SWR1-Com Shared Subunits with NuA4 and Contained Proteins with Motifs Involved in Chromatin Biology

<div><p>(A) Protein complex overlap. Purifications were performed under high stringency conditions (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020131#s4" target="_blank">Materials and Methods</a>) from Swr1-TAP, Yaf9-TAP, and untagged control strains, resolved by SDS-PAGE and stained with silver. Due to the relatively low efficiency of the Swr1-TAP purification, the wt and Swr1-TAP purifications were performed from twice the amount of starting material compared to Yaf9-TAP. Not all proteins identified by mass spectrometry were clearly visible on the gel. Arrows point to proteins that were common to the Swr1-TAP and Yaf9-TAP purifications, whereas stars point to proteins that were found only in the Yaf9-TAP purifications as judged by visual inspection and comparison of protein sizes with the data deduced from mass spectrometry. The vertical bar indicates that proteins in that area of the gel could not be clearly resolved.</p> <p>(B) Domain structure of SWR1-Com. Shown are SMART domain representations of individual proteins assigned to the SWR1-Com taken from the SMART database (<a href="http://smart.embl-heidelberg.de/" target="_blank">http://smart.embl-heidelberg.de/</a>). Domain names are included, green bars indicate coil-coiled regions, and magenta bars indicate regions of low complexity. The amino-terminal part of Swr1p is not to scale.</p></div

Chromosomal Distribution of Swr1p-Activated Genes

<div><p>(A) Histogram showing the number of Swr1p-activated genes as a function of their distance to the nearest chromosome end.</p> <p>(B) The statistical significance of the enrichment of Swr1p-activated genes as a function of distance to the nearest telomere, and the significance of the depletion of Swr1p-activated genes in regions greater than 40 kb from a telomere, were determined using the hypergeometric function (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020131#pbio-0020131-Tavazoie1" target="_blank">Tavazoie et al. 1999</a>).</p></div

Subunit Architecture of SWR1-Com and Overlap with NuA4 and Ino80-C Complexes

<p>Venn diagram showing proposed subunit compositions of the SWR1, NuA4, Ino80p-C, and Nap1p/Kap114p complexes. Assignments were based on the data shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020131#pbio-0020131-t001" target="_blank">Table 1</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020131#pbio-0020131-g002" target="_blank">Figure 2</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020131#pbio-0020131-g003" target="_blank">Figure 3</a>. Proteins used in TAP purifications are indicated by “*” and proteins encoded by essential genes are underlined.</p

Swc4p and Bdf1p Were Components of SWR1-Com

<div><p>This figure shows immunoblots of analytical-scale TAP purifications. The captured TAP-tagged protein is indicated above the gels, and the protein that was tested for association is indicated at the right side.</p> <p>(A) Association of Swc4p and Tra1p. Swc4-HA was present in purifications from Yaf9-TAP, Esa1-TAP, Rvb2-TAP, and Swr1-TAP but not Ino80-TAP. NuA4 was only present in the Yaf9-TAP and Esa1-TAP material.</p> <p>(B) Reciprocal confirmation of Swc4p being part of NuA4. Swc4-TAP and Yaf9-TAP purified material contained NuA4 components Esa1p and Tra1p.</p> <p>(C) Association of Bdf1p. Bdf1p was present in purifications from Swr1-TAP, Yaf9-TAP, and Swc4-TAP but not Esa1-TAP.</p></div