Exploring epigenetic foundations of complex transcriptional states

The National Institutes of Health National Human Genome Research Institute awarded Weill Medical College of Cornell University $100,228 on February 8, 2027, under the Human Genome Research program (CFDA 93.172) to explore epigenetic foundations of complex transcriptional states.

The recipient will apply multiome perturb-seq technology—coupling CRISPR-mediated genetic perturbations to parallel single-cell RNA sequencing and single-cell ATAC sequencing readout—to profile the role of chromatin state in mediating genetic interactions and epigenetic memory. Aim 1 tests whether perturbations inducing large-scale chromatin remodeling rewire regulatory networks that define transcriptional programs and prime cells to transition between states, investigating synergistic genetic interactions between primary perturbation targets and secondary targets whose chromatin state is modified by initial perturbations. Aim 2 seeks to discover functional drivers of epigenetic memory through transient perturbations. The work proceeds through July 31, 2029, at the recipient's location in New York, New York.

This is a Project Grant, the assistance type for investigator-initiated research under the NHGRI portfolio.

Abstract

Atlas-level transcriptional profiling efforts have characterized human cellular diversity at high resolution but lack a full understanding of the regulatory logic behind how cells establish, maintain, and transition between transcriptional states. This regulation is determined by the epigenome, which interprets the information carried by genomic sequence to direct dynamic patterns of gene expression that define cell state and persists these patterns through differentiation to define long-lived cell fates. Single-cell crispr screens allow transcriptional and epigenetic states to be separately associated with genetic perturbations, but methods to connect the transcriptional changes induced by perturbations to their regulatory foundations at high throughput have been limited. In this proposal, i apply multiome perturb-SEQ - a new technology coupling crispr-mediated genetic perturbations to parallel scrna-SEQ and scatac-SEQ readout - to profile the role of chromatin state in mediating genetic interactions and epigenetic memory. Aim 1 tests the hypothesis that perturbations leading to large-scale chromatin remodeling indicate a rewiring of the regulatory networks defining the current transcriptional program, priming the cell to transition between states. I hypothesize that state transitions are unlocked by synergistic genetic interactions between primary perturbation targets and secondary targets across the genome whose chromatin state is modified by initial perturbations. I will investigate candidate interactors by measuring the effects of diverse perturbations on the transcriptome and epigenome, computationally predicting synergistic interaction partners, and characterizing the cell states induced by applying combinatorial perturbations realizing these "primed" interactions. Aim 2 seeks to discover the functional drivers of epigenetic memory by applying transient perturbations that induce long-lived cell states. I hypothesize that these states engage cell-autonomous regulatory pathways that potentiate their properties after the initial perturbation has been withdrawn, offering a handle to study the mechanisms by which epigenetic memory is installed, maintained, and rewritten. Transiently perturbing key regulators of cell identity in populations labeled with clonal lineage barcodes, i will experimentally identify perturbations inducing memorized states and profile the regulatory networks responsible for their maintenance. Overall, the proposed research will enhance our understanding of how cells realize complex, stable phenotypes, with applications to both basic research and translationally relevant cellular engineering.