Specificity of short interfering RNA determined through gene expression signatures

被引:387
作者
Semizarov, D [1 ]
Frost, L [1 ]
Sarthy, A [1 ]
Kroeger, P [1 ]
Halbert, DN [1 ]
Fesik, SW [1 ]
机构
[1] Abbott Labs, Global Pharmaceut Res & Dev, Abbott Pk, IL 60064 USA
关键词
DNA microarray; RNA interference; gene knockdown;
D O I
10.1073/pnas.1131959100
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Short interfering RNA (siRNA) is widely used for studying gene function and holds great promise as a tool for validating drug targets and treating disease. A critical assumption in these applications is that the effect of siRNA on cells is specific, i.e., limited to the specific knockdown of the target gene. In this article, we characterize the specificity of siRNA by applying gene expression profiling. Several siRNAs were designed against different regions of the same target gene for three different targets. Their effects on cells were compared by using DNA microarrays to generate gene expression signatures. When the siRNA design and transfection conditions were optimized, the signatures for different siRNAs against the same target were shown to correlate very closely, whereas the signatures for different genes revealed no correlation. These results indicate that siRNA is a highly specific tool for targeted gene knockdown, establishing siRNA-mediated gene silencing as a reliable approach for large-scale screening of gene function and drug target validation.
引用
收藏
页码:6347 / 6352
页数:6
相关论文
共 35 条
  • [1] Bernstein E, 2001, RNA, V7, P1509
  • [2] Molecular classification of cutaneous malignant melanoma by gene expression profiling
    Bittner, M
    Meitzer, P
    Chen, Y
    Jiang, Y
    Seftor, E
    Hendrix, M
    Radmacher, M
    Simon, R
    Yakhini, Z
    Ben-Dor, A
    Sampas, N
    Dougherty, E
    Wang, E
    Marincola, F
    Gooden, C
    Lueders, J
    Glatfelter, A
    Pollock, P
    Carpten, J
    Gillanders, E
    Leja, D
    Dietrich, K
    Beaudry, C
    Berens, M
    Alberts, D
    Sondak, V
    Hayward, N
    Trent, J
    [J]. NATURE, 2000, 406 (6795) : 536 - 540
  • [3] A good antisense molecule is hard to find
    Branch, AD
    [J]. TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (02) : 45 - 50
  • [4] Cellular proteins prevent antisense phosphorothioate oligonucleotide (SdT18) to target sense RNA (rA18): Development of a new in vitro assay
    Brukner, I
    Tremblay, GA
    [J]. BIOCHEMISTRY, 2000, 39 (37) : 11463 - 11466
  • [5] Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems
    Caplen, NJ
    Parrish, S
    Imani, F
    Fire, A
    Morgan, RA
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) : 9742 - 9747
  • [6] Antisense DNAs as multisite genomic modulators identified by DNA microarray
    Cho, YS
    Kim, MK
    Cheadle, C
    Neary, C
    Becker, KG
    Cho-Chung, YS
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (17) : 9819 - 9823
  • [7] Molecular mechanisms of action of antisense drugs
    Crooke, ST
    [J]. BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION, 1999, 1489 (01): : 31 - 44
  • [8] 53BP1 functions in an ATM-dependent checkpoint pathway that is constitutively activated in human cancer
    DiTullio, RA
    Mochan, TA
    Venere, M
    Bartkova, J
    Sehested, M
    Bartek, J
    Halazonetis, TD
    [J]. NATURE CELL BIOLOGY, 2002, 4 (12) : 998 - 1002
  • [9] siRNAs can function as miRNAs
    Doench, JG
    Petersen, CP
    Sharp, PA
    [J]. GENES & DEVELOPMENT, 2003, 17 (04) : 438 - 442
  • [10] RNA interference is mediated by 21-and 22-nucleotide RNAs
    Elbashir, SM
    Lendeckel, W
    Tuschl, T
    [J]. GENES & DEVELOPMENT, 2001, 15 (02) : 188 - 200