“Degradome sequencing”的意思、由来-开放百科全书

Degradome sequencing (Degradome-Seq),^[1]^[2] also referred to as parallel analysis of RNA ends (PARE),^[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

References

1. ^¹²³{{cite journal |vauthors=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 |title=Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. |journal=Nat. Biotechnol. |volume=26 |issue=8 |pages=941–946 |year=2008 |pmid=18542052 |doi=10.1038/nbt1417}}
2. ^¹²³{{cite journal |vauthors=Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ |title=Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. |journal=Curr. Biol. |volume=18 |issue=10 |pages=758–762 |year=2008 |pmid=18472421 |doi=10.1016/j.cub.2008.04.042 |pmc=2583427}}
3. ^{{cite journal|last=Thomson|first=DW |author2=Bracken, CP |author3=Goodall, GJ|title=Experimental strategies for microRNA target identification.|journal=Nucleic Acids Research|date=2011-06-07|pmid=21652644|doi=10.1093/nar/gkr330|pmc=3167600|volume=39|issue=16 |pages=6845–6853}}
4. ^{{cite journal |vauthors=Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH |title=starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. |journal=Nucleic Acids Res. |volume= 39|issue=Database issue |pages=1–8 |year=2011 |pmid=21037263 |doi=10.1093/nar/gkq1056 |pmc=3013664}}
5. ^{{Cite journal | last1 = Henderson | first1 = I. R. | last2 = Jacobsen | first2 = S. E. | title = Sequencing sliced ends reveals microRNA targets | journal = Nature Biotechnology | volume = 26 | issue = 8 | pages = 881–882 | year = 2008 | pmid = 18688239 | doi = 10.1038/nbt0808-881 | pmc=2989925}}
6. ^{{Cite journal | last1 = Wu | first1 = L. | last2 = Zhang | first2 = Q. | last3 = Zhou | first3 = H. | last4 = Ni | first4 = F. | last5 = Wu | first5 = X. | last6 = Qi | first6 = Y. | title = Rice MicroRNA Effector Complexes and Targets | journal = The Plant Cell Online | volume = 21 | issue = 11 | pages = 3421–35 | year = 2009 | doi = 10.1105/tpc.109.070938 | pmid=19903869 | pmc=2798332}}
7. ^{{Cite journal | last1 = Pantaleo | first1 = V. | last2 = Szittya | first2 = G. | last3 = Moxon | first3 = S. | last4 = Miozzi | first4 = L. | last5 = Moulton | first5 = V. | last6 = Dalmay | first6 = T. | last7 = Burgyan | first7 = J. | title = Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis | journal = The Plant Journal | year = 2010 | doi = 10.1111/j.0960-7412.2010.04208.x | pmid=20230504 | volume=62 | issue = 6 | pages=960–76}}
8. ^{{Cite journal | last1 = Shin | first1 = C. | last2 = Nam | first2 = J. W. | last3 = Farh | first3 = K. K. H. | last4 = Chiang | first4 = H. R. | last5 = Shkumatava | first5 = A. | last6 = Bartel | first6 = D. P. | title = Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing | journal = Molecular Cell | volume = 38 | issue = 6 | pages = 789–802 | year = 2010 | pmid = 20620952 | pmc = 2942757 | doi = 10.1016/j.molcel.2010.06.005}}
9. ^{{Cite journal | last1 = Karginov | first1 = F. V. | last2 = Cheloufi | first2 = S. | last3 = Chong | first3 = M. M. W. | last4 = Stark | first4 = A. | last5 = Smith | first5 = A. D. | last6 = Hannon | first6 = G. J. | title = Diverse Endonucleolytic Cleavage Sites in the Mammalian Transcriptome Depend upon MicroRNAs, Drosha, and Additional Nucleases | journal = Molecular Cell | volume = 38 | issue = 6 | pages = 781–8 | year = 2010 | pmid = 20620951 | pmc = 2914474 | doi = 10.1016/j.molcel.2010.06.001}}
10. ^{{cite journal|last=Bracken|first=CP |author2=Szubert, JM |author3=Mercer, TR |author4=Dinger, ME |author5=Thomson, DW |author6=Mattick, JS |author7=Michael, MZ |author8=Goodall, GJ|title=Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage.|journal=Nucleic Acids Research|date=2011-03-22|pmid=21427086|pmc=3141239 |doi=10.1093/nar/gkr110|volume=39|issue=13 |pages=5658–5668}}