Johan Jakobsson

Endogenous retroviruses (ERVs) comprise a substantial fraction of the human genome, yet whether their expression can directly alter human neuronal function remains unknown. Because glutamatergic signaling is fundamental to brain function and frequently disrupted in brain disorders, we asked whether activation of the primate-specific ERV-W group, associated with neurological disease, perturbs human glutamatergic neurons. We used CRISPR activation of the LTR17-ERV-W consensus sequence to examine its effects on neuronal and synaptic function, inducing transcription from multiple proviral loci, including five with intact open reading frames. Functionally, ERV-W activation selectively altered the postsynaptic compartment, reducing PSD-95 and NMDA receptor abundance. These changes were accompanied by altered excitatory synaptic transmission and reduced intrinsic excitability, whereas activation of ERVW-1/Syncytin-1 alone did not reproduce the phenotype. Our findings identify ERV-W activation as a modulator of human neuronal function with potential relevance to ERV-associated brain disorders.

Over the past 5 to 7 million years, humans and chimpanzees have diverged in brain size, structure, and cognition despite high conservation of protein-coding genes. However, retroviral infections within host genomes have introduced numerous species-specific regulatory elements. Chimpanzees harbor lineage-specific PTERV1 endogenous retroviruses that are absent in humans, but their role in brain evolution has remained unclear. We performed an epigenomic analysis of PTERV1 insertions in chimpanzee neural organoids and found they are heavily DNA methylated, forming over 150 species-specific heterochromatin domains with the potential to influence gene regulation. We identified a chimpanzee-specific insertion on chromosome 19 that silences the long noncoding RNA LINC00662 through DNA methylation spreading. CRISPR-mediated deletion of this PTERV1 restored LINC00662 expression in chimpanzee induced pluripotent stem cells. We show that LINC00662 , a human-specific transcript expressed during brain development, plays a role in neuronal maturation, axon outgrowth, and neural organoid development. These findings reveal a mechanism by which endogenous retroviral insertions contributed to human-chimpanzee brain divergence.

Parkinson’s disease (PD) is a neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TEs) have been linked to inflammation, but their potential role in PD remains unexplored. Using bulk- and single-nuclei RNA-seq of postmortem brain tissue from four brain regions, we studied TE transcription and its correlation with PD neuroinflammation. Over a thousand TEs, including LINE-1 s and ERVs, were expressed in a cell type– and region-specific manner in the human brain. Increased TE expression was found in microglia and neurons in the substantia nigra and putamen of PD brains, but not amygdala or prefrontal cortex, compared to controls. This TE activation correlated with an innate immune response in the same brain regions. The link between an interferon response and TE activation was mechanistically confirmed using human pluripotent stem cell–derived microglia and neurons. Our findings provide insights into TE transcription in the PD brain and suggest that TEs may contribute to neuroinflammation and pathological progression in PD.

TRIM28 is an epigenetic co-repressor protein that silences transposable elements (TEs). Although loss-of-function studies in mice led to neurodevelopmental defects, a functional link between TRIM28 and human neurodevelopment has yet to be established. In this study, we describe two patients with neurodevelopmental delay who carry de novo TRIM28 missense variants. Using CRISPR-edited induced pluripotent stem cell lines and differentiated neural organoids, we demonstrate that these variants result in the loss of the histone mark H3K9me3 over TEs. This releases the regulatory potential of TEs resulting in altered expression of nearby genes. These findings could be replicated using CRISPRi-based TRIM28 silencing, which suggests that the two variants result in a loss of function. Our results highlight the critical role of TRIM28 in regulating TEs during human brain development, establishing a link between TRIM28 variants and neurodevelopmental delay. One Sentence Summary: TRIM28 variants disrupt epigenetic control of transposable elements in the developing human brain, linking them to neurodevelopmental delay.

