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LiveG4ID-seq identifies the chromatin G-quadruplex landscape in living cells

ABSTRACT: G-quadruplex (G4) structures exist in single-stranded DNA of chromatins and regulate genome function. However, the native chromatin G4 landscape in living cells has yet to be fully characterized. Herein, we fused BG4 antibody and GFP-tag to construct a live-cell G4 identifier (LiveG4ID). We first displayed its function as a high-specificity chromatin G4 probe in living cells by Dox-induced expression LiveG4ID in HEK293T cells and detecting its cellular localization, biocompatibility and G4-binding specificity. By coupling LiveG4ID with CUT&Tag technology, we established LiveG4ID-seq, a method for mapping native chromatin G4 landscape in living cells. LiveG4ID-seq can identify more chromatin G4 motifs than traditional CUT&Tag and ChIP-seq methods. Using LiveG4ID-seq, we profiled the dynamic landscape of chromatin G4 structures during the cell cycle. These data demonstrate the capacity of LiveG4ID-seq to profile a more accurate G4 landscape in living cells and promote future study on chromatin G4 structures.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE193496 | GEO | 2022/01/15

REPOSITORIES: GEO

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Project description:DNA secondary structures are important for fundamental genome functions such as transcription and replication1. The G-quadruplex (G4) structural motif has been linked to gene regulation2,3 and genome instability4,5 and may be important to cancer development and other diseases6-8. Recently, ~700,000 discrete G4s have been observed in naked human single-stranded genomic DNA using G4-seq, a high-throughput sequencing technique that detects structural features in vitro.9 It is of vital importance to investigate G4 structures within an endogenous chromatin context, which until now remained elusive10,11. Herein, we address this via the development of G4 ChIP-seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. We identified ~10,000 endogenous G4 structures and show that G4s are predominantly seen in regulatory, nucleosome-depleted, chromatin regions. G4s were enriched in the promoters and 5âUTR regions of highly transcribed genes, particularly in genes related to cancer and in somatic copy number amplifications, such as MYC. Reorganization of the chromatin landscape using a histone deacetylase inhibitor, resulted in de novo G4 formation in new and more prominent regulatory, nucleosome-depleted regions associated with increased transcriptional output. Our findings suggest a striking relationship between promoter nucleosome-depleted regions, G4 formation and elevated transcriptional activity. Comparison between normal human epidermal keratinocytes and their immortalized counterparts revealed a ï¾7-fold greater G4 abundance in immortalized cells, of which 80 % were found in regulatory, nucleosome-depleted regions common to both cell types. Consequently, cells exhibiting more G4s displayed significantly increased transcriptional output and were more sensitive to growth inhibition by a small molecule G4 ligand. Overall, our results provide new mechanistic insights into where and when DNA adopts G4 structure in vivo. Our findings show for the first time that regulatory, nucleosome-depleted chromatin and transcriptional states predominantly shape the endogenous G4 DNA landscape. Two cell lines, treated with entinostat or untreated, analyzed to detect gene expression differences, presence of G-Qudruplexes and chromatin state. Each combination of conditions replicated in duplicates or triplicates.

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LiveG4ID-seq identifies the chromatin G-quadruplex landscape in living cells

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