Degradome sequencing

Degradome sequencing (Degradome-Seq), [1][2] also referred to as parallel analysis of RNA ends (PARE), is a modified version of 5'-Rapid Amplification of cDNA Ends (RACE) using high-throughput, deep sequencing methods such as Illumina's SBS technology. The degradome encompasses the entire set of proteases that are expressed at a specific time in a given biological material, including tissues, cells, organisms, and biofluids.[3] Thus, sequencing this degradome offers a method for studying and researching the process of RNA degradation. This process is used to identify and quantify RNA degradation products, or fragments, present in any given biological sample.[4] This approach allows for the systematic identification of targets of RNA decay and provides insight into the dynamics of transcriptional and post-transcriptional gene regulation.[4]

Degradome sequencing is a complex process which includes multiple steps such as isolating RNA fragments in a given sample as well as ligation and reverse transcription to form complementary DNA (cDNA) strands.[4] This cDNA can be sequenced, and the results are compared with a transcriptome, or reference genome, in order to determine and characterize the abundance of the RNA fragments identified in this process.[4]

  1. ^ 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. S2CID 13187064.
  2. ^ 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. Bibcode:2008CBio...18..758A. doi:10.1016/j.cub.2008.04.042. PMC 2583427. PMID 18472421.
  3. ^ Trindade, Fábio; Ferreira, Rita; Amado, Francisco; Vitorino, Rui (2015-01-01), Makowski, Gregory S. (ed.), "Chapter Five - Biofluid Proteases Profiling in Diabetes Mellitus", Advances in Clinical Chemistry, 69, Elsevier: 161–207, doi:10.1016/bs.acc.2014.12.004, PMID 25934362, retrieved 2023-04-17
  4. ^ a b c d Lin, Shih-Shun; Chen, Yihua; Lu, Mei-Yeh Jade (2019). "Degradome Sequencing in Plants". Plant MicroRNAs. Methods in Molecular Biology. Vol. 1932. pp. 197–213. doi:10.1007/978-1-4939-9042-9_15. ISBN 978-1-4939-9041-2. ISSN 1940-6029. PMID 30701502. S2CID 73413403.