Academic journal article Genetics

Evolution of Gene Sequence in Response to Chromosomal Location

Academic journal article Genetics

Evolution of Gene Sequence in Response to Chromosomal Location

Article excerpt

ABSTRACT

Evolutionary forces acting on the repetitive DNA of heterochromatin are not constrained by the same considerations that apply to protein-coding genes. Consequently, such sequences are subject to rapid evolutionary change. By examining the Troponin C gene family of Drosophila melanogaster, which has euchromatic and heterochromatic members, we find that protein-coding genes also evolve in response to their chromosomal location. The heterochromatic members of the family show a reduced CG content and increased variation in DNA sequence. We show that the CG reduction applies broadly to the protein-coding sequences of genes located at the heterochromatin:euchromatin interface, with a very strong correlation between CG content and the distance from centric heterochromatin. We also observe a similar trend in the transition from telomeric heterochromatin to euchromatin. We propose that the methylation of DNA is one of the forces driving this sequence evolution.

DETAILED examination of the heterochromatic regions around eukaryotic centromeres has distinguished two subregions with differences in the structure of their chromatin and in their sequence composition (HEITZ 1934; Gatti and Pimpinelli 1992). The central region, referred to as a-heterochromatin, hosts the centromere and is the most compacted chromosome region. In the polytene chromosomes of Drosophila, it shows the lowest degree of replication and consists mainly of highly repetitive elements. The region referred to as b-heterochromatin is generally thought to be located between the a-heterochromatin and the euchro-matin of each chromosome arm. Its intermediate location also reflects the intermediate nature of its molecular and cytological characteristics. b-Heterochromatin is moderately compacted, moderately replicated in poly-tene chromosomes, and is formed by moderately repetitive elements interspersed with genes at a lower density than in euchromatic locations (ASHBURNER et al. 2004).

The β-heterochromatic genes present some unusual structural and regulatory characteristics. They span larger regions than is typical for euchromatic genes, mainly due to the possession of extremely large introns containing many insertions of transposable elements (DEVLIN et al. 1990; BIGGS et al. 1994; TULIN et al. 2002; DIMITRI et al. 2003). Although there is nothing obviously distinctive about the proteins that these genes encode, their regulation is in many ways contrary to that of euchromatic genes. Their expression is reduced when they are relocated away from centric heterochromatin (KHVOSTOVA 1939; HESSLER 1958; WAKIMOTO and HEARN 1990; EBERL et al. 1993), and suppressors or enhancers of euchromatic gene variegation often have the opposite effect on the variegation of heterochromatic genes (SCHULTZ 1936; Baker and Rein 1962; Wakimoto and Hearn 1990; Hearn et al. 1991; Lu et al. 2000; Weiler and Wakimoto 2002). Thus, both gene structure and expression appear to be influenced by a heterochromatic location.

Gene families are especially valuable for the study ofmolecular evolution since they afford the possibility of making several kinds of comparisons. One type of comparative analysis uniquely available with multi-gene families is the comparison of paralogs, those family members found within a single genome. Ideally, these analyses would make use of DNA sequence variation, both in coding and noncoding elements, gene exon structures and gene expression patterns, and known mutant phenotypes. These paralogous comparisons will help to detect conservation or divergence of function and/or structure and to deduce roles for each family member. Ultimately, this should allow us to interpret how such DNA and protein sequence changes are related to functional specializations, chromosome locations, or any other specific characteristic of the studied paralogs.

To specifically explore whether genes located near heterochromatin experience unique selective forces because of their location, we chose to examine the Troponin C (TNC) family of Drosophila melanogaster, which hasmembers in euchromatin and in b-heterochromatin (Figure 1). …

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