Nicholas T. Ingolia
Regulation of Translation Control
The translation of mRNA into protein is a central step in gene expression. We seek to understand how translation is controlled to regulate which proteins the cell synthesizes as well as to affect the function of translation products. The starting point for many of our efforts is our ribosome profiling technique, which provides comprehensive and quantitative measurements of translation. Our approach also provides information on the exact position of ribosomes on transcripts, allowing us to experimentally determine what protein is being synthesized and to monitor co-translational processes. This position-specific information has already revealed revisions to genome annotations, including the production of short proteins from supposedly non-coding RNAs.
One surprising observation that has emerged is the extensive translation occurring upstream of many genes. A significant fraction of this upstream translation results from initiation at codons other than the canonical AUG codon. We are interested in understanding the molecular causes and the physiological consequences of this phenomenon. It suggests that the classical model of initiation, in which a pre-initiation complex assembles at the beginning of a transcript and scans for the first AUG codon, may be incomplete. Furthermore, we have found that cellular growth conditions can change the pattern of upstream initiation. Determining the basis for this regulated change will provide new insight into the process of start codon selection. We will also use it to gain insights into the way in which upstream translation affects the expression of downstream genes. In some cases, such as the transcription factor Atf4, it is known to control the expression level of the principal protein encoded on the transcript. In others, such as the transcription factor C/EBP, it controls the production of alternate and functionally distinct protein isoforms. We will look more broadly to identify other genes that are affected by changes in translation initiation and understand how the 5' leader sequence on these transcripts contributes to their regulation.
Translational control plays a key role in diverse processes ranging from cellular stress responses to synaptic plasticity. We wish to understand more broadly how translation is controlled. Regulated changes in start codon selection are one mechanism, but it alone has a limited ability to target specific transcripts. We believe that, much as transcription is regulated by interactions between sequence-specific DNA-binding factors and a basal machinery, translation will be affected by RNA-binding proteins that interact with core initiation factors. Recent experiments have revealed a wealth of proteins that bind specific subsets of transcripts within the cell, but less is known about the functional consequences of this binding. We will pursue the molecular basis of interactions that mediate translational control and the influence of upstream signals that change these effects.