Analysis of Intron Sequence Features Associated with Transcriptional Regulation in Human Genes

<div><p>Although some preliminary work has revealed the potential transcriptional regulatory function of the introns in eukaryotes, additional evidences are needed to support this conjecture. In this study, we perform systemic analyses of the sequence characteristics of human introns. The results show that the first introns are generally longer and C, G and their dinucleotide compositions are over-represented relative to other introns, which are consistent with the previous findings. In addition, some new phenomena concerned with transcriptional regulation are found: i) the first introns are enriched in CpG islands; and ii) the percentages of the first introns containing TATA, CAAT and GC boxes are relatively higher than other position introns. The similar features of introns are observed in tissue-specific genes. The results further support that the first introns of human genes are likely to be involved in transcriptional regulation, and give an insight into the transcriptional regulatory regions of genes.</p> </div

Characteristic lengths of the introns.

<p>The bottom and top of the box is the 25^th percentile (the lower quartile) and 75^th percentile (the upper quartile) of lengths, respectively; the line in the box is the 50^th percentile (the median). The lowest and highest datum is the minimum and maximum not considered outliers, respectively, and outliers are not plotted. ‘+’denotes average length of introns with the same position. ‘*’ denotes that the maximum length of the first introns is more than 20000 bp which is not displayed in figure. The situations of introns whose position beyond 80 are not shown since the numbers of sequences are less than 30, hereinafter.</p

Repetitive elements in the introns.

<p>The repetitive elements are represented as black lines in the introns, where other regions are represented as gray spaces. The values along the vertical coordinates represent the numbers of introns (500 introns are selected randomly from the first introns and other introns, respectively). The directions of introns are from 5′-ends to 3′-ends. The nucleotide positions are relative to the splice sites. (A) Repetitive elements in the 5′-ends (left panel) and 3′-ends (right panel) of the first introns. (B) Repetitive elements in the 5′-ends (left panel) and 3′-ends (right panel) of the other introns position. ‘0’ at 5′-end and 3′-end denotes the position of 5′-splice site and 3′-splice site of the introns, respectively.</p

Comparison of intron lengths

<p>d: the name of each group ;</p><p>e: all sample genes;</p><p>f: the number of genes in each group;</p><p>g: the average lengths (unit: bp) of the first introns;</p><p>h: the average lengths of the non-first introns;</p><p>i: the gene proportions observed with the first intron length shorter than their expected length;</p><p>j: the gene proportions observed with the first intron length equal to their expected length;</p><p>k: the gene proportions observed with the first intron length longer than their expected length;</p><p>l: the value of KS test.</p

CpG island in the introns.

<p>(A) Frequencies of introns containing CpG islands at different positions. (B) Locations of CpG islands in the first introns. 500 introns are selected randomly from the first introns. The CpG islands are represented as black lines in the first introns where other regions are represented as gray spaces. The sequence direction is from 5′-ends to 3′-ends of the first introns.</p

Occurrence frequencies of nucleotides and dinucleotides in introns.

<p>(A) Frequencies of nucleotides and dinucleotides in the first introns and non-first introns. (B) u-values of nucleotides and dinucleotides in the first introns relative to the non-first introns. (C) u-values of nucleotides and dinucleotides in the first introns relative to the non-first introns at different positions. One colored polyline represents a group of u-values of all kinds of nucleotides and dinucleotides for the first introns vs. the non-first introns in one specific position. Since we only focus on whether some nucleotides and dinucleotides are over-represented in the first introns, the differences of nucleotide or dinucleotide content between any two position-specific non-first introns do not be concerned.</p

TATA, CAAT and GC boxes frequencies in introns

<p>TATA, CAAT and GC boxes frequencies in introns</p

Additional file 6 of Complete chloroplast of four Sanicula taxa (Apiaceae) endemic to China: lights into genome structure, comparative analysis, and phylogenetic relationships

Additional file 6: Fig. S2. Phylogenetic relationships of 13 Sanicula samples and two Eryngium species inferred from maximum likelihood (ML) analysis. A. The whole cp genome. B. Concatenation of 126 unique IGS regions