Download length of exons and introns in genes of some human chromosomes

Computational structural and functional genomics and transcriptomics
Chapter
31
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LENGTH OF EXONS AND INTRONS
IN GENES OF SOME HUMAN CHROMOSOMES
Atambaeva S.A., Ivashchenko A.T.*, Khailenko V., Boldina G., Turmagambetova A.
al-Farabi Kazakh National University, Almaty, 050038, Kazakhstan
*
Corresponding author: e-mail: [email protected]
Key words:
exon, intron, gene, genome, Homo sapiens
SUMMARY
Motivation. Length and number of introns in genes of different eukaryotes, including
human, varied within wide range of limits. It was important to clarify a quantitative
regularity is in exon-intron organization of genes. The elucidation of exon and intron
lengths variation in genes will promote determining intron function.
Results. The number of introns in genes was proportional to total length of exons and
gene length of chromosomes 1, 2, 13, 19, 21 and 22 in Homo sapiens genome. The
variations of intron and exon lengths in genes depended on number of introns in genes
and genes density of DNA region.
INTRODUCTION
Genes containing introns were more than 90 % in nuclear genomes of H. sapiens
(Venter et al., 2001). There was a considerable heterogenity of exon and intron lengths in
genes, which provided determination of regularities of exon and intron lengths variability
in every chromosome of H. sapiens genome. The number of genes including introns,
number of introns in genes and a ratio of exon and intron length varied for different
organisms (Duetsch, Long, 1999; Ivashchenko, Atambaeva, 2004). The relationship
between exon and intron lengths that depend on number of introns in genes and gene
density of DNA region in some chromosomes of H. sapiens has been determined.
METHODS
Nucleotide sequence of DNA have been extracted from GenBank
(http://www.ncbi.nlm.nih.gov/). DNA sequentially was divided into regions of 1 Mbp
length, which were put according to gene amount in groups from 1–11, 12–20, 21 and
more genes per 1 Mbp. In each group have been analyzed the samples of genes containing
1–2, 3–5, 6–9, 10–14, 15 and more introns. The average values of intron and exon
lengths, and total length of gene have been determined for each sample of genes. The
analysis of frequency of occurrence of exon lengths has been made for following length
intervals: 1–20, 21–40, 41–60 nt and so up to 400 nt and also more than 400 nt.
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RESULTS
The allocation of genes along a DNA of chromosome 1 was heterogeneously also
gene amount of region 1 Mbp length varied from zero point to 68 genes. In the group
including 1 to 11 genes per region of chromosome 1 (average value was 4 genes/Mbp)
exon length decreased from 282 to 135 nt, as well as the number of introns in genes (Nin)
increased. The average total exon lengths (Lex) in genes increased from 691 to 3163 nt
and the positive correlation between Nin and Lex variations was found out. This
relationship was described by the following equation: Nin = aLex + b, where a and b are
coefficients of linear regression. The values a and b, and coefficient of correlation (r)
were shown in the Table1. The average gene length (Lgn) containing 1–2 introns was
22485 nt and it was 146296 nt from sample of genes containing 15 and more introns.
There was a positive correlation between gene length and number of introns, which was
represented by an equation: Nin = cLgn + d, where c and d are coefficients of linear
regression (Table 1).
Table 1. Parameters of linear regressions between number of introns and length of genes or sum of exon
lengths
Genes/
Parameters of linear regressions
1 Mbp
a
b
c
d
r
r
Nu.genes
Chromosome 1
4
0.0085
-4.06
0.997
0.00018
-3.96
0.966
273
16
0.0083
-3.40
0.997
0.00025
-0.70
0.967
325
26
0.0079
-3.88
0.989
0.00043
-1.64
0.991
320
32
0.0079
-3.74
0.997
0.00066
-2.12
0.971
396
Chromosome 2
4
0.0078
- 3.15
1.000
0.00016
- 2.93
0.984
428
4
0.0072
- 3.26
0.998
0.00013
- 0.48
0.991
525
15
0,0058
- 0,71
0.983
0,00024
- 0,39
0.985
376
29
0.0076
- 2.70
0.998
0.00060
- 2.16
0.964
186
Chromosome 13
3
0.0082
-7.11
0.987
0.00008
0.91
0.983
222
15
0.0088
-4.92
0.988
0.00023
-0.24
0.970
72
Chromosome 19
5
0.0093
- 4.39
0.994
0.00043
-4.10
0.861
34
16
0.0088
- 9.89
0.886
0.00030
-2.36
0.828
83
31
0.0080
- 4.99
0.988
0.00057
- 2.43
0.998
647
35
0.0068
- 2.65
0.988
0.00053
- 0.65
0.998
644
Chromosome 21
4
0.0070
- 1.90
0.997
0.00022
-3.94
0.986
110
17
0.0088
- 5.33
0.977
0.00042
- 2.52
0.961
100
30
0.0069
- 1.92
0.956
0.00053
- 7.63
0.952
18
Chromosome 22
5
0.0061
- 0.06
0.995
0.00013
1.33
0.972
91
15
0.0069
- 1.71
0.976
0.00034
- 2.83
0.992
124
28
0.0085
- 3.42
0.998
0.00047
- 2.49
0.987
273
