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Genome organization and transcription at the beginning of development

Final Activity Report Summary - DEVELOP. GENOMICS (Genome organization and transcription at the beginning of development.)

The purpose of this project was to explore how genomic organisation impacts on regulation of gene transcription, during the early stages of embryonic development. In this research, by genomic organisation is meant variation of GC levels (percentage of Gs and Cs) along the genomic sequence, or composition. This is a convenient choice, given that it can be recognised based on sequence information and that it nicely correlates with several important structural and functional features of genomes. Among these, global levels of gene transcription: on a genome-wide scale, GC-rich genes are embedded in the GC-richer portions of the genome and are transcribed at higher levels than GC-poor ones.

On the other hand, it is generally understood that it is the information contained in a gene's cis-regulatory region that determines the time, the place and the amount at which gene transcription happens. Genes' cis-regulatory regions are built in a modular way, each module being a cluster of binding sites for the transcription factors (activators or repressors) that regulate gene expression. Appropriate mRNA production is the result of the integration of the inputs presented at these different binding sites.

Therefore, the relationship between composition of genomic context and utilisation of regulatory information is not obvious and it was explored in this work.

The experimental system utilised has been the developing sea urchin embryo, a highly accessible model system, whose genetic developmental programming is understood to a good degree. In the course of this research, the regulatory region of the gene spdri, expressed during development of the embryo has been dissected. This information has been utilised to address the main question of this research.

The spdri gene is expressed at two different times and places in the developing sea urchin embryo. Two sets of regulatory modules are needed to achieve temporally and spatially correct expression of the gene. In the early as well as in the late expression phase, three different kind of inputs are utilised: positive and globally distributed ones; negative ones (that prevent ectopic expression); positive tissue-specific ones.

Composition of spdri's cis-regulatory region matches that of its genomic context. By forcing the incorporation of a trans-gene that contained spdri's cis-regulatory region, in locations of the genome that had a lower or higher GC levels (34 % and 41 % versus 37,9 %), alterations of its expression pattern were observed. Such alterations were never random, as they could be directly related to the loss of function of regulatory modules located at the extremities of spdri's cis-regulatory region.

These results indicate that in order to work, a cis-regulatory region needs to be in a compositionally appropriate context. Otherwise, part of the regulatory information remains inaccessible to the transcriptional apparatus. To assess whether these observations refer to some peculiar property of the experimental system chosen or are instead indicative of some more general property, the genomic contexts of 80 human genes were analysed. In all cases, composition of the genomic contexts was found to match that of the cis-regulatory region considered. These results support the idea that gene localisation in genomes is not random and that genomes are integrated ensembles.