Duplication-Dependent CG Suppression of the Seed Storage Protein Genes of Maize

Genome-wide mining of perfect microsatellites and tetranucleotide orthologous microsatellites estimates in six primate species

Advancement in genome sequencing and in silico mining tools have provided new opportunities for comparative primate genomics of microsatellites. The SSRs (simple sequence repeats) numbers were not correlated with the genome size (Pearson, r=0.310, p=0.550), and were positively correlated with the total length of SSRs (Pearson, r=0.992, p=0.00). A total of 224,289 tetranucleotide orthologous microsatellites families and 367 single-copy orthologous SSRs loci were found in six primate species by homologous alignment. The inner mutation types of single-copy orthologous SSRs loci included the copy number variance, point mutation, and chromosomal translocation. The accumulated repeat times and average length of tetranucleotide orthologous microsatellites in Rhinopithecus roxellana, Papio anubis and Macaca mulatta were longer than Homo sapiens and Pan troglodytes, which showed the tetranucleotide orthologous SSRs loci had more repeat times and longer average length on the branches with earlier divergence time, one exception may be Microcebus murinus as a primitive monkey with a smallest morphology in Malagasy. Our conclusion indicated that single-copy tetranucleotide orthologous SSRs sequences accumulated individual mutation more slowly through time in H. sapiens and P. troglodytes than in R. roxellanae, P. anubis and M. mulatta. However, such divergence wouldn't arise uniformly in all branches of the primate tree. A comparison of genomic sequence assemblages would offer remarkable insights about comparisons and contrasts, and the evolutionary processes of the microsatellites involved in human and nonhuman primate species.

Differential gene expression and epiregulation of alpha zein gene copies in maize haplotypes

Multigenic traits are very common in plants and cause diversity. Nutritional quality is such a trait, and one of its factors is the composition and relative expression of storage protein genes. In maize, they represent a medium-size gene family distributed over several chromosomes and unlinked locations. Two inbreds, B73 and BSSS53, both from the Iowa Stiff Stock Synthetic collection, have been selected to analyze allelic and non-allelic variability in these regions that span between 80–500 kb of chromosomal DNA. Genes were copied to unlinked sites before and after allotetraploidization of maize, but before transposition enlarged intergenic regions in a haplotype-specific manner. Once genes are copied, expression of donor genes is reduced relative to new copies. Epigenetic regulation seems to contribute to silencing older copies, because some of them can be reactivated when endosperm is maintained as cultured cells, indicating that copy number variation might contribute to a reserve of gene copies. Bisulfite sequencing of the promoter region also shows different methylation patterns among gene clusters as well as differences between tissues, suggesting a possible position effect on regulatory mechanisms as a result of inserting copies at unlinked locations. The observations offer a potential paradigm for how different gene families evolve and the impact this has on their expression and regulation of their members.

We present here how the structure and function of a multigene family has shaped the architecture of the maize genome in a haplotype-specific manner, before and after allotetraploidization. The alpha zein gene family, the main component of storage protein genes, provides us with a model of how multicopy gene families evolve and are regulated in the plant kingdom. Indeed, gene copying might be the mechanism that helps plants adapt to variable environmental conditions. In this context, the alpha zein genes have evolved from a common ancestral copy, located on the short arm of chromosome 1, to become a 41-member gene family in the reference maize genome, B73. Different haplotypes can vary, though, as we show here, both in gene copy number and in their sequence context, the latter one being the result of the tremendous transposable element activity that the maize genome has undergone after its allotetraploidization. That had impact not only on the expression patterns of the gene family members, with newest copies contributing the most of the mRNA pool, but also on the mechanisms employed in their regulation, such as methylation of promoter sequences, which seems to be locus-specific.

DNA Methylation in Plants

DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it maybe one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression.