On Cycles in the Transcription Network of Saccharomyces cerevisiae

TL;DR

This study analyzes the cycle structure of the S. cerevisiae transcription network, revealing a dominant strongly connected component (LSCC) closely linked to the cell cycle, and highlighting its role in network hierarchy and regulation.

Contribution

It characterizes the properties and significance of cycles in the yeast transcription network, especially the LSCC's role in cell cycle regulation and network hierarchy.

Findings

Almost all cycles are in a single LSCC component.

LSCC overlaps significantly with cell cycle active interactions.

Removing cell cycle-active interactions reduces LSCC to a small subnetwork.

Abstract

We investigate the cycles in the transcription network of S. cerevisiae. Unlike a similar network of E. coli, it contains many cycles. We characterize properties of these cycles and their place in the regulatory mechanism of the cell. Almost all cycles in the transcription network of S. cerevisiae are contained in a single strongly connected component, which we call LSCC (L for ``largest''), except for a single cycle of two transcription factors. Among different physiological conditions, cell cycle has the most significant relationship with LSCC, as the set of 64 transcription interactions that are active in all phases of the cell cycle has overlap of 27 with the interactions of LSCC (of which there are 49). Conversely, if we remove the interactions that are active in all phases of the cell cycle (fewer than 1% of the total), the LSCC would have only three nodes and 5 edges, 4 of which are active only in the stress response subnetwork. LSCC has a special place in the topology of the network and it can be used to define a natural hierarchy in the network; in every physiological subnetwork LSCC plays a pivotal role. Apart from those well-defined conditions, the transcription network of S. cerevisiae is devoid of cycles. It was observed that two conditions that were studied and that have no cycles of their own are exogenous: diauxic shift and DNA repair, while cell cycle, sporulation are endogenous.