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smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites

Persson Hodén, Kristian and Hu, Xinyi and Martinez Arias, German and Dixelius, Christina (2021). smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites. International Journal of Molecular Sciences. 22 , 4267
[Research article]

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Abstract

Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (Solanum tuberosum, St) and Phytophthora infestans (Pi), initial predictions generated high numbers of cleavage site predictions, which highlighted the need of improved analytic tools. Here, we present an R package based on a deep learning convolutional neural network (CNN) in a machine learning environment to optimize discrimination of false from true cleavage sites. When applying smartPARE to our datasets on potato during the infection process by the late blight pathogen, 7.3% of all cleavage windows represented true cleavages distributed on 214 sites in P. infestans and 444 sites in potato. The sRNA landscape of the two organisms is complex with uneven sRNA production and cleavage regions widespread in the two genomes. Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed. We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs.

Authors/Creators:Persson Hodén, Kristian and Hu, Xinyi and Martinez Arias, German and Dixelius, Christina
Title:smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites
Series Name/Journal:International Journal of Molecular Sciences
Year of publishing :2021
Volume:22
Article number:4267
Number of Pages:17
ISSN:1661-6596
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 102 Computer and Information Science > 10203 Bioinformatics (Computational Biology) (applications to be 10610)
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Agricultural Science
Keywords:cleavage sites, Phytophthora infestans, potato, small RNA, Solanum tuberosum
URN:NBN:urn:nbn:se:slu:epsilon-p-111605
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-111605
Additional ID:
Type of IDID
DOI10.3390/ijms22084267
ID Code:23349
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
Deposited By: SLUpub Connector
Deposited On:26 Apr 2021 09:43
Metadata Last Modified:26 Apr 2021 09:51

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