Work

On the power and limits of evolutionary conservation—unraveling bacterial gene regulatory networks

Year: 2010

Type: review

Abstract: The National Center for Biotechnology Information (NCBI) recently announced '1000 prokaryotic genomes are now completed and available in the Genome database'. The increasing trend will provide us with thousands of sequenced microbial organisms over the next years. However, this is only the first step in understanding how cells survive, reproduce and adapt their behavior while being exposed to changing environmental conditions. One major control mechanism is transcriptional gene regulation. Here, striking is the direct juxtaposition of the handful of bacterial model organisms to the 1000 prokaryotic genomes. Next-generation sequencing technologies will further widen this gap drastically. However, several computational approaches have proven to be helpful. The main idea is to use the known transcriptional regulatory network of reference organisms as template in order to unravel evolutionarily conserved gene regulations in newly sequenced species. This transfer essentially depends on the reliable identification of several types of conserved DNA sequences. We decompose this problem into three computational processes, review the state of the art and illustrate future perspectives.

Source: Nucleic Acids Research

DOI: 10.1093/nar/gkq699

Author: Jan Baumbach

Institutions: International Computer Science Institute, Max Planck Society, Max Planck Institute for Informatics

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,992

Funders: Boehringer Ingelheim Fonds, Deutscher Akademischer Austauschdienst, Deutsche Forschungsgemeinschaft