Towards the quantitative traits regulation: fountain theory implications in comparative and developmental biology.

Abstract

A fountain mechanism of quantitative regulation of gene expression level during development is proposed. The mechanism is based on postulated ability of a special class of RNA molecules, so called fountain RNAs (fRNAs), to induce passive and selective ionic channels in the internal nuclear membrane. Ions diffuse via channel from the nuclear lumen into the chromatin compartment. An RNA-dependent battery of ion channels is assumed to produce <<a fountain>> of ions in close vicinity to the corresponding genes. An ion atmosphere, in its turn, locally changes the chromatin configuration and effectiveness of transcription and processing of transcripts. Hence this mechanism can be used to change genes productivity. It is a basic mechanism of quantitative traits regulation. A passive selective ion flux periodically stops after a threshold ion concentration induces local chromatin compactization and arrests the activity of ion channels in a given chromatin compartment. This process serves as a basis for many cellular biorhythms that are relatively temperature-independent because of the passive nature of ion channel. It is postulated that eukaryotes became eukaryotes just to obtain this fountain mechanism that allows them to perform gradual quantitative modulation of corresponding genes expression levels. The fountain mechanism is partly responsible for dominance and heterosis, X-chromosome inactivation, gene position effects, and some other epigenetic events. It plays an important role in embryonic and post-embryonic development. A significant portion of the former <<junk>> DNA can be referred to as fDNA involved in the proposed mechanism functioning. Genomic rearrangements of fDNA could lead to micro- and macroevolutionary changes in the animal and plant kingdoms. The pivotal evolutionary function of transposons could reside in their ability to contain and relocate fDNA along the chromosomes.