Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster.
RNA silencing pathways are conserved gene regulation mechanisms that elicit decay and/or translational repression of mRNAs complementary to short interfering RNAs and microRNAs (miRNAs). The fraction of the transcriptome regulated by these pathways is not known, but it is thought that each miRNA may have hundreds of targets. To identify transcripts regulated by silencing pathways at the genomic level, we examined mRNA expression profiles in Drosophila melanogaster cells depleted of four Argonaute paralogs (i.e., AGO1, AGO2, PIWI, or Aubergine) that play essential roles in RNA silencing. We also profiled cells depleted of the miRNA-processing enzyme Drosha. The results reveal that transcripts differentially expressed in Drosha-depleted cells have highly correlated expression in the AGO1 knockdown and are significantly enriched in predicted and validated miRNA targets. The levels of a subset of miRNA targets are also regulated by AGO2. Moreover, AGO1 and AGO2 silence the expression of a common set of mobile genetic elements. Together, these results indicate that the functional overlap between AGO1 and AGO2 in Drosophila is more important than previously thought.
Rehwinkel
Jan
J
EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
Natalin
Pavel
P
Stark
Alexander
A
Brennecke
Julius
J
Cohen
Stephen M
SM
Izaurralde
Elisa
E
D000818:Animals; D060565:Argonaute Proteins; D015153:Blotting, Western; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism*; D039642:Eukaryotic Initiation Factors; D020869:Gene Expression Profiling; D017344:Genes, Insect; D017930:Genes, Reporter; D049750:Genome, Insect; D008156:Luciferases / Q000378:metabolism; D010448:Peptide Initiation Factors / Q000235:genetics / Q000378:metabolism*; D011233:Precipitin Tests; D040081:Protein Array Analysis; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D034622:RNA Interference; D012333:RNA, Messenger / Q000032:analysis* / Q000378:metabolism; D034743:RNA-Induced Silencing Complex / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism*
C489654:AGO1 protein, Drosophila; C433807:AGO2 protein, Drosophila; D060565:Argonaute Proteins; D029721:Drosophila Proteins; D039642:Eukaryotic Initiation Factors; D010448:Peptide Initiation Factors; D011506:Proteins; D012333:RNA, Messenger; D034743:RNA-Induced Silencing Complex; C436124:aub protein, Drosophila; C116498:piwi protein, Drosophila; D008156:Luciferases; D043244:Ribonuclease III; C493335:drosha protein, Drosophila