations
BioProject PRJNA1124893

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Supplementary file Size Download File type/resource
GSE270033_RAW.tar 132.5 Mb (http)(custom) TAR (of BW, NARROWPEAK)
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Raw data are available in SRA

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