Related Experiment Video
Updated: Aug 9, 2026
16:24
Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Genomic data analysis using DNA structure: an analysis of conserved nongenic sequences and ultraconserved elements
Eleanor J Gardiner1, Linda Hirons, Christopher A Hunter
1Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom. e.gardiner@sheffield.ac.uk
Journal of Chemical Information and Modeling
|March 28, 2006
Summary
Conserved nongenic sequences (CNGs) and ultraconserved elements (UCEs) in human and mouse genomes lack known functions. Analysis of their structural properties using DNA octamers revealed correlations that may indicate potential functions for these highly conserved elements.
Area of Science:
- Genomics
- Bioinformatics
- Structural Biology
Background:
- Comparative genomics studies identified conserved nongenic sequences (CNGs) and ultraconserved elements (UCEs) in human and mouse genomes.
- These sequences are highly conserved, span hundreds of bases, and possess no known function.
- Lack of sequence homology between paralogous CNGs and UCEs necessitates alignment-free analytical methods.
Purpose of the Study:
- To investigate the potential functions of CNGs and UCEs by analyzing their structural properties.
- To apply an alignment-free approach for the analysis of these conserved genomic elements.
Main Methods:
- Utilized a previously compiled database of structural properties for 32,896 unique DNA octamers.
- Employed Fourier techniques to analyze CNGs and UCEs based on their octamer structural characteristics.
Main Results:
- Identified structural correlations within CNGs and UCEs.
- These correlations suggest potential functional roles for some of these highly conserved, non-coding sequences.
Conclusions:
- Structural analysis of CNGs and UCEs provides insights into their potential biological functions.
- Alignment-free methods are effective for analyzing conserved genomic elements with no detectable sequence homology.
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...
02:54Evolutionary 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...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
00:58Genomic DNA in Eukaryotes
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.