A Ribosomal Density-Mapping Procedure to Explore Ribosome Positions Along Translating mRNAs

Eldad, Naama; Arava, Yoav

doi:10.1007/978-1-59745-033-1_16

Cited by 10 publications

(8 citation statements)

References 12 publications

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“…A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs is described by Eldad et al [65]. mRNAs that entered ribosome for translation (ribosome-associated mRNA) shows better correlation with proteins than typical mRNA expression [66].…”

Section: Correlation Between Transcriptomic and Proteomic Datamentioning

confidence: 99%

Integrated Analysis of Transcriptomic and Proteomic Data

2013

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Until recently, understanding the regulatory behavior of cells has been pursued through independent analysis of the transcriptome or the proteome. Based on the central dogma, it was generally assumed that there exist a direct correspondence between mRNA transcripts and generated protein expressions. However, recent studies have shown that the correlation between mRNA and Protein expressions can be low due to various factors such as different half lives and post transcription machinery. Thus, a joint analysis of the transcriptomic and proteomic data can provide useful insights that may not be deciphered from individual analysis of mRNA or protein expressions. This article reviews the existing major approaches for joint analysis of transcriptomic and proteomic data. We categorize the different approaches into eight main categories based on the initial algorithm and final analysis goal. We further present analogies with other domains and discuss the existing research problems in this area.

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Section: Correlation Between Transcriptomic and Proteomic Datamentioning

confidence: 99%

Integrated Analysis of Transcriptomic and Proteomic Data

2013

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“…This leads to another interesting consequence-the average density of ribosomes decreases as a function of the length of the mRNA coding region. New experimental methods [20][21][22][23][24] allow for the measurements of these quantities, and we expect that a detailed comparison between theory and experiment will soon be possible.…”

Section: Introductionmentioning

confidence: 99%

Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks

2011

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We investigate the role of degradation of mRNA on protein synthesis using the totally asymmetric simple exclusion process (TASEP) as the underlying model for ribosome dynamics. mRNA degradation has a strong effect on the lifetime distribution of the mRNA, which in turn affects polysome statistics such as the number of ribosomes present on an mRNA strand of a given size. An average over mRNA of all ages is equivalent to an average over possible configurations of the corresponding TASEP-both before steady state and in steady state. To evaluate the relevant quantities for the translation problem, we first study the approach towards steady state of the TASEP, starting with an empty lattice representing an unloaded mRNA. When approaching the high density phase, the system shows two distinct phases with the entry and exit boundaries taking control of the density at their respective ends in the second phase. The approach towards the maximal current phase exhibits the surprising property that the ribosome entry flux can exceed the maximum possible steady state value. In all phases, the averaging over the mRNA age distribution shows a decrease in the average ribosome density profile as a function of distance from the entry boundary. For entry/exit parameters corresponding to the high density phase of TASEP, the average ribosome density profile also has a maximum near the exit end.

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“…Note: These will be the "Unbound" samples. 26 to extract RNA from the "input" and "unbound" samples (steps 1.13 and 1.17).…”

Section: Rapid Purificationmentioning

confidence: 99%

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Samra

Arava

2016

JoVE

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RNA-binding proteins (RBPs) play important roles in every aspect of RNA metabolism and regulation. Their identification is a major challenge in modern biology. Only a few in vitro and in vivo methods enable the identification of RBPs associated with a particular target mRNA. However, their main limitations are the identification of RBPs in a non-cellular environment (in vitro) or the low efficiency isolation of RNA of interest (in vivo). An RNA-binding protein purification and identification (RaPID) methodology was designed to overcome these limitations in yeast and enable efficient isolation of proteins that are associated in vivo. To achieve this, the RNA of interest is tagged with MS2 loops, and co-expressed with a fusion protein of an MS2-binding protein and a streptavidin-binding protein (SBP). Cells are then subjected to crosslinking and lysed, and complexes are isolated through streptavidin beads. The proteins that co-purify with the tagged RNA can then be determined by mass spectrometry. We recently used this protocol to identify novel proteins associated with the ER-associated PMP1 mRNA. Here, we provide a detailed protocol of RaPID, and discuss some of its limitations and advantages.

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A Ribosomal Density-Mapping Procedure to Explore Ribosome Positions Along Translating mRNAs

Cited by 10 publications

References 12 publications

Integrated Analysis of Transcriptomic and Proteomic Data

Integrated Analysis of Transcriptomic and Proteomic Data

Translation by Ribosomes with mRNA Degradation: Exclusion Processes on Aging Tracks

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

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