Control of gene expression in space and time plays an important role in enabling cells to know where they are in the developing embryo and what to become, a process often referred to as cellular specification. Decades of research have demonstrated numerous layers of regulation in control of gene expression, at both the transcriptional and post-transcriptional level, which coordinate this process. Translational contro of gene expression has, on the contrary, received less experimental attention. Most notably, the prevailing dogma is that at the level of protein production, the ribosome -although an immensely complex molecular machine- possesses a constitutive rather than regulatory function in translating mRNAs. Our findings unexpectedly reveal that fundamental aspects of embryonic development and tissue patterning are instead controlled by a highly regulatory function of the ribosome. Importantly, we have shown that specialized ribosomes harboring a unique protein composition or activity confer tremendous specificity to how the mammalian genome is decoded into proteins. Our recent studies have also begun to elucidate how expression information encoded within the mRNA template confers gene regulatory potential by the ribosome to guide embryonic development. In particular, our research has identified novel RNA regulons embedded within the 5'UTRs of key developmental regulators, such as entire subsets of Homeobox (Hox) genes, which direct how gene products are translated in time and space to pattern the mammalian body plan. These findings transform our understanding of gene regulation and open a new portal of understanding into an additional layer of regulation embedded within vertebrate 5'UTRs vital to control of cell specification, tissue patterning, and embryonic development. In this proposal we will undertake a highly multidisciplinary approach to characterize this novel regulatory code for translational control of key developmental transcripts that primes them for post- transcriptional regulation.
In Aim1 we will characterize a novel post-transcriptional circuitry required for control of Hox gene expression in time and space. In particular, we will undertake a multi-faceted genetic approach to uncover the functional roles of novel 5'UTR RNA Regulons including IRES-like and TIE elements in multiple Hox genes 5'UTRs towards key aspects of their expression in vivo and patterning of the vertebrate embryo.
In Aim2 we will characterize the TIE element, a newly identified RNA regulatory element with remarkable potential to functionally specialize the translation of the mammalian genome.
In Aim3 we will more broadly define the impact of RNA binding proteins on IRES-mediated translational control of key vertebrate developmental regulators. Together, these studies will open a new portal of understanding into the grammatical rules facilitated by unique RNA elements embedded within vertebrate 5'UTRs, which serves to expand developmental gene expression programs guiding organismal development.

Public Health Relevance

In humans, accumulating evidence links mutations in a number of core ribosome components and in particular ribosomal proteins (RPs) to congenital birth defects, including Diamond-Blackfan anemia (DBA) characterized by specific congenital birth defects including limb abnormalities, cleft palate, growth failure, as well as bone marrow failure. Mutations in RPL21 have also been identified in Hereditary Hypotrichosis Simplex, a disorder that is characterized by progressive hair loss early in childhood. Mutations in RPSA underlie Isolated Congenital Asplenia (ICA), where children are born without any spleens. In all of these cases, the mechanism(s) that would account for these cell and tissue specific phenotypes remain poorly understood. In this proposal we will study new mRNA sequence elements that endow the ribosome with gene regulatory specificity that will be vital for understanding the nature of a vast number of human diseases and birth defects associated with mutations in the core translation machinery.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Research Project (R01)
Project #
Application #
Study Section
Development - 1 Study Section (DEV1)
Program Officer
Coulombe, James N
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Stanford University
Anatomy/Cell Biology
Schools of Medicine
United States
Zip Code
Genuth, Naomi R; Barna, Maria (2018) The Discovery of Ribosome Heterogeneity and Its Implications for Gene Regulation and Organismal Life. Mol Cell 71:364-374
Leppek, Kathrin; Das, Rhiju; Barna, Maria (2018) Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol 19:158-174
Simsek, Deniz; Tiu, Gerald C; Flynn, Ryan A et al. (2017) The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. Cell 169:1051-1065.e18
Simsek, Deniz; Barna, Maria (2017) An emerging role for the ribosome as a nexus for post-translational modifications. Curr Opin Cell Biol 45:92-101
Shi, Zhen; Fujii, Kotaro; Kovary, Kyle M et al. (2017) Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Mol Cell 67:71-83.e7
Fujii, Kotaro; Shi, Zhen; Zhulyn, Olena et al. (2017) Pervasive translational regulation of the cell signalling circuitry underlies mammalian development. Nat Commun 8:14443