Abstract
During the first meiotic division, the entire genetic information from DNA is transcribed into mRNPs and stored in the ovoplasm in the form of mRNP particles. The 39 human nuclear HOX proteins bind to thousands of mRNAs transcribed repeatedly by lampbrush chromosomes. HOX proteins suppress processing and translation. The RNP particles containing lncRNAs+HOX proteins are the morphogens (“transcription factors,” more precisely
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There are different opinions about the origin of lncRNAs; they are by genes devoid of protein-coding capacity, intergenic regions, antisense to genes encoding proteins, pseudogenes, and protein-coding genes. Epigenetic regulatory functions have been ascribed to lncRNAs, but there is no explanation how RNA can remodel hetero- to euchromatin and to unlock new genes [3,4].
My research in developmental biology leads to different conclusions. A comparison between the fate of an mRNA in a somatic cell and the same messenger in the maturing oocyte gives new explanation about the origin and functions of long noncoding RNAs.
(1) Messenger RNAs in somatic cells. A functional gene in a differentiated cell is euchromatic. Its sense strand is bound with nonhistone homeodomain structural proteins. This gene belonging to the active euchromatin is unlocked, accessible to RNA polymerase, and starts transcription after an appropriate stimulus. No DNA methylation is needed. The mRNAs in differentiated cells can bind over 1,000 different proteins synthesized in the somatic cells (“interactom”) [5]. The somatic mRNP particles leave the nucleus as informosomes and support processing and translation.
(2) Messenger RNAs in maturing egg follicle. All genes in the oocyte bind with histones in the form of nucleosomes and belong to inactive heterochromatin, characteristics of the nuclei of eggs, spermatozoas, and the inactive chromatin of differentiated cells. These genes are locked by histones and not accessible to RNA polymerase. To start transcription, they need DNA methylation, which explains the simultaneous transcription along all lampbrush chromosomes. Further investigations are necessary to find out what exactly causes this massive transcription. Thousands of long mRNAs transcribed by the male and female chromatids by means of long DNA loops causing the appearance of lampbrush chromosomes. [6]. The newly synthesized RNAs bind HOX proteins (39 in the human karyotype). At that time, there is no protein synthesis in the ooplasm. The HOX proteins are synthesized and delivered to the oocyte by the follicular cells [7]. The HOX proteins suppress processing and translation of the mRNAs, maintaining the primary transcript intact, which is essential for the hybridization with the cDNA of the target gene.
The mRNA/HOX protein complexes leave the germinal vesicle as mRNP particles (morphogens).They accumulate in the ooplasm and can stay there for years without changes (long-lasting RNAs, maternal inheritance). The role of these transcripts is not to synthesize proteins but to control cell differentiation [8 –10]. The messenger RNAs in the somatic cells are coding. The same messengers in the oocyte are noncoding (do not translate).
There are two different ways for a gene to start transcription and two different transcription factors (TF).
(1) If the gene is locked by histones (inactive heterochromatin), DNA methylation, acetylation, or phosphorylation may interfere with histones to make DNA accessible for RNA polymerase. A historical survey shows that during the post-genomic era, the efforts of researchers to resolve cell differentiation have been focused on transcriptional mechanisms and factors that switch genes on and off. The Sanger Institute in Cambridge, United Kingdom, and Epigenomics, a Berlin-based Corporation, focused their research on gene on/off switches, the main goal of their Human Epigenome Project being to study and map DNA methylation or epigenetic changes across the entire human genome. [11]. DNA methylation affects the entire chromatid, without selection of a specific gene, and cannot cause epigenetic changes. After the activation seizes, the DNA remains heterochromatic. There is no chromatin remodeling and differentiation.
(2) If the histones from a gene are replaced by nonhistone proteins [12] or by HOX proteins [10], the gene is permanently unlocked (differentiated) (Fig. 1). The epigenetic factors leading to differentiations are the morphogens. They do not start transcription. The unlocked genes might be activated to transcribe much later. They are accessible for RNA polymerase and transcription starts after appropriate stimulation. After transcription stops, the gene remains differentiated, euchromatic, unlocked, and ready for the next stimulus to renew transcription. The TF in point A above is DNA methylation; the TF in point B is a stimulus. The process of differentiation cannot be identified with the process of transcription. The morphogens are not TF, but
Molecular mechanism for cell differentiation by morphogens (lncmRNA+HOX proteins). During replication the nucleosomal octamer–(n) splits to two tetramers, each attached to the old (parental) DNA strand. The newly synthesized antisense DNA (nA) binds histones and forms a new nucleosome (nn) with the old tetramer—a process accompanied with rotation, probably responsible for the double winding of the DNA helix around the nucleosome. The gene remains locked, belonging to the inactive heterochromatin. On the template of the old antisense strand, a new sense strand (nS) caring a gene sequence will appear. In the presence of morphogens, the complementary lncmRNA will bind the nascent DNA together with the nonhistone homeodomain proteins (dP). Since the place for histones is occupied, no formation of new nucleosomes (non) occurs. The deblocked (unlocked) differentiated gene belongs now to the active euchromatin, which is the missing nucleosome but might have only tetramers.
The lncRNAs are not a patent of the oocyte. “Homeobox genes continued to express virtually in all tissues and organs throughout the adult life” [13]. In my opinion, after G1, in preparation for mitosis, small amounts of cell-specific mRNAs bind HOX proteins, giving rise to cell-specific morphogens, which during S phase bind the complementary nascent DNA, keeping the cell differentiated in the long term. The presence of morphogens in adult cells is confirmed by transplanting a nucleus from one tissue to another differentiated cell. The implanted nucleus accepts the phenotype of the host cell under the action of the host morphogens. The transcripts of a gene in a differentiated cell might be coding or noncoding.
The conclusion is that the transcripts of each gene may be coding or noncoding, depending on the proteins they bind. The morphogens (mRNAs bind with HOX proteins) in the embryonic cells (blastomers) are synthesized in the oocyte, and during the cleavage, segregate in a special order in the blastomers, determining the body plan of the future embryo. The morphogens make the early embryonic cells pluripotent.
The two elements—HOX proteins and noncoding RNAs—applied separately cannot work as morphogens. And this is the great discovery I made studying the meiosis. The nuclear HOX proteins bind the mRNAs and suppress translation, turning them into lncRNAs. This new compound (HOX protein+mRNA) is the morphogen, which in a very elegant manner explains the molecular mechanism of cell differentiation and the great and multifaceted repertoire of RNAs.
Like each discovery, these scientific data open great possibilities for further research. Following the example of the nature showing us how the morphogens are formed, new gene engineering would be able to produce morphogens in vitro, opening bright horizons for cell therapy.
Footnotes
Author Disclosure Statement
No competing financial interests exist.