Periodic Reporting for period 1 - Evolutionary Neurogenomics (The impact of recent retrotransposon invasions on the evolution of human neural gene expression) Reporting period: 2015-06-01 to 2017-05-31 Summary of the context and overall objectives of the project In this research program, I made the first steps to determine how recent retrotransposon insertions have shaped gene-regulatory pathways involved in human brain development. Through a combination of bioinformatics and human and non-human primate stem cell cortical neuron differentiation protocols, I aimed to identify neuronally expressed genes that have become under the control of retrotransposons. Knowing exactly how each class of retrotransposons have impacted human gene expression will allow us to explore these novel gene-regulatory properties may have come indispensable for the human brain and possibly contain clues to the increased susceptibility of humans to some neurological disorders. The long term goal of my research program is to investigate how waves of retrotransposon insertions have contributed to the evolution of human gene expression patterns and how these changes relate to human-specific aspects of brain development in health and disease. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far I finalized the goals set out in work package 1 for one type of retrotransposon and obtained promising preliminary outcomes. Even though it needs to be further supported by other complementary strategies, the position of human specific retrotransposons seems to be correlated to increased inter-species gene expression differences. This is in line with what we expected. For work package 2, I setup shRNA-lentiviral transduction protocols in my lab in order to manipulate the expression of specific zinc finger genes and successfully made human ESC lines with knock down of some of them. We have performed RNA-seq analysis as planned and are now working on the analysis of the data. Finally, we have started to create CRISPR-Cas9 knock out hESC lines for some of the KRAB Zinc fingers involved in important retrotransposon repressive activities. The functional analysis of in vitro brain tissues derived from these KRAB zinc finger gene mutated stem cell lines will help us understand the genomic and genome-functional impact of each of these retrotransposon invasions and the evolutionary arms race with KRAB zinc fingers that was elicited by it. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) Even though it remains hard to predict the societal impact of this research program at this time, we have uncovered a number of exciting patterns and features of some specific retrotransposon-classes, that could potentially lead us to unravel at least one of the multiple genetic causes that underly the differential susceptibility to neurological diseases observed in the human population. Future research, building on the solid technical and intellectual foundations that I was able to lay down because of the Marie Curie Reintegration grant will allow me to assess the impact of these phenomena for the human species, in the past and today’s populations. Evolutionary arms race between KRAB zinc finger genes (predator) and Retrotransposons (prey).