Dataset Information

Hydrodynamic Models of G-Quadruplex Structures.

ABSTRACT: G-quadruplexes are noncannonical four-stranded DNA or RNA structures formed by guanine-rich repeating sequences. Guanine nucleotides can hydrogen bond to form a planar tetrad structure. Such tetrads can stack to form quadruplexes of various molecularities with a variety of types of single-stranded loops joining the tetrads. High-resolution structures may be obtained by X-ray crystallography or NMR spectroscopy for quadruplexes formed by short (?25 nt) sequences but these methods have yet to succeed in characterizing higher order quadruplex structures formed by longer sequences. An integrated computational and experimental approach was implemented in our laboratory to obtain structural models for higher order quadruplexes that might form in longer telomeric or promoter sequences. In our approach, atomic-level models are built using folding principles gleaned from available high-resolution structures and then optimized by molecular dynamics. The program HYDROPRO is then used to construct bead models of these structures to predict experimentally testable hydrodynamic properties. Models are validated by comparison of these properties with measured experimental values obtained by analytical ultracentrifugation or other biophysical tools. This chapter describes our approach and practical procedures.

SUBMITTER: Chaires JB

PROVIDER: S-EPMC5705227 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Hydrodynamic Models of G-Quadruplex Structures.

Chaires Jonathan B JB Dean William L WL Le Huy T HT Trent John O JO

Methods in enzymology 20150619

G-quadruplexes are noncannonical four-stranded DNA or RNA structures formed by guanine-rich repeating sequences. Guanine nucleotides can hydrogen bond to form a planar tetrad structure. Such tetrads can stack to form quadruplexes of various molecularities with a variety of types of single-stranded loops joining the tetrads. High-resolution structures may be obtained by X-ray crystallography or NMR spectroscopy for quadruplexes formed by short (≈25 nt) sequences but these methods have yet to succ ...[more]

PMID: 26412657

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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.

Dataset Information

Hydrodynamic Models of G-Quadruplex Structures.

Publications

Hydrodynamic Models of G-Quadruplex Structures.

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