About this Research Topic
Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view.
In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks.
In the research topic Systems Biology of Transcription Regulation we therefore welcome efforts related to:
• Signals to transcription: signaling pathways triggered by receptors and aiming TFs or chromatin remodeling;
• TF-mediated regulation: TFs, binding of a TF to DNA, TFBSs, motifs, etc.
• Chromatin-histone level: impact of chromatin structure and histone modifications on the gene expression;
• Network inference, reverse engineering;
• Mathematical modeling of the dynamic behavior of gene regulatory networks
• Multilevel modeling: bringing together data from different “levels”, e.g., different –omics data; multilayer networks; combining chromatin and TF information; etc.
We will appreciate articles representing the views on the process of transcription regulation from different perspectives and different angles, preferably combining the abovementioned issues.
Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of discussion that is welcome in this Research Topic.
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