DataSets / Project home (Nuclear bodies)
Spatial proteomic mapping of human nuclear bodies reveals new functional insights into RNA regulation
First Author: Boris J.A. Dyakov
Abstract:
  

This is the BirA* dataset associated with Dyakov et al. 2024, which is currently available as a preprint on bioRxiv.


Abstract

Nuclear bodies are diverse membraneless suborganelles with emerging links to development and disease. Explaining their structure, function, regulation, and implications in human health will require understanding their protein composition; however, isolating nuclear bodies for proteomic analysis remains challenging. We present the first comprehensive proximity proteomics-based map of nuclear bodies, featuring 140 bait proteins (encoded by 119 genes) and 1,816 unique prey proteins. We identified 641 potential nuclear body components, including 131 paraspeckle proteins and 147 nuclear speckle proteins. After validating 31 novel paraspeckle and nuclear speckle components, we discovered regulatory functions for the poorly characterised nuclear speckle- and RNA export-associated proteins PAXBP1, PPIL4, and C19ORF47, and revealed that QKI regulates paraspeckle size. This work provides a systematic framework of nuclear body composition in live cells that will accelerate future research into their organisation and roles in human health and disease.

Navigating this website

  • The data included here is by default filtered at 1% FDR as calculated by SAINTexpress ("BFDR ? 0.01"); unselect the "high confidence" buttons to view all data. To see those BioID proximity interactions that additionally scored high on the specificity filter, please refer instead to the Supplementary data (this must be updated).

  • Select "Explore baits" (left) to view all baits profiled, organized alphabetically (view as a list). Clicking on a bait will retrieve all its proximity interactors (high confidence (BFDR ? 0.01) by default) and indicates which interactions are already deposited in the BioGRID and IntAct databases. Also see the many links to excellent external resources for the baits and/or preys, including ProteinAtlas, ProteomicsDB, NCBI Gene, GeneCards and UniProt.

  • Each bait page includes a Cytoscape network in the top left corner of the page. This shows the top 25 proximal preys per bait (by prey-length normalized spectral counts). Click on this thumbnail to see a larger version. For genes which have been profiled as both N- and C-terminally tagged baits, the thumbnail at the top right shows a network where both the N- and C-term data have been unified.

  • Search for a bait or prey by Official Gene Symbol through the "Search" tab on left (or at the top). You will be able to search across all projects you have access to.

  • You may also list baits based on their compartment/nuclear body annotation via the Explore Organelles page. See Supplementary Table 1 for our detailed literature review and annotation of known human nuclear body proteins.

  • Supplementary data can be accessed through the link on the left sidebar. This includes the figures and Supplementary tables associated with Dyakov et al. 2024.

  • The SAINTexpress results for this dataset ("7013_cleaned_v2.txt") can be downloaded and exploring using our ProHits-viz suite of visualization tools.

    • Contact information

    Please contact Anne-Claude Gingras (gingras@lunenfeld.ca) for any questions regarding this dataset.


    Copyright © 2012 Gingras labs, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital.