Araştırma Makalesi
Yıl 2022,
Cilt: 3 Sayı: 1, 25 - 35, 27.10.2022
Öz
MikroRNA (miRNA), gen ekspresyonunun transkripsiyon sonrası düzenlenmesinde işlev gören küçük (~ 22 nükleotid) kodlamayan bir RNA molekülüdür. Önceki çalışmalar, miRNA’nın bitkilerin olumsuz koşullara karşı direnç kabiliyetinde önemli bir rol oynadığını göstermiştir. Bu araştırmada, önemli bir model organizma olan Arabidopsis thaliana’da miR156 ailesine dizilerin olgun, öncül ve promotor dizi karakterizasyonu yapılmıştır. Biyoinformatik yaklaşımı kullanarak, ath-miR156 gen promotörlerinde öngörülen cis düzenleyici elementleri ve aynı anda miR156 hedefli genleri tahmin edilmiştir. Sonuçlar, olgun ath-miR156 dizilerinde yüksek koruma olduğunu, ancak öncü dizilerde olmadığı görülmüştür. ath-miR156 gen promotörlerinde bulunan çeşitli cis düzenleyici elementlerin olduğu tespit edilmiştir.
Anahtar Kelimeler
Kaynakça
- 1. microRNAs – function & biogenesis [Internet]. [cited 2022 Aug 16]. Available from: https://www.tamirna.com/micrornas-function-biogenesis/
- 2. Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell. 2009 Feb;136(4):642–55.
- 3. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell. 2009 Feb;136(4):669–87.
- 4. Axtell MJ. Classification and comparison of small RNAs from plants. Annu Rev Plant Biol. 2013;64:137–59.
- 5. Sollome J, Martin E, Sethupathy P, Fry RC. Environmental contaminants and microRNA regulation: Transcription factors as regulators of toxicant-altered microRNA expression. Toxicol Appl Pharmacol. 2016 Dec;312:61–6.
- 6. Yue E, Tao H, Xu J. Genome-wide analysis of microRNA156 and its targets, the genes encoding SQUAMOSA promoter-binding protein-like (SPL) transcription factors, in the grass family Poaceae. J Zhejiang Univ Sci B. 2021 May;22(5):366–82.
- 7. Wang C, Shangguan L, Kibet KN, Wang X, Han J, Song C, et al. Characterization of microRNAs identified in a table grapevine cultivar with validation of computationally predicted grapevine miRNAs by miR-RACE. PLoS One. 2011;6(7):e21259.
- 8. Wang C, Han J, Liu C, Kibet KN, Kayesh E, Shangguan L, et al. Identification of microRNAs from Amur grape (vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics. BMC Genomics. 2012;13(1):122.
- 9. Preston JC, Hileman LC. Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family. Front Plant Sci. 2013;4:80.
- 10. Wang C, Wang Q, Zhu X, Cui M, Jia H, Zhang W, et al. Characterization on the conservation and diversification of miRNA156 gene family from lower to higher plant species based on phylogenetic analysis at the whole genomic level. Funct Integr Genomics. 2019 Nov;19(6):933–52.
- 11. Cardon G, Höhmann S, Klein J, Nettesheim K, Saedler H, Huijser P. Molecular characterisation of the Arabidopsis SBP-box genes. Gene. 1999 Sep;237(1):91–104.
- 12. Salinas M, Xing S, Höhmann S, Berndtgen R, Huijser P. Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato. Planta. 2012 Jun;235(6):1171–84.
- 13. Wang Y, Hu Z, Yang Y, Chen X, Chen G. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in grapevine. Russ J Plant Physiol [Internet]. 2010;57(2):273–82. Available from: https://doi.org/10.1134/S1021443710020160
- 14. Cho SH, Coruh C, Axtell MJ. miR156 and miR390 Regulate tasiRNA Accumulation and Developmental Timing in Physcomitrella patens . Plant Cell [Internet]. 2012;24(12):4837–49. Available from: https://doi.org/10.1105/tpc.112.103176
- 15. Willmann MR, Poethig RS. Conservation and evolution of miRNA regulatory programs in plant development. Curr Opin Plant Biol. 2007 Oct;10(5):503–11.
