miRNA analysis with Prost! reveals evolutionary conservation of organ-enriched expression and post-transcriptional modifications in three-spined stickleback and zebrafish

MicroRNAs (miRNAs) can have tissue-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variations. It remains unclear, however, which mechanisms of miRNA production or modification are tissue-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, allows accurate quantification of mature miRNAs, takes into account post-transcriptional processing, such as nucleotide editing, and helps identify mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Despite reports suggesting that stickleback had a large miRNome, results showed that stickleback has 277 evolutionary-conserved mir genes and 366 unique mature miRNAs (excluding mir430 gene replicates and the vaultRNA-derived mir733), similar to zebrafish. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, which is, for many miRNAs, evolutionarily-conserved. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms regulate miRNA post-transcriptional variations. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide editing patterns in the seed sequence in various tissues, and the editing rate was organ-specific with higher editing in the brain. In summary, Prost! is a critical new tool to identify and understand small RNAs and can help clarify a species’ miRNA biology, as shown here for an important fish model for the evolution of developmental mechanisms, and can provide insight into organ-specific expression and evolutionary-conserved miRNA post-transcriptional mechanisms.

[1]  Andrea Acquaviva,et al.  isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation , 2016, BMC Bioinformatics.

[2]  J. Iga,et al.  Elevated mRNA expression of CASPR3 in patients with schizophrenia , 2017, Nordic journal of psychiatry.

[3]  Akhilesh Pandey,et al.  miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy , 2015, PloS one.

[4]  Bronwen L. Aken,et al.  The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons , 2016, Nature Genetics.

[5]  S. Watabe,et al.  Evolution and Distribution of Teleost myomiRNAs: Functionally Diversified myomiRs in Teleosts , 2016, Marine Biotechnology.

[6]  Xavier Estivill,et al.  SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells , 2009, Nucleic acids research.

[7]  Eugene Berezikov,et al.  Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. , 2008, Genes & development.

[8]  Joost A. M. Raeymaekers,et al.  Computational identification of miRNAs, their targets and functions in three‐spined stickleback (Gasterosteus aculeatus) , 2014, Molecular ecology resources.

[9]  Peer Bork,et al.  Ancient animal microRNAs and the evolution of tissue identity , 2010, Nature.

[10]  P. Chakrabarty,et al.  The Diversity of Fishes: Biology, Evolution and Ecology. Second edition , 2010, Copeia.

[11]  S. Young,et al.  Regulation of prelamin A but not lamin C by miR-9, a brain-specific microRNA , 2012, Proceedings of the National Academy of Sciences.

[12]  Jay W. Shin,et al.  An integrated expression atlas of miRNAs and their promoters in human and mouse , 2017, Nature Biotechnology.

[13]  Ángel M. Alganza,et al.  sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments , 2014 .

[14]  K. Peterson,et al.  Do miRNAs have a deep evolutionary history? , 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

[15]  J. Postlethwait,et al.  Evolution of the miR199-214 cluster and vertebrate skeletal development , 2014, RNA biology.

[16]  Alessandro Vullo,et al.  Ensembl 2017 , 2016, Nucleic Acids Res..

[17]  Piotr Zielenkiewicz,et al.  Tools4miRs – one place to gather all the tools for miRNA analysis , 2016, Bioinform..

[18]  L. Bassas,et al.  Altered miRNA Signature of Developing Germ-cells in Infertile Patients Relates to the Severity of Spermatogenic Failure and Persists in Spermatozoa , 2015, Scientific Reports.

[19]  K. Jia,et al.  MiR-202-5p is a novel germ plasm-specific microRNA in zebrafish , 2017, Scientific Reports.

[20]  A. Keller,et al.  Distribution of miRNA expression across human tissues , 2016, Nucleic acids research.

[21]  Sebastian D. Mackowiak,et al.  miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades , 2011, Nucleic acids research.

[22]  Doron Lancet,et al.  Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification , 2005, Bioinform..

[23]  R. Andreassen,et al.  Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs , 2016, PloS one.

[24]  V. Kim,et al.  Regulation of microRNA biogenesis , 2014, Nature Reviews Molecular Cell Biology.

