Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis

Abstract

Long interspersed element-1 (LINE-1/L1) is the only autonomous transposable element in the human genome that currently mobilises in both germline and somatic tissues. Recent studies have identified correlations between altered retrotransposon expression and the fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS) in a subset of patients. The risk of an individual developing ALS is dependent on an interaction of genetic variants and subsequent modifiers during life. These modifiers could include environmental factors, which can lead to epigenetic and genomic changes, such as somatic mutations, occurring in the neuronal cells that degenerate as the disease develops. There are more than 1 million L1 copies in the human genome today, but only 80–100 L1 loci in the reference genome are considered to be retrotransposition-competent (RC) and an even smaller number of these RC-L1s loci are highly active. We hypothesise that RC-L1s could affect normal cellular function through their mutagenic potential conferred by their ability to retrotranspose in neuronal cells and through DNA damage caused by the endonuclease activity of the L1-encoded ORF2 protein. To investigate whether either an increase in the genomic burden of RC-L1s or epigenetic changes to RC-L1s altering their expression, could play a role in disease development, we chose a set of seven well characterised genomic RC-L1 loci that were reported earlier to be highly active in a cellular L1 retrotransposition reporter assay or serve as major source elements for germline and/or somatic retrotransposition events. Analysis of the insertion allele frequency of five polymorphic RC-L1s, out of the set of seven, for their presence or absence, did not identify an increased number individually or when combined in individuals with the disease. However, we did identify reduced levels of methylation of RC-L1s in the motor cortex of those individuals with both familial and sporadic ALS compared to control brains. The changes to the regulation of the loci encompassing these RC-L1s demonstrated tissue specificity and could be related to the disease process.

Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome

“…Our group has described the extra burden of L1 activity as associated with PD [12]. We have also described the increased expression of TE elements in different diseases [13][14][15]. These data indicate that TEs have an important impact on the inheritance or progression of diseases.…”

Locus specific reduction of L1 expression in the cortices of individuals with amyotrophic lateral sclerosis

“…In this cohort 70 of these L1s were detected as polymorphic; 40 of which were intact (see Additional file 4 : Table S4 for coordinates and insertion allele frequencies of each L1). Three of the polymorphic L1s identified in our analysis had been genotyped for their presence/absence using PCR amplification in our previous study [ 25 ]. The intact L1s had lower insertion allele frequencies (IAF) compared to the non-intact loci, for example non-intact L1s had a significantly higher proportion of L1s with an IAF > 0.75 compare to intact loci (50% vs 22.5%, p = 0.03) (Additional file 6 : Figure S2).…”

“…This could be related to regulation of L1s by CpG methylation, for example a recent study showed that this L1 located on chr22 is hypomethylated in the liver compared to the heart and hippocampus [ 38 ]. Our previous work analysing the methylation status of 6 highly active RC-L1s in the motor cortex identified a reduction in the DNA methylation over these elements in ALS brains compared to controls [ 25 ]. Five of these elements located in the reference genome were also analysed as part of this study quantifying their expression levels and found that four of these L1s were expressed, however they were not part of the group of L1s responsible for the majority of the expression observed.…”

“…Our previous work focussing on highly active RC-L1s in neurodegenerative diseases has identified a reduction in the methylation of selected RC-L1s in the motor cortex of individuals with ALS compared to healthy controls [ 25 ] and found that an increased burden of these elements in the germline is associated with Parkinson’s disease risk and progression [ 26 ]. Although there have been several studies evaluating the expression profile of specific families of retrotransposons in ALS there is limited data on loci specific expression, which could provide additional insight into the potential consequences of their expression.…”

TDP-43 Epigenetic Facets and Their Neurodegenerative Implications

“…Overall, TE subfamilies are species specific, but they rely on the same molecular mechanisms for their control and propagation [ 132 ], notably epigenetic mechanisms, including CpG DNA methylation. Indeed, genomes evolved defenses against their detrimental potential, and TE are generally silenced by DNA methylation and heterochromatin marks such as H3K9me3, acting as major barrier against their activation [ 133 , 134 , 135 , 136 ]. Thanks to the efforts of recent studies, TDP-43 has recently been shown to play a role in regulating them at several levels.…”