LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq]

The mechanisms underlying primate-specific genetic programs during early human development remain poorly understood. Long interspersed nuclear element 1 (L1) is the most abundant transposable element in the human genome and represents a vast source of divergent genetic information in hominoid genomes, yet its contribution to human development is largely unknown. Using multiomics profiling, we show here that thousands of hominoid-specific L1 loci are expressed in human induced pluripotent stem cells and cerebral organoids. The transcription of unique L1 elements correlates with the absence of DNA methylation and the presence of an active epigenetic state. CRISPRi silencing of L1s revealed the presence of nearly a hundred co-opted L1-derived chimeric transcripts, and silencing of these transcripts results in altered transcription of many genes involved in neural differentiation, leading to a reduction in cerebral organoid size, implicating L1s in hominoid-specific developmental processes. In conclusion, our results show that L1-derived transcripts provide a layer of primate- and human-specific transcriptome complexity that contributes to early human developmental processes. Overall design: In this study we characterized the expression profile of evolutionary young (L1HS-L1PA4), full-length L1s in hiPSCs and unguided cerebral organoids (STEMCELL cerebral organoids diff kit). We combined bulkRNA-seq, CUT&RUN, and long-read RNA and DNA sequencing to trace the promoter activity of L1s in hiPSCs (n= 3 technical replicates for bulkRNA-seq; n= 1 technical replicate for H3K4me3 and H3K9me3 CUT&RUN and long-read sequencing) and cerebral organoids (n=3 technical replicate, 3-4 organoids per replicate for bulkRNAseq; n=3 replicate, 4-5 organoids per replicate for snRNAseq; (n= 1 replicate, 5 organoids per replicate). We also performed L1 CRISPRi (via lentiviral transduction) in hiPSCs and investigated the L1 expression profile and the downstream phenotypic effects with the aforementioned technologies. Control cell line was established through lentiviral transduction using a non-targeting (LacZ) gRNA. We also differentiated these cell lines into unguided cerebral organoids and investigated the phenotype.