Johan Jakobsson

This study shows that activating ERV-W in human glutamatergic neurons disrupts postsynaptic organization and synaptic function.

The paper investigates TE transcription in Parkinson's disease brains, finding region- and cell-type-specific TE activation linked to an interferon response in microglia and neurons.

TRIM28 missense variants in individuals with neurodevelopmental delay disrupt epigenetic control of transposable elements, leading to altered gene expression and neurodevelopmental defects.

TEsingle provides locus-specific transposable element expression analysis in single-cell data, revealing cell-type-specific TE expression in Parkinson's Disease.

This paper describes a protocol for CRISPRi-mediated silencing of retrotransposons in hiPSCs, validated using a multiome approach combining RNA-seq, CUT&RUN, and proteomics.

This study shows that loss of H3K9me3 in human neural progenitor cells activates L1 retrotransposons by reducing CpG methylation at their promoters.

This study identifies a chimpanzee-specific retroviral insertion that influences gene regulation and brain development, highlighting its role in human-chimpanzee brain divergence.

This study maps cell-type specific transcriptional changes in the parkinsonian striatum across species, identifying vulnerable and resilient cell types.

The paper develops cell-type-specific transcriptomic aging clocks using single-nuclei RNA sequencing data from human prefrontal cortex tissue, showing distinct aging patterns across cell types.

This study shows that L1 retrotransposons influence human pluripotency exit and early brain development through their expression and derived transcripts.

This study shows MORC2 regulates CpG methylation of active LINE-1 retrotransposons during human neurodevelopment, similar to the piRNA pathway in the germline.

This study develops a method to efficiently generate human oligodendrocytes from induced pluripotent stem cells, which can form functional myelinating grafts in adult human brain tissue.

This study shows that systemic administration of a TNF inhibitor does not protect against α-synuclein-induced dopaminergic neuron loss in a rat model of Parkinson's disease.

This study uses bulk and single nuclear RNA-sequencing to analyze transcriptomic changes in repeat expansion ataxias, revealing distinct non-neuronal cell type-specific disease signatures across the human brain.

The paper shows that DNA methylation and the HUSH-MORC2 complex independently regulate repeat elements in human neural progenitor cells, with MORC2 binding increasing in demethylated regions.

The paper shows that sequencing ambiguity between GBA1 and its pseudogene GBAP1 affects transcriptomic analysis, revealing non-lysosomal functions in the brain and widespread annotation inaccuracies.

This study shows L1 retrotransposons contribute to human brain transcriptome complexity and functional diversification through cell-type specific transcripts and regulatory RNAs.

The paper shows that ZNF91 creates mini-heterochromatin domains that limit the regulatory impact of SVA transposons in human neural progenitor cells, contributing to XDP pathology.

The paper uses snRNA-seq to analyze TBI brain tissue, finding oligodendroglia activate endogenous retroviruses, linking them to neuroinflammation.

This study investigates miRNA biogenesis defects in HD brain tissue, finding downregulation of key enzymes and maturation defects, primarily in the striatum.

This study generates patient-derived induced dopaminergic neurons to show age-related autophagy impairments and alpha-synuclein accumulation in Parkinson's disease.

This study shows that induced neurons from Huntington's disease patients have impaired autophagy in neurites, independent of protein aggregation, and that HTT is critical for neuronal autophagy.

The paper identifies a human-specific structural variation at the ZNF558 locus that regulates a gene network involved in forebrain development by controlling SPATA18 expression through a VNTR contraction.

This study shows that activation of endogenous retroviruses during brain development leads to neuroinflammation in adult mice.

This paper develops methods to upregulate gene expression in vivo while preserving cell-type-specific regulation, demonstrating their use in studying gene function and disease mechanisms.

The paper compares protein and RNA expression levels in human and chimpanzee forebrain progenitor cells, finding that protein expression differences are more common and less correlated with RNA levels.

The paper identifies LINE-2-derived microRNAs and their target sites in human tissues, showing their role in regulating gene expression and their disruption in glioblastoma.