{"paper_id":"3114bcc8-c6d9-429e-a82b-e43e30403196","body_text":"SNPs associated with Metabolic Disorders Disrupt Structural Properties of DNA G-Quadruplexes in Regulatory Regions relevant during Tumor Development | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article SNPs associated with Metabolic Disorders Disrupt Structural Properties of DNA G-Quadruplexes in Regulatory Regions relevant during Tumor Development Angelika Lahnsteiner, Victoria Ellmer, Esther Schönauer, Markus Wiederstein, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7128220/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 14 You are reading this latest preprint version Abstract Background. The global prevalence of metabolic diseases (MetDs) is constantly rising and is associated with an increased risk of cancer development. Genome-wide association studies have identified numerous single nucleotide polymorphisms (SNPs) linked to MetDs, some of which occur in genes also implicated in tumorigenesis. G-quadruplexes (G4s) are non-canonical DNA secondary structures that regulate gene expression by serving as binding platforms for transcription factors. Alterations in their structural properties can significantly impact transcriptional efficiency. Notably, disease-associated variants have been found within or near regulatory elements. In this study, we systematically assessed the overlap between MetD-associated SNPs and G4 motifs, their impact on G4 stability and topology, and their potential to modulate the regulatory activity of G4s. Results. Approximately 0.9–1.5% of all SNPs were located within G4 motifs (G4-SNPs), varying by prediction tool. On a global level, effect alleles tended to lower G4 stability, regardless of whether the SNPs were risk or protective. Several G4-SNPs were found in regulatory regions, including the destabilizing MICB rs2855804 C/T and stabilizing PLA2G6 rs2277844 G/A variants. In vivo G4 formation was confirmed by permanganate/S1 nuclease footprinting; while circular dichroism spectroscopy and AlphaFold 3 predictions revealed allele-specific changes in G4 topology. Hi-C data, histone modifications, transcription factor binding, and luciferase reporter assays validated regulatory effects of these G4-SNPs. Conclusions. Although G4-SNPs are unlikely to be sole drivers of disease onset or progression, they significantly influence transcriptional regulation and may help explain allele-specific gene expression changes observed in MetDs and their elevated risk for certain tumors. G-quadruplex risk SNPs metabolic disease cancer risk transcription factors immune escape gene regulatory region PDAL-seq Full Text Additional Declarations No competing interests reported. Supplementary Files LAHNSTEINERG4SNPsinMetDSUPPFINAL.docx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 01 Sep, 2025 Reviews received at journal 29 Aug, 2025 Reviews received at journal 26 Aug, 2025 Reviews received at journal 24 Aug, 2025 Reviews received at journal 12 Aug, 2025 Reviewers agreed at journal 02 Aug, 2025 Reviewers agreed at journal 02 Aug, 2025 Reviewers agreed at journal 30 Jul, 2025 Reviewers agreed at journal 27 Jul, 2025 Reviewers agreed at journal 27 Jul, 2025 Reviewers invited by journal 27 Jul, 2025 Editor assigned by journal 21 Jul, 2025 Submission checks completed at journal 16 Jul, 2025 First submitted to journal 15 Jul, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {\"props\":{\"pageProps\":{\"initialData\":{\"identity\":\"rs-7128220\",\"acceptedTermsAndConditions\":true,\"allowDirectSubmit\":false,\"archivedVersions\":[],\"articleType\":\"Research Article\",\"associatedPublications\":[],\"authors\":[{\"id\":486080328,\"identity\":\"c2d8454a-16e9-47ab-b1d9-a5cdc412f86e\",\"order_by\":0,\"name\":\"Angelika 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The global prevalence of metabolic diseases (MetDs) is constantly rising and is associated with an increased risk of cancer development. Genome-wide association studies have identified numerous single nucleotide polymorphisms (SNPs) linked to MetDs, some of which occur in genes also implicated in tumorigenesis. G-quadruplexes (G4s) are non-canonical DNA secondary structures that regulate gene expression by serving as binding platforms for transcription factors. Alterations in their structural properties can significantly impact transcriptional efficiency. Notably, disease-associated variants have been found within or near regulatory elements. In this study, we systematically assessed the overlap between MetD-associated SNPs and G4 motifs, their impact on G4 stability and topology, and their potential to modulate the regulatory activity of G4s.