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

RNA-seq03:21

RNA-seq

12.4K
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...
12.4K
Ribosome Profiling02:24

Ribosome Profiling

4.3K
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...
4.3K
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

7.5K
Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
7.5K
Experimental RNAi02:15

Experimental RNAi

8.2K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
8.2K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

33.5K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
33.5K

You might also read

Related Articles

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

Sort by
Same author

Ulinastatin Treatment Associated with Lower Sepsis-Associated Encephalopathy Risk in Sepsis Patients: A Multicenter Observational Study.

Shock (Augusta, Ga.)·2026
Same author

The impact of triglyceride-glucose index on short-term prognosis in patients with acute myocarditis.

BMC cardiovascular disorders·2026
Same author

GRP78 in viral pneumonia: dual regulatory mechanisms and translational prospects.

Clinical and experimental medicine·2026
Same author

Host-guest doping strategy for achieving ultralong multicolor room-temperature phosphorescence in benzophenone-aromatic compounds.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy·2026
Same author

Systematic dysregulation of immune-related alternative polyadenylation in systemic lupus erythematosus contributes to patient stratification.

Journal of translational autoimmunity·2026
Same author

Histone deacetylase enzyme activity is not the universal anticancer target of HDAC inhibitors.

Signal transduction and targeted therapy·2026
Same journal

Progressive Cellularization of Blastoderm and Extraembryonic Tissue Formation in the Ant Camponotus floridanus.

Journal of experimental zoology. Part B, Molecular and developmental evolution·2026
Same journal

Form and Law - Rupert Riedl's Significance for Morphology.

Journal of experimental zoology. Part B, Molecular and developmental evolution·2026
Same journal

In the Spotlight-Established Researcher.

Journal of experimental zoology. Part B, Molecular and developmental evolution·2026
Same journal

In the Spotlight-Postdoc.

Journal of experimental zoology. Part B, Molecular and developmental evolution·2026
Same journal

Adding the "Eco" to the "Evo-Devo": A New Special Issue on Latin America Evo-Devo.

Journal of experimental zoology. Part B, Molecular and developmental evolution·2026
Same journal

Levels of Analysis in Evolutionary Genetics: Novel Genes and the Misuse of Homology.

Journal of experimental zoology. Part B, Molecular and developmental evolution·2026
See all related articles

Related Experiment Video

Updated: Mar 13, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

10.7K

TreeExp1.0: R Package for Analyzing Expression Evolution Based on RNA-Seq Data.

Hang Ruan1, Zhixi Su1, Xun Gu1,2

  • 1State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.

Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
|October 27, 2016
PubMed
Summary
This summary is machine-generated.

Researchers developed TreeExp, an R package for analyzing transcriptomic evolution using RNA-seq data. This tool aids in understanding gene expression changes across species and tissues, revealing insights into evolutionary developmental (evo-devo) mechanisms.

More Related Videos

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

42.4K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.9K

Related Experiment Videos

Last Updated: Mar 13, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

10.7K
Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

42.4K
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.9K

Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • RNA-sequencing (RNA-seq) advances transcriptomic evolution studies, particularly tissue-specific expression.
  • Phylogenetic analysis of transcriptomes can reveal gene expression differences driving evolutionary changes.
  • A lack of specialized software hinders phylogenetic analysis of transcriptome data.

Purpose of the Study:

  • To develop an R package, TreeExp, for phylogenetic analysis of RNA-seq data.
  • To facilitate comparative expression evolution analysis.
  • To enable mapping expression distances onto phylogenetic trees.

Main Methods:

  • Developed the R package TreeExp.
  • Included optimized input formatting, normalization, and pairwise expression distance estimation.
  • Implemented expression character tree inference and phylogenetic network analysis.

Main Results:

  • Expression trees for mammalian brain and testis largely align with known species trees.
  • Inter-tissue expression divergence (brain vs. testis) is greater than inter-species divergence.
  • Gene modules for nervous system development show distinct primate brain expression patterns.

Conclusions:

  • TreeExp provides a novel tool for transcriptomic evolution research.
  • Tissue-specific expression patterns offer insights into evo-devo mechanisms.
  • Comparative analysis reveals significant inter-tissue expression divergence in mammals.