10. Lecture WS 2008/09 Bioinformatics III 1 V10 Transcriptional regulatory networks - introduction Typical promoter region of a prokaryotic gene. The TTGACA and TATAAT sequences at positions -35 and -10 nucleotides are not essential. The preference for the correspon-ding nucleotide at each position is between 50 and 80%. Example of a gene regulatory network. Solid arrows indicate direct associations between genes and proteins (via transcription and translation), between proteins and proteins (via direct physical interactions), between proteins and metabolites (via direct physical interactions or with proteins acting as enzymatic catalysts), and the effect of metabolite binding to genes (via direct interactions). Lines show direct effects, with arrows standing for activation, and bars for inhibition. The dashed lines represent indirect associations between genes that result from the projection onto 'gene space'. For example, gene 1 deactivates gene 2 via protein 1 resulting in an indirect interaction between gene 1 and gene 2 (drawn after [Brazhnik00]).
V10 Transcriptional regulatory networks - introduction. Typical promoter region of a prokaryotic gene. The TTGACA and TATAAT sequences at positions -35 and -10 nucleotides are not essential. The preference for the correspon-ding nucleotide at each position is between 50 and 80%. - PowerPoint PPT Presentation
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Typical promoter region of a prokaryotic gene. The TTGACA and TATAAT sequences at positions -35 and -10 nucleotides are not essential. The preference for the correspon-ding nucleotide at each position is between 50 and 80%.
Example of a gene regulatory network. Solid arrows indicate direct associations between genes and proteins (via transcription and translation), between proteins and proteins (via direct physical interactions), between proteins and metabolites (via direct physical interactions or with proteins acting as enzymatic catalysts), and the effect of metabolite binding to genes (via direct interactions). Lines show direct effects, with arrows standing for activation, and bars for inhibition. The dashed lines represent indirect associations between genes that result from the projection onto 'gene space'. For example, gene 1 deactivates gene 2 via protein 1 resulting in an indirect interaction between gene 1 and gene 2 (drawn after [Brazhnik00]).
Graph representation of the gene network corresponding to the biochemical network from previous page. This figure corresponds to the lowest tier of that figure. Most genes in gene networks will have a negative effect on their own concentration because the degradation rate of their mRNA is proportional to their concentration (drawn after [Brazhnik00]).
Discovering the true connectivities from gene expression data is not trivial.
Here, three different gene connectivities may lead to similar observed co-expression patterns.
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Transcriptional regulatory network of E. coli
RegulonDB: database with information on transcriptional regulation and operon
organization in E.coli; 105 regulators affecting 749 genes
7 regulatory proteins (CRP, FNR, IHF, FIS, ArcA, NarL and Lrp) are sufficient
to directly modulate the expression of more than half of all E.coli genes.
Out-going connectivity follows a
power-law distribution In-coming connectivity follows
Dynamic representation of transript. regul. network
c, Standard statistics (global topological measures and local network motifs) describing network structures. These vary between endogenous and exogenous conditions; those that are high compared with other conditions are shaded. (Note, the graph for the static state displays only sections that are active in at least one condition, but the table provides statistics for the entire network including inactive regions.)
a, Schematics and summary of properties for the endogenous and exogenous sub-networks.
b, Graphs of the static and condition-specific networks. Transcription factors and target genes are shown as nodes in the upper and lower sections of each graph respectively, and regulatory interactions are drawn as edges; they are coloured by the number of conditions in which they are active. Different conditions use distinct sections of the network.
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Luscombe et al. Nature 431, 308 (2004)
Interpretation
Half of the targets are uniquely expressed in only one condition; in contrast, most
TFs are used across multiple processes.
The active sub-networks maintain or rewire regulatory interactions, over half of
the active interactions are completely supplanted by new ones between conditions.
Only 66 interactions are retained across ≥ 4 conditions.
They are always „on“ and mostly regulate house-keeping functions.
The calculations divide the 5 condition-specific networks into 2 categories:
endogenous and exogenous.
Endogenous processes are multi-stage, operate with an internal transcriptional
program
Exogenous processes are binary events that react to external stimuli with a
rapid turnover of expressed genes.
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Figure 2 Newly derived 'follow-on' statistics for network structures. a, TF hub usage in different cellular conditions. The cluster diagram shades cells by the normalized number of genes targeted by TF hubs in each condition. One cluster represents permanent hubs and the others condition-specific transient hubs. Genes are labelled with four-letter names when they have an obvious functional role in the condition, and seven-letter open reading frame names when there is no obvious role. Of the latter, gene names are red and italicised when functions are poorly characterized. Starred hubs show extreme interchange index values, I = 1. b, Interaction interchange (I) of TF between conditions. A histogram of I for all active TFs shows a uni-modal distribution with two extremes. Pie charts show five example TFs with different proportions of interchanged interactions. We list the main functions of the distinct target genes regulated by each example transcription factor. Note how the TFs' regulatory functions change between conditions. c, Overlap in TF usage between conditions. Venn diagrams show the numbers of individual TFs (large intersection) and pair-wise TF combinations (small intersection) that overlap between the two endogenous conditions.
Luscombe et al. Nature 431, 308 (2004)
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Bioinformatics III 30
Luscombe et al. Nature 431, 308 (2004)
Interpretation
Most hubs (78%) are transient = they are influential in one condition, but less
so in others.
Exogenous conditions have fewer transient hubs (different ).
„Transient hub“: capacity to change interactions between connections.
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a, The 70 TFs active in the cell cycle. The
diagram shades each cell by the normalized
number of genes targeted by each TF in a
phase. Five clusters represent phase-specific
TFs and one cluster is for ubiquitously active
TFs. Both hub and non-hub TFs are included.
b, Serial inter-regulation between phase-
specific TFs. Network diagrams show TFs
that are active in one phase regulate TFs in
subsequent phases. In the late phases, TFs
apparently regulate those in the next cycle.
c, Parallel inter-regulation between phase-
specific and ubiquitous TFs in a two-tiered
hierarchy. Serial and parallel inter-regulation
operate in tandem to drive the cell cycle while
balancing it with basic house-keeping
processes. Luscombe et al. Nature 431, 308 (2004)
TF inter-regulation during the cell cycle time-course
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Luscombe et al. Nature 431, 308 (2004)
Summary
Integrated analysis of transcriptional regulatory information and condition-specific
gene-expression data; post-analysis, e.g. - Identification of permanent and transient hubs- interchange index- overlap in TF usage across multiple conditions.
Large changes in underlying network architecture in response to diverse stimuli, TFs alter their interactions to varying degrees,
thereby rewiring the network some TFs serve as permanent hubs, most act transiently environmental responses facilitate fast signal propagation cell cycle and sporulation proceed via multiple stages
Many of these concepts may also apply to other biological networks.
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Luscombe et al. Nature 431, 308 (2004)
additional slides (not used)
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Cross-organism comparison
Many TF families are specific to
individual phylogenetic groups or
greatly expanded in some genomes.
Babu et al. Curr Opin Struct Biol. 14, 283 (2004)
In contrast to the high level of conservation of other regulatory and signalling
systems across the crown group eukaryotes,
some of the TF families are dramatically different in the various lineages.
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Bioinformatics III 35
Regulatory interactions across organisms
Are regulatory interactions conserved among organisms? Apparently yes.