BACKGROUND: Large deletions and duplications within the low-density lipoprotein receptor (LDLR) gene make up approximately 10% of LDLR pathogenic variants found in Czech patients with familial hypercholesterolemia. The goal of this study was to test the hypothesis that all probands with each rearrangement share identical breakpoints inherited from a common ancestor and to determine the role of Alu repetitive elements in the generation of these rearrangements. METHODS: The breakpoint sequence was determined by PCR amplification and Sanger sequencing. To confirm the breakpoint position, an NGS analysis was performed. Haplotype analysis of common LDLR variants was performed using PCR and Sanger sequencing. RESULTS: The breakpoints of 8 rearrangements within the LDLR gene were analysed, including the four most common LDLR rearrangements in the Czech population (number of probands ranging from 8 to 28), and four less common rearrangements (1-4 probands). Probands with a specific rearrangement shared identical breakpoint positions and haplotypes associated with the rearrangement, suggesting a shared origin from a common ancestor. All breakpoints except for one were located inside an Alu element. In 6 out of 8 breakpoints, there was high homology (≥ 70%) between the two Alu repeats in which the break occurred. CONCLUSIONS: The most common rearrangements of the LDLR gene in the Czech population likely arose from one mutational event. Alu elements likely played a role in the generation of the majority of rearrangements inside the LDLR gene.

• MeSH
• genová přestavba MeSH
• hyperlipoproteinemie typ II * genetika   epidemiologie   MeSH
• LDL-receptory genetika   MeSH
• lidé MeSH
• mutace MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH

Acceptor splice site recognition (3' splice site: 3'ss) is a fundamental step in precursor messenger RNA (pre-mRNA) splicing. Generally, the U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) heterodimer recognizes the 3'ss, of which U2AF35 has a dual function: (i) It binds to the intron-exon border of some 3'ss and (ii) mediates enhancer-binding splicing activators' interactions with the spliceosome. Alternative mechanisms for 3'ss recognition have been suggested, yet they are still not thoroughly understood. Here, we analyzed 3'ss recognition where the intron-exon border is bound by a ubiquitous splicing regulator SRSF1. Using the minigene analysis of two model exons and their mutants, BRCA2 exon 12 and VARS2 exon 17, we showed that the exon inclusion correlated much better with the predicted SRSF1 affinity than 3'ss quality, which were assessed using the Catalog of Inferred Sequence Binding Preferences of RNA binding proteins (CISBP-RNA) database and maximum entropy algorithm (MaxEnt) predictor and the U2AF35 consensus matrix, respectively. RNA affinity purification proved SRSF1 binding to the model 3'ss. On the other hand, knockdown experiments revealed that U2AF35 also plays a role in these exons' inclusion. Most probably, both factors stochastically bind the 3'ss, supporting exon recognition, more apparently in VARS2 exon 17. Identifying splicing activators as 3'ss recognition factors is crucial for both a basic understanding of splicing regulation and human genetic diagnostics when assessing variants' effects on splicing.

• MeSH
• alternativní sestřih genetika   MeSH
• exony genetika   MeSH
• HeLa buňky MeSH
• introny genetika   MeSH
• lidé MeSH
• místa sestřihu RNA genetika   fyziologie   MeSH
• proteiny vázající RNA metabolismus   MeSH
• regulační oblasti nukleových kyselin genetika   MeSH
• sekvence nukleotidů genetika   MeSH
• serin-arginin sestřihové faktory metabolismus   MeSH
• sestřih RNA fyziologie   MeSH
• sestřihové faktory metabolismus   fyziologie   MeSH
• sestřihový faktor U2AF metabolismus   MeSH
• spliceozomy metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Frekvence familiární hypercholesterolémie (FH) je u většiny populací asi 1/200 a je tedy možné předpokládat, že v ČR by mohlo být postiženo přibližně 50 000 osob. Řešení projektu lze rozdělit do dvou pracovních bloků (PB). PB1 je zaměřen na funkční analýzu variant genu LDLR in vitro a využívá metod průtokové cytometrie, konfokální mikroskopie na živých buňkách, qRT-PCR a sestřihových minigenových testů. Varianty LDLR budou hodnoceny na úrovni exprese, zrání, lokalizace a funkce daného proteinu a na úrovni buněčné odpovědi (aktivace tzv. unfolded protein response). PB2 je zaměřen na analýzu DNA pacientů. Metodou NGS bude provedena re-analýza pacientů s FH s dosud negativní genetickou diagnózou a budou aplikovány metody pro stanovení počtu repetic Kringle IV v genu LPA (PFGE a Southernova hybridizace) pro rozřazení pacientů do skupiny s nižšími nebo vyšší riziky předčasné aterosklerózy. Všechny uvedené přístupy mají společný cíl – identifikovat genetické varianty způsobující FH a získat nové informace o patogenitě FH.; The frequency of familial hypercholesterolemia (FH) in most populations is about 1/200, and so it is possible to predict that about 50,000 people could be affected by FH in the Czech Republic. The project solution can be divided into two work packages (WP). WP1 is focused on functional analysis of LDLR variants in vitro and methods as flow cytometry, live cell imaging microscopy, qRT-PCR, splicing minigene assay will be applied. LDLR variants will be evaluated on level of protein expression, maturation, localisation, function, and cell response (activation of the unfolded protein response). WP2 is focused on analysis of patients ́ DNA. Re-analysis of FH patients with so far negative genetic diagnosis will be performed by NGS, and methods for determination of the Kringle IV repeat number in the LPA gene (PFGE and Southern hybridisation) will be applied for stratification of patients into a group with lower or higher risk of premature atherosclerosis. All mentioned approaches have a common goal – to identify FH disease-causing variants and obtain new information about FH pathogenicity.

• Klíčová slova
• familial hypercholesterolemia, Familiální hypercholesterolémie, funkční analýza, functional analysis, confocal microscopy, konfokální mikroskopie, LDLR, LDLR, skládání proteinů, lipoprotein(a), protein folding, lipoprotein(a),

• NLK Publikační typ
• závěrečné zprávy o řešení grantu AZV MZ ČR