Mobile DNA elements in the generation of diversity and complexity in the brain

Abstract

Mobile elements are DNA sequences that can change their position (retrotranspose) within the genome. Although its biological function is largely unappreciated, DNA derived from mobile elements comprises nearly half of the human genome. It has long been thought that neuronal genomes are invariable; however, recent studies have demonstrated that mobile elements actively retrotranspose during neurogenesis, thereby creating genomic diversity between neurons. In addition, mounting data demonstrate that mobile elements are misregulated in certain neurological disorders, including Rett syndrome and schizophrenia.

Figure 1. Retrotransposons in humans

a | The retrotransposons of the long interspersed nuclear element 1 (LINE1) class are the only autonomous mobile elements that are active in humans. Full-length LINE1 elements are 6 kb long and comprise a 5′ untranslated region (UTR) sequence that contains an internal bidirectional DNA polymerase II (Pol II) promoter, followed by open reading frame 1 (ORF1) and ORF2, a 3′ UTR and a poly(A) tail. ORF1 encodes an RNA-binding protein (L1ORF1p) and the protein encoded by ORF2 (L1ORF2p) has an endonuclease (EN) domain and reverse transcriptase (RT) domain. The insertion of LINE1 into DNA during retrotransposition results in target site duplication (TSD), which flanks the new insertion. The non-autonomous elements, Alu and SINE–VNTR–Alu (SVA), are non-coding RNAs that co-opt LINE1 machinery in order to retrotranspose. Alu elements are short interspersed nuclear elements (SINEs) derived from the signal recognition particle RNA 7SL and are 280 bp long. They are transcribed by Pol III and contain A and B box sequences, left and right monomers separated by an A-rich linker and a poly(A) tail. Alu elements do not contain a Pol III termination site, so transcription continues into the flanking sequence until a Pol III termination signal (TTTT) is reached. SVA elements are a composite of other repeats, containing a CCCTCT repeat, two Alu-like sequences, a VNTR and a SINE-R region, which is homologous to the envelope (env) and long terminal repeat (LTR) sequences of human endogenous retrovirus. This is followed by a poly(A) sequence. b | The LINE1 retrotransposition cycle. LINE1 sequences are endogenously encoded in the genome. They are transcribed in the nucleus and assemble a ribonucleoprotein (RNP) complex containing LINE1 RNA, L1ORF1p and L1ORF2p in the cytoplasm. ORF1 and ORF2 sequences can also be co-opted by Alu or SVA sequences, which would result in retrotransposition of Alu or SVA. The RNP complexes can be sequestered as stress granules. The RNP complex accesses the nucleus through nuclear membrane breakdown during cell division or through an unknown import mechanism. L1ORF2p nicks the DNA at a TTAAA sequence and reverse transcribes the RNA through target-primed reverse transcription (TPRT), which results in a 3′ truncated or full-length copy of the LINE1 sequence flanked by TSDs. CC, coiled coil domain; CTD, carboxy-terminal domain; Me, methylation; OH, hydroxyl; RRM, RNA recognition motif. Part b is adapted with permission from REF. , © Elsevier (2010).

Figure 2. Consequences of germline and somatic retrotransposition events

a | As humans, chimpanzees and bonobos evolved from a common ancestor, retrotransposons actively mobilized in the ancestral germ lines, which resulted in the generation of genomic variation that natural selection then acted upon. Alu retrotransposition rates (represented by the thickness of the blue line) remained relatively similar between the three species; however, long interspersed nuclear element 1 (LINE1) retrotransposition rates (represented by the thickness of the red line) were suppressed in the human lineage. Retrotransposition of LINE, Alu and SINE–VNTR–Alu (SVA) elements continues to occur in the human germ line, which creates population variants that are present in every cell of an individual’s body and are also passed on to future generations. Whether LINE1 or Alu somatic retrotransposition rates differ between human and non-human primates is unknown. b | Somatic retrotransposition can happen at any time during embryogenesis. Retrotransposition events that occur in early pluripotent progenitor cells will result in somatic mosaicism: these unique cells will contribute to all tissues of the body of the individual, including the germ line. Somatic retrotransposition that happens after germ-layer specification and organogenesis, however, results in germ-layer- or tissue-specific insertions. These will not contribute to the germ line. c | Somatic retrotransposition increases as neural stem cells differentiate into neurons and results in neurons with unique genomes. Variability exists between the rates of retrotransposition and regions in which it occurs between individuals. High rates of retrotransposition events seem to occur in the hippocampus in some individuals^,. Figure is adapted from Muotri, A. R., Marchetto, M. C., Coufal, N. G. & Gage, F. H. The necessary junk: new functions for transposable elements. Hum. Mol. Genet. 16, R159–R167 (2007), by permission of Oxford University Press.

