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

Ribosome Profiling02:24

Ribosome Profiling

4.0K
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...
4.0K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

1.2K
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...
1.2K
Riboswitches01:56

Riboswitches

9.3K
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...
9.3K
Regulated mRNA Transport02:22

Regulated mRNA Transport

6.8K
In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
6.8K
Regulated mRNA Transport02:22

Regulated mRNA Transport

3.2K
3.2K
Translational Regulation01:29

Translational Regulation

423
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,...
423

You might also read

Related Articles

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

Sort by
Same author

MAPK-activated protein kinase 2 orchestrates memory T-cell inflation in cytomegalovirus infection.

Journal of immunology (Baltimore, Md. : 1950)·2026
Same author

Donor bone marrow together with recipient regulatory T cells induces chimerism without irradiation in kidney transplantation.

Science translational medicine·2026
Same author

IDH1-R132H enhances oncolytic HSV-1 therapy by facilitating viral entry and immune activation in glioma.

Nature communications·2026
Same author

A multiplexed, systems-based approach for prediction of antibody neutralization breadth for soluble human receptors.

Journal of immunology (Baltimore, Md. : 1950)·2026
Same author

Ensuring Reliability of Curated Electronic Health Record-Derived Data: The Validation of Accuracy for Large Language Model-/Machine Learning-Extracted Information and Data (VALID) Framework.

JCO clinical cancer informatics·2026
Same author

Donor-reactive clonotypes are overrepresented in the urinary T cell repertoire during kidney transplant rejection and show distinct dynamics in the circulation.

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons·2026

Related Experiment Video

Updated: Dec 10, 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

7.0K

Transite: A Computational Motif-Based Analysis Platform That Identifies RNA-Binding Proteins Modulating Changes in

Konstantin Krismer1, Molly A Bird2, Shohreh Varmeh3

  • 1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department for Medical and Bioinformatics, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria.

Cell Reports
|August 27, 2020
PubMed
Summary

Transite, a new computational method, identifies RNA-binding proteins (RBPs) that regulate gene expression. It revealed hnRNPC as a key factor in chemotherapy resistance in lung cancer patients.

Keywords:
DNA damage responseRNA-binding proteinschemotherapypost-transcriptional regulationsequence motifs

More Related Videos

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
12:54

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

13.9K
High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
09:44

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Published on: March 3, 2015

9.8K

Related Experiment Videos

Last Updated: Dec 10, 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

7.0K
Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
12:54

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

13.9K
High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
09:44

High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes

Published on: March 3, 2015

9.8K

Area of Science:

  • Molecular Biology
  • Computational Biology
  • Genomics

Background:

  • RNA-binding proteins (RBPs) are crucial regulators of gene expression, influencing splicing, RNA stability, and translation.
  • Stimulus-induced changes in RBP function drive global gene expression alterations, but identifying specific RBPs remains challenging.
  • Understanding RBP roles is vital for deciphering cellular responses to various stimuli and disease states.

Purpose of the Study:

  • To develop and validate Transite, a computational approach for systematically inferring RBPs that modulate gene expression via RNA stability and degradation.
  • To apply Transite to clinical data to identify RBPs involved in non-small cell lung cancer (NSCLC) and response to chemotherapy.
  • To provide a framework for identifying RBPs driving cell-state transitions using existing gene expression datasets.

Main Methods:

  • Development of Transite, a computational pipeline for inferring RBP activity from gene expression data.
  • Application of Transite to RNA sequencing data from NSCLC patients at diagnosis and post-chemotherapy recurrence.
  • Experimental validation of Transite's predictions, specifically focusing on identified RBPs and their role in chemotherapeutic resistance.

Main Results:

  • Transite successfully inferred RBPs influencing gene expression through RNA stability and degradation.
  • The analysis identified known RBP regulators of the DNA damage response in NSCLC.
  • hnRNPC was identified as a novel RBP modulating chemotherapeutic resistance, and its role was experimentally confirmed.

Conclusions:

  • Transite is an effective computational framework for identifying RBPs that drive gene expression changes and cell-state transitions.
  • The study highlights hnRNPC as a potential therapeutic target for overcoming chemoresistance in lung cancer.
  • Transite enhances the utility of public gene expression datasets for RBP discovery and understanding gene regulation.