Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

TY - JOUR

T1 - Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

AU - Khan, Aly A

AU - Betel, Doron

AU - Miller, Martin L

AU - Sander, Chris

AU - Leslie, Christina S

AU - Marks, Debora S

N1 - Keywords: Cell Line; Cell Line, Tumor; Gene Expression Profiling; Gene Expression Regulation; Gene Knockdown Techniques; Genes, cdc; Humans; MicroRNAs; Models, Genetic; RNA, Small Interfering; RNA-Induced Silencing Complex; Statistics, Nonparametric; Transfection; Up-Regulation

PY - 2009

Y1 - 2009

N2 - Transfection of small RNAs (such as small interfering RNAs (siRNAs) and microRNAs (miRNAs)) into cells typically lowers expression of many genes. Unexpectedly, increased expression of genes also occurs. We investigated whether this upregulation results from a saturation effect--that is, competition among the transfected small RNAs and the endogenous pool of miRNAs for the intracellular machinery that processes small RNAs. To test this hypothesis, we analyzed genome-wide transcript responses from 151 published transfection experiments in seven different human cell types. We show that targets of endogenous miRNAs are expressed at significantly higher levels after transfection, consistent with impaired effectiveness of endogenous miRNA repression. This effect exhibited concentration and temporal dependence. Notably, the profile of endogenous miRNAs can be largely inferred by correlating miRNA sites with gene expression changes after transfections. The competition and saturation effects have practical implications for miRNA target prediction, the design of siRNA and short hairpin RNA (shRNA) genomic screens and siRNA therapeutics.

AB - Transfection of small RNAs (such as small interfering RNAs (siRNAs) and microRNAs (miRNAs)) into cells typically lowers expression of many genes. Unexpectedly, increased expression of genes also occurs. We investigated whether this upregulation results from a saturation effect--that is, competition among the transfected small RNAs and the endogenous pool of miRNAs for the intracellular machinery that processes small RNAs. To test this hypothesis, we analyzed genome-wide transcript responses from 151 published transfection experiments in seven different human cell types. We show that targets of endogenous miRNAs are expressed at significantly higher levels after transfection, consistent with impaired effectiveness of endogenous miRNA repression. This effect exhibited concentration and temporal dependence. Notably, the profile of endogenous miRNAs can be largely inferred by correlating miRNA sites with gene expression changes after transfections. The competition and saturation effects have practical implications for miRNA target prediction, the design of siRNA and short hairpin RNA (shRNA) genomic screens and siRNA therapeutics.

U2 - 10.1038/nbt.1543

DO - 10.1038/nbt.1543

M3 - Journal article

C2 - 19465925

SN - 1087-0156

VL - 27

SP - 549

EP - 555

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 6

ER -