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Dynamic Organellar Mapping in unperturbed yeast

ABSTRACT: Sophisticated techniques are available for systematic studies of yeast cell biology. However, it remains challenging to investigate protein subcellular localization changes on a proteome-wide scale. Here, we apply Dynamic Organellar Maps (DOMs) by label-free mass spectrometry to detect localization changes of native, untagged proteins during endoplasmic reticulum (ER) stress. This dataset comprises 6 static maps generated using the newly established sample processing workflow for yeast cells. From this dataset we generated protein copy number estimates, cytosolic pool estimates and subcellular localization predictions for nearly 3000 proteins.

INSTRUMENT(S):

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast) Saccharomyces Cerevisiae

SUBMITTER: Julia Schessner

LAB HEAD: Georg H H Borner

PROVIDER: PXD061762 | Pride | 2025-12-03

REPOSITORIES: Pride

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			Action	DRS
	20230105_EXPL0_GeBo_AlDa_S436_BL114_yeastmaps_SA_LFQ_Static_map1_12k_SS_DDA.raw	Raw
	20230105_EXPL0_GeBo_AlDa_S436_BL114_yeastmaps_SA_LFQ_Static_map1_1k_SS_DDA.raw	Raw
	20230105_EXPL0_GeBo_AlDa_S436_BL114_yeastmaps_SA_LFQ_Static_map1_24k_SS_DDA.raw	Raw
	20230105_EXPL0_GeBo_AlDa_S436_BL114_yeastmaps_SA_LFQ_Static_map1_3k_SS_DDA.raw	Raw
	20230105_EXPL0_GeBo_AlDa_S436_BL114_yeastmaps_SA_LFQ_Static_map1_3k_SS_DDA_rerun.raw	Raw

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Project description:Abstract: In the yeast S. pombe, multiple chromatin-modifying enzymes are required for heterochromatin formation, yet how their actions alter chromatin structure to block access to DNAby the transcriptional machinery is unknown. We constructed high-resolution nucleosome occupancy maps of heterochromatic regions in wild-type strains and in mutants lacking the H3K9 methyltransferase Clr4 or one of the two activities of the silencing effector complex SHREC. Fourier analysis reveals that these enzymes do not increase the regularity of nucleosome spacing. Rather, their principal effect was to induce the elimination of nucleosome-free regions (NFRs). Both NFRs associated with transcription initiation sites as well as those not associated with promoters are affected. As in S. cerevisiae, repressed genes in euchromatin retain their NFRs. Thus, NFR elimination cannot be explained as a secondary consequence of repression. The maps also show that TFIIIC boundary elements have NFRs resistant to silencing, suggesting a potential role in preventing lateral spread of heterochromatin. NFR elimination offers a mechanism by which heterochromatin restricts access of the transcriptional machinery to DNA. Nucleosome positions in either heterochromatin or euchromatin were mapped in various mutants to determine whether chromatin structure is altered upon heterochromatic silencing. Eight strains were assayed for nucleosome positioning in heterochromatin while two strains were assayed for nucleosome positioning in euchromatin. Two biological replicates were assayed for each strain. No dye swaps were done. RNA transcripts were also mapped using the heterochromatin tiling arrays to determine where RNA transcripts accumulate in heterochromatin. Three strains were assayed for transcripts in heterochromatin by hybridizing cy5-labeled cDNA created from total RNA against cy3-labeled cDNA created from RNA synthesized from sonicated genomic DNA. Two biological replicates were assayed for each strain.

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Dynamic Organellar Mapping in unperturbed yeast

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