# Regulation of Protein Production Dynamics:  RNA Binding Proteins and the Ribosome Code

> **NIH NIH R35** · COLUMBIA UNIV NEW YORK MORNINGSIDE · 2020 · $127,500

## Abstract

Summary
The central dogma of molecular biology assumes a linear path of gene expression from gene to protein. It is
now clear that gene expression is tightly controlled at several levels - from transcription to translation to protein
degradation - yet the fields of molecular, cell and developmental biology have mostly focused on transcriptional
control as the primary mode of gene regulation. Yet, the mammalian genome encodes over 1,500 RNA binding
proteins (RBPs), several of which are recurrently mutated in diseases, such as cancer and neurological
disorders, suggesting that post-transcriptional gene expression regulation and especially mRNA translation are
important in both health and human disease. Furthermore, the regulatory role of the ribosome itself has so far
been under-explored. Evidence is mounting that specialized ribosomes, which vary in ribosomal protein
stoichiometry and post-translational modifications, exist that may impact the translation of specific mRNAs
through an as-yet-undefined ‘ribosome code’.
The overarching research goal of the lab is to understand the principles and mechanisms by which
translational regulation controls the dynamics of gene expression and therefore affects processes like
differentiation, stress response and pathogenesis. Over the next five years, we will focus on two specific
aspects of translational control in the context of mouse embryonic stem cell differentiation. First, we will
systematically identify and characterize RNA binding proteins (RBPs) that regulate translational changes.
Based on our previous work, we will combine high-throughput CRISPR-based screening with global
measurements of RNA dynamics, and protein production and degradation. This will link RBPs to their mRNA
targets, providing the foundation for future detailed functional follow-ups, allowing us to elucidate functional and
causal insights of how RBPs regulate mRNA translation. Second, we are looking at the extent of ribosomal
heterogeneity, testing the hypothesis that specialized ribosomes exist that selectively translate subsets of
mRNAs, thereby introducing an additional level of regulation in gene expression – a ribosome code. By
applying high accuracy mass spectrometry, we are focusing right now on two potential sources of ribosomal
heterogeneity – differential expression in core ribosomal proteins (RPs) and changes in their post-translational
modifications. Based on these measured changes in ribosome composition, we are selecting RPs and PTMs
with the strongest changes for further functional characterization. The detailed follow up will provide for a
selected set of RPs and PTMs the principles and mechanistic insight how ribosome specialization regulates
translation.
Together these two approaches will provide unprecedented insight on the dynamics of protein production in an
important physiological context, potentially unravelling novel paradigms of gene expression regulation.

## Key facts

- **NIH application ID:** 10135528
- **Project number:** 3R35GM128802-02S1
- **Recipient organization:** COLUMBIA UNIV NEW YORK MORNINGSIDE
- **Principal Investigator:** Marko Jovanovic
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $127,500
- **Award type:** 3
- **Project period:** 2018-08-01 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10135528

## Citation

> US National Institutes of Health, RePORTER application 10135528, Regulation of Protein Production Dynamics:  RNA Binding Proteins and the Ribosome Code (3R35GM128802-02S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10135528. Licensed CC0.

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