[25]  G. Hannon,et al.  A dicer-independent miRNA biogenesis pathway that requires Ago catalysis , 2010, Nature.

[26]  T. Maniatis,et al.  The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. , 2007, Molecular cell.

[27]  K Eilbeck,et al.  miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants. , 2015, Trends in genetics : TIG.

[28]  Kenneth S Kosik,et al.  MicroRNAs and Cellular Phenotypy , 2010, Cell.

[29]  E. Hovig,et al.  A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. , 2015, Annual review of genetics.

[30]  G. Obernosterer,et al.  Post-transcriptional regulation of microRNA expression. , 2006, RNA.

[31]  Selene L. Fernandez-Valverde,et al.  SOX9 Regulates MicroRNA miR-202-5p/3p Expression During Mouse Testis Differentiation1 , 2013, Biology of reproduction.

[32]  Manoj Kumar,et al.  Toward the human cellular microRNAome. , 2017, Genome research.

[33]  Benjamin M. Wheeler,et al.  The deep evolution of metazoan microRNAs , 2009, Evolution & development.

[34]  Erika Pastrana,et al.  miR-124 regulates adult neurogenesis in the SVZ stem cell niche , 2009, Nature Neuroscience.

[35]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[36]  Jian-Fu Chen,et al.  The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation , 2006, Nature Genetics.

[37]  David P. Bartel,et al.  Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals , 2008, Nature.

[38]  S. Yi,et al.  Evolution of MicroRNAs and the Diversification of Species , 2010, Genome biology and evolution.

[39]  Kannan Ranganathan,et al.  MicroRNAs - Biology and clinical applications , 2014, Journal of oral and maxillofacial pathology : JOMFP.

[40]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[41]  J. Postlethwait,et al.  Genomic conservation of erythropoietic microRNAs (erythromiRs) in white-blooded Antarctic icefish. , 2016, Marine genomics.

[42]  Tyler Risom,et al.  Evolutionary conservation of microRNA regulatory circuits: an examination of microRNA gene complexity and conserved microRNA-target interactions through metazoan phylogeny. , 2007, DNA and cell biology.

[43]  Tsuyoshi Koide,et al.  Caspr3-Deficient Mice Exhibit Low Motor Learning during the Early Phase of the Accelerated Rotarod Task , 2016, PloS one.

[44]  Kimihiro Hino,et al.  A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency , 2014, Nucleic acids research.

[45]  Yukio Kawahara,et al.  RNA editing of the microRNA‐151 precursor blocks cleavage by the Dicer–TRBP complex , 2007, EMBO reports.

[46]  R. Meuwissen,et al.  The role of microRNAs in human diseases. , 2014, Methods in molecular biology.

[47]  Monte Westerfield,et al.  ZFIN: enhancements and updates to the zebrafish model organism database , 2010, Nucleic Acids Res..

[48]  J. Postlethwait,et al.  Prost!, a tool for miRNA annotation and next generation smallRNA sequencing experiment analysis , 2015 .

[49]  S. Watabe,et al.  Evolution of the myosin heavy chain gene MYH14 and its intronic microRNA miR-499: muscle-specific miR-499 expression persists in the absence of the ancestral host gene , 2013, BMC Evolutionary Biology.

[50]  Eugene Berezikov,et al.  Mammalian mirtron genes. , 2007, Molecular cell.

[51]  E. Peles,et al.  Caspr3 and Caspr4, Two Novel Members of the Caspr Family Are Expressed in the Nervous System and Interact with PDZ Domains , 2002, Molecular and Cellular Neuroscience.

[52]  Ali M. Ardekani,et al.  The Role of MicroRNAs in Human Diseases , 2010, Avicenna journal of medical biotechnology.

[53]  Ya-song Du,et al.  The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice , 2018, Neurobiology of Disease.

[54]  J. Postlethwait,et al.  Expanding the annotation of zebrafish microRNAs based on small RNA sequencing. , 2014, Gene.

[55]  K. Nishikura,et al.  A-to-I editing of coding and non-coding RNAs by ADARs , 2015, Nature Reviews Molecular Cell Biology.

[56]  P. Ingham,et al.  Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish , 2015, BMC Genomics.

