Simple and inexpensive ribosome profiling analysis of mRNA translation.

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The development and application of ribosome profiling has markedly advanced our understanding of ribosomes and mRNA translation. The experimental approach, which relies on deep sequencing of ribosome-protected mRNA fragments generated by treatment of polyribosomes with exogenous nucleases, provides a transcriptome-wide assessment of translation. The broad application of ribosome profiling has been slowed by the complexity and expense of the protocol. Here, we provide a simplified ribosome profiling method that uses micrococcal nuclease to generate ribosome footprints in crude cellular extracts, which are then purified simply by size selection via polyacrylamide gel electrophoresis. This simplification removes the laborious or expensive purification of ribosomes that has typically been used. This direct extraction method generates gene-level ribosome profiling data that are similar to a method that includes ribosome purification. This protocol should significantly ease the barrier to entry for research groups interested in employing ribosome profiling.





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Reid, David W, Shirish Shenolikar and Christopher V Nicchitta (2015). Simple and inexpensive ribosome profiling analysis of mRNA translation. Methods (San Diego, Calif.), 91. pp. 69–74. 10.1016/j.ymeth.2015.07.003 Retrieved from

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Shirish Shenolikar

Professor Emeritus of Psychiatry and Behavioral Sciences

Protein phosphorylation controls a wide range of physiological processes in mammalian tissues. Phosphorylation state of cellular proteins is controlled by the opposing actions of protein kinases and phosphatases that are regulated by hormones, neurotransmitters, growth factors and other environmental cues. Our research attempts to understand the communication between protein kinases and phosphatases that dictates cellular protein phosphorylation and the cell's response to hormones. Over the last decade, our work has provided critical information about the role of protein phosphatase-1 (PP1) in controlling synaptic function, cell stress, gene expression and growth. We have generated a large repertoire of reagents to decipher PP1's role in signaling pathways in mammalian cells and tissues. Emerging evidence suggests that in many cells, PP1 activity is fine tuned by the protein, inhibitor-1 (I-1). A major focus of our research is to elucidate the role of I-1 in kinase-phosphatase cross-talk and impact of the altered I-1 gene expression seen in several human diseases. Our studies showed that recognition of cellular substrates by PP1 is also directed by its association with a variety of targeting subunits that are themselves also subject to physiological control. Thus, the overall focus of our research is to define the physiological mechanisms that regulate PP1 functions relevant to human health and disease.


Christopher Vincent Nicchitta

Professor of Cell Biology

  Our laboratory studies the cellular architecture and regulation of protein synthesis, with the goal of understanding how cells regulate the subcellular organization and temporal dynamics of protein synthesis. We focus on mRNA localization - the process by which cells control where and when a protein is synthesized by localizing its mRNA to a discrete location(s) in the cell. Such regulation is critical for many aspects of cell dynamics, cell signaling and cell division. Of the diverse mRNA localization phenomena that have been identified to date, the most prominent is mRNA localization to the endoplasmic reticulum (ER). mRNA localization to the ER operates on an unusually large scale (essentially the entire mRNA transcriptome is partially represented on the ER, with those mRNAs encoding secretory and membrane proteins being highly ER-enriched), and continuously– all newly exported mRNAs undergo selection for translation in the cytosol and/or the ER compartments.

We use a broad array of experimental approaches - biochemistry, cell biology, genomics, and computational biology - and are focusing on several related themes. First, we are working to identify the mRNA-encoded signals used to target mRNAs to the ER as well as the cellular factors that recognize these signals. One mechanism, in which a signal in nascent secretory and membrane proteins directs mRNA recruitment to the ER, has been previously described. It is clear though that there are multiple pathways that direct mRNAs to the ER, including pathways that direct cytosolic and nucleoplasmic protein-encoding mRNAs to the ER. We are also investigating how, once localized, mRNAs are anchored to the ER membrane. In a recent study, we reported that the cohort of mRNAs encoding organelle resident proteins(e.g., nuclear envelope, ER, Golgi, lysosomes, peroxisomes) are localized tothe ER and directly anchored to components of the ER membrane. We are very interested in understanding the cis-encoded anchoring signals and the integral membrane proteins that function in mRNA anchoring to biological membrane, and lastly, how direct mRNA anchoring influences mRNA translation and mRNA stability.

In parallel efforts, we discovered that mRNA translation is under distinct regulatory control in the cytosol and ER compartments, with translation being 3-5 fold more efficient on the ER. These differences are substantial and suggest that mRNA localization to the ER may represent an important post-transcriptional gene expression mechanism. To gain insight into the mechanisms and factors responsible for the compartmental regulation of mRNA translation we are using traditional biochemical approaches (pulse-labeling, cell fractionation, immunoprecipitation, proteomics) as well as genomic approaches (ribosome footprinting, deep sequencing).

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