Figure 3. Regulation of retrotransposition in neural progenitors

In neural stem cells, the long interspersed nuclear element 1 (LINE1) promoter is repressed by DNA methylation, H3K9me3 modifications, methyl-CpG-binding protein 2 (MECP2; which binds to the methylated (Me) DNA) and SOX2. As neural stem cells transition to progenitors, SOX2 is no longer present. The LINE1 promoter assumes an open chromatin state and becomes de-methylated. MECP2 can no longer bind. The WNT transcription factors, β-catenin and members of the TCF/LEF family activate transcription, perhaps with the cooperation of another transcription factor, YY1. This results in an increase in LINE1 transcription in the progenitor and active retrotransposition. Whether new retrotransposon insertions can occur in postmitotic mature neurons is unknown; however, the de novo insertions that occurred in the progenitor create neurons with unique LINE1 insertion sites. ORF2, open reading frame 2; UTR, untranslated region.

Figure 4. Impact of mobile element insertions on the transcriptome

Retrotransposon insertions can affect genes near the site of insertion. a | Transduction is a process through which sequences flanking the 3′ and 5′ regions of long interspersed nuclear element 1 (LINE1) elements (red and blue) can be carried by LINE1 into new locations in the genome. Transduced sequences can bring novel exons, regulatory sequences or poly(A) sequences to a new genomic location. b | LINE1 and Alu elements contain cryptic splice signals. This can cause alternative splicing of mRNA transcripts that results in LINE1 or Alu being spliced into the transcript. c | LINE1 elements also contain internal polyadenylation (pA) signals that can cause aberrant premature polyadenylation or termination of transcription. d | The 5′ untranslated region (UTR) of LINE1 encodes sense and antisense promoters. Transcripts that originate from these promoters can generate novel antisense, non-coding or chimeric transcripts. Similarly, the 3′ UTR also encodes a promoter that can initiate transcription of novel sequences. e | Mobile elements are targeted by many epigenetic mechanisms. Insertion of a mobile element can bring novel epigenetic regulation to the region, including altered levels of DNA methylation (Me) or heterochromatin formation that can initiate at the element and spread to the flanking sequence. Insertion of a mobile element can also provide novel transcription factor-binding sequences, which results in binding and activation of proximal promoters. ncRNA, non-coding RNA; siRNA, small interfering RNA. Figure is adapted with permission from REF. , © Elsevier (2010).

Figure 5. Effects of somatic mosaicism in neurons

Somatic retrotransposition in neurons might have cellular and organismal phenotypic effects. a | Under healthy conditions, a moderate level of retrotransposition (represented by curved arrows) during the differentiation of neural progenitors could expand the coding potential of the genome and create more diversity among neuronal subtypes. On an organismal level, we speculate that retrotransposition expands the variation of phenotypes and behaviours, creating an intangible variance^,. This is illustrated on the graph on the right by the grey line showing an intermediate level of variance in a normally distributed population of behavioural phenotypes. With decreased levels of retrotransposition, we speculate that phenotypes would be more similar and have a narrow distribution but unchanged mean (illustrated by the red line). Environmental stimuli may enhance variation even further (illustrated by the green line). b | Increased retrotransposition in neurodevelopmental disorders such as Rett syndrome and schizophrenia may lead to diseased neurons, with perhaps less connectivity or complexity. On an organismal level, we speculate that this may occur because phenotypes or behaviours are shifted to a more extreme mean, resulting in a disease phenotype. It is possible that targeting of insertions to certain loci or the cellular response to increased retrotransposition results in a more extreme behavioural phenotype. c | Increased long interspersed nuclear element 1 (LINE1) activity is also implicated in neurodegeneration. LINE1 may act as a DNA-damaging agent or retrotransposon transcripts may function as toxic RNAs, thereby increasing vulnerability to apoptosis.