title: Identification of Drosophila mitotic genes by combining co-expression analysis and RNA interference.
abstract: 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.
authors.affiliation: Dipartimento di Genetica e Biologia Molecolare, Istituto di Biologia e Patologia Molecolari del CNR, Rome, Italy.
authors.forename: Maria Patrizia
authors.initials: MP
authors.lastname: Somma
authors.forename: Francesca
authors.initials: F
authors.lastname: Ceprani
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Bucciarelli
authors.forename: Valeria
authors.initials: V
authors.lastname: Naim
authors.forename: Valeria
authors.initials: V
authors.lastname: De Arcangelis
authors.forename: Roberto
authors.initials: R
authors.lastname: Piergentili
authors.forename: Antonella
authors.initials: A
authors.lastname: Palena
authors.forename: Laura
authors.initials: L
authors.lastname: Ciapponi
authors.forename: Maria Grazia
authors.initials: MG
authors.lastname: Giansanti
authors.forename: Claudia
authors.initials: C
authors.lastname: Pellacani
authors.forename: Romano
authors.initials: R
authors.lastname: Petrucci
authors.forename: Giovanni
authors.initials: G
authors.lastname: Cenci
authors.forename: Fiammetta
authors.initials: F
authors.lastname: Vernì
authors.forename: Barbara
authors.initials: B
authors.lastname: Fasulo
authors.forename: Michael L
authors.initials: ML
authors.lastname: Goldberg
authors.forename: Ferdinando
authors.initials: F
authors.lastname: Di Cunto
authors.forename: Maurizio
authors.initials: M
authors.lastname: Gatti
mesh_terms: 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
chemical_list: D012330:RNA, Double-Stranded
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