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Series GSE198658 Query DataSets for GSE198658
Status Public on Nov 23, 2022
Title G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which could interact with transcription factors and chromatin remodelers to regulate cell type-specific transcriptome and shape chromatin landscapes. Based on the direct interactions between G4 and natural porphyrins, we established an in situ capture sequencing approach combining synthesized biotin-PEG4-Hemin and Cleavage Under Targets and Tagmentation (CUT&Tag) strategy to profile the Hemin binding sites in the human genome. We found that a proportion of G4s overlapped with Hemin binding sites and Hemin promoted genome-wide G4 formation at Hemin binding sites. Hemin treatments impaired gene transcription initiation and altered chromatin landscape with decreased H3K27ac and H3K4me3 modifications. Interestingly, G4 was not involved in the canonic Hemin-BACH1-NRF2-mediated enhancer activation process, highlighting an unprecedented G4-dependent mechanism for metabolic regulation of transcription. Furthermore, Hemin induced specific gene expression profiles in mouse primary hepatocytes, and block of Hemin degradation in mice by Hmox1 knockdown resulted in hepatic injury, providing in vivo insights for metabolic control of gene transcription by porphyrins.
Overall design Determination of hemin binding sites in the human genome, Determination of G4-CUT&Tag, R-loop-CUT&Tag, PRO-seq, ChIP-seq and RNA-seq in HEK293T or primary hepatocytes
Contributor(s) Liang K
Citation(s) 36522639
Submission date Mar 15, 2022
Last update date Feb 22, 2023
Contact name Yin Zhinang
Phone +8618163555312
Organization name Wuhan University
Lab Liang Lab
Street address Donghu road 185
City Wuhan
State/province Hubei
ZIP/Postal code 430071
Country China
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (48)
GSM5954447 HeLa-biotin-PEG4-hemin-CUT-Tag
GSM5954450 293T-G4-CUT-Tag
GSM5954451 293T-G4-Hemin-80uM-CUT-Tag
BioProject PRJNA816418

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Supplementary file Size Download File type/resource
GSE198658_RAW.tar 4.9 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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