Transcriptional Regulation

Although it is easy to understand that changes in the place or time of gene expression can create new or alternative molecular interactions, little information about the organization and evolution of transcriptional regulation in plants is known. However, this knowledge is essential because each gene is flanked by regulatory sequences which, together with the expression and activity of other proteins, determine the amount, place, and timing of expression. Therefore, characterizing these regulatory motifs is required in order to understand the regulatory interactions between trans-acting proteins and the promoters of thousands of genes within a eukaryotic genome. This information is also essential when studying biological processes from a holistic point of view by integrating complementary functional data sets.

We are studying the architecture of plant promoter sequences and try to identify cis-regulatory elements (or TFBS), which play an important role in transcriptional regulation. Fully sequenced plant genomes (e.g. Arabidopsis, poplar, rice, Medicago, Lotus, tomato, green algae etc.) together with extensive expression data sets are or will be used to characterize the basic composition of plant promoters (e.g. TFBS, cis-regulatory modules) and to study their evolution within the green plant lineage.

Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L., Van de Peer, Y. (2009) Unravelling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiol. 150(2):535-46.

• 
• abstract
• 
• pdf
• 
• PMID
• 
• ATCOECIS
• 
• doi
• 

---

* Piganeau, G., * Vandepoele, K., Gourbiere, S., Van de Peer, Y., Moreau, H. (2009) Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus. J. Mol. Evol. 69(3):249-59. *contributed equally

• 
• abstract
• 
• pdf
• 
• PMID
• 
• doi
• 

---

Vandenbroucke, K., Robbens, S., Vandepoele, K., Inzé, D., Van de Peer, Y., Van Breusegem, F. (2008) Hydrogen Peroxide-Induced Gene Expression across Kingdoms: A Comparative Analysis. Mol. Biol. Evol. 25(3):507-16.

• 
• abstract
• 
• pdf
• 
• supp data
• 
• PMID
• 
• doi
• 
• 
• 

---

De Bodt, S., Theissen, G., Van de Peer, Y. (2006) Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting. Mol. Biol. Evol. 23(6):1293-303.

• 
• abstract
• 
• pdf
• 
• PMID
• 
• doi
• 
• supp data
• 

---

Vandepoele, K., Vlieghe, K., Florquin, K., Hennig, L., Beemster, G.T.S., Gruissem, W., Van de Peer, Y., Inzé, D., De Veylder, L. (2005) Genome-wide identification of potential plant E2F target genes. Plant Physiol. 139(1):316-28.

• 
• abstract
• 
• pdf
• 
• PMID
• 
• doi
• 

---

* Rombauts, S., * Florquin, K., Lescot, M., Marchal, K., Rouzé, P., Van de Peer, Y. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 132(3):1162-76. *contributed equally

• 
• abstract
• 
• pdf
• 
• PMID
• 
• supp data
• 
• 
• 

---