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

The Eukaryotic Promoter Region

The Eukaryotic Promoter Region

The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

You might also read

Related Articles

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

Sort by

Same author

Flexible and scalable inference of spatially varying correlation in spatial transcriptomics with spCorr.

Genome research·2026

Same author

BioMedGraphica: an all-in-one platform for joint textual biomedical prior knowledge and numeric graph generation.

Bioinformatics (Oxford, England)·2026

Same author

IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches.

bioRxiv : the preprint server for biology·2026

Same author

Interpreting Omics Data Analysis with Large Language Models for Disease Target and Drug Discovery.

bioRxiv : the preprint server for biology·2026

Same author

Constructing stereogenic sulfur(VI) centers by catalytic desymmetrization: strategies and prospects.

Chemical communications (Cambridge, England)·2026

Same author

Spatial Mapping of the Precancer-to-Cancer Transition in Breast and Prostate.

Cancer discovery·2026

Same journal

From Pixels to Patterns: A Multidimensional Framework to Decode Cytoskeletal Organization.

Computational and structural biotechnology journal·2026

Same journal

A Large Concept Model for Mechanistic Simulation of Disease Trajectories: A Hypothesis-Generating Exemplar for Pediatric Acute Lymphoblastic Leukemia.

Computational and structural biotechnology journal·2026

Same journal

Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design.

Computational and structural biotechnology journal·2026

Same journal

High-Throughput Prediction of Protein-Protein Interactions Uncovers Hidden Molecular Networks in Biosynthetic Gene Clusters.

Computational and structural biotechnology journal·2026

Same journal

A Region-Aware Structured Framework Improves Prediction of Gene Expression from DNA Methylation.

Computational and structural biotechnology journal·2026

Same journal

Ensemble Machine Learning Approaches Predict Survival in Lower-Grade Glioma Based on Glycosphingolipid Gene Expression and Metabolic Modeling.

Computational and structural biotechnology journal·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 18, 2026

Methods to Discover Alternative Promoter Usage and Transcriptional Regulation of Murine Bcrp1

Methods to Discover Alternative Promoter Usage and Transcriptional Regulation of Murine Bcrp1

Published on: May 27, 2016

SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.

Jiang Tan^1,2,3,4, Yuqing Wu^2,3,4, Ruteja Barve^1,2,3

¹Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.

Computational and Structural Biotechnology Journal

|April 17, 2026

Summary

This summary is machine-generated.

SnakeAltPromoter automates alternative promoter analysis from RNA sequencing (RNA-seq) data, offering a unified, reproducible framework. This tool enhances the study of gene regulation and isoform diversity across various biological samples.

More Related Videos

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain

AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain

Published on: March 31, 2022

Related Experiment Videos

Last Updated: Apr 18, 2026

Methods to Discover Alternative Promoter Usage and Transcriptional Regulation of Murine Bcrp1

Methods to Discover Alternative Promoter Usage and Transcriptional Regulation of Murine Bcrp1

Published on: May 27, 2016

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain

AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain

Published on: March 31, 2022

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Alternative promoter usage drives mammalian isoform diversity and gene regulation.
Current methods like Cap Analysis of Gene Expression are costly for large-scale studies.
RNA sequencing (RNA-seq) data offers an alternative but lacks automated, reproducible analysis frameworks.

Purpose of the Study:

To develop a scalable, end-to-end workflow for automating alternative promoter analysis using RNA-seq data.
To integrate and standardize multiple RNA-seq-based promoter analysis methods for reproducible results.
To provide a framework for comparing RNA-seq-inferred promoter activity with experimental data.

Main Methods:

Developed SnakeAltPromoter, a Snakemake workflow for automated RNA-seq data processing.
Integrated junction-based, transcript-based, and first-exon-based quantification methods.
Implemented quality control, alignment, promoter classification, and differential analysis modules.
Included a benchmarking module to compare RNA-seq results with Cap Analysis of Gene Expression data.

Main Results:

SnakeAltPromoter successfully automates alternative promoter analysis from raw RNA-seq data.
The workflow demonstrated robust and complementary performance across different methods, tissues, and cell types.
Benchmarking confirmed the reliability of RNA-seq-based promoter activity inference.

Conclusions:

SnakeAltPromoter is the first unified, reproducible framework for scalable RNA-seq-based promoter analysis.
It standardizes and integrates existing tools, offering a robust platform for studying promoter-level regulation.
This framework enhances the utility of public RNA-seq data for alternative promoter research.