# Defining the regulatory roles of alternative ribosome initiation and novel peptides

> **NIH NIH K99** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2020 · $50,000

## Abstract

PROJECT SUMMARY/ABSTRACT
More than 15 years after the completion of the Human Genome Project, our understanding of the “annotated”
genome is still incomplete. Alternative ribosome initiation sites that are not part of the “annotated genome”
encode novel open reading frames (ORFs) that are either variants of annotated proteins, distinct ORFs upstream
or downstream of annotated proteins, or even ORFs on long non-coding RNAs. These novel ORFs are emerging
as a translational control mechanism to rapidly reprogram specific genes and protein synthesis networks,
especially during stress and cell-state transformations such as tumorigenesis. Furthermore, these new ORFs
encode putative peptides that remain uncharacterized. Thus, understanding the translational control
mechanisms, as well as the regulatory functions of the encoded peptides, could reveal fundamental biology and
targets for therapeutics. Existing studies of alternative initiation or alternative ORF-encoded peptides have taken
an ad hoc approach, owing to a lack of tools to profile them at genome-wide scale. Our goal is to develop and
apply deep sequencing and high-throughput, CRISPR-based methods to map the functional roles of these
nonconventional translation transcriptome-wide, using tumorigenesis as a model system. Functional genomic
approaches are uniquely poised to address the deficit in our understanding of functional alternative ORFs. In
this proposal we will aim to characterize the global utilization of nonconventional initiation sites during
tumorigenesis using ribosome profiling and RNA-seq at various time points (Aim 1). This will define novel ORFs
that are actively translated, and how the translation of these ORFs are regulated to promote expression of
oncogenic genes and peptides. Then, we will use CRISPR screens to identify ORFs necessary for tumor growth,
and define the functions of the novel peptides by characterizing localization, physical interactions, and genetic
interactions (Aim 2). Finally, we will mechanistically interrogate alternative start site usage to investigate how
translation is tuned during cell-state changes (Aim 3). Overall, the results from the proposal will address long-
standing questions about translational control, and reveal the regulatory roles of novel proteins. The combination
of mentored support, skills, and data obtained in the K99 phase will provide Dr. Chen a springboard to achieving
independence as an investigator in the R00 phase and beyond. The results of our studies will provide new
insights into fundamental aspects of translational control, and will define new paradigms relevant to biology and
disease.

## Key facts

- **NIH application ID:** 10013272
- **Project number:** 5K99GM134154-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Jin Chen
- **Activity code:** K99 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $50,000
- **Award type:** 5
- **Project period:** 2019-09-09 → 2020-10-05

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10013272

## Citation

> US National Institutes of Health, RePORTER application 10013272, Defining the regulatory roles of alternative ribosome initiation and novel peptides (5K99GM134154-02). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10013272. Licensed CC0.

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