Identification and characterization of immune-related lncRNAs and lncRNA-miRNA-mRNA networks of Paralichthys olivaceus involved in Vibrio anguillarum infection

Abstract Background Long non-coding RNAs (lncRNAs) structurally resemble mRNAs and exert crucial effects on host immune defense against pathogen infection. Japanese flounder (Paralichthys olivaceus) is an economically important marine fish susceptible to Vibrio anguillarum infection. To date, study on lncRNAs in flounder is scarce. Results Here, we reported the first systematic identification and characterization of flounder lncRNAs induced by V. anguillarum infection at different time points. A total of 2,368 lncRNAs were identified, 414 of which were differentially expressed lncRNAs (DElncRNAs) that responded significantly to V. anguillarum infection. For these DElncRNAs, 3,990 target genes (named DETGs) and 42 target miRNAs (named DETmiRs) were identified based on integrated analyses of lncRNA-mRNA and lncRNA-miRNA expressions, respectively. The DETGs were enriched in a cohort of functional pathways associated with immunity. In addition to modulating mRNAs, 36 DElncRNAs were also found to act as competitive endogenous RNAs (ceRNAs) that regulate 37 DETGs through 16 DETmiRs. The DETmiRs, DElncRNAs, and DETGs formed ceRNA regulatory networks consisting of 114 interacting DElncRNAs-DETmiRs-DETGs trinities spanning 10 immune pathways. Conclusions This study provides a comprehensive picture of lncRNAs involved in V. anguillarum infection. The identified lncRNAs and ceRNA networks add new insights into the anti-bacterial immunity of flounder.

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Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)

Planta ◽

10.1007/s00425-010-1255-1 ◽

2010 ◽

Vol 232 (6) ◽

pp. 1289-1308 ◽

Cited By ~ 83

Author(s):

Taylor P. Frazier ◽

Fuliang Xie ◽

Andrew Freistaedter ◽

Caitlin E. Burklew ◽

Baohong Zhang

Keyword(s):

Nicotiana Tabacum ◽

Target Genes ◽

Identification And Characterization

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Systematic identification and characterization of porcine snoRNAs: structural, functional and developmental insights

Animal Genetics ◽

10.1111/j.1365-2052.2012.02363.x ◽

2012 ◽

Vol 44 (1) ◽

pp. 24-33 ◽

Cited By ~ 2

Author(s):

Nan Liu ◽

Bang Xiao ◽

Hong-Yan Ren ◽

Zhong-Lin Tang ◽

Kui Li

Keyword(s):

Systematic Identification ◽

Identification And Characterization

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Identification and characterization of the binding sequences and target genes of p53 lacking the 1st transactivation domain

Cancer Science ◽

10.1111/cas.14279 ◽

2020 ◽

Vol 111 (2) ◽

pp. 451-466

Author(s):

Shiori Suzuki ◽

Shuichi Tsutsumi ◽

Yu Chen ◽

Chikako Ozeki ◽

Atsushi Okabe ◽

...

Keyword(s):

Target Genes ◽

Transactivation Domain ◽

Identification And Characterization

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Identification and characterization of the prepro-vasoactive intestinal peptide gene from the teleost Paralichthys olivaceus

Veterinary Immunology and Immunopathology ◽

10.1016/j.vetimm.2008.10.320 ◽

2009 ◽

Vol 127 (3-4) ◽

pp. 249-258 ◽

Cited By ~ 6

Author(s):

Bo-Hye Nam ◽

Young-Ok Kim ◽

Hee Jeong Kong ◽

Woo-Jin Kim ◽

Sang-Jun Lee ◽

...

Keyword(s):

Vasoactive Intestinal Peptide ◽

Paralichthys Olivaceus ◽

Peptide Gene ◽

Identification And Characterization

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Systematic Identification and Characterization of Carboxylesterases in Cynomolgus Macaques

Drug Metabolism and Disposition ◽

10.1124/dmd.114.059972 ◽

2014 ◽

Vol 42 (12) ◽

pp. 2002-2006 ◽

Cited By ~ 10

Author(s):

Yasuhiro Uno ◽

Shotaro Uehara ◽

Masakiyo Hosokawa ◽

Teruko Imai

Keyword(s):

Cynomolgus Macaques ◽

Systematic Identification ◽

Identification And Characterization

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Identification and characterization of kiss2 and kissr2 homologs in Paralichthys olivaceus

Fish Physiology and Biochemistry ◽

10.1007/s10695-016-0199-1 ◽

2016 ◽

Vol 42 (4) ◽

pp. 1073-1092 ◽

Cited By ~ 5

Author(s):

Huayu Song ◽

Mengxun Wang ◽

Zhongkai Wang ◽

Haiyang Yu ◽

Zhigang Wang ◽

...

Keyword(s):

Paralichthys Olivaceus ◽

Identification And Characterization

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Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Genes ◽

10.3390/genes10070536 ◽

2019 ◽

Vol 10 (7) ◽

pp. 536 ◽

Cited By ~ 2

Author(s):

Xiaobo Zhao ◽

Liming Gan ◽

Caixia Yan ◽

Chunjuan Li ◽

Quanxi Sun ◽

...

Keyword(s):

Large Scale ◽

Target Genes ◽

Sequencing Data ◽

Regulatory Processes ◽

Genome Wide ◽

Non Coding Rnas ◽

Identification And Characterization ◽

Lower Expression ◽

Weighted Correlation

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.

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MyDGR: a server for identification and characterization of diversity-generating retroelements

Nucleic Acids Research ◽

10.1093/nar/gkz329 ◽

2019 ◽

Vol 47 (W1) ◽

pp. W289-W294 ◽

Cited By ~ 5

Author(s):

Fatemeh Sharifi ◽

Yuzhen Ye

Keyword(s):

Target Gene ◽

Target Genes ◽

Web Server ◽

Nucleotide Sequences ◽

Bacterial Genomes ◽

Fasta Format ◽

Reverse Transcriptases ◽

Identification And Characterization ◽

The Web

Abstract MyDGR is a web server providing integrated prediction and visualization of Diversity-Generating Retroelements (DGR) systems in query nucleotide sequences. It is built upon an enhanced version of DGRscan, a tool we previously developed for identification of DGR systems. DGR systems are remarkable genetic elements that use error-prone reverse transcriptases to generate vast sequence variants in specific target genes, which have been shown to benefit their hosts (bacteria, archaea or phages). As the first web server for annotation of DGR systems, myDGR is freely available on the web at http://omics.informatics.indiana.edu/myDGR with all major browsers supported. MyDGR accepts query nucleotide sequences in FASTA format, and outputs all the important features of a predicted DGR system, including a reverse transcriptase, a template repeat and one (or more) variable repeats and their alignment featuring A-to-N (N can be C, T or G) substitutions, and VR-containing target gene(s). In addition to providing the results as text files for download, myDGR generates a visual summary of the results for users to explore the predicted DGR systems. Users can also directly access pre-calculated, putative DGR systems identified in currently available reference bacterial genomes and a few other collections of sequences (including human microbiomes).

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