Related papers: The evolution of complex gene regulation by low sp…
The diversity of expressed genes plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across cell types and is orchestrated by intricate,…
Genetic regulatory networks (GRNs) have been widely studied, yet there is a lack of understanding with regards to the final size and properties of these networks, mainly due to no network currently being complete. In this study, we analyzed…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
The diverse, specialized genes in today's lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and…
Mathematical models of stem cell differentiation are commonly based upon the concept of subsequent cell fate decisions, each controlled by a gene regulatory network. These networks exhibit a multistable behavior and cause the system to…
Transcription factors are proteins that regulate the expression of genes by binding to specific genomic regions known as Transcription Factor Binding Sites (TFBSs), typically located in the promoter regions of those genes. Accurate…
Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site…
A proof is presented that gene regulatory networks (GRNs) based solely on transcription factors cannot control the development of complex multicellular life. GRNs alone cannot explain the evolution of multicellular life in the Cambrian…
The maintainance of a stable periodicity during the yeast metabolic cycle involving approximately half of the genome requires a very strict and efficient control of gene expression. For this reason, the metabolic cycle is a very good…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…
Robust systems, like the molecular networks of living cells are often resistant to single hits such as those caused by high-specificity drugs. Here we show that partial weakening of the Escherichia coli and Saccharomyces cerevisiae…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…