Fission yeast Scm3 mediates stable assembly of Cnp1/CENP-A into centromeric chromatin

Abstract

Mis16 and Mis18 are subunits of a protein complex required for incorporation of the histone H3 variant CenH3 (Cnp1/CENP-A) into centromeric chromatin in Schizosaccharomyces pombe and mammals. How the Mis16-Mis18 complex performs this function is unknown. Here, we report that the Mis16-Mis18 complex is required for centromere localization of Scm3(Sp), a Cnp1-binding protein related to Saccharomyces cerevisiae Scm3. Scm3(Sp) is required for centromeric localization of Cnp1, while Scm3(Sp) localizes at centromeres independently of Cnp1. Like the Mis16-Mis18 complex but unlike Cnp1, Scm3(Sp) dissociates from centromeres during mitosis. Inactivation of Scm3(Sp) or Mis18 increases centromere localization of histones H3 and H2A/H2B, which are largely absent from centromeres in wild-type cells. Whereas S. cerevisiae Scm3 is proposed to replace histone H2A/H2B in centromeric nucleosomes, the dynamic behavior of S. pombe Scm3 suggests that it acts as a Cnp1 assembly/maintenance factor that directly mediates the stable deposition of Cnp1 into centromeric chromatin.

Figure 1. Fission Yeast Scm3 is a Conserved Fungal Protein that Physically Interacts and Co-localizes with Cnp1 at the Central Core of the Centromere

A. A schematic of Scm3 from selected fungal species showing the area of homology in the N-terminus consisting of approximately 50 amino acids. Alignment of this domain in S. pombe Scm3 and its homologs in A. nidulans, N. crassa, and S. cerevisiae is presented. Black background indicates identical residues, and light shading indicates similar residues. B. Yeast two-hybrid interactions showing that Scm3 self-interacts and interacts with Cnp1. C. Co-immunoprecipitation of GST-Scm3 with Cnp1-GFP. Extracts of cells expressing Cnp1-GFP and nmt1-GST-Scm3 or nmt1-GST-Cds1^1-190 (Boddy et al., 2000) were immunoprecipitated using glutathione sepharose. GFP-Cnp1 co-immunoprecipitated with GST-Scm3 but not with GST-Cds1^1-190. D. Scm3 co-localizes with Cnp1. Live cells expressing both Scm3-CFP (red) and Cnp1-GFP (green) were photographed. Images were merged in the right panel. E. ChIP analysis was performed using extracts expressing Scm3 tagged with the Flag epitope. The position of centromere probes cnt1, imr1, dg and euchromatic lys1 are indicated. Mis18-FLAG was used as a positive control.

Figure 2. Fission Yeast Scm3 is Essential for Centromere Function

A. Scm3 is an essential protein. Tetrad analysis of an scm3⁺/scm3::kanMX6 diploid revealed that scm3::kanMX6 spores germinate but do not proliferate. All viable spores are Kan^-. B. Loss of viability of scm3-ts mutants at high temperature. The scm3-6 and scm3-19 mutants were grown at 25°C and then shifted to 35.5°C for the indicated periods of time. Cells were plated onto YES agar and colonies were counted following incubation at 25°C for 3 days. The untagged control strain is PR110. C. The scm3-ts mutants are rescued by Cnp1 overexpression. The indicated strains expressing GFP-vector, Scm3, or Cnp1 under control of the nmt41 thiamine-repressible promoter were spotted in 10-fold serial dilutions onto selective medium containing thiamine. Leaky expression of Scm3 or Cnp1 from the nmt41 promoter in the presence of thiamine was sufficient to rescue scm3-6 and scm3-19. Rescue was also observed in the absence of thiamine (our unpublished data). D. The scm3-ts mutants display unequal chromosome/centromere segregation. Missegregation of centromere I was observed in the scm3-6 and scm3-19 mutants grown for 6 hrs at 30°C. DAPI staining revealed binucleate cells with asymmetric nuclei. E. Minichromosome 16 (Ch16) is unstable in scm3-ts mutants. The Ch16 loss assay (see Experimental Procedures) was performed following growth at 30°C for 16 h.

