Cell type-specific intronic RNAs shape genome architecture during neuronal lineage specification

Cell differentiation towards neurons is accompanied by widespread changes in three-dimensional (3D) genome organization and gene expression. Nuclear RNAs (nucRNAs) have been proposed to be important regulators of such changes; however, the type, abundance, and functions of nucRNAs during neurodifferentiation remain largely unexplored. Here, we integrate multi-omic data generated in the frame of the Functional ANnoTation Of the Mammalian genome (FANTOM6) to chart 3D genome, RNA-DNA contactome, and transcriptome changes during in vitro differentiation of human induced pluripotent stem cells to neural stem cells and neurons. We find that most RNA-DNA contacts form between transcripts and their source gene; however, a group of intronic RNAs engages in chromatin contacts with distal loci on the same or on different chromosomes. We detect such trans-contacting intronic RNAs (TIRs) in all cell types profiled by FANTOM6, but most prominently in neurons, where TIRs are produced from highly expressed, neuron-specific, long (mean length: 400 kilobases, kb) protein-coding genes. In neurons, TIRs accumulate in the nucleus forming large clouds around their source loci, and they occasionally spread across the nucleus. TIRs engage in local and distal contacts with a set of genomic regions (named TIR-contacted regions or TIRCs) carrying much shorter (mean length: 30 kb) neuron-specific genes that become upregulated and move towards the nuclear center during neurodifferentiation, forming high-connectivity hubs. TIR source genes, and especially their introns, are strongly enriched in risk loci for neurodevelopmental disorders (NDDs). Notably, knockdown of a single TIR by antisense oligonucleotides leads to downregulation of multiple genes implicated in NDDs and of source genes of most other TIRs. We propose that TIRs orchestrate cell type-specific gene expression during neurodifferentiation and might be pathogenically linked to NDDs.