Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway.
In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character-as is found in small interfering RNAs (siRNAs)-directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. Here, we show that while most Drosophila miRNAs are bound to Ago1, miRNA* strands accumulate bound to Ago2. Like siRNA loading, efficient loading of miRNA* strands in Ago2 favors duplexes with a paired central region and requires both Dcr-2 and R2D2. Those miRNA and miRNA* sequences bound to Ago2, like siRNAs diced in vivo from long double-stranded RNA, typically begin with cytidine, whereas Ago1-bound miRNA and miRNA* disproportionately begin with uridine. Consequently, some pre-miRNA generate two or more isoforms from the same side of the stem that differentially partition between Ago1 and Ago2. Our findings provide the first genome-wide test for the idea that Drosophila small RNAs are sorted between Ago1 and Ago2 according to their duplex structure and the identity of their first nucleotide.
Ghildiyal
Megha
M
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,Worcester, Massachusetts 01605, USA.
Xu
Jia
J
Seitz
Hervé
H
Weng
Zhiping
Z
Zamore
Phillip D
PD
D000818:Animals; D060565:Argonaute Proteins; D001483:Base Sequence / Q000502:physiology; D001665:Binding Sites / Q000235:genetics; D004330:Drosophila / Q000196:embryology / Q000235:genetics*; D029721:Drosophila Proteins / Q000378:metabolism; D004625:Embryo, Nonmammalian; D039642:Eukaryotic Initiation Factors / Q000378:metabolism; D035683:MicroRNAs / Q000032:analysis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D034622:RNA Interference / Q000502:physiology*; D034443:RNA Transport / Q000235:genetics / Q000502:physiology; D034741:RNA, Small Interfering / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D034743:RNA-Induced Silencing Complex / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics
C489654:AGO1 protein, Drosophila; C433807:AGO2 protein, Drosophila; D060565:Argonaute Proteins; D029721:Drosophila Proteins; D039642:Eukaryotic Initiation Factors; D035683:MicroRNAs; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex