Relationship between regulatory element organization, gene function and gene expression in Arabidopsis thaliana : toward the regulatory element annotation.

My Ph.D. defense

Promoteur

Proteins are synthetised with both, the transcription of DNA in RNA, and the translation of RNA in protein. Mechanisms involved during transcription and translation are well known. On the other hand, when and how genes are expressed are questions for which there is only the beginning of answer. The genes expression is regulated by a lot of processes. A better knowledge of this regulation is particularly interesting to be able to predict the gene expression conditions.

The transcription initiation is an essential process which contributes to the regulation of gene expression. The regulatory element presence in promoter of genes is involved in this process. Their presence regulates the gene expression in definite conditions, in reply to a stress or in specific tissues. A better knowledge of the promoter architecture and therefore a better knowledge of the gene expression regulation are today possible at the genomic level for A. thaliana, by exploiting the available transcripts. However, the actual analyses often consider only the regulatory element identification, without taking into account their organization in the promoters, or the function of linked genes. By considering this organization and linking it up with the functional annotation of A. thaliana genes, we propose to ameliorate the regulatory element annotation.

Functional regulatory elements may be conserved during the evolution at a preferential position relative to the transcription start site. They can be identified by searching overrepresented sequences in a definite position. Besides, one waits for regulatory elements involved in the same biological pathway co-present in promoters. Genes having a same promoter organization put in an obvious place a functional link therefore between the co-present regulating elements.

TATAWA distribution

Out of A. thaliana promoters, I characterized regulatory elements by their preferential positions relative to the transcription start site. I grouped them according to their biased co-presence within the promoters. This analysis put in an obvious place the functional bias of genes linked to a precise organization of regulatory elements in the core-promoter. This result is a first step in the functional annotation of regulatory elements. At present I focus my work on the core-promoter analysis. The regulatory elements which are present in this area are linked together and they are conserved at a very strict position within the promoters.

The general research of functional biases within genes having a same promoter organization will allow following this regulatory elements annotation.