\\u003c/p\\u003e\\n\\u003cp\\u003eResults. Approximately 0.9–1.5% of all SNPs were located within G4 motifs (G4-SNPs), varying by prediction tool. On a global level, effect alleles tended to lower G4 stability, regardless of whether the SNPs were risk or protective. Several G4-SNPs were found in regulatory regions, including the destabilizing \\u003cem\\u003eMICB\\u003c/em\\u003ers2855804 C/T and stabilizing \\u003cem\\u003ePLA2G6\\u003c/em\\u003e rs2277844 G/A variants. \\u003cem\\u003eIn vivo\\u003c/em\\u003eG4 formation was confirmed by permanganate/S1 nuclease footprinting; while circular dichroism spectroscopy and AlphaFold 3 predictions revealed allele-specific changes in G4 topology. Hi-C data, histone modifications, transcription factor binding, and luciferase reporter assays validated regulatory effects of these G4-SNPs.\\u003c/p\\u003e\\n\\u003cp\\u003eConclusions. Although G4-SNPs are unlikely to be sole drivers of disease onset or progression, they significantly influence transcriptional regulation and may help explain allele-specific gene expression changes observed in MetDs and their elevated risk for certain tumors.\\u003c/p\\u003e\",\"manuscriptTitle\":\"SNPs associated with Metabolic Disorders Disrupt Structural Properties of DNA G-Quadruplexes in Regulatory Regions relevant during Tumor Development\",\"msid\":\"\",\"msnumber\":\"\",\"nonDraftVersions\":[{\"code\":1,\"date\":\"2025-07-18 19:37:03\",\"doi\":\"10.21203/rs.3.rs-7128220/v1\",\"editorialEvents\":[{\"type\":\"communityComments\",\"content\":0},{\"type\":\"decision\",\"content\":\"Revision requested\",\"date\":\"2025-09-01T11:40:25+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2025-08-29T17:46:46+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2025-08-26T09:46:38+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2025-08-25T03:13:10+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"editorInvitedReview\",\"content\":\"\",\"date\":\"2025-08-12T07:50:12+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"216998789138617930876600787552647452575\",\"date\":\"2025-08-02T10:27:48+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"242726580272403210854101709242019779441\",\"date\":\"2025-08-02T08:26:32+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"228968605577485141881631852154502430672\",\"date\":\"2025-07-30T17:35:40+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"259394018950859226649354991830136584675\",\"date\":\"2025-07-28T00:43:25+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewerAgreed\",\"content\":\"24813091983342646897941761787148352306\",\"date\":\"2025-07-28T00:36:13+00:00\",\"index\":\"hide\",\"fulltext\":\"\"},{\"type\":\"reviewersInvited\",\"content\":\"\",\"date\":\"2025-07-28T00:10:43+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"editorAssigned\",\"content\":\"\",\"date\":\"2025-07-21T09:38:13+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"checksComplete\",\"content\":\"\",\"date\":\"2025-07-16T04:39:48+00:00\",\"index\":\"\",\"fulltext\":\"\"},{\"type\":\"submitted\",\"content\":\"Genome Biology\",\"date\":\"2025-07-15T08:26:43+00:00\",\"index\":\"\",\"fulltext\":\"\"}],\"status\":\"published\",\"journal\":{\"display\":true,\"email\":\"info@researchsquare.com\",\"identity\":\"genome-biology\",\"isNatureJournal\":false,\"hasQc\":true,\"allowDirectSubmit\":false,\"externalIdentity\":\"gbio\",\"sideBox\":\"Learn more about [Genome Biology](https://genomebiology.biomedcentral.com/)\",\"snPcode\":\"13059\",\"submissionUrl\":\"https://submission.springernature.com/new-submission/13059/3\",\"title\":\"Genome Biology\",\"twitterHandle\":\"\",\"acdcEnabled\":true,\"dfaEnabled\":true,\"editorialSystem\":\"stoa\",\"reportingPortfolio\":\"BMC/SO AJ\",\"inReviewEnabled\":true,\"inReviewRevisionsEnabled\":true}}],\"origin\":\"\",\"ownerIdentity\":\"b5f735af-84a7-4c0f-8450-58210e38492a\",\"owner\":[],\"postedDate\":\"July 18th, 2025\",\"published\":true,\"recentEditorialEvents\":[],\"rejectedJournal\":[],\"revision\":\"\",\"amendment\":\"\",\"status\":\"under-review\",\"subjectAreas\":[],\"tags\":[],\"updatedAt\":\"2026-03-25T08:10:16+00:00\",\"versionOfRecord\":[],\"versionCreatedAt\":\"2025-07-18 19:37:03\",\"video\":\"\",\"vorDoi\":\"\",\"vorDoiUrl\":\"\",\"workflowStages\":[]},\"version\":\"v1\",\"identity\":\"rs-7128220\",\"journalConfig\":\"researchsquare\"},\"__N_SSP\":true},\"page\":\"/article/[identity]/[[...version]]\",\"query\":{\"redirect\":\"/article/rs-7128220\",\"identity\":\"rs-7128220\",\"version\":[\"v1\"]},\"buildId\":\"XKTyCvWXoU3ODBz1xrDgd\",\"isFallback\":false,\"isExperimentalCompile\":false,\"dynamicIds\":[84888],\"gssp\":true,\"scriptLoader\":[]}","source_license":"CC-BY-4.0","license_restricted":false}