{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T09:26:32Z","timestamp":1740129992353,"version":"3.37.3"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T00:00:00Z","timestamp":1680652800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"National Key Research and Development Program for Active Health and Aging Response","award":["2020YFC2008200"],"award-info":[{"award-number":["2020YFC2008200"]}]},{"name":"Key Research and Development Program of Zhejiang Province","award":["2023C03031","2021C03102","2020C03036"],"award-info":[{"award-number":["2023C03031","2021C03102","2020C03036"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81830027"],"award-info":[{"award-number":["81830027"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Major Scientific and Technological Innovation Project of WenZhou","award":["ZY2020013"],"award-info":[{"award-number":["ZY2020013"]}]},{"name":"Internal Fund Project of Eye Hospital of Wenzhou Medical University","award":["KYQD20210702"],"award-info":[{"award-number":["KYQD20210702"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The susceptibility single nucleotide polymorphisms (SNPs) obtained by genome-wide association studies leave some thorny questions, such as prioritization, false positives and unknown pathogenesis. Previous studies suggested that genetic variation may perturb the RNA secondary structure, influence protein recruitment and binding and ultimately affect splicing processes. Therefore, exploring the perturbation of SNPs to structure\u2013function correlations may provide an effective bridge toward understanding the genetic contribution to diseases. Here, aiming to decipher the regulatory mechanism of myopia susceptibility variants, we systematically evaluated the roles of SNP-induced structural changes during splicing. In addition, 7.53% of myopia-related SNPs exhibited significant global structural changes, 19.53% presented noteworthy local structural disturbance and there were wide-ranging structural perturbations in the splice-related motifs. We established a comprehensive evaluation system for structural disturbance in the splicing-related motifs and gave the priority ranking for the SNPs at RNA structural level. These high-priority SNPs were revealed to widely disturb the molecular interaction properties between splicing-related proteins and pre-mRNAs by HDOCK. Moreover, mini-gene assays confirmed that structural perturbation could influence splicing efficiency through structural remodelling. This study deepens our understanding of the potential molecular regulatory mechanisms of susceptible SNPs in myopia and contributes to personalized diagnosis, personalized medicine, disease-risk prediction and functional verification study by guiding the prioritization of the susceptibility SNPs.<\/jats:p>","DOI":"10.1093\/hmg\/ddad057","type":"journal-article","created":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T12:02:21Z","timestamp":1680696141000},"page":"2229-2240","source":"Crossref","is-referenced-by-count":1,"title":["Impact of the RNA allosteric effect triggered by single nucleotide polymorphisms on the splicing process"],"prefix":"10.1093","volume":"32","author":[{"given":"Youyuan","family":"Zhuang","sequence":"first","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyan","family":"Lu","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Lin","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyu","family":"Wang","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoran","family":"Sheng","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chong","family":"Chen","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guosi","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyi","family":"Wang","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Changqiu","family":"Mei","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jia","family":"Qu","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Center of Optometry International Innovation of Wenzhou, Eye Valley , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liangde","family":"Xu","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Center of Optometry International Innovation of Wenzhou, Eye Valley , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong","family":"Wang","sequence":"additional","affiliation":[{"name":"National Engineering Research Center of Ophthalmology and Optometry , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"State Key Laboratory of Ophthalmology , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Optometry and Visual Science, Eye Hospital, , Wenzhou 325027 , China"},{"name":"National Clinical Research Center for Ocular Diseases , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Wenzhou Medical University , Eye Hospital, , Wenzhou 325027 , China"},{"name":"Center of Optometry International Innovation of Wenzhou, Eye Valley , Wenzhou 325027 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,5]]},"reference":[{"key":"2023062021510384300_ref1","doi-asserted-by":"crossref","first-page":"5866","DOI":"10.1093\/hmg\/ddu309","article-title":"Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes","volume":"23","author":"Ezkurdia","year":"2014","journal-title":"Hum. Mol. Genet."},{"key":"2023062021510384300_ref2","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng.259","article-title":"Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing","volume":"40","author":"Pan","year":"2008","journal-title":"Nat. Genet."},{"key":"2023062021510384300_ref3","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/j.cell.2009.02.009","article-title":"The spliceosome: design principles of a dynamic RNP machine","volume":"136","author":"Wahl","year":"2009","journal-title":"Cell"},{"key":"2023062021510384300_ref4","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.tibs.2009.10.004","article-title":"Role of RNA structure in regulating pre-mRNA splicing","volume":"35","author":"Warf","year":"2010","journal-title":"Trends Biochem. Sci."},{"key":"2023062021510384300_ref5","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.molcel.2016.04.028","article-title":"In vivo mapping of eukaryotic RNA interactomes reveals principles of higher-order organization and regulation","volume":"62","author":"Aw","year":"2016","journal-title":"Mol. Cell"},{"key":"2023062021510384300_ref6","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1016\/j.cell.2016.10.026","article-title":"Genetic drivers of epigenetic and transcriptional variation in human immune cells","volume":"167","author":"Chen","year":"2016","journal-title":"Cell"},{"key":"2023062021510384300_ref7","first-page":"1354","article-title":"Three different cone opsin gene array mutational mechanisms with genotype-phenotype correlation and functional investigation of cone opsin variants","volume":"35","author":"Gardner","year":"2014","journal-title":"Hum. Mutat."},{"key":"2023062021510384300_ref8","doi-asserted-by":"crossref","first-page":"12","DOI":"10.3389\/fmolb.2018.00012","article-title":"Alternative splicing in neurogenesis and brain development","volume":"5","author":"Su","year":"2018","journal-title":"Front. Mol. Biosci."},{"key":"2023062021510384300_ref9","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1111\/opo.12682","article-title":"A novel deep intronic COL2A1 mutation in a family with early-onset high myopia\/ocular-only stickler syndrome","volume":"40","author":"Sun","year":"2020","journal-title":"Ophthalmic Physiol. Opt."},{"key":"2023062021510384300_ref10","doi-asserted-by":"crossref","first-page":"e0200739","DOI":"10.1371\/journal.pone.0200739","article-title":"Evaluation of serum sphingolipids and the influence of genetic risk factors in age-related macular degeneration","volume":"13","author":"Pujol-Lereis","year":"2018","journal-title":"PLoS One"},{"key":"2023062021510384300_ref11","doi-asserted-by":"crossref","first-page":"1990","DOI":"10.1177\/15353702211017292","article-title":"Differential expression and alternative splicing of transcripts in orbital adipose\/connective tissue of thyroid-associated ophthalmopathy","volume":"246","author":"Wu","year":"2021","journal-title":"Exp. Biol. Med. (Maywood)"},{"key":"2023062021510384300_ref12","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/519276a","article-title":"The myopia boom","volume":"519","author":"Dolgin","year":"2015","journal-title":"Nature"},{"key":"2023062021510384300_ref13","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s40662-021-00255-1","article-title":"Design, methodology, and baseline of whole city-million scale children and adolescents myopia survey (CAMS) in Wenzhou, China","volume":"8","author":"Xu","year":"2021","journal-title":"Eye Vis. (Lond.)"},{"key":"2023062021510384300_ref14","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1016\/j.ophtha.2011.03.012","article-title":"Myopia as a risk factor for open-angle glaucoma: a systematic review and meta-analysis","volume":"118","author":"Marcus","year":"2011","journal-title":"Ophthalmology"},{"key":"2023062021510384300_ref15","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1136\/bjo.2009.157727","article-title":"The epidemiology of rhegmatogenous retinal detachment: geographical variation and clinical associations","volume":"94","author":"Mitry","year":"2010","journal-title":"Br. J. Ophthalmol."},{"key":"2023062021510384300_ref16","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/S0161-6420(01)01024-7","article-title":"Prevalence and progression of myopic retinopathy in an older population","volume":"109","author":"Vongphanit","year":"2002","journal-title":"Ophthalmology"},{"key":"2023062021510384300_ref17","doi-asserted-by":"crossref","first-page":"107778","DOI":"10.1016\/j.exer.2019.107778","article-title":"An overview of myopia genetics","volume":"188","author":"Cai","year":"2019","journal-title":"Exp. Eye Res."},{"key":"2023062021510384300_ref18","doi-asserted-by":"crossref","first-page":"194401","DOI":"10.1016\/j.bbagrm.2019.07.002","article-title":"The regulation properties of RNA secondary structure in alternative splicing","volume":"1862","author":"Bartys","year":"2019","journal-title":"Biochim. Biophys. Acta Gene Regul. Mech."},{"key":"2023062021510384300_ref19","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1016\/j.cell.2006.08.032","article-title":"Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements","volume":"126","author":"Korostelev","year":"2006","journal-title":"Cell"},{"key":"2023062021510384300_ref20","doi-asserted-by":"crossref","first-page":"10505","DOI":"10.1128\/MCB.24.24.10505-10514.2004","article-title":"Influence of RNA secondary structure on the pre-mRNA splicing process","volume":"24","author":"Buratti","year":"2004","journal-title":"Mol. Cell. Biol."