Coding and noncoding molecular mechanisms of a bifunctional gene in multiple cellular contexts

The National Institute of General Medical Sciences, National Institutes of Health, awarded the Trustees of Indiana University $871,750 on September 9, 2025, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate the coding and noncoding molecular mechanisms of a bifunctional gene across multiple cellular contexts.

The research addresses the functional and mechanistic characterization of genes that possess both coding and noncoding regulatory elements. The project focuses on long noncoding RNA genes that unexpectedly contain small open reading frames translated into microproteins of less than 100 amino acids, which may regulate cellular processes distinct from those of their parent genes. By determining how bifunctional genes are regulated and how they control fundamental cellular processes, the work aims to reveal mechanisms that could lead to more specific therapeutic targets for human disease.

Performance takes place in Indianapolis, Indiana. The award period extends through July 31, 2030.

Abstract

Dysfunctional cellular processes contribute to the pathogenesis of many human diseases. Genes and their functional products are central to the molecular mechanisms of all cellular processes. As such, determining the regulation and molecular mechanisms of uncharacterized genes may reveal mechanisms controlling cellular processes that could be exploited to improve disease. Long noncoding RNA genes (lncrnas) are a type of regulatory noncoding RNA that contain 200 or more nucleotides and DON't encode proteins. They are increasingly recognized as critical cell and context specific regulators of cellular functions. There are potentially tens of thousands of lncrna genes; however, the function and molecular mechanism of most are unknown. Determining these may reveal mechanisms regulating cellular processes that could lead to more specific ways of targeting cellular defects that contribute to human disease. Lncrnas are not supposed to code for proteins, but recent systematic analyses found an appreciable proportion contain unrecognized small open reading frames (sorfs) that are translated into functional microproteins of less than 100 amino acids. Some microproteins regulate key cellular processes; however, the vast majority of putative microproteins encoded by lncrnas remain functionally and mechanistically unvalidated. Furthermore, some microproteins encoded by lncrna genes exhibit functions distinct from those of their parent lncrnas. These "bifunctional" genes (i.e., possess coding and noncoding functional elements) are poorly understood and pose intriguing questions about their regulation and cellular mechanisms. Our long-term goal is to understand how bifunctional genes are regulated and how they control fundamental cellular processes. Towards this goal, we have identified a bifunctional gene currently annotated as a lncrna that is mainly expressed in t cells and cortical neurons. Its microprotein-dependent effects play a crucial role in protecting against pathogenic t cell responses, while both its microprotein-dependent and independent effects regulate cytokine responses of t cells. However, its transcriptional and translational regulation and the molecular mechanisms of its microprotein and lncrna molecule are undefined. In addition, its regulation, function, and molecular mechanism in neurons are unknown. Here, we propose using this bifunctional gene as a model and leveraging our expertise in lncrna and microprotein cellular and molecular biology to address the following questions: 1) what are the transcriptional and translational mechanisms regulating its RNA and microprotein expression? 2) what are the molecular mechanisms of its RNA molecule and microprotein? 3) how do different cellular contexts influence the regulation of expression and the molecular mechanisms of its microprotein and RNA products? By addressing these questions, we will establish a template for characterizing bifunctional genes thereby enhancing understanding of this growing group of genes and their contributions to human disease.