Insertions and Deletions of Introns in Human and Dog Aligned
with Boreoeutherian (ancestral) Genome
Sharndeep Kaur
Abstract
Many genome-scale studies show the losses and gains of introns occurring during
evolution of the major eukaryotic lineages but studies focused on more recent
evolutionary periods have found more examples of losses than gains [1] . Studies
conducted by Fedorov et al. did not detect any recently gained introns with in genome
sequences of human, Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis
thaliana [1]. The focus of this paper is the pattern of introns in humans and dogs
compared to the Boreoeutherian (ancestral) genome. Using the two-way alignment to
determine the patterns of insertions and deletions, it was determined that dog had more
insertions and deletions than human.
Introduction
In our advanced world of science, it is surprising to find how little we know about the
origin of introns. The existence of intervening sequences of non-coding DNA
interrupting the coding region of nuclear genes, only to be later removed from transcribed
nuclear pre-mRNAs by spliceosomes, poses fundamental questions [2]. What is the
significance and origin of introns? How do they spread in genes? What is the primary
process by which new introns are created? These are just a few questions that arise about
introns.
In 1977, a surprising phenomenon was discovered — introns. These are non-protein
coding sequences of DNA that occur within functional genes. All genes begin with
exons (the protein-coding segments), but most have a variable number of introns, within
them that alternate with the exons [3]. There are eight major classes of introns, each
occurring in different locations. The most common introns in the genome of eukaryotes
are the GU-AG introns (named for their splice sites). AU-AC introns, also named for
their splice site, along with some Group I introns are also found in eukaryotic genomes.
Group I and II introns are also found in organelle and some bacterial 3 RNAs. Group III
introns and twintrons are found entirely in organelle RNAs. Pre-tRNA introns are found
in eukaryotic nuclear pre-tRNA, and archeal introns are found in various RNAs in
archaebacteria. Lastly, vertebrate introns contain several conserved sequences. The 5’
end of the intron contains a 5’ splice site, of the sequence GU (guanine-uracil). The 3’
end of the intron contains a 3’ splice site, of the sequence AG (adenine-guanine) [4].
It is hard to conclude the exact function of introns but because they have been carried
over for a long time indicates that introns might carry some genetic significance because
of their presence through out evolution. There are two major hypotheses of intron
evolution: “introns early” and “introns late.” The introns early theory states that introns
were originated early in the genomic evolution process and are slowly being removed
from eukaryotic genomes. In contrast, the introns late theory states that introns are a
recent development in the genome and are accumulating in rather than disappearing from
eukaryotic genomes [4].
There has been several hypotheses for functions of introns. One theory claims that it
separates the exons into the functional subunits of the product for which they code.
Another one states that introns allow exon shuffling, which would account for the
tremendous variability in proteins (and their nearly instantaneous production) in
eukaryotes [5]. And another interesting one is that if RNA was the original genetic
material (and there is lots of evidence to suggest it is more primitive than DNA), then
introns may have pinched out to function as the first enzymes [5].
In this paper, Boreoeutherian genome was used as an ancestral genome to compare the
patterns of introns in humans and dogs. Boreoeutherian ancestor is the most common
ancestor because boreoeutheria are the largest clade, or group of species, of mammals.
Also, the reconstruction of boreoeutherian genome is 98 percent accurate. The time
stamp for boreoeutherian ancestors is still unknown but scientists agree that it was more
than 70 million years ago [6].
Materials and Methods
An exon.txt file was used from the class directory (bme230/Winter05/projects/intron) and
was converted using a perl script, getIntron.pl, into intron.bed to read the chromosome
number, start and end of introns, gene-id, scores and strand. Intron.bed was then used by
Robert Baertsch to find the two-way alignment, dog with ancestor (outDog.axt) and
human with ancestor genome (outHuman.axt ). getIdAlign.pl was then used on the data
that was obtained from two-way alignment to generate files that contain the counts of
insertions and deletions in human and dog. These files: humanDel.data, dogDel.data,
humanIns.data, and dogIns.data, can also be obtained from the class project directory.
Results
Table 1: Counts of introns inserted and deleted in human and dog genome .
Lineages
Counts
Human Insertions
7343
Human Deletions
1218
Dog Insertions
8757
Dog Deletions
1629
Discussion
Table 1, contains the data of introns deleted and inserted in two different lineages. These
insertions and deletions are of introns that are greater than 100 base pairs. Deletions and
insertions less than 100 base pairs were regarded as noise and were not used in the count
of intron insertions and deletions for human and dog.
From the data above, it is evident that more insertions occurred over evolution, in both
human and dog. In human lineage, 7,343 introns were inserted but only 1,218 introns
were deleted. Similarly, dog’s genome inserted 8,757 introns , but deleted only 1,629
introns.
My data supports the “introns late” theory which states that introns are accumulating in
the eukaryotic genomes rather than disappearing. More insertions than deletions in both
human and dog rules out the “intron early” theory.
It would be great to find correlations between the insertion/deletions of introns in dog and
human for they can lead to further knowledge about the common function of intron. Dog
genome is a great choice to compare the human genome with because it is similar in size
to the genomes of humans and other mammals, containing approximately 2.5 billion
DNA base pairs [7].
Literature Cited
Coghlan A, Wolfe KH: Origins of recently gained introns in Caenorhabditis.
Proc Natl Acad Sci USA 2004, 101:11362-11367
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