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Status
Public on Sep 12, 2006
Title
Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity
Organism
Homo sapiens Experiment type
Expression profiling by array
Summary
Transfected siRNAs and miRNAs regulate numerous transcripts that have only limited complementarity to the active strand of the RNA duplex. This process reflects natural target regulation by miRNAs, but is an unintended (“off-target”) consequence of siRNA-mediated silencing. Here we demonstrate that this unintended off-target silencing is widespread, and occurs in a manner reminiscent of target silencing by miRNAs. A high proportion of unintended transcripts silenced by siRNAs showed 3’ UTR sequence complementarity to the seed region of the siRNA. Base mismatches within the siRNA seed region reduced the set of original off-target transcripts but generated new sets of silenced transcripts with sequence complementarity to the mismatched seed sequence. An inducible shRNA silenced a subset of transcripts that were silenced by an siRNA of the same sequence, demonstrating that unintended silencing is sequence-mediated and is independent of delivery method. In all cases, off-target transcript silencing was accompanied by loss of the corresponding protein and occurred with similar dependence on siRNA concentration as silencing of the target transcript. These results demonstrate that short stretches of sequence complementarity to the seed region of the siRNA are key to the silencing of unintended transcripts, and that this limits the specificity of siRNA-mediated transcript silencing. Because these off-target events are sequence-dependent, inclusion of multiple independent siRNAs to the target of interest can help to distinguish true positives from false positives in functional genetic analyses.
Overall design
For details, please see A.L. Jackson, et al. 2006. RNA 12(7): 1179-1187. We used consensus genelists for clustering. Please see attached tables for genelists.
Contributor(s)
Jackson AL , Burchard J , Schelter J , Chau N , Cleary M , Lim L , Linsley PS Citation(s)
16682560 Submission date
Sep 11, 2006
Last update date
Jul 24, 2015
Contact name
Aimee Jackson
Organization name
Regulus Therapeutics
Street address
1896 Rutherford Rd
City
Carlsbad
State/province
CA
ZIP/Postal code
92008
Country
USA
Platforms (3)
GPL2029 Rosetta/Merck Human 25k v2.2.1 microarray
GPL3991 Human 3.0 A1
GPL3992 Functional ID v2.0 Array 1
Samples (68)
GSM133543 HT29tTSTetOH1_PLK1_Doxycycline_0ng/ml_24h vs. HT29tTSTetOH1_PLK1_Doxycycline_50ng/ml_24h
GSM133684 HeLa, mock, vs. HeLa, 193-MAPK14, pos 19 mut
GSM133685 HeLa, mock, vs. HeLa, 193-MAPK14, pos 13 mut
GSM133686 HeLa, mock, vs. HeLa, 193-MAPK14, pos 11 mut
GSM133687 HeLa, mock, vs. HeLa, 193-MAPK14, pos 18 mut
GSM133688 HeLa, mock, vs. HeLa, 193-MAPK14, pos 1 mut
GSM133689 HeLa, mock, vs. HeLa, 193-MAPK14, pos 2 mut
GSM133690 HeLa, mock, vs. HeLa, 193-MAPK14, pos 17 mut
GSM133691 HeLa, mock, vs. HeLa, 193-MAPK14, pos 16 mut
GSM133692 HeLa, mock, vs. HeLa, 193-MAPK14, pos 15 mut
GSM133693 HeLa, mock, vs. HeLa, 193-MAPK14, pos 14 mut
GSM133694 HeLa, mock, vs. HeLa, 193-MAPK14, pos 12 mut
GSM133695 HeLa, mock, vs. HeLa, 193-MAPK14, pos 10 mut
GSM133696 HeLa, mock, vs. HeLa, 193-MAPK14, pos 9 mut
GSM133697 HeLa, mock, vs. HeLa, 193-MAPK14, pos 8 mut
GSM133698 HeLa, mock, vs. HeLa, 193-MAPK14, pos 7 mut
GSM133699 HeLa, mock, vs. HeLa, 193-MAPK14, pos 6 mut
GSM133700 HeLa, mock, vs. HeLa, 193-MAPK14, pos 4 mut
GSM133701 HeLa, mock, vs. HeLa, 193-MAPK14, pos 3 mut
GSM133702 HeLa, mock, vs. HeLa, 193-MAPK14, normal
GSM133703 Hela, mock vs. HeLa, Luc
GSM134466 Hela mock 24hr vs. HeLa PLk1319, 24 hr
GSM134467 HeLa, mock, 24 hrs vs. HeLa, 1721-PLK-772, 24 hrs
GSM134468 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, normal, 24 hr
GSM134469 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 19 mut, 24 hr, a
GSM134470 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 18 mut, 24 hr, a
GSM134471 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 17 mut, 24 hr, a
GSM134472 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 16 mut, 24 hr, a
GSM134473 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 15 mut, 24 hr, a
