Primerjava regulatornih regij genov Pparg, Ppargc1a in Ppargc1b pri debeli in vitki liniji miši

Markež, Ana (author), Kunej, Tanja (mentor), Horvat, Simon (comentor)

Debelost in druge presnovne bolezni postajajo vedno večji svetovni zdravstveni in ekonomski problem in so običajno posledica porušenega ravnotežja med vnosom in porabo energije. Vzdrževanje tega ravnotežja omogočajo med drugim tudi produkti genov jedrnega receptorja Pparg in transkripcijskih kofaktorjev Ppargc1a in Ppargc1b. V raziskavi smo s pomočjo znanstvene literature, podatkovnih zbirk in bioinformacijskih orodij izvedli in silico analizo različic posameznega nukleotida (SNP) pri poligenih selekcioniranih linijah debelih (F) in vitkih (L) miši, znotraj regij različnih ravni regulacije. Preučili smo ravni regulacije na katere imajo lahko direkten vpliv SNP-ji v nukleotidnem zaporedju genov in sicer regulatorne elemente, alternativno poliadenilacijo (APA), alternativno izrezovanje introna (AS), metilacijo DNA, mikroRNA (miRNA) in potranslacijske modifikacije (PTM). Med mišjima linijama so bile ugotovljene razlike v številu in biotipu SNP-jev pri vseh treh preučevanih genih glede na referenčni mišji genom, Pparg (L = 0 in F = 3), Ppargc1a (L = 631 in F = 0), Ppargc1b (L = 3 in F = 140). V regulatornih elementih (ojačevalcih in promotorjih) so bili SNP-ji prisotni pri vseh treh genih, in sicer pri Pparg mišje linije F (n = 1), Ppargc1a mišje linije L (n = 45) in Ppargc1b mišje linije F (n = 14). To kaže na možnost sprememb v izražanju v času, lokaciji in ravni vseh treh genov, še posebej gena Ppargc1a mišje linije L in gena Ppargc1b mišje linije F. En SNP (rs244748170) se pri genu Ppargc1a mišje linije L prekriva s tremi skupki mest alternativne poliadenilacije (PAS), vendar se ne prekriva s posameznimi PAS znotraj skupkov. Iz tega sklepamo, da najverjetneje ne vpliva na regulacijo z APA. Pri nobeni od mišjih linij SNP-ji niso prisotni v regulatornih regijah AS, metilacije DNA, PTS in vezavnih mestih preučenih miRNA v maščobnem tkivu. Dodatno smo v zaporedju gena Ppargc1a mišje linije L našli drugačnosmiselen SNP (rs265764749), ki povzroči zamenjavo aminokisline arginin v cistein na mestu 629 in ima napovedan škodljiv vpliv na funkcijo proteina. Povzroči lahko porušenje strukture proteina zaradi razlik v lastnostih zamenjanih aminokislin, kar se lahko odraža v spremembi funkcije, stabilnosti in aktivnosti proteina. Identificirane spremembe lahko pripomorejo k razlagi razlik v nalaganju maščob med mišjima linijama, s čimer raziskava omogoča dodatni vpogled in podaja usmeritve ter odpira nova vprašanja v razumevanju kompleksnega mehanizma debelosti in vitkosti.

• Language: Slovenian
• Keywords: debelost, regulacija genov, genetska raznolikost, SNP, bioinformatika
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: BF - Biotechnical Faculty
• Year: 2023
• PID: 20.500.12556/RUL-147470
• COBISS.SI-ID: 157927939
• Publication date in RUL: 06.07.2023

Secondary language

• Language: English
• Title: Comparison of regulatory regions in Pparg, Ppargc1a and Ppargc1b genes between fat and lean mouse lines

Abstract

Obesity and other metabolic diseases are a growing problem worldwide, usually because of an imbalance between energy intake and energy expenditure. This balance is maintained by various factors, including the products of the nuclear receptor gene Pparg and the genes of the transcription cofactor Ppargc1a and Ppargc1b. In this study, we performed an in silico analysis of single nucleotide polymorphisms (SNP) within the regulatory regions of these genes in polygenic selected lines of obese (F) and lean (L) mice by analyzing scientific publications, databases and bioinformatics tools. We examined SNPs in the regulatory regions that can affect various levels of gene expression such as regulatory elements alternative polyadenylation (APA), alternative splicing (AS), DNA methylation, microRNAs (miRNA) and post-translational modifications (PTM). We found differences in the number and biotype of SNPs in the Pparg (L = 0, F = 3), Ppargc1a (L = 631, F = 0), and Ppargc1b (L = 3, F = 140) genes between the two mouse lines. In regulatory elements (enhancers and promoters), SNPs were present in all three genes, namely Pparg of mouse line F (n = 1), Ppargc1a of mouse line L (n = 45) and Ppargc1b of mouse line F (n = 14). These findings suggest that differential expression in time, location and level of these genes between the F and L lines is possible, especially for the Ppargc1a gene of the L mouse line and the Ppargc1b gene of the F mouse line. The SNP (rs244748170) observed in the Ppargc1a gene of L mouse line overlaps with three clusters of alternative polyadenylation sites (PAS), but does not overlap with individual PAS within the clusters, indicating that it most likely does not affect regulation through APA. None of the SNPs in any of the mouse lines are present in regulatory regions of PTM, AS, DNA methylation, and binding sites of studied microRNA in adipose tissue. Additionally, we identified a missense SNP (rs265764749) of the Ppargc1a gene of the L mouse line that causes an amino acid substitution from arginine to cysteine at position 629 and could potentially disrupt the protein's structure, leading to changes in protein function, stability, and activity. Our results may help to explain the differences in body fat accretion between the two mouse lines, thus providing additional insights, directions and raising new questions in the understanding of the complex mechanism of obesity and leanness.

• Keywords: obesity, gene regulation, genetic diversity, SNP, bioinformatics