7 August 2009. Synchrony and uniformity tend to characterize line dancers, but they may elude neurons when LINE-1 (long interspersed element 1) retrotransposons take the stage. According to new data from Fred Gage, of Salk Institute for Biological Studies, La Jolla, California, and colleagues, the human hippocampus and other brain regions are potentially rich with LINE-1 elements—more so than other organs such as the heart or liver. The study, published 5 August in the advance online edition of Nature, raises the possibility that these “jumping genes” could help explain individual differences in brain connectivity and function, and that dysfunctional retrotransposition may contribute to neurological disease.
Roughly a fifth of the human genome is made up of LINEs, which can copy and insert themselves at new sites, thereby enlarging the genome and potentially disrupting specific genes. Earlier work from the Gage lab showed that LINE-1 elements introduced into transgenic mice are active in neuronal precursors (Muotri et al., 2005 and ARF related news story). The current study addressed whether this phenomenon also occurs in the human brain.
To assess retrotransposition, first author Nicole Coufal and colleagues designed an expression construct containing a human LINE-1 along with an “indicator.” They placed a reversed copy of the enhanced green fluorescent protein (EGFP) in the 3’ untranslated region of LINE-1 such that cells transfected with the construct turn green only if the element gets retrotransposed. The researchers transfected the construct into neural stem cells isolated from human fetal brain, and into neural progenitors derived from human embryonic stem cell lines. In both sets of analyses, green cells emerged that co-expressed neural stem cell markers and could differentiate down both neuronal and glial pathways, indicating that LINE-1 could retrotranspose in undifferentiated cells.
But this assay only measured activity of a single LINE-1. What about the other 80-100 active LINE-1 elements that are replicated throughout the human genome? To estimate the extent of endogenous LINE-1 activity in the human brain, Gage’s team designed a quantitative multiplex PCR strategy that measured relative LINE-1 content in brain and other tissues. They ran the PCR assay on genomic DNA from hippocampus, cerebellum, heart, and liver tissue of three adults, and found, in each case, more copies of LINE-1 in the hippocampus compared to the heart and liver. Furthermore, when the researchers extended their analysis to 10 brain regions in three additional people, they found that amounts of LINE-1 differed greatly between brain areas and among individuals. By spiking liver and heart DNA with known quantities of the LINE-1 plasmid, they determined that genomic DNA from hippocampal neurons contained about 80 times more LINE-1 copies per cell than did heart or liver DNA.
To get at why LINE-1 activity seems to shoot up in brain compared to other tissues, Coufal and colleagues turned their attention to the LINE-1 promoter. They analyzed genomic DNA from brain and skin tissues of two human fetuses. In both cases, the skin LINE-1 promoter had more methylation—a measure that correlates with DNA inaccessibility and transcriptional repression—compared to the same region in matched brain samples.
Though the new data make a strong case for potential genetic mosaicism in the human brain, whether this actually occurs, and how extensive or meaningful it is, remain unclear. It is tempting to speculate that retrotransposons could play a role in development, as prior work by Gage’s group has shown that LINE insertions in the promoter of the PSD-95 gene (which encodes a synaptic marker) can shift neural fates (Muotri et al., 2005). In an e-mail to ARF, he wrote that his lab is also analyzing the brains of people with various neurodegenerative diseases to see if they have dysregulated gene-jumping frequencies compared to healthy people.—Esther Landhuis.
Coufal NG, Garcia-Perez JL, Peng GE, Yeo GW, Mu Y, Lovci MT, Morell M, O’Shea KS, Moran JV, Gage FH. L1 retrotransposition in human neural progenitor cells. Nature. 2009 August 5. Abstract