Thursday, September 21, 2017  – 2:00 pm
Location – Biomedical Sciences, Room 200
Host – Professor David Haussler


The cerebral cortex has undergone rapid changes in size and complexity in the primate lineage, yet the molecular processes underlying primate brain development are poorly understood. We have developed a common protocol for generating cortical organoids from human, chimpanzee, orangutan, and rhesus pluripotent stem cells that recapitulates early events in cortical development and enables comparative molecular analysis of this process. Here we focus on long non-coding RNAs (lncRNAs), which as a class have been implicated in gene regulation and differentiation of pluripotent cells into specific tissues. Despite their potential importance in driving the developmental processes, studies focusing on lncRNAs have been impeded by the low sequence conservation and tissue-specific expression patterns of functionally relevant lncRNAs. For this reason, we developed a new approach focusing on the sequence, gene structure, and expression conservation of lncRNAs in equivalent tissues among closely related primate species. To use these aspects of conservation in concert, we collected RNA for high throughput total transcriptome sequencing at weekly time points during the differentiation protocol and identified thousands of multi-exonic lncRNAs in each species. Of the 2,975 expressed multi-exonic lncRNAs in human, 2,143 were conserved in gene structure to chimpanzee, 1,731 to orangutan, and 1,290 to rhesus. Among these were 386 human transiently expressed (TrEx) lncRNAs, defined as primarily induced at one time point during differentiation and off by week 5. This expression pattern was  conserved among great apes for at least 51% of transcripts. Many of these transiently expressed transcripts were also associated with specific neural developmental cell subtypes including neuroepithelium, radial glia, and Cajal-Retzius cells as determined by single cell RNA-sequencing. 8 with specific expression in these cell types were tested and found found to influence key transcription factors in correlated gene networks by endogenous locus activation via CRISPRa. This study provides a rich resource of expression data in early cortical development in human, chimpanzee, orangutan, and rhesus at equivalent time points and a framework for identifying new, potentially functional lncRNAs expressed during human differentiation by their gene structure and expression conservation in closely related species.