Spatio-temporal characterization of ERV expression and regulation in primate brain development

• Applicants: Professorin Johanna Klughammer, Ph.D.; Dr. Michelle Vincendeau
• Subject Area: Developmental Neurobiology ; Developmental Biology ; Virology ; Cell Biology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 497803923

Approximately 99% of our genome is identical to that of our closest relative, the chimpanzee. However, we clearly differ from chimpanzee. Especially the human brain shows substantially higher neuronal complexity. Still, molecular mechanisms that lead to differences in neuronal number, diversity and complexity remain poorly understood. Transposable Elements (TE) account for a stunning proportion (45%) of the human genome, thereby raising questions about their roles in human biology. Among TEs, endogenous retroviruses (ERVs) have colonized the mammalian genome, which include ~500.000 solitary long terminal repeats (LTRs) scattered throughout the genome. Many ERV LTRs have been used as regulators of gene expression networks and are fine-tuned by the largest family of ERV controllers, the KRAB-containing zinc finger proteins (KZFPs). Interestingly, the rise of ERVs during evolution occurred in parallel to KZFPs. KZFPs are highly expressed in the human brain suggesting that the specific regulation of ERVs plays an important role during human brain development. In line with this hypothesis, we recently could show that activation of a specific ERV group, HERV-K(HML-2), at early stages of cortical development has a negative impact on human cortical neuron differentiation as well as human forebrain patterning. These findings show that a developmental time point–specific control of HERV-K(HML-2) is important for human cortical neurogenesis. Also our preliminary data show increased ERV expression in iPSCs as well as in brain samples from cynomolgus macaques, whereas ERV expression was repressed in human iPSCs. Among the upregulated ERVs in monkey iPSCs, we also identified HERV-K(HML-2). Based on these notions, we want to further investigate how differences in ERV activity and their gene-regulatory implications during brain development have contributed to the human-specific features of human brain development, taking spatial as well as temporal expression variability into account. We want to generate new single cell expression and matched spatial transcriptomics datasets of human and non-human microglia containing brain organoids during developmentally important time points. Using systems-level computational approaches to analyze and integrate this dataset we will comprehensively study the expression of ERVs alongside the protein-coding transcriptome in situ and at single cell resolution, generating an integrated ERV Map that charts spatio-temporal interactions between ERV expression, cellular expression phenotypes, and tissue morphology. This approach will allow us to select several ERV groups of which we will decipher their specific functions using CRISPR technologies and 3D brain organoids in the context of human brain development. This project will not only strengthen our understanding of ERVs in the context of human brain development and evolution but also produce a universal spatio-molecular reference map for primate brain development research.

• DFG Programme: Research Grants