Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Nucleic Acid Structure

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

Ribosome Profiling

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...

RNA-seq

RNA-seq

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 microarray-based...

Ribosomes

Ribosomes

Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.Ribosome Structure and AssemblyRibosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome production. Within the...

Ribosomes

Ribosomes

Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome production. Within...

Nucleic Acids

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...

You might also read

Related Articles

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

Sort by

Same author

Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction.

Science advances·2026

Same author

Structure-informed mutagenesis identifies combinatorial contributions to mouse insulin receptor IRES function.

RNA (New York, N.Y.)·2026

Same author

Epstein-Barr Virus Encoded lncRNAs Control the Viral Lytic Switch.

bioRxiv : the preprint server for biology·2025

Same author

Controlling intermolecular base pairing in Drosophila germ granules by mRNA folding and its implications in fly development.

Nature communications·2025

Same author

Telomerase RNA structural heterogeneity in living human cells detected by DMS-MaPseq.

Nature communications·2025

Same author

DMS-MapSeq Analysis of Antisense Oligonucleotide Binding to lncRNA PANDA.

Current protocols·2024

Search research articles

Related Experiment Video

Updated: Jun 5, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites.

Adam Sychla¹, Pierre Bongrand¹, Grant Yang^1,2

¹Department of Microbiology, Harvard Medical School, Boston & 02115, USA.

Biorxiv : the Preprint Server for Biology

|June 4, 2026

Summary

New research reveals novel Internal Ribosome Entry Site (IRES) structures and functions in viral RNA genomes. An AI model, Albatross, accurately predicts IRES structures, advancing our understanding of viral translation and bioengineering applications.

More Related Videos

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Published on: February 25, 2011

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

Related Experiment Videos

Last Updated: Jun 5, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

Published on: February 25, 2011

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution

Published on: July 8, 2019

Area of Science:

Virology
Molecular Biology
Bioinformatics

Background:

Viral RNA genomes are highly information-dense.
Internal Ribosome Entry Sites (IRESes) are crucial for picornavirus translation.
Previous studies had limitations in IRES characterization.

Purpose of the Study:

To profile full-length IRESes across different cell types.
To investigate the activity and tissue tropism of IRES elements.
To develop and validate an AI model for predicting IRES structures.

Main Methods:

Profiling 96 full-length IRESes across six cell types.
Introducing Albatross, an RNA language model fine-tuned on 50,000 IRES sequences.
Comparing Albatross predictions with chemical probing and covariation analysis.

Main Results:

Type V IRESes were found to double the activity of EMCV.
Most IRESes demonstrated significant tissue tropism.
Albatross predicted IRES structures with precision comparable to chemical probing.
Structural discovery scaled with model size.

Conclusions:

Newly identified IRESes offer enhanced activity for bioengineering.
IRES activity is significantly influenced by cell type, indicating tissue tropism.
Albatross represents a breakthrough in predicting RNA structures from sequence alone.
The study provides structural maps for thousands of IRES elements, facilitating future research.