Zhang F., Lupski J.R. 2015. Non-coding genetic variants in human disease. Hum. Mol. Genet. 24 (R1), R102‒R110. https://doi.org/10.1093/hmg/ddv259
Article CAS PubMed PubMed Central Google Scholar
Babushkina N.P., Postrigan A.E., Kucher A.N. 2021. Involvement of variants in the genes encoding BRCA1-associated genome surveillance complex (BASC) in the development of human common diseases. Mol. Biol. (Moscow) 55 (2), 278–296. https://doi.org/10.31857/S0026898421020038
Babushkina N.P., Postrigan A.E., Kucher A.N. 2018. Involvement of genes of DNA repair systems in the development of cardiovascular pathology. In Molekulyarno-biologicheskie tekhnologii v meditsinskoi praktike. (Molecular Biological Technologies in Medical Practice). Maslennikov A.B., Ed. Novosibirsk: Akademizdat, pp. 48‒62.
Babushkina N.P., Postrigan A.E., Khitrinskaya E.Yu., Kucher A.N. 2019. Environmental effects on the association of genes of proteins of DNA repair systems with bronchial asthma. VII S”ezd Vavilovskogo obschestva genetikov i selektsionerov (VOGiS) Sankt-Peterburg, Rossiya. Sbornik tezisov. (VII Congress of the Vavilov Society of Geneticists and Breeders (VOGiS), St. Petersburg, Russia. Abstracts of Papers). p. 788.
Babushkina N.P., Postrigan A.E., Khitrinskaya E.Yu., Kucher A.N. 2019. Involvement of polymorphic gene variants of DNA repair systems in the development of multifactorial diseases. In Sbornik: Genetika cheloveka i patologiya: aktual’nye problemy klinicheskoi i molekulyarnoi tsitogenetiki. (Collection of Papers: Human Genetics and Pathology: Actual Problems of Clinical and Molecular Cytogenetics). Stepanov V.A., Ed. Tomsk: Literaturnoe byuro, p. 5–6.
Babushkina N.P., Postrigan A.E., Kucher A.N. 2020. Genes Encoding DNA repair proteins and longevity. Med. Genet. 19 (5), 99–100. https://doi.org/10.25557/2073-7998.2020.05.99-100
Babushkina N.P., Postrigan A.E., Kucher A.N., Kuzheleva E.A., Garganeeva A.A. 2020. Associations of gene polymorphisms of DNA repair systems with lipid metabolism indices. Sbornik: Kardiologiya 2020—novye vyzovy i novye resheniya. Kazan’. Sbornik tezisov. (Cardiology 2020—New Challenges and New Solutions, Kazan, Abstracts of Papers), Kazan, p. 811.
Postrigan A.E., Babushkina N.P., Kucher A.N. 2020. The involvement of the NBN gene polymorphism in the formation of predisposition to dystrophic diseases. Med. Genet. 19 (8), 98–99. https://doi.org/10.25557/2073-7998.2020.08.98-99
Peakall R., Smouse P.E. 2012. GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics. 28 (19), 2537‒2539. https://doi.org/10.1093/bioinformatics/bts460
Article CAS PubMed PubMed Central Google Scholar
Taverna S.D., Li H., Ruthenburg A.J., Allis C.D., Patel D.J. 2007. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14 (11), 1025‒1040. https://doi.org/10.1038/nsmb1338
Article CAS PubMed PubMed Central Google Scholar
Hoon D.S.B., Rahimzadeh N., Bustos M.A. 2021. EpiMap: fine-tuning integrative epigenomics maps to understand complex human regulatory genomic circuitry. Signal. Transduct. Target Ther. 6 (1), 179. https://doi.org/10.1038/s41392-021-00620-5
Article PubMed PubMed Central Google Scholar
Fu Y., Sinha M., Peterson C.L., Weng Z. 2008. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4 (7), e1000138. https://doi.org/10.1371/journal.pgen.1000138
Article CAS PubMed PubMed Central Google Scholar
