Michael Ratz

In eukaryotic cells, ~50% of the nucleus is filled with proteins and RNAs, many of which are closely associated with DNA. In exciting preliminary work, we discovered a new class of nuclear RNAs that form genome-wide, long-range contacts with DNA and mainly consist of intronic sequences. During neurodifferentiation, these trans-contacting intronic RNAs (TIRs) are produced from very long, neuronally expressed, protein-coding genes enriched in risk loci for neurodevelopmental disorders (NDDs). TIRs form an intricate localization pattern in the nucleus, which we hypothesize is critical for shaping the local and global 3D genome structure, as well as for coordinating gene expression in brain cells. Here, we tackle this hypothesis by first charting TIRs in neurons/glial cells differentiated from hESCs/iPSCs either from healthy donors or NDD subjects (Aim1). We then pioneer MARINDA for simultaneous all-way profiling of DNA and RNA contacts in single cells and apply it to reconstruct the 3D DNA-DNA, RNA-DNA, and RNA-RNA connectome in mouse brain cells (Aim2). Finally, we combine antisense oligonucleotide and genetic engineering techniques to silence selected TIRs or re-localize them within the nucleus and then measure the effects of these perturbations at the genetic, epigenetic, and phenotypic level in neurons (Aim 3). This project has the potential to establish a new fundamental role of nuclear RNAs in neurobiology and uncover new pathomechanisms for NDDs.

The human genome contains several thousand genes that encode the brain’s connectome, a precise assembly of neural connections with trillions of synapses. How is genomic information translated into synapse-specific connectivity underlying behavior and cognition? Answering this fundamental question will provide important insights about the general principles underlying nervous system development and is relevant for human disease. Here I propose to develop a novel approach based on genetic barcoding and single-cell Spatial Transcriptomics that permits a comprehensive understanding about neural network assembly via the large-scale measurement of molecular, cellular, and circuit-level mechanisms in the mouse brain. Compared to current efforts that require vast scientific resources to map synaptic connectivity among a few cells or small tissue volumes, my approach will enable routine measurements of neural connections among thousands of cells with molecular detail using standard laboratory equipment. I will systematically reveal the connectivity rules underlying the spatiotemporal development of neural circuits from diverse cell types in the mouse cortex and employ CRISPR perturbations to engineer neural circuitry in vivo. My work will provide an innovative experimental platform and reveal mechanistic insights into the developmental algorithms that the genome uses to encode the connectome.