Profiling post-translational modifications of proteins that regulate gene expression
© Hornbeck et al; licensee BioMed Central Ltd. 2010
Published: 11 October 2010
The aggregation of over 100,000 non-redundant, experimentally-determined post-translational modification sites on human proteins in PhosphoSitePlus (PSP) has enabled system-wide analyses of modification sites on proteins that regulate gene expression. The location of modification sites within specific domains or motifs, their distribution on subsets of proteins and in specific locations within the cell presumably underlie the flow of information within signaling networks that regulate gene expression. We will present the results of analyses of the structure, location and distribution of phosphoryl, acetyl, ubiquitinyl, and methyl modification sites on proteins that regulate transcription. The goals of this work are to gain an overview of protein modifications and identify novel modification sites that may regulate gene expression.
Materials and methods
Analyses of the PSPlogo profiles of modification sites differ significantly between subsets of proteins that regulate gene expression, presumably reflecting differential signaling networks, and implicating different enzymes in these various networks. For example, the profile of all phosphoserine sites in nucleosomal proteins (Figure 1a) indicates that multiple kinase families are active in this compartment (proline-directed, DNA damage, and AGC kinases). Molecular visualization software allows for the identification of modification sites that may regulate gene expression such as the three phosphotyrosines at the mouth of the H4-K20me2-binding cage of 53BP1 (Figure 1b).
Post-translational profiling using the data and algorithms available in PSP can be a useful tool for developing testable hypotheses about protein modifications that might regulate gene expression.
This article is published under license to BioMed Central Ltd.