GSM134474 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 14 mut, 24 hr, a
GSM134475 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 13 mut, 24 hr, a
GSM134476 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 12 mut, 24 hr, a
GSM134477 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 11 mut, 24 hr, a
GSM134478 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 10 mut, 24 hr, a
GSM134479 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 9 mut, 24 hr, a
GSM134480 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 8 mut, 24 hr, a
GSM134481 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 7 mut, 24 hr, a
GSM134482 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 6 mut, 24 hr, a
GSM134483 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 5 mut, 24 hr, a
GSM134484 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 4 mut, 24 hr, a
GSM134485 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 3 mut, 24 hr, a
GSM134486 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 2 mut, 24 hr, a
GSM134487 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 1 mut, 24 hr, a
GSM134488 HeLa, mock , 24 hr vs. HeLa, MAPK14-193 , 24 hr
GSM134489 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 1 mut, 24 hr, c
GSM134490 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 2 mut, 24 hr, c
GSM134491 HeLa, mock, 24hr vs. HeLa, MAPK14, normal, 24hr
GSM134492 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 19 mut, 24 hr, b
GSM134493 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 18 mut, 24 hr, b
GSM134494 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 17 mut, 24 hr, b
GSM134495 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 16 mut, 24 hr, b
GSM134496 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 15 mut, 24 hr, b
GSM134497 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 14 mut, 24 hr, b
GSM134498 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 13 mut, 24 hr, b
GSM134499 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 12 mut, 24 hr, b
GSM134500 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 11 mut, 24 hr, b
GSM134501 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 10 mut, 24 hr, b
GSM134502 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 9 mut, 24 hr, b
GSM134503 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 8 mut, 24 hr, b
GSM134504 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 7 mut, 24 hr, b
GSM134505 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 6 mut, 24 hr, b
GSM134506 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 5 mut, 24 hr, b
GSM134507 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 4 mut, 24 hr, b
GSM134508 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 3 mut, 24 hr, b
GSM134509 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 2 mut, 24 hr, b
GSM134510 HeLa, mock, 24 hr vs. HeLa, 193-MAPK14, pos 1 mut, 24 hr, b
GSM134511 HeLa, mock, 24 hr vs. HeLa, PIK3CB-6338, 24 hr
GSM134512 HeLa, mock, 24 hr vs. HeLa, PIK3CB-6340, 24 hr
Relations BioProject
PRJNA97197
MAPK14_genelist_mut_walk_Fig3A header descriptions Primary Sequence Name Sequence Code
Data table Primary Sequence Name Sequence Code LOC441347
AL050136
ARMC8
NM_015396
RBM7
NM_016090
NPTN
NM_017455
SETD7
Contig57582_RC
NPTN
NM_012428
CRIPT
NM_014171
EXPH5
AB014524
UBP1
NM_014517
ANKFY1
AB033081
RTN4R
Contig45454_RC
LOC440203
Contig54980_RC
CDC42SE2
AF131831
KLHL24
Contig50396_RC
N-PAC
NM_018459
C20orf11
Contig1924_RC
C14orf46
Contig41736_RC
BTRC
Contig65663
ZNF706
Contig46375_RC
ARPC5L
Contig3398_RC
52 <1 Kbytes .MAPK14_genelist_sig_Fig3B header descriptions Primary Sequence Name Sequence Code
Data table Primary Sequence Name Sequence Code KIAA0376
AB002374
AURKAIP1
NM_017900
RPS6KA4
NM_003942
CTPS
NM_001905
MAPKAPK5
NM_003668
NARF
NM_012336
CAMTA1
Contig54761_RC
STK10
NM_005990
SREBF2
NM_004599
RNF40
NM_014771
MKNK2
NM_017572
USP46
AF070557
HAGH
NM_005326
TAF7
NM_005642
HIST1H2BD
AJ223353
SUMO3
NM_006936
CKS1B
NM_001826
PCID2
NM_018386
MAPRE1
NM_012325
CNDP2
NM_018235
95 1 Kbytes .Supplementary file Size Download File type/resource GSE5814_RAW.tar
180.0 Kb
(http) (custom) TAR
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