MicroTrout: A comprehensive, genome-wide miRNA target prediction framework for rainbow trout, Oncorhynchus mykiss

被引:21
|
作者
Mennigen, Jan A. [1 ]
Zhang, Dapeng [2 ]
机构
[1] Univ Ottawa, Dept Biol, 20 Marie Curie, Ottawa, ON K1N 6N5, Canada
[2] Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA
来源
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS | 2016年 / 20卷
关键词
MEDIATED REPRESSION; MICRORNAS; EXPRESSION; IDENTIFICATION; ZEBRAFISH; EVOLUTION; DIFFERENTIATION; PROLIFERATION; CONSEQUENCES; TRANSLATION;
D O I
10.1016/j.cbd.2016.07.002
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Rainbow trout represent an important teleost research model and aquaculture species. As such, rainbow trout are employed in diverse areas of biological research, including basic biological disciplines such as comparative physiology, toxicology, and, since rainbow trout have undergone both teleost- and salmonid-specific rounds of genome duplication, molecular evolution. In recent years, microRNAs (miRNAs, small non-protein coding RNAs) have emerged as important posttranscriptional regulators of gene expression in animals. Given the increasingly recognized importance of miRNAs as an additional layer in the regulation of gene expression and hence biological function, recent efforts using RNA- and genome sequencing approaches have resulted in the creation of several resources for the construction of a comprehensive repertoire of rainbow trout miRNAs and isomiRs (variant miRNA sequences that all appear to derive from the same gene but vary in sequence due to post-transcriptional processing). Importantly, through the recent publication of the rainbow trout genome (Berthelot et al., 2014), mRNA 3'UTR information has become available, allowing for the first time the genome-wide prediction of miRNA-target RNA relationships in this species. We here report the creation of the microtrout database, a comprehensive resource for rainbow trout miRNA and annotated 3'UTRs. The comprehensive database was used to implement an algorithm to predict genome-wide rainbow trout-specific miRNA-mRNA target relationships, generating an improved predictive framework over previously published approaches. This work will serve as a useful framework and sequence resource to experimentally address the role of miRNAs in several research areas using the rainbow trout model, examples of which are discussed. (C) 2016 Elsevier Inc. All rights reserved.
引用
收藏
页码:19 / 26
页数:8
相关论文
共 50 条
  • [1] Computational prediction of micrornas and their target genes in rainbow trout (Oncorhynchus mykiss)
    Huang, Yong
    Ma, Xiu Ying
    Yang, You Bing
    Gao, Xiao Chan
    Ren, Hong Tao
    Zhang, Chun Nuan
    RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY, 2016, 42 (03) : 282 - 293
  • [2] Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)
    Huang, Tianqing
    Gu, Wei
    Liu, Enhui
    Shi, Xiulan
    Wang, Bingqian
    Wu, Wenhua
    Dong, Fulin
    Xu, Gefeng
    GENOMICS, 2021, 113 (06) : 3533 - 3543
  • [3] Single-Step Genome-Wide Association Study for Resistance to Piscirickettsia salmonis in Rainbow Trout (Oncorhynchus mykiss)
    Barria, Agustin
    Marin-Nahuelpi, Rodrigo
    Caceres, Pablo
    Lopez, Maria E.
    Bassini, Liane N.
    Lhorente, Jean P.
    Yanez, Jose M.
    G3-GENES GENOMES GENETICS, 2019, 9 (11): : 3833 - 3841
  • [4] Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)
    Paul, Katy
    Restoux, Gwendal
    Phocas, Florence
    GENETICS SELECTION EVOLUTION, 2024, 56 (01)
  • [5] Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss)
    Reis Neto, Rafael Vilhena
    Yoshida, Grazyella Massako
    Paul Lhorente, Jean
    Manuel Yanez, Jose
    MOLECULAR GENETICS AND GENOMICS, 2019, 294 (03) : 563 - 571
  • [6] Physical Enrichment Triggers Brain Plasticity and Influences Blood Plasma Circulating miRNA in Rainbow Trout (Oncorhynchus mykiss)
    Cardona, Emilie
    Brunet, Valentin
    Baranek, Elodie
    Milhade, Leo
    Skiba-Cassy, Sandrine
    Bobe, Julien
    Calandreau, Ludovic
    Roy, Jerome
    Colson, Violaine
    BIOLOGY-BASEL, 2022, 11 (08):
  • [7] A MicroRNA Repertoire for Functional Genome Research in Rainbow Trout (Oncorhynchus mykiss)
    Salem, Mohamed
    Xiao, Caide
    Womack, Jonah
    Rexroad, Caird E., III
    Yao, Jianbo
    MARINE BIOTECHNOLOGY, 2010, 12 (04) : 410 - 429
  • [8] Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss)
    Wang, Jian
    Fu, Liyuan
    Koganti, Prasanthi P.
    Wang, Lei
    Hand, Jacqelyn M.
    Ma, Hao
    Yao, Jianbo
    MARINE BIOTECHNOLOGY, 2016, 18 (02) : 271 - 282
  • [9] Circulating miRNA measurements are reflective of cholesterol-based changes in rainbow trout (Oncorhynchus mykiss)
    Zhu, Tengfei
    Corraze, Genevieve
    Plagnes-Juan, Elisabeth
    Skiba-Cassy, Sandrine
    PLOS ONE, 2018, 13 (11):
  • [10] Genome-wide association study and genomic prediction of tolerance to acute hypoxia in rainbow trout
    Prchal, M.
    D'Ambrosio, J.
    Lagarde, H.
    Lallias, D.
    Patrice, P.
    Francois, Y.
    Poncet, C.
    Desgranges, A.
    Haffray, P.
    Dupont-Nivet, M.
    Phocas, F.
    AQUACULTURE, 2023, 565