G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes

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. 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