[57]  Anton J. Enright,et al.  MicroRNA targets in Drosophila , 2003, Genome Biology.

[58]  Chun-Nan Hsu,et al.  Identification of homologous microRNAs in 56 animal genomes. , 2010, Genomics.

[59]  J. Bienertová-Vašků,et al.  Muscle-specific microRNAs in skeletal muscle development. , 2016, Developmental biology.

[60]  C. Croce,et al.  MicroRNAs in cancer. , 2014, Annual review of pathology.

[61]  H. Kaessmann,et al.  Conserved microRNA editing in mammalian evolution, development and disease , 2014, Genome Biology.

[62]  P. Seeburg,et al.  Modulation of microRNA processing and expression through RNA editing by ADAR deaminases , 2006, Nature Structural &Molecular Biology.

[63]  M. O’Connell,et al.  Editing independent effects of ADARs on the miRNA/siRNA pathways , 2009, The EMBO journal.

[64]  Andreas Keller,et al.  A comprehensive, cell specific microRNA catalogue of human peripheral blood , 2017, Nucleic acids research.

[65]  C. Langford,et al.  5′ isomiR variation is of functional and evolutionary importance , 2014, Nucleic acids research.

[66]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[67]  Michael Hackenberg,et al.  sRNAtoolbox: an integrated collection of small RNA research tools , 2015, Nucleic Acids Res..

[68]  Kohta Yoshida,et al.  RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks , 2013, BMC Genomics.

[69]  Pasko Rakic,et al.  Microarray analysis of microRNA expression in the developing mammalian brain , 2004, Genome Biology.

[70]  Paul Verkade,et al.  MiR-3120 Is a Mirror MicroRNA That Targets Heat Shock Cognate Protein 70 and Auxilin Messenger RNAs and Regulates Clathrin Vesicle Uncoating , 2012, The Journal of Biological Chemistry.

[71]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[72]  D. Bartel,et al.  Intronic microRNA precursors that bypass Drosha processing , 2007, Nature.

[73]  K. Skryabin,et al.  Identification of novel microRNA genes in freshwater and marine ecotypes of the three‐spined stickleback (Gasterosteus aculeatus) , 2016, Molecular ecology resources.

[74]  Stefan L Ameres,et al.  Diversifying microRNA sequence and function , 2013, Nature Reviews Molecular Cell Biology.

[75]  M. Bhaskaran,et al.  MicroRNAs: history, biogenesis, and their evolving role in animal development and disease. , 2014, Veterinary pathology.

[76]  A. Sinclair,et al.  The potential role of microRNAs in regulating gonadal sex differentiation in the chicken embryo , 2011, Chromosome Research.

[77]  MicroRNA-202 (miR-202) controls female fecundity by regulating medaka oogenesis , 2018, bioRxiv.

[78]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[79]  A. Hatzigeorgiou,et al.  Redirection of Silencing Targets by Adenosine-to-Inosine Editing of miRNAs , 2007, Science.

[80]  C. Croce,et al.  MicroRNAs in Cancer. , 2009, Annual review of medicine.

[81]  R. Gregory,et al.  Many roads to maturity: microRNA biogenesis pathways and their regulation , 2009, Nature Cell Biology.

[82]  Tsuyoshi Koide,et al.  Cell adhesion molecule contactin‐associated protein 3 is expressed in the mouse basal ganglia during early postnatal stages , 2016, Journal of neuroscience research.

[83]  C. Bracken,et al.  IsomiRs--the overlooked repertoire in the dynamic microRNAome. , 2012, Trends in genetics : TIG.

[84]  David W. Taylor,et al.  A Novel miRNA Processing Pathway Independent of Dicer Requires Argonaute2 Catalytic Activity , 2010, Science.

[85]  Feng Chen,et al.  A challenge for miRNA: multiple isomiRs in miRNAomics. , 2014, Gene.

[86]  L. Ribas,et al.  Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture , 2014, Front. Genet..

[87]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[88]  Michelle S. Scott,et al.  From snoRNA to miRNA: Dual function regulatory non-coding RNAs , 2011, Biochimie.

[89]  Bastian Fromm,et al.  Big Strides in Cellular MicroRNA Expression. , 2018, Trends in genetics : TIG.