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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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 helps...
Riboswitches01:56

Riboswitches

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.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
RNA Splicing01:32

RNA Splicing

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...
Types of RNA01:23

Types of RNA

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.
RNA...
Types of RNA01:20

Types of RNA

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 regulating 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.
RNA Performs Diverse...

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Related Experiment Video

Updated: Jun 10, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

RNA-binding protein transcripts reflect composition of target mRNAs.

Thomas H Kapral1,2,3, Bojan Žagrović1,2

  • 1Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria.

Nucleic Acids Research
|June 8, 2026
PubMed
Summary
This summary is machine-generated.

Messenger RNAs (mRNAs) preferentially bind to RNA-binding proteins (RBPs) with similar nucleotide compositions in their own transcripts. This RNA composition bias shapes global RNA-protein networks and nuclear mRNA organization.

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Novel RNA-Binding Proteins Isolation by the RaPID Methodology
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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Related Experiment Videos

Last Updated: Jun 10, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Novel RNA-Binding Proteins Isolation by the RaPID Methodology
11:19

Novel RNA-Binding Proteins Isolation by the RaPID Methodology

Published on: September 30, 2016

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA-protein interactions are crucial for gene regulation.
  • The large-scale organization of RNA-protein networks is not fully understood.

Purpose of the Study:

  • To investigate the organizing principles of RNA-protein networks.
  • To understand how nucleotide composition influences RNA-protein interactions and mRNA localization.

Main Methods:

  • Analysis of a comprehensive human eCLIP dataset (>11,000 mRNAs, 150 RBPs).
  • Statistical analysis controlling for transcript length, expression, and sequence motifs.
  • Validation using in vitro HTR-SELEX data.

Main Results:

  • mRNAs associate with RBPs whose transcripts share similar nucleotide composition.
  • This pattern holds across all four nucleotides and is statistically significant.
  • Nucleotide composition predicts mRNA enrichment in nuclear speckles, particularly guanine-rich transcripts and arginine-binding RBPs.

Conclusions:

  • mRNA nucleotide composition is a fundamental organizing principle of RNA-protein networks.
  • Compositional bias provides specificity in RNA-protein interactions and influences nuclear mRNA organization.
  • A link exists between RNA coding and binding, mediated by nucleotide composition.