Identification of Drosophila mitotic genes by combining co-expression analysis and RNA interference.
RNAi screens have, to date, identified many genes required for mitotic divisions of Drosophila tissue culture cells. However, the inventory of such genes remains incomplete. We have combined the powers of bioinformatics and RNAi technology to detect novel mitotic genes. We found that Drosophila genes involved in mitosis tend to be transcriptionally co-expressed. We thus constructed a co-expression-based list of 1,000 genes that are highly enriched in mitotic functions, and we performed RNAi for each of these genes. By limiting the number of genes to be examined, we were able to perform a very detailed phenotypic analysis of RNAi cells. We examined dsRNA-treated cells for possible abnormalities in both chromosome structure and spindle organization. This analysis allowed the identification of 142 mitotic genes, which were subdivided into 18 phenoclusters. Seventy of these genes have not previously been associated with mitotic defects; 30 of them are required for spindle assembly and/or chromosome segregation, and 40 are required to prevent spontaneous chromosome breakage. We note that the latter type of genes has never been detected in previous RNAi screens in any system. Finally, we found that RNAi against genes encoding kinetochore components or highly conserved splicing factors results in identical defects in chromosome segregation, highlighting an unanticipated role of splicing factors in centromere function. These findings indicate that our co-expression-based method for the detection of mitotic functions works remarkably well. We can foresee that elaboration of co-expression lists using genes in the same phenocluster will provide many candidate genes for small-scale RNAi screens aimed at completing the inventory of mitotic proteins.
Somma
Maria Patrizia
MP
Dipartimento di Genetica e Biologia Molecolare, Istituto di Biologia e Patologia Molecolari del CNR, Rome, Italy.
Ceprani
Francesca
F
Bucciarelli
Elisabetta
E
Naim
Valeria
V
De Arcangelis
Valeria
V
Piergentili
Roberto
R
Palena
Antonella
A
Ciapponi
Laura
L
Giansanti
Maria Grazia
MG
Pellacani
Claudia
C
Petrucci
Romano
R
Cenci
Giovanni
G
Vernì
Fiammetta
F
Fasulo
Barbara
B
Goldberg
Michael L
ML
Di Cunto
Ferdinando
F
Gatti
Maurizio
M
D000818:Animals; D020090:Chromosome Segregation; D048749:Cytokinesis; D004330:Drosophila / Q000235:genetics* / Q000378:metabolism; D015870:Gene Expression; D017344:Genes, Insect; D008938:Mitosis / Q000235:genetics*; D034622:RNA Interference; D012330:RNA, Double-Stranded / Q000378:metabolism; D008941:Spindle Apparatus / Q000235:genetics / Q000378:metabolism
D012330:RNA, Double-Stranded
J Cell Biol. 2002 May 27;157(5):749-60
12034769
Mol Biol Cell. 1994 Oct;5(10):1145-58
7865880
J Cell Biol. 2004 Jul 5;166(1):61-71
15240570
Curr Biol. 2002 Nov 19;12(22):1952-8
12445390
Nature. 2006 Feb 23;439(7079):1009-13
16496002
Nat Methods. 2006 Oct;3(10):833-8
16964256
Genes Dev. 1999 Jul 1;13(13):1664-77
10398680
Curr Biol. 2001 Mar 6;11(5):295-307
11267866
J Cell Sci. 1993 Sep;106 ( Pt 1):87-98
8270646
PLoS One. 2007 May 30;2(5):e478
17534428
J Cell Sci. 2006 Jun 1;119(Pt 11):2354-61
16723741
Nature. 2005 Aug 11;436(7052):861-5
16094371
J Cell Biol. 1992 Aug;118(4):759-73
1339459
Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15986-91
15514020
Am J Hum Genet. 2007 Mar;80(3):485-94
17273969
Mol Biol Cell. 2001 Dec;12(12):4054-65
11739800
Nat Cell Biol. 2001 Aug;3(8):730-9
11483958
J Biol. 2003;2(4):27
14527345
Curr Biol. 2004 Sep 21;14(18):1685-93
15380073
J Cell Biol. 2002 Sep 2;158(5):873-84
12213835
Cell. 2005 Apr 22;121(2):223-34
15851029
Curr Biol. 2002 Nov 19;12(22):1959-64
12445391
Genome Res. 2007 Aug;17(8):1146-60
17623812
Nat Methods. 2006 Oct;3(10):777-9
16990807
J Cell Biol. 1997 Jun 16;137(6):1337-54
9182666
Nature. 2006 Sep 21;443(7109):359-63
16964239
Curr Biol. 2003 Apr 15;13(8):647-53
12699620
J Cell Sci. 2002 Mar 1;115(Pt 5):949-61
11870214
J Cell Biol. 2003 Sep 15;162(6):1079-88
12975351
J Mol Biol. 1988 Sep 20;203(2):425-37
3199441
Curr Biol. 2006 Dec 19;16(24):2406-17
17112726
Mol Biol Cell. 2004 Nov;15(11):5053-63
15371536
J Biol. 2004;3(5):21
15588312
Development. 2004 Oct;131(20):5053-63
15459099
Cancer Res. 2004 May 1;64(9):2998-3001
15126332
Cell. 2006 Dec 1;127(5):955-67
17113138
J Cell Biol. 2006 Feb 13;172(4):517-28
16476773
Chromosoma. 2007 Aug;116(4):385-402
17333235
Genetics. 2000 Apr;154(4):1693-710
10747063
J Biol. 2002;1(1):5
12144710
Nat Cell Biol. 2006 Feb;8(2):137-47
16378099
Curr Biol. 2007 Feb 20;17(4):293-303
17306545
J Cell Sci. 2007 Oct 15;120(Pt 20):3522-33
17895365
Nature. 2004 Dec 23;432(7020):980-7
15616552
Mol Biol Cell. 1993 Nov;4(11):1161-74
8305737
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
9843981
Nat Genet. 2001 Oct;29(2):206-11
11544477
J Cell Biol. 1996 Mar;132(6):1093-104
8601587
Nature. 1998 Dec 17;396(6712):643-9
9872311
J Cell Biol. 2003 Sep 15;162(6):1003-16
12975346
Science. 2004 Feb 6;303(5659):832-5
14764878
Nature. 2004 Dec 23;432(7020):1036-40
15616564
Mol Biol Cell. 2002 Jul;13(7):2448-60
12134082
Curr Biol. 2006 Jan 24;16(2):195-201
16431372
Nature. 1996 Aug 1;382(6590):420-5
8684481
Science. 2002 Jan 4;295(5552):127-31
11778048
Science. 2007 Apr 20;316(5823):417-21
17412918
Genes Dev. 2000 Jul 15;14(14):1765-76
10898791
Science. 2003 Oct 10;302(5643):249-55
12934013
Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):716-21
10639145
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D489-94
16381918
Genes Dev. 2005 Sep 1;19(17):2041-53
16140985
PLoS Biol. 2004 Dec;2(12):e379
15547975