Vladimir M. Jovanović*1,2, Jeong-Eun Költzow1, Amanda Jager Fonseca1, Sebastian Streblow1, Katja Ettig3, Stefano Berto4, Katja Nowick1
1 Human Biology and Primate Evolution Group, Freie Universität Berlin, Berlin, Germany
2 Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
3 Rudolf-Schönheimer-Institut für Biochemie, Leipzig, Germany
4 Medical University of South Carolina, Charleston, USA
vladimir.jovanovic [at] fu-berlin.de
Abstract
Despite near-identical protein sequences, humans exhibit striking phenotypic differences from other primates. These differences likely stem from subtle changes in gene regulation, not just gene sequences. The transcription factor ZEB2, known for its diverse roles in development and cancer, has emerged as a key player in brain development and neuronal differentiation. We investigated its functional divergence in primates by performing ChIP-Seq with a ZEB2 antibody and RNA-Seq following ZEB2 knockdown in human, chimpanzee, and orangutan B-lymphoblastoid cell lines. Our results showed that ZEB2 binding extends beyond its canonical motif, revealing diverse, potentially species-specific, regulatory preferences. Numerous binding sites within promoter regions exhibited significantly higher affinity in humans, suggesting accelerated evolution of these regulatory elements. While a conserved core of immune-related ZEB2 targets was identified across species, we uncovered 437 potential human-specific targets enriched for chromatin organization and DNA replication functions. Notably, an exceptionally high number of non-coding RNA genes was seen among human-specific targets. Furthermore, ZEB2 knockdown induced a unique pattern of differential gene expression in humans, affecting genes involved in neural development and synaptic organization. This highlights a human-specific functional shift in ZEB2 regulation towards brain-related processes. Our findings not only illuminate ZEB2’s potential role in the evolution of uniquely human traits but also provide valuable gene candidates for further functional studies into the genetic basis of our species’ distinctive features.
Keywords: human evolution, gene regulation, multi-omics, ZEB2, DNA binding motif