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G-quadruplex DNA structure is a positive regulator of MYC transcription

ABSTRACT: G-quadruplex DNA structure is a positive regulator of MYC transcription

PROVIDER: PRJNA925884 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26244700_1.fastq.gz	Fastqsanger.gz
	SRR26244700_2.fastq.gz	Fastqsanger.gz
	SRR26244800_1.fastq.gz	Fastqsanger.gz
	SRR26244800_2.fastq.gz	Fastqsanger.gz
	SRR26244900_1.fastq.gz	Fastqsanger.gz

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G-quadruplex DNA structure is a positive regulator of MYC transcription

Project description:DNA structure can regulate genome function. Four-stranded DNA G-quadruplex (G4) structures have been implicated in transcriptional regulation; however, previous studies have not directly addressed the role of an individual G4 within its endogenous cellular context. Using CRISPR to genetically abrogate endogenous G4 structure folding, we directly interrogate the G4 found within the upstream regulatory region of the critical human MYC oncogene. G4 loss leads to suppression of MYC transcription from the P1 promoter that is mediated by the deposition of a de novo nucleosome alongside alterations in RNA polymerase recruitment. We also show that replacement of the endogenous MYC G4 with a different G4 structure from the KRAS oncogene restores G4 folding and MYC transcription. Moreover, we demonstrate that the MYC G4 structure itself, rather than its sequence, recruits transcription factors and histone modifiers. Overall, our work establishes that G4 structures are important features of transcriptional regulation that coordinate recruitment of key chromatin proteins and the transcriptional machinery through interactions with DNA secondary structure, rather than primary sequence.

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G4 Quadruplex Binding Proteins

Project description:In this study we discover proteins that bind to G4 quadruplex DNA structure. We use modified c-myc quadruplex as a bait, and compare it to the control bait - T15 oligo. We use spectral counts and G-test to determine significant binders. T15 and G4 datafiles are uploaded

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Comprehensive analysis of genomic G-quadruplex forming oligonucleotides homologous to NHEIII1 of c-MYC promoter on leukemia cell growth inhibition and c-MYC expression

Project description:The c-MYC onco-protein regulates a large array of genes playing an important role in basic cell functions. Because of its central role in growth regulation, c-MYC expression must be tightly regulated. The NHEIII1 located upstream of the P1 promoter regulates up to 80% of c-MYC transcription, and includes a C/G rich region (Pu27) which forms a G-quadruplex structure. We have identified seventeen genomic G-quadruplex-forming motifs which have more than 90% identity with Pu27 found on different chromosomes throughout the human genome. Of thirteen members of the Pu27 family tested, all interact specifically with NHEIII1 sequence and inhibit leukemic cells proliferation to differing degrees. Further characterization of three Pu27 homologous sequences (Pu5-, Pu9- and Pu27) reveals a dose/time dependent response on growth inhibition in four leukemia cell lines and down regulation of c-MYC at RNA and protein level. The three Pu27 family members selectively alter expression of genes involved in cell cycle progression/regulation, DNA damage/repair and histone modification. In conclusion, we have identified sixteen genomic G-quadruplex-forming sequences homologous to Pu27 of c-MYC promoter sharing the same structure and function. It is likely that these sequences play important biologic roles in c-MYC regulation and provide an ideal tool for targeted cancer therapy.

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G-Quadruplex structures are stable and detectable in human genomic DNA.

Project description:The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. Our high sensitivity structure-based pull-down strategy enables the isolation of genomic DNA fragments bearing a single as well as multiple G-quadruplex structures. Stable G-quadruplex structures are found in sub-telomeres, gene bodies and gene regulatory regions. For a sample of identified target genes, we show that G-quadruplex stabilizing ligands can modulate transcription. These results confirm the existence of G-quadruplex structures and their persistence in human genomic DNA. Four independent libraries have been enriched in DNA G-quadruplex structures using a G-quadruplex-specific probe. One genomic input library was sequenced as control. Deep-sequencing of these libraries allowed the mapping of G-quadruplexes on the genome.

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RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF

Project description:It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex forming capacity promote exon inclusion. Destroying G-quadruplex forming capacity while keeping G-tracts intact abrogates exon inclusion. Analysis of RNA binding protein footprints revealed that G-quadruplexes are enriched in hnRNPF-binding sites and near hnRNPF-regulated alternatively spliced exons in the human transcriptome. Moreover, hnRNPF regulates an EMT-associated CD44 isoform switch in a G-quadruplex-dependent manner, which results in inhibition of EMT. Mining breast cancer TCGA datasets, we demonstrate that hnRNPF negatively correlates with an EMT gene signature and positively correlates with patient survival. These data suggest a critical role for RNA G-quadruplexes in regulating alternative splicing. Modulation of G-quadruplex structural integrity may control cellular processes important for tumor progression.

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Project description:Analysis of the gene expression profile between MYC positive and MYC negative germinal center B-cells. Total RNA isolated from MYC positive and MYC negative GC B-cells, isolated by FACS from 10 day sheep red blood cell immunized mice MycEGFP (a Myc reporter allele, in which a MYC-EGFP fusion protein (MYCEGFP) is expressed from the endogenous Myc locus, Huan, CY et al Eur J Immunol 2008)

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G-Quadruplex structures are stable and detectable in human genomic DNA.

2013-05-08 | GSE45241 | GEO

Direct mapping of G-quadruplex anchored 3D chromatin structure via ViCAR

Project description:Direct mapping of G-quadruplex anchored 3D chromatin structure via ViCAR

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Genome wide analysis of germinal center MYC positive B-cells

Project description:Analysis of the gene expression profile between MYC positive and MYC negative germinal center B-cells.

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