Expansion of the Ago gene family in the teleost clade

Lindsey McFarlane, Terje Svingen, Ingo Braasch, Peter Koopman, Manfred Schartl, Dagmar Wilhelm

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

AGO proteins are universal effectors of eukaryotic small RNA-directed regulatory pathways. In this study, we used a comparative genomics approach to explore the AGO sub-family in the teleost clade. We identified five Ago homologues in teleost genomes, one more than encoded in other vertebrate clades. The additional teleost homologue was preserved most likely due to the differential retention of regulatory elements following the fish-specific genome duplication event that occurred approximately 350 million years ago. Analysis of all five Ago genomic loci in teleosts revealed that orthologues contain specific, conserved sequence elements in non-coding regions indicating that the teleost Ago paralogues are differentially regulated. This was supported by qRT-PCR analysis that showed differential expression of the zebrafish homologues across development and between adult tissues indicating stage and tissue-specific function of individual AGO proteins. Multiple sequence alignments showed not only that all teleost homologues possess critical residues for AGO function, but also that teleost homologues contain multiple orthologue-specific features, indicative of structural diversification. Notably, these are retained throughout the vertebrate lineage arguing these may be important for orthologue-specific functions.
Original languageEnglish
JournalDevelopment, Genes and Evolution
Volume221
Issue number2
Pages (from-to)95-104
Number of pages10
ISSN0949-944X
DOIs
Publication statusPublished - 2011
Externally publishedYes

Keywords

  • Amino Acid Sequence
  • Animals
  • Conserved Sequence
  • Eukaryotic Initiation Factor-2
  • Evolution, Molecular
  • Fishes
  • Gene Duplication
  • Genome
  • Molecular Sequence Data
  • Multigene Family
  • Oryzias
  • Phylogeny
  • RNA, Small Untranslated
  • Sequence Alignment
  • Takifugu
  • Tetraodontiformes
  • Zebrafish
  • amino acid
  • argonaute protein
  • argonaute gene
  • article
  • cladistics
  • controlled study
  • fish genetics
  • gene deletion
  • gene duplication
  • gene insertion
  • gene sequence
  • genetic code
  • genetic conservation
  • genetic difference
  • molecular evolution
  • nonhuman
  • nucleotide sequence
  • priority journal
  • protein function
  • protein localization
  • regulator gene
  • reverse transcription polymerase chain reaction
  • sequence alignment
  • sequence homology
  • structure analysis
  • teleost
  • zebra fish
  • Danio rerio
  • Eukaryota
  • Teleostei
  • Vertebrata
  • AGO
  • Argonaute
  • Fish
  • Non-coding RNA
  • Chordata Animalia (Animals, Chordates, Nonhuman Vertebrates, Vertebrates) - Vertebrata [85150] vertebrate common
  • Pisces Vertebrata Chordata Animalia (Animals, Chordates, Fish, Nonhuman Vertebrates, Vertebrates) - Osteichthyes [85206] Danio rerio species zebrafish common Tetraodon nigroviridis species Takifugu rubripes species Oryzias latipes species Gasterosteus aculeatus species teleost common
  • Danio rerio Ago gene family [Osteichthyes] expression
  • Gasterosteus aculeatus Ago gene family [Osteichthyes] expression
  • Oryzias latipes Ago gene family [Osteichthyes] expression
  • Takifugu rubripes Ago gene family [Osteichthyes] expression
  • Tetraodon nigroviridis Ago gene family [Osteichthyes] expression
  • AGO proteins
  • regulatory element
  • 03502, Genetics - General
  • 03506, Genetics - Animal
  • 03509, Genetics - Population genetics
  • 10062, Biochemistry studies - Nucleic acids, purines and pyrimidines
  • Molecular Genetics
  • Population Genetics
  • multiple sequence alignment
  • species genome
  • structural diversification
  • Biochemistry and Molecular Biophysics
  • Population Studies
  • NP036331 GenBank, EMBL, DDJB nucleotide sequence
  • quantitative real-time polymerase chain reaction qRT-PCR laboratory techniques, genetic techniques
  • CELL
  • EVOLUTIONARY
  • DEVELOPMENTAL
  • WHOLE-GENOME DUPLICATION
  • RNA INTERFERENCE
  • ARGONAUTE PROTEINS
  • PASSENGER-STRAND
  • EVOLUTION
  • IDENTIFICATION
  • PATHWAY
  • CLEAVAGE
  • SLICER
  • SIRNA

Cite this

McFarlane, L., Svingen, T., Braasch, I., Koopman, P., Schartl, M., & Wilhelm, D. (2011). Expansion of the Ago gene family in the teleost clade. Development, Genes and Evolution, 221(2), 95-104. https://doi.org/10.1007/s00427-011-0363-7