A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.
Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after knockdown of nucleotidyltransferase enzymes. The PAPD4 nucleotidyltransferase adenylates a wide range of miRNA loci, but adenylation does not appear to affect miRNA stability on a genome-wide scale. Adenine addition appears to reduce effectiveness of miRNA targeting of mRNA transcripts while deep-sequencing of RNA bound to immunoprecipitated Argonaute (AGO) subfamily proteins EIF2C1-EIF2C3 revealed substantial reduction of adenine addition in miRNA associated with EIF2C2 and EIF2C3. Our findings show 3' addition events are widespread and conserved across animals, PAPD4 is a primary miRNA adenylating enzyme, and suggest a role for 3' adenine addition in modulating miRNA effectiveness, possibly through interfering with incorporation into the RNA-induced silencing complex (RISC), a regulatory role that would complement the role of miRNA uridylation in blocking DICER1 uptake.
Burroughs
A Maxwell
AM
Omics Science Center (OSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan. burrough@gsc.riken.jp
Ando
Yoshinari
Y
de Hoon
Michiel J L
MJ
Tomaru
Yasuhiro
Y
Nishibu
Takahiro
T
Ukekawa
Ryo
R
Funakoshi
Taku
T
Kurokawa
Tsutomu
T
Suzuki
Harukazu
H
Hayashizaki
Yoshihide
Y
Daub
Carsten O
CO
D020413:3' Untranslated Regions / Q000235:genetics*; D000225:Adenine / Q000378:metabolism*; D000818:Animals; D060565:Argonaute Proteins; D002460:Cell Line; D015852:Eukaryotic Initiation Factor-2 / Q000378:metabolism; D039642:Eukaryotic Initiation Factors / Q000378:metabolism; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D009000:Monocytes; D009713:Nucleotidyltransferases / Q000235:genetics / Q000378:metabolism*; D011062:Polynucleotide Adenylyltransferase; D020871:RNA Stability; D039221:mRNA Cleavage and Polyadenylation Factors
D020413:3' Untranslated Regions; C115848:AGO1 protein, human; C517143:AGO3 protein, human; D060565:Argonaute Proteins; D015852:Eukaryotic Initiation Factor-2; D039642:Eukaryotic Initiation Factors; D035683:MicroRNAs; D039221:mRNA Cleavage and Polyadenylation Factors; D009713:Nucleotidyltransferases; D011062:Polynucleotide Adenylyltransferase; C550174:TENT2 protein, human; D000225:Adenine