Distance constraints between microRNA target sites dictate efficacy and cooperativity.
MicroRNAs (miRNAs) have the potential to regulate the expression of thousands of genes, but the mechanisms that determine whether a gene is targeted or not are poorly understood. We studied the genomic distribution of distances between pairs of identical miRNA seeds and found a propensity for moderate distances greater than about 13 nt between seed starts. Experimental data show that optimal down-regulation is obtained when two seed sites are separated by between 13 and 35 nt. By analyzing the distance between seed sites of endogenous miRNAs and transfected small interfering RNAs (siRNAs), we also find that cooperative targeting of sites with a separation in the optimal range can explain some of the siRNA off-target effects that have been reported in the literature.
Saetrom
Pål
P
Division of Molecular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
Heale
Bret S E
BS
Snøve
Ola
O
Aagaard
Lars
L
Alluin
Jessica
J
Rossi
John J
JJ
D020413:3' Untranslated Regions / Q000737:chemistry; D001665:Binding Sites; D002460:Cell Line; D015536:Down-Regulation; D006367:HeLa Cells; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA
D020413:3' Untranslated Regions; D035683:MicroRNAs; D034741:RNA, Small Interfering