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Updated: May 16, 2026
09:06
High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
Published on: October 5, 2018
UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks
Slavica Dimitrieva1, Philipp Bucher
1Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland. slavica.dimitrieva@epfl.ch
Nucleic Acids Research
|November 30, 2012
Summary
UCNEbase is a new resource detailing ultra-conserved non-coding elements (UCNEs) and their genomic organization across 18 species. It aids researchers studying these key developmental gene regulators.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Ultra-conserved non-coding elements (UCNEs) are crucial for regulating developmental genes.
- Understanding their genomic organization and evolution is vital for biological research.
Purpose of the Study:
- To present UCNEbase, a comprehensive web resource for UCNEs.
- To provide a structured database for studying UCNE evolution and genomic organization.
Main Methods:
- Development of a relational database system for UCNE data.
- Integration with the UCSC Genome Browser for data visualization.
- Creation of a systematic nomenclature and cross-linking for orthologous and paralogous UCNEs.
Main Results:
- UCNEbase curates 4351 UCNEs across 18 species.
- The database organizes UCNEs into individual elements and ultra-conserved genomic regulatory blocks (UGRBs).
- Provides detailed synteny maps and custom track files for visualization.
Conclusions:
- UCNEbase offers a valuable, accessible platform for researchers.
- Facilitates the study of conserved non-coding DNA elements in vertebrates.
- Supports computational, experimental, and evolutionary biology investigations.
Related Concept Videos
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
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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...
02:02Cis-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...
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