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.

Public Health Relevance

Relevancy Statement Gene expression is tightly controlled in time and space. RNA binding proteins and ribosomal proteins, essential regulators of mRNA translation, one of the fundamental steps of gene expression, are recurrently mutated in diseases such as immunoregulatory and neurological disorders, as well as cancer. Understanding how these translational regulators control gene expression dynamics would have a strong impact on biology, disease development and therapeutic applications.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Unknown (R35)
Project #
5R35GM128802-02
Application #
9737981
Study Section
Special Emphasis Panel (ZGM1)
Program Officer
Reddy, Michael K
Project Start
2018-08-01
Project End
2023-07-31
Budget Start
2019-08-01
Budget End
2020-07-31
Support Year
2
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Biology
Type
Graduate Schools
DUNS #
049179401
City
New York
State
NY
Country
United States
Zip Code
10027
Emmott, Edward; Jovanovic, Marko; Slavov, Nikolai (2018) Ribosome Stoichiometry: From Form to Function. Trends Biochem Sci :