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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 Profiling02:24

Ribosome Profiling

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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.
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
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Translational Regulation01:29

Translational Regulation

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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria
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Mapping the small RNA interactome in bacteria using RIL-seq.

Sahar Melamed1, Raya Faigenbaum-Romm1, Asaf Peer1

  • 1Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.

Nature Protocols
|December 8, 2017
PubMed
Summary
This summary is machine-generated.

We developed RIL-seq, a method to map bacterial small RNA (sRNA) targets in vivo. This technique captures native sRNA-target interactions without sRNA overexpression, revealing regulatory networks.

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Area of Science:

  • Bacterial gene regulation
  • RNA biology
  • Molecular genetics

Background:

  • Small RNAs (sRNAs) are key post-transcriptional regulators in bacteria.
  • Understanding sRNA-target interactions is crucial for deciphering gene expression control.

Purpose of the Study:

  • To develop a transcriptome-wide method for mapping bacterial sRNA-target pairs in vivo.
  • To capture these interactions under native cellular conditions without sRNA overexpression.

Main Methods:

  • RNA interaction by ligation and sequencing (RIL-seq) combines co-immunoprecipitation of Hfq-bound RNAs, ligation, and sequencing.
  • A computational pipeline identifies statistically significant chimeric fragments representing sRNA-target interactions.
  • The method utilizes the Hfq protein to capture interacting RNA molecules.

Main Results:

  • RIL-seq successfully maps sRNA-target interactions in vivo.
  • The method does not require sRNA overexpression, capturing native regulatory interactions.
  • It allows for the identification of novel sRNAs and their targets.

Conclusions:

  • RIL-seq provides a powerful tool for studying bacterial post-transcriptional regulatory networks.
  • It offers insights into the dynamics of the sRNA interactome under various conditions.
  • The method is adaptable for studying protein-mediated RNA-RNA interactions in diverse bacteria.