Allopolyploidy alters gene expression in the highly stable hexaploid wheat

Hexaploid wheat (Triticum aestivum) contains triplicated genomes derived from three distinct species. To better understand how different genomes are coordinated in the same nucleus of the hexaploid wheat, we globally compared gene expression of a synthetic hexaploid wheat with its diploid (Aegilops tauschii) and tetraploid (T. turgidum) parents by cDNA-AFLP display. The results suggested that the expression of a significant fraction of genes was altered in the synthetic hexaploid; most appeared to be diminished and some were activated. We characterized nine cDNA clones in details. Cytogenetic as well as genomic sequence analyses indicated that the gene silencing was not due to chromosome/DNA loss but was caused by gene regulation. Northern and RT-PCR divided these genes into three groups: (I) four genes were down-regulated nonspecifically, likely involving both parental orthologues; (II) four genes were down-regulated in an orthologue-dependent manner; (III) one gene was activated specifically in the synthetic hexaploid wheat. These genes were often altered non-randomly in different synthetic hexaploids as well as natural hexaploid wheat, suggesting that many of the gene expression changes were intrinsically associated with polyploidy.     

Does CTCF mediate between nuclear organization and gene expression?

The multifunctional zinc‐finger protein CCCTC‐binding factor (CTCF) is a very strong candidate for the role of coordinating the expression level of coding sequences with their three‐dimensional position in the nucleus, apparently responding to a “code” in the DNA itself. Dynamic interactions between chromatin fibers in the context of nuclear architecture have been implicated in various aspects of genome functions. However, the molecular basis of these interactions still remains elusive and is a subject of intense debate. Here we discuss the nature of CTCF‐DNA interactions, the CTCF‐binding specificity to its binding sites and the relationship between CTCF and chromatin, and we examine data linking CTCF with gene regulation in the three‐dimensional nuclear space. We discuss why these features render CTCF a very strong candidate for the role and propose a unifying model, the “CTCF code,” explaining the mechanistic basis of how the information encrypted in DNA may be interpreted by CTCF into diverse nuclear functions.     

Epigenetics and plant evolution

A fundamental precept of evolutionary biology is that natural selection acts on phenotypes determined by DNA sequence variation within natural populations. Recent advances in our understanding of gene regulation, however, have elucidated a spectrum of epigenetic molecular phenomena capable of altering the temporal, spatial, and abundance patterns of gene expression. These modifications may have morphological, physiological, and ecological consequences, and are heritable across generations, suggesting they are important in evolution. A corollary is that genetic variation per se is not always a prerequisite to evolutionary change. Here, we provide an introduction to epigenetic mechanisms in plants, and highlight some of the empirical studies illustrative of the possible connections between evolution and epigenetically mediated alterations in gene expression and morphology.