Rubio E.D., Reiss D.J., Welcsh P.L., Disteche C.M., Filippova G.N., Baliga N.S., Aebersold R., Ranish J.A., Krumm A. 2008. CTCF physically links cohesin to chromatin. Proc. Natl. Acad. Sci. U. S. A. 105 (24), 8309‒8314. https://doi.org/10.1073/pnas.0801273105
Article PubMed PubMed Central Google Scholar
Mishiro T., Ishihara K., Hino S., Tsutsumi S., Aburatani H., Shirahige K., Kinoshita Y., Nakao M. 2009. Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. EMBO J. 28 (9), 1234‒1245. https://doi.org/10.1038/emboj.2009.81
Article CAS PubMed PubMed Central Google Scholar
Shoaib M., Chen Q., Shi X., Nair N., Prasanna C., Yang R., Walter D., Frederiksen K.S., Einarsson H., Svensson J.P., Liu C.F., Ekwall K., Lerdrup M., Nordenskiöld L., Sørensen C.S. 2021. Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. Nat. Commun. 12 (1), 4800. https://doi.org/10.1038/s41467-021-25051-2
Article CAS PubMed PubMed Central Google Scholar
Hansen K.H., Bracken A.P., Pasini D., Dietrich N., Gehani S.S., Monrad A., Rappsilber J., Lerdrup M., Helin K. 2008. A model for transmission of the H3K27me3 epigenetic mark. Nat. Cell Biol. 10 (11), 1291‒1300. https://doi.org/10.1038/ncb1787
Article CAS PubMed Google Scholar
Vandamme J., Sidoli S., Mariani L., Friis C., Christensen J., Helin K., Jensen O.N., Salcini A.E. 2015. H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic Acids Res. 43 (20), 9694‒9710. https://doi.org/10.1093/nar/gkv1063
Article CAS PubMed PubMed Central Google Scholar
Yang W., Bai Y., Xiong Y., Zhang J., Chen S., Zheng X., Meng X., Li L., Wang J., Xu C., Yan C., Wang L., Chang C.C., Chang T.Y., Zhang T., Zhou P., Song B.L., Liu W., Sun S.C., Liu X., Li B.L., Xu C. 2016. Potentiating the antitumour response of CD8+ T cells by modulating cholesterol metabolism. Nature. 531 (7596), 651‒655. https://doi.org/10.1038/nature17412
Article CAS PubMed PubMed Central Google Scholar
Fornes O., Castro-Mondragon J.A., Khan A., van der Lee R., Zhang X., Richmond P.A., Modi B.P., Correard S., Gheorghe M., Baranasic D., Santana-Garcia W., Tan G., Cheneby J., Ballester B., Parcy F., Sandelin A., Lenhard B., Wasserman W.W., Mathelier A. 2020. J-ASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48 (D1), D87‒D92. https://doi.org/10.1093/nar/gkz1001
Article CAS PubMed Google Scholar
Lesurf R., Cotto K.C., Wang G., Griffith M., Kasaian K., Jones S.J., Montgomery S.B., Griffith O.L.; Open Regulatory Annotation Consortium. 2016. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 44 (D1), D126‒D132. https://doi.org/10.1093/nar/gkv1203
Article CAS PubMed Google Scholar
Kazachenka A., Bertozzi T.M., Sjoberg-Herrera M.K., Walker N., Gardner J., Gunning R., Pahita E., Adams S., Adams D., Ferguson-Smith A.C. 2018. Identification, characterization, and heritability of murine metastable epialleles: implications for non-genetic inheritance. Cell. 175 (5), 1259‒1271.e13. https://doi.org/10.1016/j.cell.2018.09.043
Article CAS PubMed PubMed Central Google Scholar
Li M.J., Wang L.Y., Xia Z., Sham P.C., Wang J. 2013. GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. Nucleic Acids Res. 41 (W1), W150‒W158. https://doi.org/10.1093/nar/gkt456
Article PubMed PubMed Central Google Scholar
Huang D., Yi X., Zhang S., Zheng Z., Wang P., Xuan C., Sham P.C., Wang J., Li M.J. 2018. GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits. Nucleic Acids Res. 46 (W1), W114‒W120. https://doi.org/10.1093/nar/gky407
