Degradome sequencing

From Wikipedia, the free encyclopedia

Degradome sequencing (Degradome-Seq),[1][2] also referred to as parallel analysis of RNA ends (),[1][2] is a modified version of 5'-Rapid Amplification of cDNA Ends (RACE) using high-throughput, deep sequencing methods such as Illumina's SBS technology. Degradome sequencing provides a comprehensive means of analyzing patterns of RNA degradation.

Degradome sequencing has been used to identify microRNA (miRNA) cleavage sites,[3] because miRNAs can cause endonucleolytic cleavage of mRNA by extensive and often perfect complementarity to mRNAs.[1][2] Degradome sequencing revealed many known and novel plant miRNA (siRNA) targets.[1][2][4][5][6][7] Recently, degradome sequencing also has been applied to identify animal (human and mouse) miRNA-derived cleavages.[8][9][10]

External links[]

  • starBase database: a database for exploring microRNA cleavage sites from degradome sequencing (Degradome-Seq) data.

References[]

  1. ^ a b c d German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC, Green PJ (2008). "Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends". Nat. Biotechnol. 26 (8): 941–946. doi:10.1038/nbt1417. PMID 18542052.
  2. ^ a b c d Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ (2008). "Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome". Curr. Biol. 18 (10): 758–762. doi:10.1016/j.cub.2008.04.042. PMC 2583427. PMID 18472421.
  3. ^ Thomson, DW; Bracken, CP; Goodall, GJ (2011-06-07). "Experimental strategies for microRNA target identification". Nucleic Acids Research. 39 (16): 6845–6853. doi:10.1093/nar/gkr330. PMC 3167600. PMID 21652644.
  4. ^ Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH (2011). "starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data". Nucleic Acids Res. 39 (Database issue): 1–8. doi:10.1093/nar/gkq1056. PMC 3013664. PMID 21037263.
  5. ^ Henderson, I. R.; Jacobsen, S. E. (2008). "Sequencing sliced ends reveals microRNA targets". Nature Biotechnology. 26 (8): 881–882. doi:10.1038/nbt0808-881. PMC 2989925. PMID 18688239.
  6. ^ Wu, L.; Zhang, Q.; Zhou, H.; Ni, F.; Wu, X.; Qi, Y. (2009). "Rice MicroRNA Effector Complexes and Targets". The Plant Cell Online. 21 (11): 3421–35. doi:10.1105/tpc.109.070938. PMC 2798332. PMID 19903869.
  7. ^ Pantaleo, V.; Szittya, G.; Moxon, S.; Miozzi, L.; Moulton, V.; Dalmay, T.; Burgyan, J. (2010). "Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis". The Plant Journal. 62 (6): 960–76. doi:10.1111/j.0960-7412.2010.04208.x. PMID 20230504.
  8. ^ Shin, C.; Nam, J. W.; Farh, K. K. H.; Chiang, H. R.; Shkumatava, A.; Bartel, D. P. (2010). "Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing". Molecular Cell. 38 (6): 789–802. doi:10.1016/j.molcel.2010.06.005. PMC 2942757. PMID 20620952.
  9. ^ Karginov, F. V.; Cheloufi, S.; Chong, M. M. W.; Stark, A.; Smith, A. D.; Hannon, G. J. (2010). "Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases". Molecular Cell. 38 (6): 781–8. doi:10.1016/j.molcel.2010.06.001. PMC 2914474. PMID 20620951.
  10. ^ Bracken, CP; Szubert, JM; Mercer, TR; Dinger, ME; Thomson, DW; Mattick, JS; Michael, MZ; Goodall, GJ (2011-03-22). "Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage". Nucleic Acids Research. 39 (13): 5658–5668. doi:10.1093/nar/gkr110. PMC 3141239. PMID 21427086.


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