THE FREQUENCY AND FITNESS OF m6A-ASSOCIATED VARIANTS COULD BE MODULATED BY THE THERMODYNAMIC STABILITY OF AN OVERLAPPING G-QUADRUPLEX

Year 2023, Volume: 6 Issue: 3, 219 - 228, 24.10.2023

Çağrı Güleç

https://doi.org/10.26650/JARHS2023-1349345

Abstract

Objective: Post-transcriptional modifications like m6A (N6-methyladenosine) and secondary structures like G-quadruplex (G4) are formations that play a vital role in RNA processing. Their synergy also has functional consequences. Since m6A is known to be enzymatically created in the DRACH-motif, and that genetic variants can create a novel DRACH-motif or abolish a pre-existing DRACH-motif, we can hypothesize that variants which affect the gene product level through modulating m6A-G4 colocalization, may also consequently affect fitness and change the allele frequency. To test this hypothesis, the rare and common variants in selected human genes were investigated to determine their effect on DRACH-G4 colocalization.
Material and Methods: Genomic sequences and variant information were retrieved from the GRCh37/hg19 and Biomart-Ensembl databases. Experimentally determined G4 sequences were obtained from two different studies.
Results: Common variants leading to the formation of a novel DRACHmotif were found to be significantly higher inside the G4 structure than outside. In contrast, rare variants with the same feature were higher outside the G4-structure and had uneven distribution alongside the premRNA. The uneven distribution of the DRACH-creating rare variants was observed to correlate with their effect on thermodynamic stability of the overlapping G4.
Conclusion: Selective DRACH-G4 colocalization suggests that m6A is evolutionally favorable when overlapping with G4. The thermodynamic stability could lead to uneven distribution of DRACH-G4 colocalization, favorable in 3-prime-side, but not in 5-prime-side. We can conclude that the fitness, and consequently frequency of a DRACH-creating variant is prone to become higher or lower depending in its position and effect on the overlapping-G4 stability.

Keywords

RNA modification, N6-methyladenosine, G-quadruplex, allele frequency

m6A İLE İLİŞKİLİ VARYANTLARIN SIKLIĞI, ÖRTÜŞTÜĞÜ G-KUADRUPLEKS YAPISININ TERMODİNAMİK KARARLILIĞI İLE DEĞİŞEBİLİR

Abstract

Amaç: M6A (N6-metiladenozin) gibi post-transtranskripsiyonel modifikasyonlar ve G-kuadrupleks (G4) gibi ikincil yapılar, RNA işlenmesinde önemli rol oynayan oluşumlardır. Bu iki oluşumun birlikteliğinin de işlevsel sonuçları vardır. M6A oluşumunun DRACH motifi üzerinde enzimatik olarak meydana geldiği, genetik varyantların yeni DRACH motifi oluşturabildiği veya var olan bir DRACH motifini ortadan kaldırabildiği dikkate alındığında, bu tür varyantların, mRNA üzerinde m6A-G4 örtüşme durumunu değiştirerek gen ürün düzeyini etkileyebileceğini, bunun da nesiller boyunca ilgili varyantın alel sıklığını değiştireceğini varsayabiliriz. Bu hipotezi test etmek için seçilmiş hastalık ilişkili genlerdeki nadir ve sık varyantlar DRACH-G4 örtüşmesi yönünden incelendi.
Gereç ve Yöntemler: Genomik diziler ve varyant bilgileri sırasıyla GRCh37/ hg19 ve Biomart-Ensembl veritabanlarından çekildi. Deneysel olarak saptanmış G4 dizileri iki farklı çalışmadan elde edildi.
Bulgular: Yeni bir DRACH motifi oluşumuna yol açan yaygın varyantlar, G4 yapısı içinde yüksek bulundu. Aynı özelliğe sahip nadir varyantlar ise G4 yapısı dışında yüksek bulunurken, pre-mRNA üzerinde eşit dağılım göstermedikleri belirlendi. Yeni bir DRACH motifi oluşumuna yol açan nadir varyantların eşit olmayan dağılımı, örtüştüğü G4 yapısının termodinamik kararlılığı üzerindeki etkisi ile ilişkili bulundu.
Sonuç: Beklenenden sık gözlenen DRACH-G4 örtüşmesi, m6A modifikasyonunun G4 ile örtüştüğü durumların evrimsel bir avantaj sağlıyor olabileceğini düşündürmektedir. Nadir varyantlara bağlı ortaya çıkan DRACH-G4 örtüşmelerinin pre-mRNA’da eşit dağılım göstermemesi ise, m6A’nın G4 termodinamik kararlılığını değiştirmesi ve bu değişikliğin pre-mRNA’nın 5’ kısmına göre 3’ kısmında daha fazla tolere ediliyor olmasına bağlı görünmektedir. Sonuç olarak, DRACH motifi oluşturan varyantların seçilim baskısı ve bunun sonucunda biçimlenen alel sıklığı, bu varyantın pre-mRNA üzerindeki konumuna ve örtüştüğü G4 oluşumunun kararlılığı üzerindeki etkisine göre değişiklik göstermektedir.

Keywords

RNA modifikasyonu, N6-metiladenozin, G-kuadrupleks, alel sıklığı

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