Article CAS PubMed PubMed Central Google Scholar
Huang D., Zhou Y., Yi X., Fan X., Wang J., Yao H., Sham P.C., Hao J., Chen K., Li M.J. 2022. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Res. 50 (D1), D1408‒D1416. https://doi.org/10.1093/nar/gkab853
Article CAS PubMed Google Scholar
Lee R., Kang M.K., Kim Y.J., Yang B., Shim H., Kim S., Kim K., Yang C.M., Min B.G., Jung W.J., Lee E.C., Joo J.S., Park G., Cho W.K., Kim H.P. 2022. CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates. Nucleic Acids Res. 50 (1), 207‒226. https://doi.org/10.1093/nar/gkab1242
Article CAS PubMed Google Scholar
Putt W., Palmen J., Nicaud V., Tregouet D.A., Tahri-Daizadeh N., Flavell D.M., Humphries S.E., Talmud P.J.; EARSII group. 2004. Variation in USF1 shows haplotype effects, gene:gene and gene:environment associations with glucose and lipid parameters in the European Atherosclerosis Research Study II. Hum. Mol. Genet. 13 (15), 1587‒1597. https://doi.org/10.1093/hmg/ddh168
Article CAS PubMed Google Scholar
Laurila P.P., Naukkarinen J., Kristiansson K., Ripatti S., Kauttu T., Silander K., Salomaa V., Perola M., Karhunen P.J., Barter P.J., Ehnholm C., Peltonen L. 2010. Genetic association and interaction analysis of USF1 and APOA5 on lipid levels and atherosclerosis. Arterioscler. Thromb. Vasc. Biol. 30 (2), 346‒352. https://doi.org/10.1161/ATVBAHA.109.188912
Article CAS PubMed Google Scholar
Taghizadeh E., Mirzaei F., Jalilian N., Ghayour Mobarhan M., Ferns G.A., Pasdar A. 2020. A novel mutation in USF1 gene is associated with familial combined hyperlipidemia. IUBMB Life. 72 (4), 616‒623. https://doi.org/10.1002/iub.2186
Article CAS PubMed Google Scholar
Pollard K.S., Hubisz M.J., Rosenbloom K.R., Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20 (1), 110–121. https://doi.org/10.1101/gr.097857.109
Article CAS PubMed PubMed Central Google Scholar
Caron B., Luo Y., Rausell A. 2019. NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans. Genome Biol. 20 (1), 32. https://doi.org/10.1186/s13059-019-1634-2
Article PubMed PubMed Central Google Scholar
Siepel A. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15 (8), 1034‒1035. https://doi.org/10.1101/gr.3715005
Article CAS PubMed PubMed Central Google Scholar
Hubisz M.J., Pollard K.S., Siepel A. 2011. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 12 (1), 41–51. https://doi.org/10.1093/bib/bbq072
Article CAS PubMed Google Scholar
Zerbino D.R., Achuthan P., Akanni W., Amode M.R., Barrell D., Bhai J., Billis K., Cummins C., Gall A., Giron C.G., Gil L., Gordon L., Haggerty L., Haskell E., Hourlier T., Izuogu O.G., Janacek S.H., Juettemann T., To J.K., Laird M.R., Lavidas I., Liu Z., Loveland J.E., Maurel T., McLaren W., Moore B., Mudge J., Murphy D.N., Newman V., Nuhn M., Ogeh D., Ong C.K., Parker A., Patricio M., Riat H.S., Schuilenburg H., Sheppard D., Sparrow H., Taylor K., Thormann A., Vullo A., Walts B., Zadissa A., Frankish A., Hunt S.E., Kostadima M., Langridge N., Martin F.J., Muffato M., Perry E., Ruffier M., Staines D.M., Trevanion S.J., Aken B.L., Cunningham F., Yates A., Flicek P. 2018. Ensembl 2018. Nucleic Acids Res. 46 (D1), D754‒D761. https://doi.org/10.1093/nar/gkx1098
Article CAS PubMed Google Scholar
Gulko B., Hubisz M.J., Gronau I., Siepel A. 2015. A method for calculating probabiliti
留言 (0)