Evolution of the AMP-Activated Protein Kinase Controlled Gene Regulatory Network
| Autor: | Markus Bönn, Ivo Grosse, Katharina Strödecke, Ioana Lemnian, Constance Mehlgarten, Ralf Eggeling, André Gohr, Karin D. Breunig, Martin Nettling, Carolin Kleindienst |
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| Rok vydání: | 2017 |
| Předmět: |
Genetics
Regulation of gene expression 0303 health sciences Computer science 030302 biochemistry & molecular biology MAPK7 Gene regulatory network Context (language use) Computational biology Autophagy-related protein 13 Divergent evolution 03 medical and health sciences Tree (data structure) Adaptation 030304 developmental biology |
| Zdroj: | Information-and Communication Theory in Molecular Biology ISBN: 9783319547282 |
| DOI: | 10.1007/978-3-319-54729-9_9 |
| Popis: | Alterations in gene regulation are considered major driving forces in divergent evolution. This is reflected in different species by the variable architecture of regulatory networks controlling highly conserved metabolic pathways. While many regulatory proteins are surprisingly conserved their wiring has evolved more rapidly. This project focuses on the adaptation to nutrient limitation, which requires the activation of the conserved AMP-activated protein kinase (AMPK alias Snf1 in yeast) and its downstream effectors. The goal is to uncover basic principles of adaptation and steps in the evolutionary process associated with regulatory network rearrangement. This requires improving the prediction of gene regulation based experimental data, DNA sequence information and information theory. In this project Context Tree (CT) models and Parsimonious Context Tree (PCT) models and the corresponding algorithms for extended Context Tree Maximization (CTM) and extended Parsimonious Context Tree Maximization (PCTM) are derived, implemented, and applied. Computational predictions and experimental validation will establish an iterative cycle to improve algorithms in each cycle leading to a growing set of experimentally verified and falsified predictions, finally allowing a deeper understanding of the evolution of the transcriptional regulatory network controlling energy metabolism, one of the most fundamental processes conserved across all kingdoms of life. |
| Databáze: | OpenAIRE |
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