An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors

Abstract

Traditionally the gene expression pathway has been regarded as being comprised of independent steps, from RNA transcription to protein translation. To date there is increasing evidence of coupling between the different processes of the pathway, specifically between transcription and splicing. To study the interplay between these processes we derived a transcription-splicing integrated network. The nodes of the network included experimentally verified human proteins belonging to three groups of regulators: transcription factors, splicing factors and kinases. The nodes were wired by instances of predicted transcriptional and alternative splicing regulation. Analysis of the network indicated a pervasive cross-regulation among the nodes; specifically, splicing factors are significantly more connected by alternative splicing regulatory edges relative to the two other subgroups, while transcription factors are more extensively controlled by transcriptional regulation. Furthermore, we found that splicing factors are the most regulated of the three regulatory groups and are subject to extensive combinatorial control by alternative splicing and transcriptional regulation. Consistent with the network results, our bioinformatics analyses showed that the subgroup of kinases have the highest density of predicted phosphorylation sites. Overall, our systematic study reveals that an organizing principle in the logic of integrated networks favor the regulation of regulatory proteins by the specific regulation they conduct. Based on these results, we propose a new regulatory paradigm postulating that gene expression regulation of the master regulators in the cell is predominantly achieved by cross-regulation.

Author Summary

The operation of a living cell depends on its ability to regulate its different functions. The master regulators in the cell are proteins, which control the function of many other genes by several mechanisms. Transcription factors can differentially activate or repress the transcription of genes by binding to their regulatory elements. A second major mechanism of gene expression regulation occurs at the level of alternative splicing. Alternative splicing is regulated by splicing factors that bind to short regulatory motifs on the RNA and dictate the final gene architecture. To date there is increasing evidence of coupling between transcription and splicing. In this study, we modeled a network integrating the two regulations. Analysis of the network indicated that splicing factors were more often regulated by alternative splicing while transcription factors were more extensively controlled by transcriptional regulation. Overall, we postulate that regulatory proteins in the cell are controlled preferentially by the specific regulation they conduct.