},{"key":"2023062021510384300_ref21","doi-asserted-by":"crossref","first-page":"1387","DOI":"10.1128\/MCB.24.3.1387-1400.2004","article-title":"RNA folding affects the recruitment of SR proteins by mouse and human polypurinic enhancer elements in the fibronectin EDA exon","volume":"24","author":"Buratti","year":"2004","journal-title":"Mol. Cell. Biol."},{"key":"2023062021510384300_ref22","doi-asserted-by":"crossref","first-page":"e204","DOI":"10.1371\/journal.pgen.0030204","article-title":"Pre-mRNA secondary structures influence exon recognition","volume":"3","author":"Hiller","year":"2007","journal-title":"PLoS Genet."},{"key":"2023062021510384300_ref23","first-page":"405","article-title":"A highly stable duplex structure sequesters the 5\u2032 splice site region of hnRNP A1 alternative exon 7B","volume":"3","author":"Blanchette","year":"1997","journal-title":"RNA (New York, N.Y.)"},{"key":"2023062021510384300_ref24","doi-asserted-by":"crossref","first-page":"4036","DOI":"10.1128\/MCB.20.11.4036-4048.2000","article-title":"Aberrant splicing of tau pre-mRNA caused by intronic mutations associated with the inherited dementia frontotemporal dementia with parkinsonism linked to chromosome 17","volume":"20","author":"Jiang","year":"2000","journal-title":"Mol. Cell. Biol."},{"key":"2023062021510384300_ref25","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/nar\/gkl1050","article-title":"Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes","volume":"35","author":"Singh","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023062021510384300_ref26","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1006\/jmbi.1995.0458","article-title":"Beta-tropomyosin pre-mRNA folding around a muscle-specific exon interferes with several steps of spliceosome assembly","volume":"251","author":"Sirand-Pugnet","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2023062021510384300_ref27","doi-asserted-by":"crossref","first-page":"9203","DOI":"10.1073\/pnas.0900342106","article-title":"The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing","volume":"106","author":"Warf","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2023062021510384300_ref28","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/s41587-020-0712-z","article-title":"Determination of isoform-specific RNA structure with nanopore long reads","volume":"39","author":"Aw","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"2023062021510384300_ref29","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1038\/nature12946","article-title":"Landscape and variation of RNA secondary structure across the human transcriptome","volume":"505","author":"Wan","year":"2014","journal-title":"Nature"},{"key":"2023062021510384300_ref30","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.neuron.2015.06.012","article-title":"RNA structures as mediators of neurological diseases and as drug targets","volume":"87","author":"Bernat","year":"2015","journal-title":"Neuron"},{"key":"2023062021510384300_ref31","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.1038\/s41467-018-04110-1","article-title":"Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes","volume":"9","author":"Garcia-Lopez","year":"2018","journal-title":"Nat. Commun."},{"key":"2023062021510384300_ref32","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1038\/nrm.2017.103","article-title":"Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them","volume":"19","author":"Leppek","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023062021510384300_ref33","doi-asserted-by":"crossref","first-page":"194403","DOI":"10.1016\/j.bbagrm.2019.07.004","article-title":"How RNA structure dictates the usage of a critical exon of spinal muscular atrophy gene","volume":"1862","author":"Singh","year":"2019","journal-title":"Biochim. Biophys. Acta Gene Regul. Mech."},{"key":"2023062021510384300_ref34","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"The genotype-tissue expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"Human genomics","year":"2015","journal-title":"Science (New York, N.Y.)"},{"key":"2023062021510384300_ref35","doi-asserted-by":"crossref","first-page":"235","DOI":"10.21037\/atm-20-4275","article-title":"Elongated axial length and myopia-related fundus changes associated with the Arg130Cys mutation in the LIM2 gene in four Chinese families with congenital cataracts","volume":"9","author":"Wang","year":"2021","journal-title":"Ann. Transl. Med."},{"key":"2023062021510384300_ref36","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1261\/rna.078662.120","article-title":"Co-transcriptional splicing efficiencies differ within genes and between cell types","volume":"27","author":"Bedi","year":"2021","journal-title":"RNA (New York, N.Y.)"