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

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...

lncRNA - Long Non-coding RNAs

lncRNA - Long Non-coding RNAs

siRNA - Small Interfering RNAs

siRNA - Small Interfering RNAs

Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the...

piRNA - Piwi-interacting RNAs

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...

Causality in Epidemiology

Causality in Epidemiology

Causality or causation is a fundamental concept in epidemiology, vital for understanding the relationships between various factors and health outcomes. Despite its importance, there's no single, universally accepted definition of causality within the discipline. Drawing from a systematic review, causality in epidemiology encompasses several definitions, including production, necessary and sufficient, sufficient-component, counterfactual, and probabilistic models. Each has its strengths and...

What is Gene Expression?

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...

You might also read

Related Articles

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

Sort by

Same author

Molecular architecture of the tumor microenvironment caused by <i>BRCA1</i> and <i>BRCA2</i> somatic mutations in human lung adenocarcinoma.

eLife·2026

Same author

Pan-cancer analysis of single-cell profiles with polygenic signals reveals genetic influences on tumor immunity across cancers.

Communications biology·2026

Same author

Interplay between Donor Identity and Sulfur Oxidation in Regulating the Photophysics of Phenothiazine-Based D-A Molecules.

The journal of physical chemistry. A·2026

Same author

Piezo1 aggravates diabetic vascular calcification by enhancing OGT-mediated RUNX2 O-GlcNAcylation in vascular smooth muscle cells.

Biochemical pharmacology·2026

Same author

Trifluoromethyl Engineered 9-Amino-Si-Xanthene with Distinct p<i>K</i><sub>a</sub> and Emission Shift for Imaging Ethanol-Induced Gastric Ulcer.

Analytical chemistry·2026

Same author

Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases.

Nature aging·2025

Search research articles

Related Experiment Video

Updated: Feb 5, 2026

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Published on: February 1, 2019

Capturing functional long non-coding RNAs through integrating large-scale causal relations from gene perturbation

Jinyuan Xu¹, Aiai Shi¹, Zhilin Long¹

¹College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.

|September 5, 2018

Summary

This study introduces LnCAR, a computational method that identifies long noncoding RNA (lncRNA) functions by analyzing gene perturbation data. It reveals lncRNAs critical for cancer invasion, metastasis, and immune evasion, offering potential biomarkers for cancer progression and immunotherapy response.

Keywords:

Cancer Function Gene perturbation Immunotherapy lncRNA

More Related Videos

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Overexpressing Long Noncoding RNAs Using Gene-activating CRISPR

Overexpressing Long Noncoding RNAs Using Gene-activating CRISPR

Published on: March 1, 2019

Related Experiment Videos

Last Updated: Feb 5, 2026

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Published on: February 1, 2019

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Overexpressing Long Noncoding RNAs Using Gene-activating CRISPR

Overexpressing Long Noncoding RNAs Using Gene-activating CRISPR

Published on: March 1, 2019

Area of Science:

Genomics
Computational Biology
Cancer Research

Background:

Characterizing long noncoding RNA (lncRNA) functions is challenging due to limited understanding of their regulatory roles.
Gene perturbation expression profiles are valuable for inferring causal relationships between genes and their responses.

Purpose of the Study:

To develop a novel computational approach (LnCAR) for inferring lncRNA functions using large-scale gene perturbation data.
To identify lncRNAs involved in cancer hallmark processes and evaluate their clinical relevance.

Main Methods:

Annotated over 600 genome-wide gene perturbation profiles to identify >354,000 causal relationships involving lncRNAs.
Developed and applied the LnCAR computational approach to infer lncRNA functions, comparing its accuracy to co-expression methods.
Investigated the association of identified lncRNAs with cancer hallmarks, including invasion, metastasis, and immune evasion.

Main Results:

LnCAR demonstrated higher accuracy in inferring lncRNA functions compared to co-expression based approaches.
Identified 38 lncRNAs associated with distinct carcinogenic processes.
lncRNAs linked to "activating invasion & metastasis" predicted metastatic progression across various cancers.
lncRNAs related to "evading immune destruction" correlated with immune infiltration and predicted response to anti-PD-1 immunotherapy.

Conclusions:

The developed LnCAR approach offers a systematic method for revealing lncRNA functions.
Identified lncRNAs hold potential as biomarkers for cancer metastasis and predicting immunotherapy response.
This resource facilitates further experimental validation and clinical translation of lncRNA research.