It was established the change of the average exon length, when the number of introns
in genes increased. For example, the average exon length decreased from 274 to 135 nt in
16 genes/Mbp group, sum of exon lengths increased from 706 to 2946 nt, length of genes
increased from 5108 to 77198 nt accordingly for 1–2 introns genes and for genes
containing 15 and more introns. The positive correlation between the sum of exon lengths
and the number of introns in genes is shown (Table 1). The average intron length of the
first gene group was 10576 nt and for the second gene group was 4128 nt. The result of
the decrease of intron length was the contraction of the average gene length for all gene
samples and accordingly a variation of linear regression parameters between gene length
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and intron amount in genes (Table 1). While further increasing the gene density per 1
Mbp this tendency was observed too (Table 1). For example, in a gene group, where the
density was 32 genes/Mbp, the average exon length decreased from 304 to 144 nt, the
sum of exon lengths increased from 745 to 3308 nt, the gene length increased from 3918
to 32856 nt accordingly in 1–2 intron genes and in genes containing 15 and more introns.
The relationship between the number of intron in genes and the total exon length for
genes of four groups from chromosome 1 were shown in a Fig. 1. The correlation
coefficients have been obtained from the great samples of genes and testify to a high
reliability of this relationship (р < 0.001).
Figure 1. Correlations between total exon length (a), gene lengths (b) and number of introns in genes of
chromosome 1. Regions having of gene density: 4 genes/Mbp – ■, 16 genes/Mbp – ●, 26 genes/Mbp –
▲ and 32 genes/Mbp – ♦; x-axis – sum of exon lengths (a) and gene lengths (b), nt; y-axis – number of
introns in genes.
The greatest average density of genes/Mbp has chromosome 19 and two gene groups
were formed a high gene density (Table 1). In both gene groups the relationship between
sum of exon lengths and number of intron in genes was similar and was characterized by
high correlation coefficients. Chromosome 13 has the lowest average density of
genes/Mbp, however in two groups of genes the relationship between sum of exon lengths
and number of introns in genes was similar and the high correlation coefficients were also
presented too (Table 1). In the group with low gene density (3 genes/Mbp) the gene
lengths increased from 27194 nt (1–2 introns in a gene) to 332554 nt (15 and more introns
in a gene). The chromosomes 2, 21 and 22 had essential heterogeneity of gene distribution
along a DNA. In all groups of genes between the sum of exon lengths and the number of
introns in genes the relationship clearly appeared and had a high correlation coefficient
(Table 1). The value of parameter a was similar for linear regressions of all the gene
groups of every chromosomes. It obvious, the revealed connection is universal for all
investigated human chromosomes and reflects an unknown intron function as sharing the
protein coding part of a gene into segments.
The exon and intron share in the range of length 1–400 nt and more than 400 nt
changed depending on gene sample in all the gene groups. In genes of H. sapiens
chromosomes 1, 2, 13, 19, 21 and 22 the share of exons having length more than 400 nt
decreased when increasing of number of introns in a gene, thus the share of exon having
length 60–180 nt increased. For example, in the chromosomes 1 and 13 the share of exon
with the length of more than 400 nt in 1-2 introns genes was 27.2 and 31.0 %, and in
genes containing 15 and more introns 2.1 and 2.8 % accordingly (Fig. 2). The obtained
data testify to the fact, that the genes having different intron number and located in
different gene density regions have no the same exon-intron organization. The tendency
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of increasing the number of intron in a gene, and the sum of exon lengths increased,
testify to correcting function of introns on while unknown gene properties.
Figure 2. Variation of exon lengths in genes of the chromosome 1 (a) and chromosome 13 (b): ■ – exons
lengths in 1–2 introns genes; ● – exons lengths in genes with 15 and more introns. x-axis – exon lengths,
nt; y-axis – share exons, %.
REFERENCES
Venter J.C., Adams M.D., Myers E.W. et al. (2001) The sequence of the human genome. Science, 291,
1304–1351.
Duetsch M., Long M. (1999) Intron-exon structure of eukaryotic model organisms. Nucl. Acids Res., 27,
3219–3228.
Ivashchenko A., Atambaeva S. (2004) Variation in lengths of introns and exons in genes of the
Arabidopsis thaliana nuclear genome. Rus. J. Genet., 40, 1179–1181.
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