SavedAdd your journal

Journals / Turkish Journal of Botany / 2019 / Cilt: 43 - Sayı: 2

G-Quadruplex enrichment analysis reveals their role as intronic regulatory elements in plants

Osman DOLUCA
Pages
151–166
Publication Date
2022-11-03
DOI
—
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

The results indicate that G-quadruplex distribution has gone through significant changes with the evolution of higherplants and, for the first time, that G-quadruplexes enriched at the beginning of introns may have a regulatory role during transcription.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:G-Quadruplexes, a class of noncanonical but highly stable nucleic acid structures, have the potential to be part of theregulatory mechanism of cells.
📊
Key Findings & Data:They can form in the genome where the double-stranded helix is unwound to facilitate formation of aG-quadruplex.
💡
Conclusion & Impact:The results indicate that G-quadruplex distribution has gone through significant changes with the evolution of higherplants and, for the first time, that G-quadruplexes enriched at the beginning of introns may have a regulatory role during transcription.
🔬Design:Research Article
📍Scope:Comprehensive Sample
⚙️Variables:Domain Parameters

Abstract

G-Quadruplexes, a class of noncanonical but highly stable nucleic acid structures, have the potential to be part of theregulatory mechanism of cells. They can form in the genome where the double-stranded helix is unwound to facilitate formation of aG-quadruplex. The biological significance of these structures is yet to be understood entirely. This work presents a novel approach andinvestigates common characteristics in the distribution of G-quadruplexes relative to genes in plants through analysis of genomes andgene expressions. The results indicate that G-quadruplex distribution has gone through significant changes with the evolution of higherplants and, for the first time, that G-quadruplexes enriched at the beginning of introns may have a regulatory role during transcription.

🔖

Cite This Article

DOLUCA, O. (2022). G-Quadruplex enrichment analysis reveals their role as intronic regulatory elements in plants. Turkish Journal of Botany, Cilt: 43 - Sayı: 2, 151–166. https://ajindex.com/articles/600844

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (5)

  1. Andorf CM, Kopylov M, Dobbs D, Koch KE, Stroupe ME et al. (2014). G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation. Journal of Genetics and Genomics 41 (12): 627–647. doi: 10.1016/j.jgg.2014.10.004 Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G et al. (2011). The genome of Theobroma cacao. Nature Genetics 43 (2): 101-108.
  2. Beaudoin JD, Perreault JP (2013). Exploring mRNA 3’-UTR Gquadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Nucleic Acids Research 41 (11): 5898-5911. doi: 10.1093/nar/gkt265 Biswas B, Kandpal M, Jauhari UK, Vivekanandan P (2016). Genomewide analysis of G-quadruplexes in herpesvirus genomes. BMC Genomics 17 (1): 949. doi: 10.1186/s12864-016-3282-1
  3. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006). Quadruplex DNA: sequence, topology and structure. Nucleic Acids Resesearch 34 (19): 5402-5415. doi: 10.1093/nar/gkl655 Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J et al. (2010). Draft genome sequence of the oilseed species Ricinus communis. Nature Biotechnology 28 (9): 951-956.
  4. Cogoi S, Xodo LE (2006). G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Research 34 (9): 2536-2549. doi: 10.1093/ nar/gkl286 Davidson RM, Gowda M, Moghe G, Lin H, Vaillancourt B et al. (2012). Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. The Plant Journal 71 (3): 492-502. doi: 10.1111/j.1365-313X.2012.05005.x Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F et al. (2014). The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature 505 (7484): 546- 549. Eddy A, Galloway DJ, John DM, Tittley I (1992). Lower plant diversity. In: Groombridge B (editor). Global Biodiversity. Dordrecht, the Netherlands: Springer, pp. 55-63.
  5. Eddy J, Maizels N (2006). Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Research 34 (14): 3887-3896. doi: 10.1093/nar/gkl529 Fernando H, Reszka AP, Huppert J, Ladame S, Rankin S et al. (2006). A conserved quadruplex motif located in a transcription activation site of the human c-kit oncogene. Biochemistry 45 (25): 7854-7860. doi: 10.1021/bi0601510 Fletcher TM, Sun D, Salazar M, Hurley LH (1998). Effect of DNA secondary structure on human telomerase activity