Ribosome profiling (ribosome footprinting, ribosome protected fragment profiling, translation profiling)

AbstractThe recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we used a 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.

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Selective mRNA translation in erythropoiesis

Biochemical Society Transactions ◽

10.1042/bst20150009 ◽

2015 ◽

Vol 43 (3) ◽

pp. 343-347 ◽

Cited By ~ 1

Author(s):

Klaske A.M.H. Thiadens ◽

Marieke von Lindern

Keyword(s):

Translation Initiation ◽

High Throughput Sequencing ◽

Gene Expression Regulation ◽

Mrna Translation ◽

Ribosome Profiling ◽

Daily Production ◽

Cellular Processes ◽

Global Mapping ◽

Ribosome Footprinting ◽

Control Translation

The daily production of up to 1011 erythrocytes is tightly controlled to maintain the number of erythrocytes in peripheral blood between narrow boundaries. Availability of growth factors and nutrients, particularly iron, control the proliferation and survival of precursor cells partly through control of mRNA translation. General translation initiation mechanisms can selectively control translation of transcripts that carry specific structures in the UTRs. This selective mRNA translation is an important layer of gene expression regulation in erythropoiesis. Ribosome profiling is a recently developed high throughput sequencing technique for global mapping of translation initiation sites across the transcriptome. Here we describe what is known about control of mRNA translation in erythropoiesis and how ribosome profiling will help to further our knowledge. Ribosome footprinting will give insight in transcript-specific translation at codon resolution, which is of great value to understand many cellular processes during erythropoiesis. It will be of particular interest to understand responses to iron availability and reactive oxygen species (ROS), which affects translation initiation of transcripts harbouring upstream ORFs (uORF) and potential alternative downstream ORFs (aORF).

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riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data

10.1101/169862 ◽

2017 ◽

Cited By ~ 1

Author(s):

Fabio Lauria ◽

Toma Tebaldi ◽

Paola Bernabò ◽

Ewout J.N. Groen ◽

Thomas H. Gillingwater ◽

...

Keyword(s):

Visual Inspection ◽

R Package ◽

Ribosome Profiling ◽

Precise Estimation ◽

Genome Wide ◽

Protected Fragment ◽

Multiple Case ◽

Multiple Case Studies ◽

Nucleotide Resolution ◽

Optimal Localization

ABSTRACTRibosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies.Availability and ImplementationriboWaltz was implemented in R and is available at https://github.com/LabTranslationalArchitectomics/[email protected] or [email protected]

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