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Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

RNA-seq

RNA-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...

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Related Experiment Video

Updated: Sep 23, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

RSAT 2022: regulatory sequence analysis tools.

Walter Santana-Garcia¹, Jaime A Castro-Mondragon², Mónica Padilla-Gálvez³

¹Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.

Nucleic Acids Research

|May 11, 2022

Summary

This summary is machine-generated.

Regulatory Sequence Analysis Tools (RSAT) offers over 50 integrated tools for discovering and analyzing cis-regulatory elements in genomes. It supports diverse access methods and thousands of genomes, aiding biological research.

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Published on: May 31, 2011

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Last Updated: Sep 23, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Cis-regulatory elements are crucial for gene expression control.
Discovering and analyzing these elements is essential for understanding biological processes.
Existing tools may lack comprehensive functionality or broad genomic support.

Purpose of the Study:

To present the updated capabilities and accessibility of the Regulatory Sequence Analysis Tools (RSAT) software suite.
To highlight RSAT's utility for de novo motif discovery, sequence scanning, motif analysis, regulatory variation analysis, and comparative genomics.
To showcase RSAT's flexible access modes and extensive genome support.

Main Methods:

RSAT provides a suite of over 50 integrated tools accessible via web servers, command-line, and programmatic web services.
The software supports de novo motif discovery from various datasets (e.g., ChIP-seq, ATAC-seq) and scanning with known motifs.
It facilitates motif analysis, regulatory variation analysis, comparative genomics, and gene regulatory network construction.

Main Results:

RSAT offers multi-modal access, supporting diverse user needs and over 10,000 genomes.
Recent updates include an expanded REST API, enhanced genome and motif collection support, and a new tool for gene regulatory network analysis.
The platform provides extensive documentation, tutorials, and is open-source.

Conclusions:

RSAT is a versatile and comprehensive resource for the analysis of cis-regulatory elements across a wide range of genomes.
Its flexible access and continuous development make it a valuable tool for diverse biological research communities.
The open-source nature and extensive support foster collaboration and advancement in regulatory genomics.