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

12.2K
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...
12.2K
Ribosome Profiling02:24

Ribosome Profiling

4.2K
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...
4.2K
Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

16.0K
In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps...
16.0K

You might also read

Related Articles

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

Sort by
Same author

Transcriptomic analysis reveals regulation of adipogenesis via long non-coding RNA, alternative splicing, and alternative polyadenylation.

Scientific reports·2024
Same author

The precise function of alphaherpesvirus tegument proteins and their interactions during the viral life cycle.

Frontiers in microbiology·2024
Same author

Duck STING mediates antiviral autophagy directing the interferon signaling pathway to inhibit duck plague virus infection.

Veterinary research·2024
Same author

METTL3-mediated chromatin contacts promote stress granule phase separation through metabolic reprogramming during senescence.

Nature communications·2024
Same author

Clinical risk factors and outcomes of carbapenem-resistant <i>Escherichia coli</i> nosocomial infections in a Chinese teaching hospital: a retrospective study from 2013 to 2020.

Microbiology spectrum·2024
Same author

Integrative and conjugative elements of <i>Pasteurella multocida</i>: Prevalence and signatures in population evolution.

Virulence·2024

Related Experiment Video

Updated: Feb 25, 2026

3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

11.1K

Polyadenylation Site-Based Analysis of Transcript Expression by 3'READS.

Dinghai Zheng1, Bin Tian2

  • 1Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Cancer Institute of New Jersey, 205 South Orange Avenue, Newark, NJ, 07103, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 3, 2017
PubMed
Summary

Deep sequencing of poly(A)+ RNA can misidentify cleavage sites. 3'READS+ accurately identifies polyadenylation sites (PAS) and measures transcript abundance, even with limited RNA input.

Keywords:
3′ end sequencing3′READS+Alternative cleavage and polyadenylationDeep sequencingRNA-seq

More Related Videos

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.5K
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

54.3K

Related Experiment Videos

Last Updated: Feb 25, 2026

3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

11.1K
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.5K
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

54.3K

Area of Science:

  • Molecular Biology
  • Genomics
  • RNA Biology

Background:

  • Deep sequencing of poly(A)+ RNA is crucial for identifying cleavage and polyadenylation sites (PAS) and quantifying transcript abundance.
  • Oligo-dT priming in reverse transcription can lead to mispriming in A-rich regions, causing inaccurate PAS identification.
  • Existing ligation-based methods for 3' end RNA sequencing are often inefficient.

Purpose of the Study:

  • To develop an accurate and sensitive method for deep sequencing of the 3' end of poly(A)+ RNA.
  • To overcome the challenge of mispriming in A-rich regions during PAS identification.
  • To provide a method suitable for small RNA input amounts and cost-effective gene expression analysis.

Main Methods:

  • The study introduces 3'READS+, a novel method for deep sequencing of the 3' end of poly(A)+ RNA.
  • It utilizes partial RNase H digestion of the poly(A) tail hybridized to a locked nucleic acid (LNA)/DNA oligo.
  • This approach optimizes the number of sequenced terminal A's for improved accuracy in A-rich regions.

Main Results:

  • 3'READS+ enhances sequencing quality and accuracy in identifying PAS, particularly in challenging A-rich regions.
  • The method demonstrates high efficiency, making it suitable for limited amounts of input RNA.
  • 3'READS+ proves to be a cost-effective approach for gene expression analysis.

Conclusions:

  • 3'READS+ offers an accurate and sensitive solution for deep sequencing of poly(A)+ RNA 3' ends.
  • The method effectively resolves issues related to mispriming and ligation inefficiency.
  • 3'READS+ is a valuable tool for PAS identification and gene expression profiling, especially with low RNA input.