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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Riboswitches

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Updated: Feb 23, 2026

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome.

Lorenzo Calviello1, Uwe Ohler2

  • 1Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin 13125, Germany; Department of Biology, Humboldt Universität zu Berlin, Unter den Linden 6, Berlin 10117, Germany.

Trends in Genetics : TIG
|September 10, 2017
PubMed
Summary

Ribosome profiling (Ribo-seq) maps translating ribosomes to study gene expression. This review overviews diverse Ribo-seq methods and computational strategies for analyzing translation, emphasizing standardization needs.

Keywords:
Ribo-seqbioinformaticsgenomicstranscriptomicstranslation

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Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Ribosome profiling (Ribo-seq) is a key technique for studying gene expression at the translational level.
  • Numerous experimental modifications and computational analyses exist for Ribo-seq data.
  • The diversity in protocols necessitates standardization for robust and reproducible research.

Purpose of the Study:

  • To provide a comprehensive overview of Ribo-seq methodologies.
  • To discuss various computational strategies for Ribo-seq data analysis.
  • To highlight the importance of standardization in Ribo-seq protocols.

Main Methods:

  • Review of existing literature on ribosome profiling techniques.
  • Analysis of different computational approaches for Ribo-seq data interpretation.
  • Comparison of protocol variations and their assumptions.

Main Results:

  • Identification of diverse Ribo-seq protocols and their applications.
  • Overview of computational tools for analyzing translation.
  • Discussion on the strengths and limitations of various methodologies.

Conclusions:

  • Ribo-seq is a versatile tool for transcriptome-wide translation studies.
  • Standardization of protocols and analysis is crucial for advancing the field.
  • Ribo-seq integrates with other omics data to elucidate the role of translation in cellular processes.