Figure 3. Centromere Localization of Cnp1 Requires Scm3

A. Cnp1 foci formation is abolished in the scm3-ts mutants at the restrictive temperature. Cnp1-GFP localization was determined in scm3-6, scm3-19 or mis18-262 strains grown at 26°C or shifted to 36°C for 8 h. Microscopy was performed following methanol fixation. Quantitation of cells with a Cnp1 dot is shown to the right. B. Cnp1-GFP protein levels are not altered in the scm3-ts mutants at the restrictive temperature. Whole cell extracts were prepared following growth at 25°C or shift to 36°C for 8 h. Immunoblotting was performed with antibodies to GFP or Cdc2 (PSTAIR). C. Mis18-GFP foci formation is unaffected by incubation of scm3-ts mutants at 36°C. Loss of Mis18-GFP foci in the mis18-262 cells is shown as a positive control.

Figure 4. Synthetic Genetic Interactions Between scm3-ts and mis-ts Alleles

A. Overexpression of GFP-Scm3 is toxic in cnp1-ts and mis-ts strains. The indicated strains were transformed with pSK248 plasmids containing cnp1⁺ or mis⁺ genes, or pRep41-GFP plasmids containing scm3⁺ expressed from the nmt41 promoter. Cells were streaked onto minimal medium in the presence or absence of thiamine to repress (+Thi) or induce (-Thi) expression of GFP-Scm3. The table summarizes the toxicity of overexpression (+++ is most toxic). B. Synthetic genetic interactions of scm3-ts with mis6-ts or mis16-ts mutations. Ten-fold serial dilutions of cells on YES agar were incubated at 25°C, 28°C or 30°C for 2-3 days. Two individual isolates for scm3-6 mis6-302 or scm3-6 mis16-53 double mutants are shown.

Figure 5. Mis6, Mis16 and Mis18 are Required for Scm3 Localization at Centromeres

A. Localization of Scm3 at centromeres requires Mis6, Mis16, and Mis18. Strains were grown at 20°C and then shifted to 36°C for 6 h. Microscopy was performed following methanol fixation. B. Yeast two-hybrid assay showing that Scm3 interacts with Mis16 and Cnp1 but not Mis18.

Figure 6. Scm3 Dissociates from Centromeres During Mitosis

A. Scm3 is localized to centromeres during interphase, but not in mitosis. Colocalization of GFP-tagged Scm3 (green) and RFP-tagged Mis12 (red) was performed using cells grown at 20°C and fixed in methanol. The merged image is on the right. Representative images are displayed. White arrows indicate cells undergoing mitosis in which the nuclear dot corresponding to Scm3 has been lost but the dot for Mis12 persists. B. Scm3 dissociates from centromeric chromatin during mitosis. ChIP assays were performed using wild type or nda3-KM311 cells expressing FLAG-tagged Cnp1 and Pk-tagged Scm3. Cells were grown at 20°C (restrictive temperature for the cold-sensitive nda3-KM311 mutation) for 8 h prior to harvesting. ChIP quantitation is provided below.

Figure 7. Scm3 and Mis18 Regulate Cnp1, H3 and H2B Occupancy at Centromeres

A. ChIP analysis of Cnp1 and canonical histone occupancy at the centromere in scm3-ts and mis18-262 cells. Cells were incubated at 36°C prior to harvesting. Compared to wild type, Cnp1-GFP enrichment at cnt1 and imr1 is reduced in the mutants while H2B and H3 enrichment is increased. Quantitation for Cnp1-GFP, H2B, and H3 is shown below; quantitation for H4 and acetylated-H4 is in Figure S9. B. H2A and H2B are largely absent from the central core of the centromere. ChIP was performed using strains expressing Cnp1, H2A, or H2B tagged with GFP. The level of H4 at each of the centromere regions was determined as a control.