Abstract
BackgroundMany cellular programs are regulated through the integration of specific transcriptional signals originated from external stimuli, being cooperation between transcription factors a key feature in this process. In this work, we studied how transcriptional cooperativity in yeast is aimed at integrating different regulatory inputs rather than controlling particular cellular functions from a organizational, evolutionary and functional point of view.FindingsOur results showed that cooperative transcription factor pairs co-evolve and are essential for the life of the cell. When organized into a layered regulatory network, we observed that cooperative transcription factors were preferentially placed in the middle layers, which highlights a role in regulatory signal integration. We also observed significant co-activity and co-evolution between members of the same cooperative pairs, but a lack of common co-expression profile.ConclusionsOur results suggest that transcriptional cooperativity has a specific role within the regulatory control scheme of the cell, focused in the amplification and integration of cellular signals rather than control of particular cellular functions. This information can be used for better characterization of regulatory interactions between transcription factors, aimed at determining the spatial and temporal control of gene expression.
Highlights
Many cellular programs are regulated through the integration of specific transcriptional signals originated from external stimuli, being cooperation between transcription factors a key feature in this process
Our results suggest that transcriptional cooperativity has a specific role within the regulatory control scheme of the cell, focused in the amplification and integration of cellular signals rather than control of particular cellular functions
This information can be used for better characterization of regulatory interactions between transcription factors, aimed at determining the spatial and temporal control of gene expression
Summary
Many cellular programs are regulated through the integration of specific transcriptional signals originated from external stimuli, being cooperation between transcription factors a key feature in this process. In eukaryotes, the process of cooperativity enables a small number of TFs to combine their regulatory influences to execute a large number of regulatory decisions [1,2] This can be achieved through different mechanisms, such as interaction between adjacent TFs on the promoter, interaction between distantly located cis-regulatory elements or even through mechanisms devoid of protein contacts [3,4,5,6]. Previous studies have devised methods for computationally detecting and measuring transcriptional cooperativity based on different mechanisms of cooperation such as co-expression, co-binding to the promoter or TF-TF interaction These works produced different lists of cooperative transcription factor pairs (CTFPs) [3,4,5,6,7,8,9]. In a previous work we found that a core of the predicted CTFPs shared some particular characteristics when analyzed in terms of their placement in the protein interaction network and in the regulatory network [10]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
