Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985556%3A_____%2F23%3A00576660" target="_blank" >RIV/67985556:_____/23:00576660 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68378050:_____/23:00576660

Výsledek na webu

<a href="https://genome.cshlp.org/content/33/8/1395" target="_blank" >https://genome.cshlp.org/content/33/8/1395</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1101/gr.277694.123" target="_blank" >10.1101/gr.277694.123</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Genome Research

ISSN

1088-9051

e-ISSN

1549-5469

Svazek periodika

33

Číslo periodika v rámci svazku

8

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

15

Strana od-do

1395-1408

Kód UT WoS článku

001077365500001

EID výsledku v databázi Scopus

2-s2.0-85173558258