RNA Genes: Retroelements and Virally Retroposable microRNAs in Human Embryonic Stem Cells

Abstract

Embryonic stem cells (ESCs) are capable of undergoing self-renewal, and their developmental ability is known as the stemness. Recently, microRNAs (miRNAs) as regulators have been isolated from ESCs. Although Dicer and DiGeorge syndrome critical region gene 8 (DGCR8) are essential factors for the biogeneration of miRNA, Dicer-knockout (KO) ESCs have showed to fail to express differentiation markers and DGCR8-KO ESCs have showed to be arrest in the G1 phase. Furthermore, Dicer-KO ESCs lost the ability to epigenetically silence retroelemtns (REs). REs are expressed and transposed in ESCs, whose transcripts control expression of miRNAs, and their transposable retroelement (TE) expression is, therefore related to ESC proliferation and differentiation, suggesting that the interplay between miRNAs and REs may have a deep responsibility for the stemness including a short G1/S transition and for RE regulation in ESCs.

Keywords: ES cell; HIV-1; RNA wave.; microRNA; retrotransposon.

Fig. (1)

A model of TE-controlled miRNA expression mechanisms. (A) Transposable elements (TEs) in the genome. The architecture of the genome for TEs was represented. (B) Alu-genomic miRNA switching. Clusters of miRNAs in human chromosome 19 (Chr19) and murine chromosome 7 are represented. These genomic miRNA genes are closely or overlapping localized in TEs, such as Alu and B1. The direction of TEs may not matter. TE could promote the expression of pri-miRNA (Alu-pri-miRNA) and genomic miRNAs from the pri-miRNA can be silence on translation of target mRNAs in ESCs. (C) ESC specific resident miRNAs for self-renewal and differentiation. Human ESCs express self-renewal specific set of miRNAs. The cluster of miR-371, 372 and 373 is related to the self-renewal of ESCs. The cluster of miR-290 in murine is also specific for ESC self-renewal and the murine miR-290 cluster genes are transferred from ESCs to neighboring cells by ESC microvesicles (ESMVs). For differentiation of ESCs, other resident miRNAs are presented and then the profile of miRNAs in differentiated cells, such as granulocytes and monocytes is greatly different from that of ESCs.

Fig. (2)

DGCR8- or Dicer-null ESCs. DGCR8-null ESCs lack differentiation ability, and, in turn DGCR8 is essential for the silencing of self-renewal. Dicer-null ESCs also lack differentiation ability. But both null cells remain alive and pluripotent markers still continue to be expressed. In Fig. (1B), there is self-renewal set of human miRNAs (miR-371 cluster in C19MC), suggesting that the resident miRNAs are present independently and the resident miRNAs might play important role in the ESCs’ self-renewal program. These data are based on the criteria of the RNA wave.

Fig. (3)

A model of epigetic on/off switching mechanism of transposable miRNAs. (A) Epigenetic silencing off by the resident small RNAs is shown. The function of nnRNA is similar to that of siRNA. Alu-pri-miRNAs as the TE could be targeted by nnRNA during transcription epigenetically. This process induces complete silencing off, that starts translation of mRNAs for differentiation of ESCs. The Ago/nnRNA complex circulized as a Buddhist rosary (‘Jyuzu’ in Japanease) and the ring of nnRNA may epigentically lock Alu-pri-miRNA transcription by methylation of histone by Clr4-like human methyltransferase (HMT) enzyme, Suv39 associated with Swi6/HP1 and chromo domain-containing protein 1 (Chp1) plus RNA-induced transcriptional silencing complex protein 3 (Tas3) binding to H3K9me+ histone following CpG methylation by DNA methyltransferase (DNMT) [111]. (B) The HIV-1 latency model. The Weinberg and Morris model [97] is shown with minor modifications. The HIV-1 3’LTR U3 region contains at least three genomic miRNA genes: MIR#4, MIRN367 and MIRH1. The 5’LTR/gag/pol/env region may be corresponding to Alu TE. These genomic miRNAs yeild silencing of HIV-1 proviral expression (Switch OFF). Environmental factors, such as the resident miRNA in ESMV, IL-2, X-ray, dietary food etc. affect the profile of miRNAs in cells, nnRNA from digestion of the resident miRNAs, retroposable miRNAs or mobile miRNAs completely stopped expression of Alu-pri-miRNA described in (A). This is the mechanism of latency. Dominant transcriptional factor induces HIV-1 mRNA transcription (Switch ON). In this state, iPS cells may be produced; however, since there is no step of complete silencing on, iPS cells may occasionally change into tumour cells. Therefore, the differentiation set of the resident miRNAs should be completely switched off to reprogram the somatic cell.

Fig. (4)

A model of tanslational tuning by virally mobile miRNAs. (A) G-G repeats in the miRNAs. The viral miRNAs of HIV-1 (i), self-renewal-related miRNAs (ii) and differentiation-related miRNAs (iii) contained GG repeats (black dots). The calculated FMO values were represented as a radar-circle, which could be represented as wings by Excel software (Microsoft corp.). Shaded diamonds are represented as the region of the seed. The FMO values of each atom of bases were calculated by winMOPAC software version 3 (SCIGRESS MO Compact Professional: Fujitsu Corp. Tokyo, Japan) and each panel was illustrated by EXCEL (Microsoft Corp. USA). (B) Quantum theory of the RNA wave in translational tuning. The model of Fabian et al. in the Sonenberg laboratory (2009) is modified and the modified model is represented. (i) Circularized viral HIV-1 RNA (mRNA) via eIF4G-PAGP interaction and viral miRNAs, such as MIR#4, MIRN367 and MIRH1 are circularized via Ago2 and GW182. (ii) miRNA targets mRNA. Black shaded regions represented appropriate mage of unbalanced electron distribution. (iii) Circularized mRNA by cap-binding factor eIF4E plus eIF4G and poly(A)-binding protein PABP could make miRISC into linear strand of mRNA. miRISC is the link of the miRNA ring and circularized miRNAs are superposed. Electrons on the virally circular miRNAs would move from one base to another neighboring base, whereas electrons may spin round. Depended on the direction of the rotating electron, the direction of the magnetic field would go up or down. The superposing of the magnetic direction of electrons according to quantum theory may be the code of RNA as in quantum computing (Fujii, 2008). (iv) The mobile miRNAs can tune silencing ON (Switch ON) and repeat to (i) ~ (iv) in very short time (see Movie S1).