Related Experiment Video
Updated: Aug 11, 2026
12:36
Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
Published on: May 9, 2011
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA
F Chiaromonte1, S Yang, L Elnitski
1Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA.
Summary
Genomic regions with more repetitive DNA show less divergence in noncoding sequences between humans and mice. This suggests some genome areas are more evolutionarily flexible than others.
Area of Science:
- Comparative Genomics
- Evolutionary Biology
- Genetics
Background:
- Noncoding genomic DNA alignment between human and mouse varies across different genomic regions.
- Repetitive DNA content also varies significantly across these regions.
Purpose of the Study:
- To investigate the correlation between DNA sequence divergence and repetitive DNA content in noncoding genomic regions.
- To understand the evolutionary flexibility of different genomic areas.
Main Methods:
- Analysis of aligned noncoding nonrepetitive DNA and repetitive DNA fractions in four large human and mouse genomic regions (5.89 Mb total).
- Sliding window analysis (10 kb) to assess local correlations.
- Randomization study to validate findings by relocating repetitive elements.
Main Results:
- A strong negative correlation was observed between the fraction of aligned noncoding nonrepetitive DNA and the fraction of repetitive DNA.
- Regions with fewer point mutations since primate-rodent divergence also had fewer retrotransposition events.
- Genomic regions exhibit varying evolutionary flexibility, accommodating different rates of mutation and insertion.
Conclusions:
- The rates of different evolutionary processes, such as point mutation and retrotransposition, are correlated across noncoding DNA.
- Genomic regions can be characterized as 'flexible' or 'rigid' based on their evolutionary change rates.
- Conservation patterns in noncoding DNA must consider this correlated variation when inferring functional importance or selection.
Related Concept Videos
02:07Organization of Genes
Overview
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...
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...
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...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
02:32Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...