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Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells

ABSTRACT: Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells

PROVIDER: PRJNA911792 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22715414_1.fastq.gz	Fastqsanger.gz
	SRR22715414_2.fastq.gz	Fastqsanger.gz
	SRR22715419_1.fastq.gz	Fastqsanger.gz
	SRR22715419_2.fastq.gz	Fastqsanger.gz
	SRR22715424.fastq.gz	Fastqsanger.gz

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Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [CUT&Tag]

Project description:Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [CUT&Tag]

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Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [RNA-seq]

Project description:Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [RNA-seq]

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Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [CUT&Tag]

Project description:i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences and in acidic conditions in vitro. However, their formation and distribution in cells is still under debate. Here we performed CUT&Tag sequencing using the anti-iM antibody iMab and showed that iMs form within the human genome in live cells. We mapped native iMs in two different human cell lines and recovered C-rich sequences that were confirmed to fold into iMs in vitro. We found that iMs in cells are mainly present at actively transcribing gene promoters and that their abundance and distribution are specific to each cell type. iMs with both long and short C-tracts were recovered, further extending the relevance of iMs throughout the genome. By simultaneously mapping G-quadruplexes (G4s), four-stranded structures that form at guanine-rich regions, and comparing the results with iMs, we proved that the two structures can form in independent genomic regions; however, when both iMs and G4s are present in the same genomic tract, their formation is favored. Our findings support the in vivo formation of iM structures and provide new insights into their interplay with G4s as new regulatory elements in the human genome.

2023-08-02 | GSE220878 | GEO

Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells [RNA-seq]

2023-08-02 | GSE220881 | GEO

Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells.

Project description:i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences in acidic conditions in vitro. Their formation in cells is still under debate. We performed CUT&Tag sequencing using the anti-iM antibody iMab and showed that iMs form within the human genome in live cells. We mapped iMs in two human cell lines and recovered C-rich sequences that were confirmed to fold into iMs in vitro. We found that iMs in cells are mainly present at actively transcribing gene promoters, in open chromatin regions, they overlap with R-loops, and their abundance and distribution are specific to each cell type. iMs with both long and short C-tracts were recovered, further extending the relevance of iMs. By simultaneously mapping G-quadruplexes (G4s), which form at guanine-rich regions, and comparing the results with iMs, we proved that the two structures can form in independent regions; however, when both iMs and G4s are present in the same genomic tract, their formation is enhanced. iMs and G4s were mainly found at genes with low and high transcription rates, respectively. Our findings support the in vivo formation of iM structures and provide new insights into their interplay with G4s as new regulatory elements in the human genome.

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Genome-wide mapping of i-Motifs reveals their association with transcription regulation in live human cells

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