- 16. Cui J, You C, Chen X. The evolution of microRNAs in plants. Curr Opin Plant Biol. 2017 Feb;35:61–7.
- 17. Ren G, Wang B, Zhu X, Mu Q, Wang C, Tao R, et al. Cloning, expression, and characterization of miR058 and its target PPO during the development of grapevine berry stone. Gene [Internet]. 2014;548(2):166–73. Available from: https://www.sciencedirect.com/science/article/pii/S037811191400804X
- 18. Yang J, Liu X, Xu B, Zhao N, Yang X, Zhang M. Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of Brassica juncea. BMC Genomics. 2013 Jan;14:9.
- 19. Sunkar R, Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol. 2008 Apr;8:37.
- 20. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev. 2002 Jul;16(13):1616–26.
- 21. Cardon GH, Höhmann S, Nettesheim K, Saedler H, Huijser P. Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J. 1997 Aug;12(2):367–77.
- 22. Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014 Jan;42(Database issue):D68-73.
- 23. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016 Jul;33(7):1870–4.
- 24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007 Nov;23(21):2947–8.
- 25. About Arabidopsis thaliana [Internet]. [cited 2022 Aug 16]. Available from: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
- 26. YAPP Eukaryotic Core Promoter Predictor [Internet]. [cited 2022 Aug 16]. Available from: http://www.bioinformatics.org/yapp/cgi-bin/yapp.cgi
- 27. Genome Information Database System for Innovation of Crop and Livestock Production [Internet]. [cited 2022 Aug 16]. Available from: https://sogo.dna.affrc.go.jp/cgi-bin/sogo.cgi?lang=en
- 28. Thrall JMH, Goodrich JA. Promoters. In: Maloy S, Hughes K, editors. Brenner’s Encyclopedia of Genetics. Second Edi. Massachusetts: Academic Press; 2013. p. 472–4.
- 29. Maher C, Stein L, Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 2006 Apr;16(4):510–9.
- 30. Bektas Y. The synthetic elicitors 2,6-dichloro-isonicotinic acid (INA) and 2,4-dichloro-6-{(E)-[(3-methoxyphenyl)imino]methyl}phenol (DPMP) enhances tomato resistance against bacterial canker disease with different molecular mechanisms. Physiol Mol Plant Pathol [Internet]. 2021;116:101740. Available from: https://www.sciencedirect.com/science/article/pii/S0885576521001417
- 31. Gandikota M, Birkenbihl RP, Höhmann S, Cardon GH, Saedler H, Huijser P. The miRNA156/157 recognition element in the 3’ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J. 2007 Feb;49(4):683–93.
- 32. Wu G, Poethig RS. Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development. 2006 Sep;133(18):3539–47.
- 33. Usami T, Horiguchi G, Yano S, Tsukaya H. The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in the control of heteroblasty. Development. 2009 Mar;136(6):955–64.
- 34. Wang J-W, Schwab R, Czech B, Mica E, Weigel D. Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell. 2008 May;20(5):1231–43.
- 35. Schwarz S, Grande A V, Bujdoso N, Saedler H, Huijser P. The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol Biol. 2008 May;67(1–2):183–95.
Toplam 35 adet kaynakça vardır.
Ayrıntılar
| Birincil Dil | Türkçe |
|---|---|
| Konular | Mühendislik |
| Bölüm | Araştırma Makalesi |
| Yazarlar | |
| Yayımlanma Tarihi | 27 Ekim 2022 |
| Gönderilme Tarihi | 16 Ağustos 2022 |
| Yayımlandığı Sayı | Yıl 2022 Cilt: 3 Sayı: 1 |
