Abstract
Constitutive heterochromatin is a ubiquitous and still unveiled component of eukaryotic genomes, within which it comprises large portions. Although constitutive heterochromatin is generally considered to be transcriptionally silent, it contains a significant variety of sequences that are expressed, among which about 300 single-copy coding genes have been identified by genetic and genomic analyses in the last decades. Here, we report the results of the evolutionary analysis of Yeti, an essential gene of Drosophila melanogaster located in the deep pericentromeric region of chromosome 2R. By FISH, we showed that Yeti maintains a heterochromatin location in both D. simulans and D. sechellia species, closely related to D. melanogaster, while in the more distant species e.g., D. pseudoobscura and D. virilis, it is found within euchromatin, in the syntenic chromosome Muller C, that corresponds to the 2R arm of D. melanogaster chromosome 2. Thus, over evolutionary time, Yeti has been resident on the same chromosomal element, but it progressively moved closer to the pericentric regions. Moreover, in silico reconstruction of the Yeti gene structure in 19 Drosophila species and in 5 non-drosophilid dipterans shows a rather stable organization during evolution. Accordingly, by PCR analysis and sequencing, we found that the single intron of Yeti does not undergo major intraspecies or interspecies size changes, unlike the introns of other essential Drosophila heterochromatin genes, such as light and Dbp80. This implicates diverse evolutionary forces in shaping the structural organization of genes found within heterochromatin. Finally, the results of dS - dN tests show that Yeti is under negative selection both in heterochromatin and euchromatin, and indicate that the change in genomic location did not affected significantly the molecular evolution of the gene. Together, the results of this work contribute to our understanding of the evolutionary dynamics of constitutive heterochromatin in the genomes of higher eukaryotes.
Highlights
Constitutive heterochromatin is commonly found in large blocks near centromeres and telomeres; it consists mostly of repetitive DNA sequences and maintains its characteristic organization on both homologous chromosomes
To map Yeti in D. simulans and D. sechellia, we used the D. melanogaster Yeti cDNA probe (RE36623), while PCR speciesspecific probes were used in D. pseudoobscura and D. virilis
Virilis the Yeti signal is found at region 53E, in the distal euchromatin of chromosome 5. Independently of their genome localization, in the analysed species Yeti lies in the syntenic chromosome Muller C, that corresponds to the 2R arm of D. melanogaster chromosome 2
Summary
Constitutive heterochromatin is commonly found in large blocks near centromeres and telomeres; it consists mostly of repetitive DNA sequences and maintains its characteristic organization on both homologous chromosomes. Distinctive antagonistic properties compared to the rest of the genome were identified: 1) strongly reduced level of meiotic recombination; 2) low gene density; 3) mosaic inactivation of the expression of euchromatic genes when moved nearby (position effect variegation, PEV); 4) late replication during S phase; 5) transcriptional inactivity; 6) enrichment in the so-called ‘‘junk’’ repetitive DNA, such as satellite sequences and truncated transposable element remnants. Together, these properties led to the view of constitutive heterochromatin as a ‘‘desert’’ of genetic functions [5]. In Drosophila melanogaster, more than 40 genes essential for viability or fertility have been mapped to pericentric heterochromatin [12,13,14,15,16,17]
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