Functionally significant features in the 5 ' untranslated region of the ABCA1 gene and their comparison in vertebrates

Kód výsledku v IS VaVaI

RIV/75010330:_____/19:00012660 - isvavai.cz

Nalezeny alternativní kódy

RIV/00216208:11140/19:10394875

Výsledek na webu

https://www.mdpi.com/2073-4409/8/6/623

DOI - Digital Object Identifier

10.3390/cells8060623

Jazyk výsledku

angličtina

Název v původním jazyce

Functionally significant features in the 5 ' untranslated region of the ABCA1 gene and their comparison in vertebrates

Popis výsledku v původním jazyce

Single nucleotide polymorphisms located in 5 ' untranslated regions (5 ' UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5 ' UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5 ' UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5 ' UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5 ' UTRs, such as GC content variation, hairpin structure conservation or 5 ' UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.

Název v anglickém jazyce

Functionally significant features in the 5 ' untranslated region of the ABCA1 gene and their comparison in vertebrates

Popis výsledku anglicky

Single nucleotide polymorphisms located in 5 ' untranslated regions (5 ' UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5 ' UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5 ' UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5 ' UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5 ' UTRs, such as GC content variation, hairpin structure conservation or 5 ' UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

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

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2019

Kód důvěrnosti údajů

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

Název periodika

Cells

ISSN

2073-4409

e-ISSN

—

Svazek periodika

8

Číslo periodika v rámci svazku

6

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

24

Strana od-do

623

Kód UT WoS článku

000475309200111

EID výsledku v databázi Scopus

—