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Fig. 1. Structure of eukaryotic regulatory networks. (A) The basic building blocks
of regulatory networks are interactions between transcription factor proteins
and cis-regulatory DNA sequences, protein–protein interactions
affecting availability or activity of transcription factors, and hybridization
of microRNAs to their targets. (B) Interactions among these factors form local
regulatory motifs such as feed-forward loops, single input modules, multiple
input modules, autoregulation, feed-back loops and regulator chains. In the
diagrams, circles represent proteins, squares represent genes, and solid
arrows represent regulatory interactions. Broken lines indicate protein
production from a gene. (C) Regulatory pathways controlling biological
processes (especially development) have hierarchical structure. Pathways
controlling wing development in D. melanogaster at mid-embryonic
(top), late embryonic (middle) and late larval (bottom) stages are reproduced
from Abouheif and Wray (Abouheif and Wray,
2002 ). Reprinted with permission from AAAS. Layers of regulatory
proteins interact before the ultimate activation of effector genes that give
differentiated cells their characteristic properties. (D) Genes functioning in
multiple pathways form an integrated genomic network. The transcriptional
regulatory network for S. cerevisiae is shown here, modified from
Babu et al. (Babu et al.,
2004), with permission from Elsevier. (E) The genomic regulatory
network for S. cerevisiae has a hierarchical structure similar to
individual pathways. Image is modified from Yu and Gerstein
(Yu and Gerstein, 2006,
Proc. Natl. Acad. Sci. USA 103, 14724-14731), with permission.
Copyright (2006) National Academy of Sciences, USA.
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