Spliceosome database: a tool for tracking components of the spliceosome

Abstract

The spliceosome is the extremely complex macromolecular machine responsible for pre-mRNA splicing. It assembles from five U-rich small nuclear RNAs (snRNAs) and over 200 proteins in a highly dynamic fashion. One important challenge to studying the spliceosome is simply keeping track of all these proteins, a situation further complicated by the variety of names and identifiers that exist in the literature for them. To facilitate studies of the spliceosome and its components, we created a database of spliceosome-associated proteins and snRNAs, which is available at http://spliceosomedb.ucsc.edu and can be queried through a simple browser interface. In the database, we cataloged the various names, orthologs and gene identifiers of spliceosome proteins to navigate the complex nomenclature of spliceosome proteins. We also provide links to gene and protein records for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, we created tools to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes. Together, the information in the database provides an easy reference for spliceosome components and will support future modeling of spliceosome structure and dynamics.

Figure 1.

Spliceosome ‘Component Search’. (A) Quick Search queries all SpliceosomeDB data, whereas additional parameters can be used to limit results. The search results in a table showing matching components that can be further refined using the ‘Filter current table’ tool or sorted by columns. Gene/protein names are linked to a page displaying additional information about the gene/protein. Checkboxes can be used in conjunction with the ‘Mass Spec Comparison’ button to generate a table showing MS experiments in which the selected proteins were identified. (B) Portion of browser view displaying individual gene/protein information linked to additional sources of information. At the bottom of the page, MS experiments identifying the protein are listed along with the number of unique peptides by which the protein was identified.

Figure 1.

Spliceosome ‘Component Search’. (A) Quick Search queries all SpliceosomeDB data, whereas additional parameters can be used to limit results. The search results in a table showing matching components that can be further refined using the ‘Filter current table’ tool or sorted by columns. Gene/protein names are linked to a page displaying additional information about the gene/protein. Checkboxes can be used in conjunction with the ‘Mass Spec Comparison’ button to generate a table showing MS experiments in which the selected proteins were identified. (B) Portion of browser view displaying individual gene/protein information linked to additional sources of information. At the bottom of the page, MS experiments identifying the protein are listed along with the number of unique peptides by which the protein was identified.

Figure 2.

Comparing the composition of spliceosome complexes. Portion of ‘Compare Complexes’ browser view displaying the components of selected complexes grouped by classification. Each component is linked to its individual information page.

Figure 3.

‘Mass Spec Experiments’ (A) MS experiments can be queried by a general ‘Quick Search’ or by specific attributes to return a list of matching experiments. Each experiment is linked to a page displaying the entire experimental results and to the PubMed entry of the corresponding publication. Checkboxes can be used in conjunction with the ‘Mass Spec Comparison’ button to generate a table comparing the results of the selected MS experiments. (B) Portion of browser view displaying an individual MS experiment result. Gene/protein names of identified proteins are linked to a page displaying additional information and the number of unique peptides by which proteins were identified is given.

Figure 4.

Comparison of MS experiment results. Generated with the ‘Mass Spec Comparison’ tool, columns in the comparison table display results of individual MS experiments, typically shown as the number of unique peptides used to identify the proteins represented in the different rows. Descriptions for each MS ‘Experiment ID’ are displayed in a legend and linked to individual experiment results.