DOI: 10.5061/dryad.sbcc2frjh
title: Data from: Cypin regulates K63-linked polyubiquitination to shape synaptic content

description: 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.
description: # Data from: Cypin regulates K63-linked polyubiquitination to shape
 synaptic content Dataset DOI:
 [10.5061/dryad.sbcc2frjh](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](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