Enhanced epigenome editing technologies for controlling mammalian gene expression

The National Institute of General Medical Sciences, part of the Department of Health and Human Services, awarded the University of Illinois $526,483 on May 14, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to develop enhanced epigenome editing technologies for controlling mammalian gene expression.

The award funds development of a toolkit of programmable epigenome editors capable of activating gene expression in vivo through three integrated aims. Aim 1 applies phylogenetic diversity and directed evolution to identify histone acetyltransferase P300 variants with enhanced gene activation capabilities. Aim 2 develops machine-learning models that integrate target-site sequence features and nucleosome architecture to predict actionable acetylation sites for efficient gene activation. Aim 3 engineers split-intein and ultracompact epigenome editors compatible with single or dual adeno-associated virus vectors to enable in vivo gene activation, addressing current incompatibility barriers that limit clinical applications of dCas9-P300 systems.

The work is performed in Urbana, Illinois, with period of performance through February 28, 2030. The research team assembles multidisciplinary expertise in epigenome editing, computational biology, and AAV gene delivery across the University of Illinois.

Abstract

Genome editing is rapidly transforming biology and medicine by enabling the precise modification of DNA sequences in vivo. The technologies used for genome editing have also provided a means to modulate the expression of a target gene by facilitating the recruitment of transcriptional effector domains to a target site. One such tool capable of recreating the native mechanisms of gene activation consists of catalytically inactive CAS9 (DCAS9) fused with the histone acetyltransferase P300, which, by acetylating histones near a target site, can activate gene expression through a nearly physiological approach. Nonetheless, current DCAS9-P300 systems are inefficient, unpredictable, and incompatible with adeno-associated virus (AAV) delivery, which hinders future applications of this technology. Here, we propose to integrate state-of-the-art techniques including protein engineering, machine learning, and viral-vector design to create an innovative toolkit of epigenome editors that can be used to activate gene expression in vivo. Aim 1 will leverage phylogenetic diversity and directed evolution in mammalian cells to identify P300 variants with enhance gene activation capabilities. In aim 2, we will develop machine-learning models that integrate target-site sequence features and nucleosome architecture to predict actionable target sites for efficient acetylation and gene activation. And, in aim 3, we will engineer split-intein and ultracompact epigenome editors that can be packaged within single or dual AAV vectors to enable in vivo gene activation. To accomplish these objectives, we have assembled a multidisciplinary team with collective expertise in epigenome editing (DR. Perez-pinera), computational biology (DR. Song) and AAV gene delivery (DR. GAJ). Our collaborative efforts will: (1) yield a toolkit of programmable, tunable, and deliverable gene-activation tools, (2) facilitate the discovery of fundamental principles for epigenome editor design, and (3) enable the development of therapeutic applications for multiple disorders including developmental and metabolic disorders. We anticipate that the innovative and interdisciplinary nature of this proposal will yield technologies that will broadly impact biotechnology and medicine.