NDLI: Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize

Content Provider	Springer Nature : BioMed Central
Author	Fan, Chunyan Hao, Zhiqiang Yan, Jiahong Li, Guanglin
Abstract	Background Long intergenic noncoding RNAs (lincRNAs) are endogenous non-coding RNAs (ncRNAs) that are transcribed from ‘intergenic’ regions of the genome and may play critical roles in regulating gene expression through multiple RNA-mediated mechanisms. MicroRNAs (miRNAs) are single-stranded small ncRNAs of approximately 21–24 nucleotide (nt) that are involved in transcriptional and post-transcriptional gene regulation. While miRNAs functioning as mRNA repressors have been studied in detail, the influence of miRNAs on lincRNAs has seldom been investigated in plants. Methods LincRNAs as miRNA targets or decoys were predicted via GSTAr.pl script with a set of rules, and lincRNAs as miRNA targets were validated by degradome data. Conservation analysis of lincRNAs as miRNA targets or decoys were conducted using BLASTN and MAFFT. The function of lincRNAs as miRNA targets were predicted via a lincRNA-mRNA co-expression network, and the function of lincRNAs as miRNA decoys were predicted according to the competing endogenous RNA (ceRNA) hypothesis. Results In this work, we developed a computational method and systematically predicted 466 lincRNAs as 165 miRNA targets and 86 lincRNAs as 58 miRNA decoys in maize (Zea mays L.). Furthermore, 34 lincRNAs predicted as 33 miRNA targets were validated based on degradome data. We found that lincRNAs acting as miRNA targets or decoys are a common phenomenon, which indicates that the regulated networks of miRNAs also involve lincRNAs. To elucidate the function of lincRNAs, we reconstructed a miRNA-regulated network involving 78 miRNAs, 117 lincRNAs and 8834 mRNAs. Based on the lincRNA-mRNA co-expression network and the competing endogenous RNA hypothesis, we predicted that 34 lincRNAs that function as miRNA targets and 86 lincRNAs that function as miRNA decoys participate in cellular and metabolic processes, and play role in catalytic activity and molecular binding functions. Conclusions This work provides a comprehensive view of miRNA-regulated networks and indicates that lincRNAs can participate in a layer of regulatory interactions as miRNA targets or decoys in plants, which will enable in-depth functional analysis of lincRNAs.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-015-2024-0.pdf
Ending Page	19
Page Count	19
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-015-2024-0
Journal	BMC Genomics
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-10-15
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Maize miRNAs lincRNAs Targets Decoys
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

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