Transposable elements (TEs) are mobile genetic sequences that can generate new copies of themselves via insertional mutations. These viral-like sequences comprise nearly half the human genome and are present in most genome wide sequencing assays. While only a small fraction of genomic TEs have retained their ability to transpose, TE sequences are often transcribed from their own promoters or as part of larger gene transcripts. Accurately assessing TE expression from each individual genomic TE locus remains an open problem in the field, due to the highly repetitive nature of these multi-copy sequences. These issues are compounded in single-cell and single-nucleus transcriptome experiments, where additional complications arise due to sparse read coverage and unprocessed mRNA introns. Here we present our tool for single-cell TE and gene expression analysis, TEsingle. Using synthetic datasets, we show the problems that arise when not properly accounting for intron retention events, failing to address uncertainty in alignment scoring, and failing to make use of unique molecular identifiers for transcript resolution. Addressing these challenges has enabled an accurate TE analysis suite that simultaneously tracks gene expression as well as locus-specific resolution of expressed TEs. We showcase the performance of TEsingle using single-nucleus profiles from substantia nigra (SN) tissues of Parkinsons Disease (PD) patients. We find examples of young and intact TEs that mark dopaminergic neurons (DA) as well as many young TEs from the LINE and ERV families that are elevated in PD neurons and glia. These results demonstrate that TE expression is highly cell-type and cellular-state specific and elevated in particular subsets of neurons, astrocytes, and microglia from PD patients.

Heterochromatin is characterized by an inaccessibility to the transcriptional machinery and is associated with the histone mark H3K9me3. However, studying the functional consequences of heterochromatin loss in human cells has been challenging. Here, we used CRISPRi-mediated silencing of the histone methyltransferase SETDB1 to remove H3K9me3 heterochromatin in human neural progenitor cells. Despite a major loss of H3K9me3 peaks resulting in genome-wide reorganization of heterochromatin domains, silencing of SETDB1 had a limited effect on cell viability. Cells remained proliferative and expressed appropriate marker genes. We found that a key event following the loss of SETDB1-mediated H3K9me3 was the expression of evolutionarily young L1 retrotransposons. Derepression of L1s was associated with a loss of CpG DNA methylation at their promoters, suggesting that deposition of H3K9me3 at the L1 promoter is required to maintain DNA methylation. In conclusion, these results demonstrate that loss of H3K9me3 in human neural somatic cells transcriptionally activates evolutionary young L1 retrotransposons.

Over the past 5 to 7 million years, humans and chimpanzees have diverged in brain size, structural complexity, and cognitive abilities despite high conservation of protein-coding genes. Notably, the endogenization and proliferation of retroviral infections within host genomes has introduced numerous species-specific regulatory elements that have the potential to influence gene regulation. However, the role of these endogenous retroviruses in hominoid brain evolution remains unclear. A burst of lineage-specific PTERV1 retroviruses recently invaded the chimpanzee genome but are absent in humans. We conducted an epigenomic analysis of PTERV1 insertions in chimpanzee neural organoids and found that they are heavily covered by DNA methylation, representing more than 150 species-specific heterochromatin domains with the capacity to influence gene regulatory networks. We identified one such chimpanzee-specific PTERV1 insertion on chromosome 19 that blocks the expression of the long noncoding RNA LINC00662, via DNA methylation spread to the adjacent genomic region. The expression of LINC00662 was restored in chimpanzee induced pluripotent stem cells when we deleted the PTERV1 insertion using CRISPR editing. We found that LINC00662, a human-specific RNA, is highly expressed in the developing brain and plays an important role in the posttranscriptional control of neuronal maturation, axon outgrowth, and neural organoid development. In summary, our findings describe how endogenous retroviral insertions contributed to the functional divergence of the human and chimpanzee brains. This provides a new mechanism by which retroviral pandemics influenced primate brain speciation.

Summary: This protocol describes a workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). It illustrates how to design gRNAs to target TE families or unique TE loci and how to validate the efficiency and specificity of large-scale CRISPRi-based silencing using a multiome approach that combines bulk RNA sequencing, CUT&RUN epigenetic profiling, and proteomics. This unique framework optimizes performance and interpretation of in vitro functional studies based on transcriptional manipulation of TEs in hiPSC models. For complete details on the use and execution of this protocol, please refer to Adami et al . (2025) ¹ . Graphical

Summary: The progressive degeneration of dopaminergic projections to the striatum is a key disease mechanism in Parkinson’s disease (PD). To define the cellular landscape in the parkinsonian striatum, we mapped the cell-type specific transcriptional landscape in early and progressive PD mouse models and in human PD stages. Our analyses revealed substantial transcriptomic changes across both neuronal and glial populations, with astrocytes and oligodendrocytes exhibiting distinct disease-associated gene expression profiles. Notably, progressive dopamine depletion uncovered differential neuronal vulnerability, identifying eccentric striatal projection neurons (SPNs) and Chst9-expressing direct-pathway SPNs as among the most resilient subtypes in both species. This cross-species resource establishes a comprehensive framework for investigating cell-state dynamics in the parkinsonian striatum and uncovers selectively vulnerable and resistant cell types that can inspire new therapeutic strategies.