Data processing workflow. The primary dataset is a complete list of proteins identified in IP experiments that were used to map the Chromatin Central proteomic environment in any of the two yeasts. After removal of ribosomal proteins, all hits together with their A-indices were compiled into a non-redundant master table and grouped according to IP rounds. To accurately determine the scaffold protein complexes, we further removed from the master table proteins having A-index = 1 that were identified only in one IP experiment and common background proteins. Using the average A-index of background proteins as a selection threshold, the remaining proteins were sorted into two large groups: proteins enriched in corresponding IP experiments and proteins whose abundance remained at the background level. Proteins in the first group were considered as genuine interactors and were assigned to complexes, assuming IP experiments in which they were identified. From the second group, only proteins that were validated by a reciprocal IP experiment were assigned to the corresponding complexes.

Representative Coomassie stained polyacrylamide gels of immunoaffinity isolations used for deciphering the Chromatin Central environment in S. pombe. These baits were selected for IP experiments as plausible proteomic hyperlinks. Bands, in which corresponding proteins were identified by mass spectrometry, are indicated with arrows for each lane. The full list of identified proteins is presented in Table S4 in Additional data file 1.

Genetic interactions support the proteomic observations. (a) Scatter plots of correlation coefficients between genetic profiles for the two Set3C subunits, Set3 and Hos2, in S. cerevisiae and S. pombe across 239 direct homologs between the two species. In both species Sif2 (Hif2) is highly correlated with both Set3 and Hos2, consistent with its being a subunit of the core Set3C, whilst Hst1 (part of the Sc_Set3C extension) is uncorrelated with either Set3 or Hos2. Pho23 (Png2), a subunit of Rpd3C(L), correlates better with Set3 and Hos2 than does Rco1 (Cph1), a subunit of Rpd3C(S). The 90th percentile of the data is indicated. (b) Subunits of the core Set3C and Set3C extension show different genetic interaction patterns. Shown are genetic interactions between Set3C core and extension subunits and Swr1C, SAGA and Prefoldin subunits. Color-coding of the interaction magnitude (shown in the key) is as follows: shades of cyan indicate synthetic sick/lethal (negative) interactions typically observed between genes acting on parallel pathways; shades of yellow represent suppressive (positive) interactions seen primarily between genes acting on the same pathway and within stable protein complexes. (c) Msc1 in S. pombe is a member of Swr1C, while its S. cerevisiae ortholog (Ecm5) is not. Genetic profiles of members of the complex in the two species are shown with Msc1 and Ecm5 profiles aligned at the bottom. Genetic pattern of Msc1 is very similar to the rest of the complex and positive genetic interactions with the other members indicate that it is a bona fide member of Swr1C in S. pombe. Color-coding is as for (b). (d) A scatter plot of pair-wise correlation coefficients of genetic profiles of members of Swr1C in S. cerevisiae and S. pombe. Consistent with (c), data-points corresponding to pairs containing Msc1 or Ecm5 form an outlier group and are strongly correlated in S. pombe, but not in S. cerevisiae.

New protein complexes in Chromatin Central. (a) Immuno-isolation of the Sc_Snt2C complex and (b) domain structure of its subunits. (c) Immuno-isolation of the Sp_ASTRA complex and (d) domain structure of its subunits. In (a, c), only the relevant protein bands are annotated. The full list of identified proteins is provided in Table S1 in Additional data file 1.

Chromatin Central proteomic environment in S. cerevisiae. Individual protein complexes are boxed; TAP-tagged subunits are indicated with asterisks. The proteomic hyperlinks (proteins shared between the individual complexes) are shown between the complexes in grey diamonds. The hyperlink from Tra1 to the SAGA/SLIK complex is designated with a dashed line/filled arrow because it was not identified in this work, but inferred from published evidence. Gene names designated with a minus (-) symbol indicate that their TAP tagging/immunoaffinity purification failed. Several relatively abundant (A-index > 1.75) pair-wise interactors, also identified in proteome-wide screens [101,102], are mapped onto the scheme (dashed line/unfilled arrow). Set3C complex was previously characterized by TAP-tagging method in [10].

Chromatin Central proteomic environment in S. pombe. Individual protein complexes are boxed; color coding designates the protein complexes that are orthologous to the corresponding complexes in S. cerevisiae as shown in Figure 2. TAP-tagged subunits are designated by asterisks; minus (-) signs indicate that the IP experiment failed; proteomic hyperlinks are shown between the complexes in grey diamonds. Certain confident pair-wise interactors, discussed in the text, are designated with dashed arrows.

Several divergent proteomic hyperlinks between S. cerevisiae and S. pombe are due to gene duplications. Hence, hyperlinks provide a mechanism for the fixation of gene duplications.