0576660 20250313101252.920231018235959.9 85173558258 001077365500001 10.1101/gr.277694.123 15 s. cav_un_epca*02530541088-9051338 (2023)1395-1408Cold Spring Harbor Laboratory Press IMMUNODEFICIENCY-VIRUS TYPE-1 HIV-1 INTEGRATION HUMAN GENOME cav_un_auth*0358546 Miklík Dalibor UMG-J Oddělení virové a buněčné genetiky Laboratory of Viral and Cellular Genetics 12 12 Ústav molekulární genetiky AV ČR, v. v. i. cav_un_auth*0101091 Grim Jiří UTIA-B Rozpoznávání obrazu Department of Pattern Recognition RO RO Ústav teorie informace a automatizace AV ČR, v. v. i. cav_un_auth*0105358 Elleder Daniel UMG-J Oddělení virové a buněčné genetiky Laboratory of Viral and Cellular Genetics 12 12 Ústav molekulární genetiky AV ČR, v. v. i. cav_un_auth*0105375 Hejnar Jiří UMG-J Oddělení virové a buněčné genetiky Laboratory of Viral and Cellular Genetics 12 12 K Ústav molekulární genetiky AV ČR, v. v. i. https://genome.cshlp.org/content/33/8/1395 LX22NPO5103 GA MŠk CZ cav_un_auth*0433948 GA19-23407S GA ČR CZ cav_un_auth*0456716 A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Given that the majority of target sequences are not palindromic, the current model explains the symmetry by an overlap of the nonpalindromic motif present on one of the half-sites of the sequences. Here, we show that the implementation of multicomponent mixture models allows for different interpretations consistent with the existence of both palindromic and nonpalindromic submotifs in the sets of integration site sequences. We further show that the weak palindromic motifs result from freely combined site-specific submotifs restricted to only a few positions proximal to the site of integration. The submotifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Using the mixture models, we also identify HIV-1-favored palindromic sequences in Alu repeats serving as local hotspots for integration. The application of the novel statistical approach provides deeper insight into the selection of retroviral integration sites and may prove to be a valuable tool in the analysis of any type of DNA motifs. 10000 10600 10608 2024 4 UTIA-B 10000 10200 10201 4 O 4o 2rh 20241111130635.1 2 R hod 20250310154451.7 20250313101252.9 RVO:67985556 RVO:68378050 https://hdl.handle.net/11104/0346204 Article Biochemistry Molecular Biology|Biotechnology Applied Microbiology|Genetics Heredity A BIOTECHNOLOGY&APPLIEDMICROBIOLOGY|BIOCHEMISTRY&MOLECULARBIOLOGY|GENETICS&HEREDITY 8.4 1.1 12.2 0.03298 4.727 42932 338 4.403 66.9 6.11 3425 Q1 6.100 132 Q1 87.3 Q1* Q1* 1.65 Q1 88.2 2023 Soubory v repozitáři: grim-576660.pdf, genome-miklík-23.pdf GENOME RESEARCH 1088-9051 2023 33 8 85173558258 SCOPUS 001077365500001 WOS cav_un_epca*0253054 Genome Research 1088-9051 1549-5469 Roč. 33 č. 8 2023 1395 1408 Cold Spring Harbor Laboratory Press