Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases.
The life span of a mammalian mRNA is determined, in part, by the binding of regulatory proteins and small RNA-guided complexes. The conserved endonuclease activity of Argonaute2 requires extensive complementarity between a small RNA and its target and is not used by animal microRNAs, which pair with their targets imperfectly. Here we investigate the endonucleolytic function of Ago2 and other nucleases by transcriptome-wide profiling of mRNA cleavage products retaining 5' phosphate groups in mouse embryonic stem cells (mESCs). We detect a prominent signature of Ago2-dependent cleavage events and validate several such targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in site-specific mRNA cleavage. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events that functionally regulate mRNA levels in mESCs, including one in the Dgcr8 mRNA. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals.
Karginov
Fedor V
FV
Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
Cheloufi
Sihem
S
Chong
Mark M W
MM
Stark
Alexander
A
Smith
Andrew D
AD
Hannon
Gregory J
GJ
D000818:Animals; D060565:Argonaute Proteins; D002460:Cell Line; D019295:Computational Biology; D053595:Embryonic Stem Cells / Q000378:metabolism; D004722:Endoribonucleases / Q000378:metabolism*; D015852:Eukaryotic Initiation Factor-2 / Q000378:metabolism*; D020869:Gene Expression Profiling; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D010766:Phosphorylation; D011506:Proteins / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins; D043244:Ribonuclease III / Q000378:metabolism*
C526735:Ago2 protein, mouse; D060565:Argonaute Proteins; C474044:Dgcr8 protein, mouse; D015852:Eukaryotic Initiation Factor-2; D035683:MicroRNAs; D011506:Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D004722:Endoribonucleases; C513400:Drosha protein, mouse; D043244:Ribonuclease III