Tag Archives: Transposable Element

Retrotransposons as regulatory elements

In a paper from 2004, Peaston et al reported on the expression of various retrotransposons (RTEs) in the mouse oocyte and pre-implantation embryo, finding widespread RTE transcription and the presence of chimeric transcripts composed of host genes and RTEs.

In a cDNA library constructed from full grown oocyte (FGO) transcripts, 12% of sequences were derived from MT (mouse transcript, a member of the MaLR family of nonautonomous LTR class III retrotransposons), whilst in a library from 2 cell stage embryos, 3% of cDNAs were derived from murine ERV-L (another class III  LTR RTE). Expression of these and other RTEs tailed off to nothing by the blastocyst stage. The differential developmental expression profile of these RTEs is interesting: MT is a large component of the maternally contributed RNA in the oocyte, whilst MuERV-L must be expressed zygotically very early in development.

The most important finding of this paper was that the cDNA libraries from FGO and 2 cell embryos contained many chimeric gene transcripts in which the 5′ sequence was derived from retrotransposons. These chimeric mRNAs made up 3% of the FGO library and 1.4% of the 2 cell stage embryo library. A large variety of RTEs contribute to chimeras in the FGO library but 51% of them involved MT. 56% of chimeric transcripts in the 2 cell stage had 5′ contributions from MuERV-L and it’s relatives, so RTE composition of the chimeric transcripts correlated with specific RTE abundance. The genes expressed as chimeric transcripts didn’t show any particular functional bias.

When the chimeric transcripts were compared with genomic sequence it was found that the cognate RTEs were either located within the gene locus or upstream of it. If the RTE was encoded within the gene, the chimeric transcript lacked any exons upstream of it. When the RTE was located upstream of the gene, the chimeric mRNA often lacked one or more 5′ exons (2/3rds of the time).

Therefore it appears that RTE sequences act as cis-regulatory elements driving oocyte and pre-implantation embryo specific expression of a population of alternatively spliced transcripts encoding (generally) variant proteins. The notion of RTEs as alternative promoters is close to that of transposons as “controlling elements” put forward by their discoverer Barbara McClintock. The authors note that RTE insertions could give rise to co-regulated gene expression and that RTE driven transcription of multiple host genes “provides grounds for selection of new modes of gene regulation by introducing variation”.

In a review of this work Shapiro uses this as evidence for a “functionalist” perspective, in which he regards mobile elements as “distributed genomic control modules”. This does seem to overstate the purposiveness of TE insertion. One potentially forgets all the cases of deleterious mutations leaving no issue. However, there is no doubt that through evolutionary time, host/parasite arms races can become coevolved integrated functions. An interesting finding in Peaston et al was that sense and antisense transcripts were found in relatively equal ratio when MuERV-L was expressed. This suggested that dsRNA would be formed, triggering RNAi that could seed heterochromatin formation to repress RTE expression. This is again open to a dichotomy of interpretation: in that this is part of a host mechanism to inhibit genomic parasites, or conversely (as Shapiro does) “another mechanism by which RTE insertions can influence the expression of nearby coding sequences and act to construct distributed suites of co-ordinately regulated loci”.

See also: On Transposable Elements and Regulatory Evolution 

Peaston AE, Evsikov AV, Graber JH, de Vries WN, Holbrook AE, Solter D, & Knowles BB (2004). Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Developmental cell, 7 (4), 597-606 PMID: 15469847

Shapiro JA (2005). Retrotransposons and regulatory suites. BioEssays : news and reviews in molecular, cellular and developmental biology, 27 (2), 122-5 PMID: 15666350

Virophages and the evolution of transposable elements

Fischer, M., & Suttle, C. (2011). A Virophage at the Origin of Large DNA Transposons Science, 332 (6026), 231-234 DOI: 10.1126/science.1199412

This paper reports the discovery and characterisation of a virophage, Mavirus, and postulates that it’s similarities with a family of transposable elements suggest a common evolutionary origin.

Mavirus (white arrows) in the virion factory of CroV (CroV viral particles white arrow head, black arrow - a potentially defective CroV capsid)

Mavirus is the second virophage so far discovered. Both it and the other, Sputnik, parasitize giant viruses that infect protists. There is some controversy as to whether these viruses should be classified as virophages or a new class of satellite viruses. Virophages are predicted to have no nuclear phase in their infection cycle, to replicate in the virion factory of the host virus and to be dependent on enzymes provided by the host virus rather than the host cell. Mavirus is associated with the Cafeteria roenbergensis virus (CroV) that infects the marine phagotrophic flagellate C. roenbergensis. Mavirus can’t replicate in the absence of CroV, and CroV production and host cell lysis was reduced when infected with Mavirus.

The Mavirus has a 19kb circular double stranded DNA genome that is predicted to contain 20 protein coding genes (fig 1).  Between each gene the researchers found promoters that are highly similar to the predicted late promoter motif in CroV, implying that Mavirus gene expression is activated by the transcription machinery of CroV. Only four Mavirus genes showed homology with those on Sputnik, the other known virophage (including those encoding the capsid protein and a DNA pumping ATPase).

Figure 1. Genome diagram of Mavirus. Genes conserved with MP TEs are in red. Genes sometimes found in MP TEs in blue.

More genetic homology is found between Mavirus and a class of DNA transposons: the self-synthesising Maverick or Polinton Transposable elements (MP TEs). MP TEs are between 9 and 22kb long and encode up to 20 proteins. A conserved subset of genes is found in all MP TEs including a retroviral integrase (rve-INT) (responsible for DNA integration), a protein primed DNA polymerase B (PolB), an ATPase similar to those responsible for packaging dsDNA in viruses, and a cysteine protease with adenoviral homologues. Genes for all four of these proteins were found in Mavirus as well as another three often encountered in MP TEs.

The best evidence for a close evolutionary relationship between Mavirus and MP TEs was the identification of a region of synteny between Mavirus and a genomic fragment from the slime mold Polysphondylium pallidum that contains a MP TE-like fragment (fig 2).

Fig 2. Comparison of gene organisation between Mavirus and a truncated MP TE from P. pallidum. homologous genes are the same colour and the syntenic region shown in green.

Another resemblance between MP TEs and Mavirus relates to genome structure. MP TEs have terminal inverted repeats of several hundred nucleotides, and highly conserved ends starting with 5′-AG and ending with CT-3′. Although the Mavirus genome is a circular molecule at one point it encodes a ~50bp inverted repeat with the potential to adopt a hairpin structure. The adenine at the top of this hairpin was designated position 1 of the genome. Cutting the Mavirus genome between nucleotides 19,063 and 1 would result in the same termini as MP TEs and inverted repeats.

All these parallels between MP TEs and Mavirus suggest that the two are derived from a common ancestor. The question is whether the common ancestor was a transposable element or a virophage? The authors consider that the more parsimonious explanation is that a Mavirus ancestor (MVA) gave rise to MP TEs, and go on to suggest a possible evolutionary scenario. In early eukaryotic cells susceptible to infection by large DNA viruses there would be selective pressure on the host cells to stabilise relationships with a MVA. The acquisition of a retroviral integrase gene by MVA and integration in the host cell genome could have conferred protection against the large DNA virus. Various endogenisation of virophage events would create provirophages that may have led to various MP TEs. The close relationship between retroviruses and retrotransposons has long been known. This characterisation of the links between a DNA virus and a class of DNA transposable element yields similar insight into the evolution of mobile DNA and it’s importance in genomic evolution.