It is widely accepted that gene expression regulation is a stochastic event. The common approach for its computer simulation requires detailed information on the interactions of individual molecules, which is often not available for the analyses of biological experiments. As an alternative approach, we employed a more intuitive model to simulate the experimental result, the Markov-chain model, ...

BACKGROUND Promoter methylation is associated with gene repression; however, little is known about its mechanism. It was proposed that the repression of methylated genes is achieved through the recruitment of methyl binding proteins (MBPs) that participate in closing the chromatin. An alternative mechanism suggests that methylation interferes with the binding of either site specific activators ...

A gene network gives the knowledge of the regulatory relationships among the genes. Each gene has its activators and inhibitors that regulate its expression positively and negatively respectively. Genes themselves are believed to act as activators and inhibitors of other genes. They can even activate one set of genes and inhibit another set. Identifying gene networks is one of the most crucial ...

Induction of local defence, as well as systemic resistance, of plants is associated with transcriptional reprogramming. Here we report on defence gene induction by natural and synthetic stimulants of plant immunity. Gene expression changes in Arabidopsis thaliana were monitored in response to several plant immunity stimulants (plant activators) using Northern blotting and an application-based a...

Anthocyanin is a class of water-soluble flavonoids found in Chinese bayberry (Morella rubra) that not only responsible for the variety colors visible nature but also has numerous health-promoting benefits humans. Through comparative transcriptomics, we isolated and identified transcription factor (TF) R2R3-MYB type, MrMYB9, order to explore anthocyanin biosynthesis pathway red white bayberries....

DNA methylation and chromatin modification operate along a common pathway to repress transcription; accordingly, several experiments demonstrate that the effects of DNA methylation can spread in cis and do not require promoter modification. In order to investigate the molecular details of the inhibitory effect of methylation, we microinjected into Xenopus oocytes a series of constructs containi...

The circadian clock uses a widely expressed pair of clock activators to drive tissue-specific rhythms in target gene expression. A new study sheds light on this tissue specificity by showing that binding of clock activators and tissue-specific transcription factors to closely associated target sites enables cooperative activation of target genes in different tissues.

The transcription apparatus (TA) is a huge molecular machine. It detects the time-varying concentrations of transcriptional activators and initiates mRNA transcripts at appropriate rates. Based on the general structural organizations of the TA, we propose how the TA dynamically orchestrates transcriptional responses. The activators rapidly cycle in and out of a clamp-like space temporarily form...