Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

Kouzine, Fedor; Wójtowicz, Damian; Baranello, Laura; Yamane, Arito; Nelson, Stacy A. C.; Resch, Wolfgang; Kieffer-Kwon, Kyong-Rim; Benham, Craig J.; Casellas, Rafael; Przytycka, Teresa M.; Levens, David

doi:10.1016/j.cels.2017.01.013

Cited by 187 publications

(232 citation statements)

References 109 publications

(194 reference statements)

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“…The detected G-quadruplexes in cells account for less than 1% of the genomic G4-sites identified by G4-seq [179] or predicted by G4 algorithms [81], suggesting the in vivo formation of G-quadruplex is highly context-dependent. In addition, the endogenous potential G4 sites were detected in live human cells by chemical footprinting combined with high-throughput sequencing and were found to enrich in regions involving chromatin reorganization and gene transcription [180]. G-quadruplex formation in vivo was also detected by small molecules probes, such as the radiolabeled Gquadruplex-ligands 360A [181], and fluorescent G-quadruplexligands BMVC [182,183] and DAOTA-M2 [184].…”

Section: G-quadruplex Detection In Vivomentioning

confidence: 99%

G-Quadruplex DNA and RNA

Yang

2019

Methods in Molecular Biology

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G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5 0 -and 3 0 -untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure. G-quadruplexes have been found to form in specific human guanine-rich sequences with functional significance, such as telomeres, oncogene-promoter regions, and 5 0 -and 3 0 -untranslated region (UTR) of mRNA, as well as in nonhuman genomes. G-Quadruplexes in TelomeresThe first biologically relevant G-quadruplex was observed in telomeric DNA. Telomeres are specific DNA-protein complexes at the ends of linear chromosomes, providing protection against gene erosion from cell divisions, chromosomal nonhomologous end-joinings, and nuclease attacks [19][20][21]. Telomeric G-quadruplexes were first reported as novel intramolecular structures containing guanine-guanine base-pairs in single-stranded telomeric sequences of several organisms [22], and as guaninetetrads between hairpin loops of the Tetrahymena telomeric DNA [23]. The importance of monovalent cations in the stabilization of G-quadruplex structures was revealed by Williamson, Cech in their monovalent cation-induced square-planar G-quartet model using the Oxytricha and Tetrahymena telomeric DNA [14]. Human telomeres consist of tandem repeats of the hexanucleotide d (TTAGGG) n 5-10 kb in length, which terminate in a singlestranded 3 0 -overhang of 35-600 bases [24]. Telomeres of cancer cells do not shorten upon replication, mainly due to the activation of a reverse transcriptase, telomerase, that extends the telomeric sequence at the chromosome ends [25]. Telomerase is activated in 80-85% of hu...

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Section: G-quadruplex Detection In Vivomentioning

confidence: 99%

G-Quadruplex DNA and RNA

Yang

2019

Methods in Molecular Biology

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“…Recently, permanganate mapping has revealed single‐stranded DNA and other non‐B‐DNA structures across the genome . This method effectively detected the predicted single‐stranded DNA generated at transcription bubbles.…”

Section: Non‐b‐dna Is Found Throughout the Genomementioning

confidence: 99%

DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond

Zaytseva

Quinn

2018

BioEssays

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Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its regulation. Dissection of regulatory regions within the MYC promoter provided the first hint that intimate feedback between DNA topology and associated DNA remodeling proteins is critical for moderating transcription. As evidence of such regulation is also found in the context of many other genes, here we expand on the prototypical example of the MYC promoter, and also explore DNA architecture in a genome-wide context as a global mechanism of transcriptional control.

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“…MCM binding; (2) ORC abundance(Dellino et al, 2013); (3) DNA replication, based on BrdU incorporation(Davis et al, 2018); (4) GC content; (5) the presence of single-stranded DNA (ssDNA), as measured by a KMnO 4 -based assay(Kouzine et al, 2017);(6)tendency to form G4 quadruplexes, based on the "G4 hunter" algorithm(Bedrat, Lacroix, & Mergny, 2016); (7) DNase-hypersensitivity(Davis et al, 2018); and (8) histone modifications associated with ORC binding and replication initiation(Davis et al, 2018) (see each pairwise r value inSupplementary Data…”

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Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans

Foss

Sripathy

Gatbonton-Schwager

et al. 2019

Preprint

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The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during Sphase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we identified the binding sites of the Mcm2-7 helicase complex, a key component of the pre-RC that is required for initiation of DNA replication, in budding yeast, fission yeast and mouse. In budding yeast, we detected Mcm2 binding in sharply focused peaks, generally with a single double hexamer bound at known origins of replication. In fission yeast, Mcm2 binding, while still concentrated at known origins, was more diffuse, often with 6 to 8 helicase complexes distributed along 0.5-1.5 kb sized origins, and with significantly more binding between origins. Finally, in mouse, we found even more diffuse Mcm2-7 distribution, with the density of Mcm2-7 binding in G1 recapitulating to a remarkable degree the replication program implemented in S-phase. Computer simulations that assign each licensed origin an equal probability of firing show that the observed Mcm2-7 density distribution in G1 across all three species largely recapitulated the DNA replication program. We conclude that the pattern of origin licensing from yeast to mammals is sufficient to explain most differences in replication timing without invoking an overarching temporal program of origin firing. ResultsInitiation of DNA replication requires activation of the MCM2-7 helicase complex (Mcm2-7) at sites at which this complex was loaded during the preceding G2/M and G1 phases [1][2][3][4].However, the order in which different regions of the genome complete replication is widely assumed to reflect not only the locations of Mcm2-7 loading but also a program of control above the level of loading, in which certain complexes are activated before others [5,6]. The distribution of Mcm2-7 is therefore expected to constrain but not fully determine the program of genome replication. Mcm2-7 encircles approximately 60 base pairs (bp) of DNA as a double hexamer whose monomer components are juxtaposed head-to-head at their N-termini with C-

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Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome

Cited by 187 publications

References 109 publications

G-Quadruplex DNA and RNA

G-Quadruplex DNA and RNA

DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond

Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans

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