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Related Concept Videos

RNA-seq03:21

RNA-seq

11.8K
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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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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.
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.
The technique...
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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Related Experiment Video

Updated: Jan 17, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

8.5K

Using SPIDRs to map the RNA-protein web.

Carson C Thoreen1

  • 1Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA.

Molecular Cell
|September 19, 2025
PubMed
Summary

Researchers developed SPIDR, a new method for mapping RNA-protein interactions. This technique revealed novel interactions regulated by the mTOR pathway, offering new insights into cellular nutrient sensing.

Area of Science:

  • Molecular Biology
  • Genomics
  • Cellular Signaling

Background:

  • RNA-binding proteins (RBPs) play crucial roles in gene regulation.
  • Understanding RBP-RNA interactions is essential for deciphering cellular processes.
  • Current methods for profiling these interactions can be limited in scale.

Purpose of the Study:

  • To introduce a novel, high-throughput method for profiling RNA-protein interactions.
  • To investigate the role of the nutrient-regulated mTOR pathway in controlling RNA-protein interactions.

Main Methods:

  • Development and application of SPIDR (Sequencing Protein-protein Interaction Discovery and Retrieval), a massively multiplexed variant of CLIP (Crosslinking Immunoprecipitation).
  • Simultaneous profiling of targets for numerous RNA-binding proteins.

More Related Videos

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Related Experiment Videos

Last Updated: Jan 17, 2026

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
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A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

Published on: July 10, 2019

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Main Results:

  • SPIDR enables the simultaneous profiling of targets for an arbitrary number of RNA-binding proteins.
  • The study uncovered previously unknown RNA-protein interactions.
  • These interactions are demonstrated to be under the control of the nutrient-regulated mTOR pathway.

Conclusions:

  • SPIDR is a powerful tool for large-scale mapping of RNA-protein interactions.
  • The mTOR pathway regulates a complex network of RNA-protein interactions impacting cellular responses to nutrients.