},{"key":"2023062021510384300_ref37","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2017.05.045","article-title":"Dynamic RNA modifications in gene expression regulation","volume":"169","author":"Roundtree","year":"2017","journal-title":"Cell"},{"key":"2023062021510384300_ref38","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/nrm.2016.132","article-title":"Post-transcriptional gene regulation by mRNA modifications","volume":"18","author":"Zhao","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023062021510384300_ref39","doi-asserted-by":"crossref","first-page":"D819","DOI":"10.1093\/nar\/gkw1139","article-title":"The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data","volume":"45","author":"Wong","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023062021510384300_ref40","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1007\/BF00455162","article-title":"Increased aggregation and arachidonic acid transformation by psoriatic platelets: evidence that platelet-derived 12-hydroxy-eicosatetraenoic acid increases keratinocyte DNA synthesis in vitro","volume":"278","author":"Kragballe","year":"1986","journal-title":"Arch. Dermatol. Res."},{"key":"2023062021510384300_ref41","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The Ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"2023062021510384300_ref42","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023062021510384300_ref43","doi-asserted-by":"crossref","first-page":"D884","DOI":"10.1093\/nar\/gkaa942","article-title":"Ensembl 2021","volume":"49","author":"Howe","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023062021510384300_ref44","first-page":"920","article-title":"Machine learning annotation of human branchpoints","volume":"34","author":"Signal","year":"2018","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023062021510384300_ref45","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/s12864-020-6484-5","article-title":"Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants","volume":"21","author":"Leman","year":"2020","journal-title":"BMC Genomics"},{"key":"2023062021510384300_ref46","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1101\/gr.182899.114","article-title":"Genome-wide discovery of human splicing branchpoints","volume":"25","author":"Mercer","year":"2015","journal-title":"Genome Res."},{"key":"2023062021510384300_ref47","doi-asserted-by":"crossref","first-page":"D480","DOI":"10.1093\/nar\/gkaa1100","article-title":"UniProt: the universal protein knowledgebase in 2021","volume":"49","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023062021510384300_ref48","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1007\/978-1-0716-1851-6_3","article-title":"RBPmap: a tool for mapping and predicting the binding sites of RNA-binding proteins considering the motif environment","volume":"2404","author":"Paz","year":"2022","journal-title":"Methods Mol. Biol."},{"key":"2023062021510384300_ref49","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms for molecular biology: AMB"},{"key":"2023062021510384300_ref50","doi-asserted-by":"crossref","first-page":"5381","DOI":"10.1093\/nar\/gky285","article-title":"bpRNA: large-scale automated annotation and analysis of RNA secondary structure","volume":"46","author":"Danaee","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023062021510384300_ref51","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1002\/humu.22273","article-title":"RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs","volume":"34","author":"Sabarinathan","year":"2013","journal-title":"Hum. Mutat."},{"key":"2023062021510384300_ref52","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1016\/j.csbj.2023.01.007","article-title":"RNAsmc: a integrated tool for comparing RNA secondary structure and evaluating allosteric effects","volume":"21","author":"Wang","year":"2023","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2023062021510384300_ref53","doi-asserted-by":"crossref","first-page":"W365","DOI":"10.1093\/nar\/gkx407","article-title":"HDOCK: a web server for protein-protein and protein-DNA\/RNA docking based on a hybrid strategy","volume":"45","author":"Yan","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2023062021510384300_ref54","article-title":"3dRNA v2.0: an updated web server for RNA 3D structure prediction","volume":"20","author":"Wang","year":"2019","journal-title":"Int. J. Mol. Sci."},{"key":"2023062021510384300_ref55","doi-asserted-by":"crossref","first-page":"D437","DOI":"10.1093\/nar\/gkaa1038","article-title":"RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences","volume":"49","author":"Burley","year":"2021","journal-title":"Nucleic Acids Res."}],"container-title":["Human Molecular Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/hmg\/advance-article-pdf\/doi\/10.1093\/hmg\/ddad057\/50202620\/ddad057.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hmg\/article-pdf\/32\/13\/2229\/50659767\/ddad057.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hmg\/article-pdf\/32\/13\/2229\/50659767\/ddad057.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T05:23:42Z","timestamp":1687325022000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hmg\/article\/32\/13\/2229\/7107871"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,5]]},"references-count":55,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2023,4,5]]},"published-print":{"date-parts":[[2023,6,19]]}},"URL":"https:\/\/doi.org\/10.1093\/hmg\/ddad057","relation":{},"ISSN":["0964-6906","1460-2083"],"issn-type":[{"type":"print","value":"0964-6906"},{"type":"electronic","value":"1460-2083"}],"subject":[],"published-other":{"date-parts":[[2023,7,1]]},"published":{"date-parts":[[2023,4,5]]}}}