Environmental genomics: a tale of two fishes.

The influence of the environment on two congeneric fishes, Gillichthys mirabilis and Gillichthys seta, that live in the Gulf of California at temperatures of 10-25 degrees C, and up to 42-44 degrees C, respectively, was addressed by analyzing their genomes. Compared with G. mirabilis, G. seta showed some striking features. Substitution rates in the mitochondrial genes were found to be extremely fast, in fact faster than in noncoding control regions (D-loops), from which a divergence time of less than 0.66-0.75 Mya could be estimated. In the nuclear genome, 1) both AT --> GC/GC --> AT and transversion: transition ratios in coding sequences (CDSs) were relatively high; moreover, the ratios of nonsynonymous/synonymous changes (Ka/Ks) suggested that some genes were under positive selection; 2) DNA methylation showed a very significant decrease; and 3) a GC-rich minisatellite underwent a 4-fold amplification in the gene-rich regions. All these observations clearly indicate that the environment (temperature and the accompanying hypoxia) can rapidly mold the nuclear as well as the mitochondrial genome. The stabilization of gene-rich regions by the amplification of the GC-rich minisatellite and by the GC increase in nuclear CDSs is of special interest because it provides a model for the formation of the GC-rich and gene-rich isochores of the genomes of mammals and birds.

Mapping DNase-I hypersensitive sites on human isochores.

Mapping DNase-I hypersensitive sites (HS) was used in the past to identify regulatory elements of specific genes. More recently, thousands of HS were identified in the human genome by using high-throughput methods. These approaches showed a general enrichment of HS near or within known genes, within CpG islands, within human-mouse conserved regions and in GC-rich regions of the genome. Here we show that HS: (i) are characterized by a much higher GC level (approximately 56%) than the average GC level of the human genome (approximately 41%); (ii) are overwhelmingly located in the GC-richest compartment of the genome, which is predominantly associated with an open chromatin structure; (iii) and are slightly more and slightly less frequent than genes, respectively, in the gene-rich and in the gene-poor isochore families.

Extrapolating ENCODE data to the whole human genome.

The ENCODE (ENCyclopedia Of DNA Elements) project was launched three years ago with the purpose of identifying all of the functional elements in the human genome. ENCODE was started with 44 target sequences, which comprise 1% of the human genome. A crucial question about ENCODE is how representative it is of the human genome. Indeed, this is not a negligible problem if one considers that only 1% of the genome was selected for the project, and, more importantly, that the choice of the large DNA segments was based on two major criteria, namely the presence of extensively characterized genes and/or other functional elements, and the availability of a substantial amount of comparative sequence data. We found that the ENCODE data lead to an unbalanced representation of the compositional pattern of the human genome, especially for the GC-poorest and GC-richest regions. This unbalanced representativity of ENCODE can, however, be corrected by multiplying ENCODE data by a G/E factor (the ratio of whole genome data over ENCODE data), so amplifying the potential interest of ENCODE.

Isochore pattern and gene distribution in the chicken genome.

We report here investigations on the isochore pattern and the distribution of genes in the chromosomes of chicken. In spite of large differences in genome size and karyotype, the compositional properties and the gene distribution of the chicken genome are very similar to those recently published for the human genome, which is a good representative of most mammalian genomes. In fact, this similarity, which extends to the relative amounts and, also, to a large extent at least, to the average base composition of isochore families, is most interesting in view of the very large distance of mammals and birds for a common ancestor, which goes back to 310-340 million years ago. This raises important questions about genome evolution in vertebrates.

Ammonium channel expression is essential for brain development and function in the larva of Ciona intestinalis.

Ammonium uptake into the cell is known to be mediated by ammonium transport (Amt) proteins, which are present in all domains of life. The physiological role of Amt proteins remains elusive; indeed, loss-of-function experiments suggested that Amt proteins do not play an essential role in bacteria, yeast, and plants. Here we show that the reverse holds true in the tunicate Ciona intestinalis. The genome of C. intestinalis contains two AMT genes, Ci-AMT1a and Ci-AMT1b, which we show derive from an ascidian-specific gene duplication. We analyzed Ci-AMT expression during embryo development. Notably, Ci-AMT1a is expressed in the larval brain in a small number of cells defining a previously unseen V-shaped territory; these cells connect the brain cavity to the external environment. We show that the knockdown of Ci-AMT1a impairs the formation of the brain cavity and consequently the function of the otolith, the gravity-sensing organ contained in it. We speculate that the normal mechanical functioning (flotation and free movement) of the otolith may require a close regulation of ammonium salt(s) concentration in the brain cavity, because ammonium is known to affect both fluid density and viscosity; the cells forming the V territory may act as a conduit in achieving such a regulation.

Euchromatic and heterochromatic compositional properties emerging from the analysis of Solanum lycopersicum BAC sequences.

The consortium responsible for the sequencing of the tomato (Solanum lycopersicum) genome initially focused on the sequencing of the euchromatic regions using a BAC-by-BAC strategy. We analyzed the compositional features of the whole collection of BAC sequences publically available. This analysis highlights specific peculiarities of heterochromatic and euchromatic BACs, in particular: the whole BAC collection has i) a large variability in repeat and gene content, ii) a positive and significant correlation of LTR retrotransposons of the Gypsy class with the repeat content and iii) the preferential location of the SINEs (short interspersed nuclear elements) in BAC sequences showing a low repeat content. Our results point out a typical design of the tomato chromosomes and pave the way for further investigations on the relationship between DNA primary structure and chromatin organization in Solanaceae genomes.

The early apoptotic DNA fragmentation targets a small number of specific open chromatin regions.

We report here that early apoptotic DNA fragmentation, as obtained by using an entirely new approach, is the result of an attack at a small number of specific open chromatin regions of interphase nuclei. This was demonstrated as follows: (i) chicken liver was excised and kept in sterile tubes for 1 to 3 hours at 37 degrees C; (ii) this induced apoptosis (possibly because of oxygen deprivation), as shown by the electrophoretic nucleosomal ladder produced by DNA preparations; (iii) low molecular-weight DNA fragments (approximately 200 bp) were cloned, sequenced, and shown to derive predominantly from genes and surrounding 100 kb regions; (iv) a few hundred cuts were produced, very often involving the same chromosomal sites; (v) at comparable DNA degradation levels, micrococcal nuclease (MNase) also showed a general preference for genes and surrounding regions, but MNase cuts were located at sites that were quite distinct from, and less specific than, those cut by apoptosis. In conclusion, the approach presented here, which is the mildest and least intrusive approach, identifies a preferred accessibility landscape in interphase chromatin.