We have employed a novel in vivo approach to study the structure and function of the eukaryotic kinetochore multiprotein complex. RNA interference (RNAi) was used to block the synthesis of centromere protein A (CENP-A) and Clip-170 in human cells. By coexpression, homologous kinetochore proteins from Saccharomyces cerevisiae were then tested for the ability to complement the RNAi-induced phenotypes. Cse4p, the budding yeast CENP-A homolog, was specifically incorporated into kinetochore nucleosomes and was able to complement RNAi-induced cell cycle arrest in CENP-A-depleted human cells. Thus, Cse4p can structurally and functionally substitute for CENP-A, strongly suggesting that the basic features of centromeric chromatin are conserved between yeast and mammals. Bik1p, the budding yeast homolog of human CLIP-170, also specifically localized to kinetochores during mitosis, but Bik1p did not rescue CLIP-170 depletion-induced cell cycle arrest. Generally, the newly developed in vivo complementation assay provides a powerful new tool for studying the function and evolutionary conservation of multiprotein complexes from yeast to humans.Centromeres are eukaryotic cellular structures that are essential for faithful chromosomal segregation during mitotic and meiotic cell division. The kinetochore complex is a defined multiprotein structure on the mitotic chromosome that adheres to the centromere (18, 61). The kinetochore serves as the site of attachment for spindle microtubules, which facilitate the alignment and separation of chromosomes during mitosis (12,13). Although the centromere's function is highly conserved among eukaryotes, centromeric morphology varies significantly, ranging from small, simple kinetochores in the budding yeast Saccharomyces cerevisiae to complex centromeres in multicellular eukaryotes (14). In mammalian cells, the centromere forms a visible primary constriction during metaphase and the kinetochore is a distinct structure that can be resolved into subregions (45,47,67). Finally, in holokinetic organisms such as the nematode Caenorhabditis elegans, multiple centromeres are dispersed throughout the chromosomes (1, 2). The primary nucleotide sequences of centromeric DNAs are also not conserved across phylogenies. The absolute size of the centromeric DNA can vary from ca. 125 bp in S. cerevisiae to tens of megabases in higher eukaryotes (11). Beyond the lack of size and sequence conservation between organisms, the centromere's function may be established not only at predefined sequences, but also at noncentromeric DNA elements, as illustrated by neocentromeres in human (11) and plant (93) cells. Finally, while in budding yeast the centromere DNA alone can nucleate centromere formation de novo, centromeres of metazoan cells strongly depend on epigenetic factors rather than DNA sequences for their activity (90). Thus, there is no primary sequence determinant in centromeric DNA that is conserved among eukaryotic species.At the protein level, a series of kinetochore components show homology to proteins...