Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA

Duquette, Michelle L.; Handa, Priya; Vincent, Jack A.; Taylor, Andrew F.; Maizels, Nancy

doi:10.1101/gad.1200804

Cited by 482 publications

(522 citation statements)

References 78 publications

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“…Persistent R-loops can become deleterious, however. These aberrant R-loops are generally stabilized by the formation of G-quadruplexes in the displaced, G-rich nontemplate strand, which can trigger gene down-regulation or DNA double-strand breaks through as-yet unclear mechanisms (39,41). To date, two distinct mechanisms for R-loop formation in neurodegeneration have been proposed, depending on the genetic insult.…”

Section: Discussionmentioning

confidence: 99%

“…R-loop formation is limited by the rapid association of RNA-binding proteins with the nascent RNA during transcription and splicing, preventing hybridization to the DNA template, and is actively resolved by RNA:DNA helicase activity and RNase H1/H2 activity (39,40). The presence of G-rich nontemplate strands can stabilize R-loops by folding into G-quadruplexes and further contribute to double-strand break formation (39,41). Knockdown of RNA splicing and transport factors has been associated with increased R-loop formation and DNA damage (42,43).…”

Section: Smnmentioning

confidence: 99%

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SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Jangi

Fleet

Cullen

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

107

111

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Spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disease, is the leading monogenic cause of infant mortality. Homozygous loss of the gene survival of motor neuron 1 (SMN1) causes the selective degeneration of lower motor neurons and subsequent atrophy of proximal skeletal muscles. The SMN1 protein product, survival of motor neuron (SMN), is ubiquitously expressed and is a key factor in the assembly of the core splicing machinery. The molecular mechanisms by which disruption of the broad functions of SMN leads to neurodegeneration remain unclear. We used an antisense oligonucleotide (ASO)-based inducible mouse model of SMA to investigate the SMN-specific transcriptome changes associated with neurodegeneration. We found evidence of widespread intron retention, particularly of minor U12 introns, in the spinal cord of mice 30 d after SMA induction, which was then rescued by a therapeutic ASO. Intron retention was concomitant with a strong induction of the p53 pathway and DNA damage response, manifesting as γ-H2A.X positivity in neurons of the spinal cord and brain. Widespread intron retention and markers of the DNA damage response were also observed with SMN depletion in human SH-SY5Y neuroblastoma cells and human induced pluripotent stem cell-derived motor neurons. We also found that retained introns, high in GC content, served as substrates for the formation of transcriptional R-loops. We propose that defects in intron removal in SMA promote DNA damage in part through the formation of RNA:DNA hybrid structures, leading to motor neuron death.

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Section: Discussionmentioning

confidence: 99%

Section: Smnmentioning

confidence: 99%

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

Jangi

Fleet

Cullen

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

107

111

View full text Add to dashboard Cite

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“…(47) However, EM data of these sequences in vitro have been interpreted as suggesting G-quartet formation. (49) Recent examples of well-studied non-B DNA structures, which are pathologically relevant are described below.…”

Section: Lymphoid Translocations: An Overviewmentioning

confidence: 99%

DNA structures at chromosomal translocation sites

Raghavan

Lieber

2006

BioEssays

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SummaryIt has been unclear why certain defined DNA regions are consistently sites of chromosomal translocations. Some of these are simply sequences of recognition by endogenous recombination enzymes, but most are not. Recent progress indicates that some of the most common fragile sites in human neoplasm assume non-B DNA structures, namely deviations from the Watson-Crick helix. Because of the single strandedness within these non-B structures, they are vulnerable to structure-specific nucleases. Here we summarize these findings and integrate them with other recent data for non-B structures at sites of consistent constitutional chromosomal translocations.

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“…Although there is no demonstration yet that the G-quadruplex forms in the cell for human telomeric DNA, recent studies of the telomeres of Stylonychia macronuclei indicated that G-quadruplexes can indeed form in vivo (11), and their formation is controlled by telomere end binding proteins in vivo (12). In addition, intracellular formation of the G-quadruplex was observed in the nontemplate G-rich sequence during transcription (13).…”

mentioning

confidence: 99%

Extreme conformational diversity in human telomeric DNA

Lee

Okumuş

Kim

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

260

353

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DNA with tandem repeats of guanines folds into G-quadruplexes made of a stack of G-quartets. In vitro, G-quadruplex formation inhibits telomere extension, and POT1 binding to the singlestranded telomeric DNA enhances telomerase activity by disrupting the G-quadruplex structure, highlighting the potential importance of the G-quadruplex structure in regulating telomere length in vivo. We have used single-molecule spectroscopy to probe the dynamics of human telomeric DNA. Three conformations were observed in potassium solution, one unfolded and two folded, and each conformation could be further divided into two species, long-lived and short-lived, based on lifetimes of minutes vs. seconds. Vesicle encapsulation studies suggest that the total of six states detected here is intrinsic to the DNA. Folding was severely hindered by replacing a single guanine, showing only the shortlived species. The long-lived folded states are dominant in physiologically relevant conditions and probably correspond to the parallel and antiparallel G-quadruplexes seen in high-resolution structural studies. Although rare under these conditions, the shortlived species determine the overall dynamics because they bridge the different long-lived species. We propose that these previously unobserved transient states represent the early and late intermediates toward the formation of stable G-quadruplexes. The major compaction occurs between the early and late intermediates, and it is possible that local rearrangements are sufficient in locking the late intermediates into the stably folded forms. The extremely diverse conformations of the human telomeric DNA may have mechanistic implications for the proteins and drugs that recognize G-rich sequences.FRET ͉ G-quadruplex ͉ single molecule ͉ telomere ͉ vesicle encapsulation E ukaryotic chromosomes have a novel nucleoprotein structure at both ends called a telomere. Telomeres are indispensable for protection against genome degradation and have implications in cellular aging and cancer (1-3). In many organisms, a telomeric DNA is composed of tandem repeats of short DNA sequences. In vitro, this guanine-rich region forms G-quadruplex (4), which blocks the binding of telomerase (5). The potential importance of Gquadruplex structure was further implied by the recent demonstration in vitro that the human POT1, which binds to the singlestranded form of human telomeric DNA (6), facilitates the telomerase activity by disrupting G-quadruplex (7). Human disease helicases, BLM and WRN, also were shown to disrupt Gquadruplexes in vitro (8,9). Because extension of the telomere is critical for generation and growth of cancer cells, the human telomeric G-quadruplex is considered a target for anticancer agents. Structure-based design of chemotherapeutic drugs would require an understanding of a range of conformations that can be adopted by the G-rich sequences, and indeed it was shown to be possible to design molecules that are specific to different types of G-quadruplex structures (10). Although there is no demonstr...

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Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA

Cited by 482 publications

References 78 publications

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage

DNA structures at chromosomal translocation sites

Extreme conformational diversity in human telomeric DNA

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