Related Experiment Video
Updated: May 21, 2026
08:49
Improving Small RNA-seq: Less Bias and Better Detection of 2'-O-Methyl RNAs
Published on: September 16, 2019
StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts
Ida Shinder1,2, Geo Pertea3, Richard Hu4,5
1Cross Disciplinary Graduate Program in Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. ishinde1@jhmi.edu.
Nature Methods
|May 19, 2026
Summary
StringTie3 improves RNA sequencing (RNA-seq) by distinguishing nascent from mature transcripts, reducing errors in total RNA-seq assembly and analysis. This advancement aids in understanding gene regulation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Accurate RNA sequencing (RNA-seq) assembly is crucial but challenged by conflating nascent and mature RNA.
- Existing methods lead to misassemblies and quantification errors in total RNA sequencing.
Purpose of the Study:
- To introduce StringTie3, an updated assembler for total RNA-seq, designed to differentiate nascent and mature transcripts.
- To improve the accuracy of RNA-seq assembly and analysis, particularly for total RNA samples.
Main Methods:
- StringTie3 incorporates a nascent mode to model co-transcriptional splicing, separating nascent from mature transcripts.
- A refined long-read module distinguishes true polyadenylation sites from artifacts.
- Evaluated across short-, long-, and hybrid-read datasets.
Main Results:
- StringTie3 significantly reduces assembly errors compared to existing tools.
- Nascent-mode analysis in Argonaute knockout experiments showed distinct effects on nascent vs. mature RNA.
- Discordant nascent and mature expression in breast cancer samples suggests posttranscriptional regulation.
Conclusions:
- StringTie3 offers a robust framework for analyzing total RNA-seq data.
- The tool enhances the investigation of transcriptional and posttranscriptional regulatory processes.
- StringTie3 improves the accuracy of RNA isoform assembly and quantification.
Related Concept Videos
03:21RNA-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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
01:32RNA Splicing
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
01:32RNA Splicing
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
02:24Ribosome 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...
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...
01:32Pre-mRNA Processing: RNA Splicing
Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
01:23RNA Structure
Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...