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Highlights d Single-cell genomic analysis of hippocampal neurons reveals a somatic L1 insertion d The donor L1 is slightly 5ʹ truncated and lacks a conserved YY1 binding site d Young L1s with truncated or mutated YY1 binding sites are globally hypomethylated d L1 is able to mobilize in the brain because of locus-specific exceptions to repression

LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants.DOI: http://dx.doi.org/10.7554/eLife.13926.001

The role of microglia cells in Alzheimer’s disease (AD) is well recognized, however their molecular and functional diversity remain unclear. Here, we isolated amyloid plaque-containing (using labelling with methoxy-XO4, XO4+) and non-containing (XO4−) microglia from an AD mouse model. Transcriptomics analysis identified different transcriptional trajectories in ageing and AD mice. XO4+ microglial transcriptomes demonstrated dysregulated expression of genes associated with late onset AD. We further showed that the transcriptional program associated with XO4+ microglia from mice is present in a subset of human microglia isolated from brains of individuals with AD. XO4− microglia displayed transcriptional signatures associated with accelerated ageing and contained more intracellular post-synaptic material than XO4+ microglia, despite reduced active synaptosome phagocytosis. We identified HIF1α as potentially regulating synaptosome phagocytosis in vitro using primary human microglia, and BV2 mouse microglial cells. Together, these findings provide insight into molecular mechanisms underpinning the functional diversity of microglia in AD.

Transposable elements are in a constant arms race with the silencing mechanisms of their host genomes. One silencing mechanism commonly used by many eukaryotes is dependent on cytosine methylation, a covalent modification of DNA deposited by C5 cytosine methyltransferases (DNMTs). Here, we report how two distantly related eukaryotic lineages, dinoflagellates and charophytes, have independently incorporated DNMTs into the coding regions of distinct retrotransposon classes. Concomitantly, we show that dinoflagellates of the genus Symbiodinium have evolved cytosine methylation patterns unlike any other eukaryote, with most of the genome methylated at CG dinucleotides. Finally, we demonstrate the ability of retrotransposon DNMTs to methylate CGs de novo, suggesting that retrotransposons could self-methylate retrotranscribed DNA. Together, this is an example of how retrotransposons incorporate host-derived genes involved in DNA methylation. In some cases, this event could have implications for the composition and regulation of the host epigenomic environment.

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26Alzheimer's disease (AD) is a heterogeneous disease that is largely dependent on the complex 27 cellular microenvironment in the brain. This complexity impedes our understanding of how 28 individual cell types contribute to disease progression and outcome. To characterize the 29 molecular and functional cell diversity in the human AD brain we utilized single nuclei RNA-30 seq in AD and control patient brains in order to map the landscape of cellular heterogeneity in 31 AD. We detail gene expression changes at the level of cells and cell subclusters, highlighting 32 specific cellular contributions to global gene expression patterns between control and 33 Alzheimer's patient brains. We observed distinct cellular regulation of APOE which was 34 repressed in oligodendrocyte progenitor cells (OPCs) and astrocyte AD subclusters, and highly 35 enriched in a microglial AD subcluster. In addition, oligodendrocyte and microglia AD 36 subclusters show discordant expression of APOE. Integration of transcription factor regulatory 37 modules with downstream GWAS gene targets revealed subcluster-specific control of AD cell 38 fate transitions. For example, this analysis uncovered that astrocyte diversity in AD was under 39 the control of transcription factor EB (TFEB), a master regulator of lysosomal function and 40 which initiated a regulatory cascade containing multiple AD GWAS genes. These results 41 establish functional links between specific cellular sub-populations in AD, and provide new 42 insights into the coordinated control of AD GWAS genes and their cell-type specific 43 contribution to disease susceptibility. Finally, we created an interactive reference web resource 44 which will facilitate brain and AD researchers to explore the molecular architecture of subtype 45 and AD-specific cell identity, molecular and functional diversity at the single cell level. 46Highlights 47 • We generated the first human single cell transcriptome in AD patient brains 48 • Our study unveiled 9 clusters of cell-type specific and common gene expression 49 patterns between control and AD brains, including clusters of genes that present 50 properties of different cell types (i.e. astrocytes and oligodendrocytes) 51 • Our analyses also uncovered functionally specialized sub-cellular clusters: 5 52 microglial clusters, 8 astrocyte clusters, 6 neuronal clusters, 6 oligodendrocyte 53 clusters, 4 OPC and 2 endothelial clusters, each enriched for specific ontological 54 gene categories 55 • Our analyses found manifold AD GWAS genes specifically associated with one 56 cell-type, and sets of AD GWAS genes co-ordinately and differentially regulated 57 between different brain cell-types in AD sub-cellular clusters 58 • We mapped the regulatory landscape driving transcriptional changes in AD brain, 59 and identified transcription factor networks which we predict to control cell fate 60 transitions between control and AD sub-cellular clusters 61 • Finally, we provide an interactive web-resource that allows the user to further 62 visua...

The important role of microglia, the brain’s resident immune cells, in Alzheimer’s disease (AD) is now well recognized, however their molecular and functional diversity and underlying mechanisms still remain controversial. To transcriptionally and functionally characterize the diversity of microglia in AD and aging, we isolated the amyloid plaque-containing (XO4+) and non-containing (XO4−) microglia from an AD mouse model. Transcriptomics analysis unveiled independent transcriptional trajectories in ageing and AD. XO4+ microglial transcriptomes linked plaque phagocytosis to altered expression of bona fide late onset AD genetic risk factors. We further revealed that the XO4+ transcriptional program is present in a subset of human microglia from AD patients and is a direct and reversible consequence of Aβ plaque phagocytosis. Conversely, XO4− microglia in AD displayed an accelerated ageing signature and contained more intracellular post synaptic material than plaque-containing microglia, despite reduced active synaptosome phagocytosis. Mechanistically, we predicted HIF1α as a core regulator of the XO4−/XO4+ axis, and further validated the mechanism in vitro using human stem cell-derived microglia like cells and primary human microglia. Together these findings unveiled the molecular mechanism underpinning the functional diversity of microglia in AD, providing opportunities to develop treatments targeted at subset specific manipulation of the microglial niche.