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

Article  CAS  Google Scholar 

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

Article  Google Scholar 

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

Article  Google Scholar 

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