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A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein, whereas a mRNA is translated into a protein. The ncRNAs include highly abundant and functionally important RNAs such as transfer RNA (tRNA), ribosomal RNA (rRNA), as well as small ncRNA and long ncRNA. The main classes of small ncRNAs are miRNA, short interfering RNA (siRNA), and PIWI-interacting RNA (piRNA), and all of them play an important role in RNA interference (RNAi) pathway. Many reports suggest that long ncRNAs are involved in structure of functional nuclear domain.
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In eukaryotic cells, there are a lot of regulatory mechanisms, which control quality of mRNA in various steps from processing of precursor mRNA (pre-mRNA) in nucleus to translation into protein through cytoplasmic ribosome. Among these processes, RBPs play a primary role in regulating the behavior of the functionally related genes by forming the ribonucleoprotein (RNP) clusters.
Recent transcriptome analyses have revealed that transcription occurs at more than 90% of human genomic DNA regions, and more than 95% of transcripts are predicted to be ncRNAs. That is to say, most of the transcribed RNAs are ncRNAs. Although annotation of ncRNAs has been started in several species, the functions of most of them are still unknown. Some of them have been confirmed to be mRNA-like ncRNAs that undergo post-transcriptional processing, such as 5'-capping, splicing and 3'-polyadenylation, without being translated. As the study on RNA became an active area of research, it has been unveiled little by little that the most of the mRNA-like ncRNAs reside in the nucleus and function as an essential structural determinant of nuclear functional domains. ncRNAs and RBPs are aligned and regulated in a spatiotemporally specific manner in each nuclear functional domain. These findings support the noticeable concept, ‘RiboCluster’, propounded by MBL.
To understand, what kind of mechanism resolves this typically linguistic problem of removing homonym indefiniteness, it is necessary firstly to postulate a mechanism for the context-wave orientations of ribosomes in order to resolve the problem of a precise selection of amino acid during protein synthesis [Maslow, Gariaev 1994].
Numerous and unclear events of distant “recognition” of the antigene-antibody and tRNA anticodon-iRNA codon pairs, as well as complementary mutual recognitions of DNA single chains, self-construction of ribosomes, recognition sites of ferments, careful piloting and landing of transposons in the DNA and so on, are also well contained within the frames of these processes.
In this paper, we are trying to produce more developed opinions of some possible synthesis mechanisms and functions of wave genetic structures, attributable to higher biosystems, as well as of the methods applicable for simulation of sign wave processes in chromosomes and model units simulating chromosome field functions and transferring wave genes.
On the other side, if we know the principles of ribosome operation in a context orientation mode, then we can successfully fight HIV in a ribosomal wave (laser, solitonic, polarization and radio wave) regulation zone.
Laser-like radiations, emitted by the participants in this process and correcting the order of insertion of the amino acid components into a peptide, also function on the ribosome in addition to and/or together with the resonance regulations of a mutual dislocation of the codon-anticodon continuums.
It is possible to postulate a qualitative, simplified, initial version of substance-wave control over the amino acids' line-up order, dictated by the associates of aminoacylated tRNA, the predecessors of proteins.
Indeed, the code is likely to be a multi-letter fractal and heteromultiplet structure coding both individual proteins and functionally-linked protein associates.
In  an important idea, very close to ours, was put forward: the influence of the mRNA context on monosemantic incorporation of amino acids into a peptide chain reflects some basic, still unstudied, laws of genetic information coding in the protein synthesis process.
Here, the translation context effect is clearly seen as a strategic influence of distant mRNA codons on the inclusion (or non-inclusion) of certain amino acids in the composition of a protein being synthesized.
That’s why mRNA, acting as a “phrase”, should operate in the protein synthesis process as an integral coding system, non-locally determining the sequence of amino acids at the level of tRNA aminoacylated associates, which interact in a global and complementary way with the entire mRNA molecule.