Yin Yang 1 contains G-quadruplex structures in its promoter and 5′-UTR and its expression is modulated by G4 resolvase 1

Cells engage numerous signaling pathways in response to oxidative stress that together repair macromolecular damage or direct the cell toward apoptosis. As a result of DNA damage, mitochondrial DNA or nuclear DNA has been shown to enter the cytoplasm where it binds to "DNA sensors," which in turn initiate signaling cascades. Here we report data that support a novel signaling pathway in response to oxidative stress mediated by specific guanine-rich sequences that can fold into G-quadruplex DNA (G4DNA). In response to oxidative stress, we demonstrate that sequences capable of forming G4DNA appear at increasing levels in the cytoplasm and participate in assembly of stress granules. Identified proteins that bind to endogenous G4DNA in the cytoplasm are known to modulate mRNA translation and participate in stress granule formation. Consistent with these findings, stress granule formation is known to regulate mRNA translation during oxidative stress. We propose a signaling pathway whereby cells can rapidly respond to DNA damage caused by oxidative stress. Guanine-rich sequences that are excised from damaged genomic DNA are proposed to enter the cytoplasm where they can regulate translation through stress granule formation. This newly proposed role for G4DNA provides an additional molecular explanation for why such sequences are prevalent in the human genome.

Section: Discussionmentioning

confidence: 58%

Section: Resultsmentioning

confidence: 99%

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress

Byrd¹,

Zybailov

Maddukuri³

et al. 2016

“…Although the structural and biophysical characterization of G-quadruplexes has progressed rapidly, the mechanistic basis for their recognition and remodeling is poorly understood. RHAU has emerged as a primary quadruplex resolvase in eukaryotic cells, and the functional consequences of quadruplex remodeling has been established in a small number of important processes (17,18,21,41,42). Therefore, our goal was to make biophysical inroads to the process by examining the recognition of G-quadruplexes by the N-terminal region of RHAU that contains the RSM, a required region for quadruplex recognition.…”

Section: Discussionmentioning

confidence: 99%

“…Microarray studies have implicated RHAU in broad spectrum transcriptional regulation and mRNA stability (20). In support, RHAU has been shown to control gene expression through direct binding to quadruplexes within the promoter of the YY1 gene (21). RHAU can also modulate quadruplex structures in the context of non-coding RNAs.…”

mentioning

confidence: 99%

Binding of G-quadruplexes to the N-terminal Recognition Domain of the RNA Helicase Associated with AU-rich Element (RHAU)

Meier

Patel

Booy

et al. 2013

Background:The helicase RHAU requires an N-terminal extension to bind quadruplex structures. Results: This extension adopts an elongated shape and interacts with the guanine tetrad face of quadruplexes. Conclusion: We provide a basis for the understanding of quadruplex binding by the N-terminal domain. Significance: The N-terminal region does not require the 2Ј-OH of the ribose to mediate the protein-quadruplex interaction.

“…RHAU and G4R1) is of particular interest for general G4 disruption activity because it is highly expressed, comprises the bulk of the DNA G4 disruption activity in a human cell lysate, and is one of only two helicases known to disrupt RNA G4s (14)(15)(16). DHX36 has been implicated as a regulator of RNA folding and assembly (17,18), RNA localization, translation (19), pre-mRNA processing (20), and transcription (21), most simply suggesting that it functions in both the cytoplasm and nucleus and interacts with both RNA and DNA G4s. Underscoring the importance of this protein and potentially G4s in vivo, DHX36 is an essential gene in mouse (22)(23)(24).…”

Section: ___________________________________mentioning

confidence: 99%

The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism

Yangyuoru

Bradburn

et al. 2018

Single-stranded DNA (ssDNA) and RNA regions that include at least four closely spaced runs of three or more consecutive guanosines strongly tend to fold into stable G-quadruplexes (G4s). G4s play key roles as DNA regulatory sites and as kinetic traps that can inhibit biological processes, but how G4s are regulated in cells remains largely unknown. Here, we developed a kinetic framework for G4 disruption by DEAH-box helicase 36 (DHX36), the dominant G4 resolvase in human cells. Using tetramolecular DNA and RNA G4s with four to six G-quartets, we found that DHX36-mediated disruption is highly efficient, with rates that depend on G4 length under saturating conditions (k cat ) but not under subsaturating conditions (k cat /K M ). These results suggest that a step during G4 disruption limits the k cat value and that DHX36 binding limits k cat /K M . Similar results were obtained for unimolecular DNA G4s. DHX36 activity depended on a 3′ ssDNA extension and was blocked by a polyethylene glycol linker, indicating that DHX36 loads onto the extension and translocates 3′-5′ toward the G4. DHX36 unwound dsDNA poorly compared with G4s of comparable intrinsic lifetime. Interestingly, we observed that DHX36 has striking 3′-extension sequence preferences that differ for G4 disruption and dsDNA unwinding, most likely arising from differences in the rate-limiting step for the two activities. Our results indicate that DHX36 disrupts G4s with a conventional helicase mechanism that is tuned for great efficiency and specificity for G4s. The dependence of DHX36 on the 3′-extension sequence suggests that the extent of formation of genomic G4s may not track directly with G4 stability. ___________________________________Single-stranded DNA and RNA segments that include at least four closely-spaced runs of three or more consecutive guanosine nucleotides have a strong intrinsic propensity to fold into stable G-quadruplex structures (G4s) (1) (Fig. 1A, top left). The genomes of humans and many other eukaryotes are replete with putative G4-forming sequences, and pronounced, conserved patterns have been observed in their distribution, suggesting that Gquadruplex structures form at least transiently in cells and perform conserved functions (2-6). Supporting this hypothesis, G4s have been detected in cells for both .To function as regulatory elements, G4s must be folded and disrupted in a regulated way. In addition, processes that require single-stranded DNA or RNA, such as replication and translation, require that G4s be temporarily disrupted. The high stability and long intrinsic lifetime of G4s suggest Mechanism of G4 disruption by DHX362 that their efficient disruption requires the activity of ATP-dependent enzymes such as helicases.Supporting this view, incorporation of sequences predicted to form particularly stable G4s leads to genetic instability in yeast, suggesting that these G4 structures are not processed efficiently and pose blocks to replication (12). Indeed, several helicases have been shown to possess G4 disruption acti...