Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

23.7K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
23.7K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
Ribosome Profiling02:24

Ribosome Profiling

3.5K
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...
3.5K
Transcription Initiation01:47

Transcription Initiation

16.3K
Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
The promoters and enhancers and their accessory proteins allow tight regulation of...
16.3K
RNA-seq03:21

RNA-seq

9.8K
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...
9.8K
RNA Stability01:53

RNA Stability

33.3K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
33.3K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A scalable approach to investigating sequence-to-function predictions from personal genomes.

Nature methods·2026
Same author

BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.

bioRxiv : the preprint server for biology·2026
Same author

Gene regulatory networks define human airway epithelial cell types and their distinct responses to type I interferon.

bioRxiv : the preprint server for biology·2026
Same author

Single nucleus RNA sequencing of juvenile dermatomyositis skeletal muscle identifies altered angiogenic signaling.

bioRxiv : the preprint server for biology·2026
Same author

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2.

Nature biotechnology·2026
Same author

Memory T cell rapid recall is driven by memory-specific AP-1 recruitment determined by epigenome and co-factor interactions.

bioRxiv : the preprint server for biology·2026
Same journal

Layered social competition coordinates reproductive hierarchy formation in ants.

bioRxiv : the preprint server for biology·2026
Same journal

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas.

bioRxiv : the preprint server for biology·2026
Same journal

Loss of LanC-like proteins delays post-injury regeneration of aging skeletal muscles.

bioRxiv : the preprint server for biology·2026
Same journal

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets.

bioRxiv : the preprint server for biology·2026
Same journal

Confidence-supported label-free metabolic imaging with FPhaS phase autofluorescence microscopy.

bioRxiv : the preprint server for biology·2026
Same journal

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Jun 9, 2025

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

6.6K

Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes.

Alexander Sasse1,2,3,4, Debashish Ray2, Kaitlin U Laverty1,2,4,5

  • 1Department of Molecular Genetics, University of Toronto, Toronto, ON Canada.

Biorxiv : the Preprint Server for Biology
|October 28, 2024
PubMed
Summary
This summary is machine-generated.

EuPRI is a new database of RNA motifs for 34,736 RNA-binding proteins (RBPs) across eukaryotes. This resource significantly expands known RBP motifs, aiding gene regulation studies.

Keywords:
KHPost-transcriptional regulationRNA binding interfaceRNA binding proteinsRNA-binding specificityRNAcompeteRRMmotif evolutionrecognition code

More Related Videos

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
09:45

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

11.0K
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

53.4K

Related Experiment Videos

Last Updated: Jun 9, 2025

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

6.6K
An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes
09:45

An Oligonucleotide-based Tandem RNA Isolation Procedure to Recover Eukaryotic mRNA-Protein Complexes

Published on: August 18, 2018

11.0K
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

53.4K

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA-binding proteins (RBPs) are crucial for regulating gene expression.
  • Understanding RBP-RNA interactions is essential for deciphering cellular processes.
  • Existing resources for RBP motifs are limited in scope and coverage.

Purpose of the Study:

  • To introduce EuPRI, a comprehensive resource for eukaryotic protein-RNA interactions.
  • To expand the repertoire of known RNA motifs for a vast number of RBPs.
  • To provide tools for inferring RBP function and evolutionary relationships.

Main Methods:

  • Development of a new computational platform, Joint Protein-Ligand Embedding (JPLE), for motif reconstruction.
  • Collection and integration of in vitro binding data, including new RNAcompete data.
  • Analysis of motif conservation and evolution across eukaryotic clades.

Main Results:

  • EuPRI provides RNA motifs for 34,736 RBPs from 690 eukaryotes, quadrupling the number of known motifs.
  • The resource includes binding data for 504 RBPs and assigns motifs to most human RBPs.
  • Significant expansion of RBP motif knowledge in flowering plants, e.g., 7-fold increase for Arabidopsis thaliana.
  • Predicted roles for 12 Arabidopsis thaliana RBPs in RNA stability.
  • Identified rapid evolution of post-transcriptional regulatory networks in worms and plants.

Conclusions:

  • EuPRI is a valuable, freely available resource for studying gene regulation across eukaryotes.
  • The platform facilitates the prediction of RBP function and evolutionary dynamics.
  • EuPRI enhances our understanding of RNA-binding protein roles in diverse organisms.