Data from: Cypin regulates K63-linked polyubiquitination to shape synaptic content
Data files
Jul 17, 2025 version files 116.91 MB
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Supplementary_Figure_4.zip
1.91 MB
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Figure_5.zip
3.08 MB
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Figure_3.zip
2.88 MB
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Supplementary_Figure_5.zip
2.35 MB
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Figure_6.zip
13.73 MB
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Supplementary_Figure_3.zip
538.87 KB
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Supplementary_Figure_2.zip
1.80 MB
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Figure_2.zip
7.69 MB
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Figure_7.zip
26.87 MB
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Supplementary_Figure_1.zip
48.10 MB
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Supplementary_Figure_6.zip
1.17 MB
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Figure_1.zip
3.32 MB
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Figure_4.zip
3.46 MB
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README.md
3.11 KB
Abstract
An open question in neuroscience is how protein posttranslational modifications regulate synaptic site targeting. Polyubiquitination plays a role in proteasome-mediated protein turnover; however, additional functions for specific types of polyubiquitin linkages have been identified. One type of polyubiquitination, K63-polyubiquitin (K63-polyUb), has been studied for its role in signal transduction within the context of cancer, but little has been done to uncover its role regarding neuronal and synaptic function. Here, we report an emerging function for the cytosolic PSD-95 interactor, cypin, in the regulation of synaptic content by K63-polyUb during neuronal development in vitro and in adult mice in vivo. We identify cypin-promoted K63-polyUb on postsynaptic proteins and also find an important role for cypin in presynaptic function. Our work demonstrates for the first time that cypin-promoted changes to K63-polyUb can regulate synaptic content and function on both sides of the synapse, adding important insight into basic mechanisms of neuronal signaling.
Dataset DOI: 10.5061/dryad.sbcc2frjh
Description of the data and file structure
Data for each figure are in folders corresponding to the figure number.
For Figures 1, 2, 3, 4, 5 and supplementary Figures 1, 2, 3, 4, 5:
All Western blot images (that were quantitated for the final graphs) are in .tif files in a folder labeled Raw files. All quantitation is in Excel spreadsheets corresponding to the proteins probed for in their respective figures, and analysis files are in Graphpad Prism files (Fc – Fold change in respect to control). All individual panels for figures are stored in.tif files.
Figure 2: “Total Lysate_cypin OE_in vitro.xlsx” file contains proteomics data from GFP or cypin-GFP overexpression in in vitro. Sheets labeled as Final are used for subsequent analysis, Processed contains the analyzed data, and Raw contains pre-processed intensity values.
Figure 4: “Synaptosomes_cypin OE_in vivo_For SynGO.xls” contains Expression log ratio, p-value and q-value from proteomics data from isolated synaptosomes from cypin overexpression mice. The “SynGO_id_convert” folder contains files that contain protein IDs of mouse proteins converted to their human equivalents.
Figure 6: Contains Origin Pro files comparing the cypin overexpression (OE) or cypin knockout (KO) using the data isolated from synGo analysis. “Processed” folder contains the excel sheets “Total lysate_cypin OE_in vivo.xlsx” or “Total lysate_cypin KO_in vivo.xlsx” from proteomics analysis of samples from either cypin overexpression or knockout from mice and are subsequently used in synGO portal to make respective graphs in Origin Pro. “OE & KO_ common genes.xls” contains the expression log ratio of common genes that are altered with cypin overexpression or knockout.
Figure 7: Contains Origin Pro files comparing the cypin overexpression (OE) in isolated synaptosomes or K63-polyUbiquitin enrichment. “cypin OE_synaptosomes and K63 enrichment_in vivo_IPA.xls” contains commonly enriched genes from isolated synaptosomes or K63-polyubiquitin enrichment in cypin overexpressed mice.
“Processed_For IPA_q 0.1_Fc+or-0.1” folder contains the .xlsx files used in Qiagen IPA analysis. These files contains sheets labeled as “Final” which are used for subsequent analysis, “Processed” contains the analyzed data, and “Raw” contains pre-processed intensity values.
Supplementary Figure 1 & 4: Contains .xlsx files of quantified fluorescent (S1) or luminescence (S4) intensity values.
Code/software
Software:
Excel for .xlsx,Previewer or Imageviewer for .tif and .png, Graphpad Prism for .pzfx Origin Pro for .opju, Notepad for .txt files.
Code: N/A
Access information
Other publicly accessible locations of the data:
- ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE [98] partner repository with the dataset identifier PXD055383 and 10.6019/PXD055383
Data was derived from the following sources:
- N/A