J Korean Med Sci.  2004 Dec;19(6):783-792. 10.3346/jkms.2004.19.6.783.

Alu and L1 Retroelements Are Correlated with the Tissue Extent and Peak Rate of Gene Expression, Respectively

• Kim TM
• Jung YC
• Rhyu MG

• KMID: 1778557
• DOI: http://doi.org/10.3346/jkms.2004.19.6.783

Abstract

We exploited the serial analysis of gene expression (SAGE) libraries and human genome database in silico to correlate the breadth of expression (BOE; housekeep-ing versus tissue-specific genes) and peak rate of expression (PRE; high versus low expressed genes) with the density distribution of the retroelements. The BOE status is linearly associated with the density of the sense Alus along the 100 kb nucleotides region upstream of a gene, whereas the PRE status is inversely correlated with the density of antisense L1s within a gene and in the up- and downstream regions of the 0-10 kb nucleotides. The radial distance of intranuclear position, which is known to serve as the global domain for transcription regulation, is reciprocally correlated with the fractions of Alu (toward the nuclear center) and L1 (toward the nuclear edge) elements in each chromosome. We propose that the BOE and PRE statuses are related to the reciprocal distribution of Alu and L1 elements that formulate local and global expression domains.

Keyword

Alu Elements; Long Interspersed Nucleotide Elements; Gene Expression

MeSH Terms

Alu Elements/*genetics
Chromosome Mapping/*methods
Comparative Study
Databases, Genetic
Gene Expression Profiling/*methods
Gene Expression Regulation/*genetics
Genome, Human
Humans
Long Interspersed Nucleotide Elements/*genetics
Retroelements/genetics
Sequence Analysis, DNA/*methods
Statistics
Tissue Distribution

Figure

• 

  Fig. 1 Distribution of 5,037 gene expressions skewed toward low breadth of expression (BOE) and low peak rate of expression (PRE). The total of 6,776 expressed genes and the 5,037 genes reliably matched to a transcriptional unit are similarly divided into four BOE-PRE groups using the median values of the expression parameters. The table above the graph represents the proportion of 6,776 expressed genes and 5,037 matched genes present in the four BOE-PRE groups. The 5,036 expressed genes are plotted against the BOE and PRE parameters and are divided into four quadrants indicated by dotted lines. The correlation between the BOE and log-transformed PRE is shown by the best-fit line.

• 

  Fig. 2 Relationships between breadth (BOE) and peak rate (PRE) of expression and retroelement families. The 5,037 gene expressions are categorized into four BOE-PRE pair-wise groups, high-BOE and high-PRE (blue), high-BOE and low-PRE (black), low-BOE and high-PRE (green), and low-BOE and low-PRE (red). The densities of the retroelements in the 100 kb nucleotides regions, upstream and downstream of the genes, are fractionated into 10 kb nucleotides bins, and separately plotted for the four BOE-PRE groups. The sense and antisense copies of each retroelement indicate the same and opposite orientation, respectively, in relation to the nearest gene. The intragenic density of the retroelements is indicated above the "Gene".

• 

  Fig. 3 Regional relationships between the BOE and PRE statuses and density distributions of sense Alu and antisense L1 elements. The BOE and PRE statuses are divided into three levels, high (red), intermediate (black), and low (blue). Sense Alu and antisense L1 elements in the extragenic and intragenic regions are separately plotted according to the levels of BOE and PRE in 10 kb nucleotide bins along 100 kb nucleotides regions upstream and downstream of the coding regions. Statistically significant differences (p<0.05) in the Alu and L1 densities between high and intermediate levels (red) and between intermediate and low levels (blue) of expression are indicated by closed circles along the intragenic and extragenic regions. The cutoff points for the BOE and PRE levels were described in the Methods section. The intragenic density of the retroelements is indicated above the "Gene".

• 

  Fig. 4 Comparison of BOE-Alu relation among the five gene groups sorted in the order of chromosomal (Alu and L1 fractions and intranuclear position) and genomic (gene density and GC content) parameters. Sense Alu density differences between the high and intermediate (red) and the low and intermediate (blue) levels of the BOE status are calculated for each chromosome or gene group. Density differences are indicated by shaded bars in statistically significant cases (p<0.05). The cutoff values for gene grouping were described in the Methods section. The mean densities of the sense Alus per 10 kb segment along the 100 kb upstream region of a gene are selected and depicted below the corresponding histogram (see legend to Fig. 3).

• 

  Fig. 5 Comparison of PRE-L1 relation among the five gene groups sorted in the order of chromosomal (Alu and L1 fractions and intranuclear position) and genomic (gene density and GC content) parameters. Density differences of antisense L1s between the high and intermediate (red) and the low and intermediate (blue) levels of the PRE status are calculated for each chromosome or gene group. Density differences are indicated by shaded bars in statistically significant cases (p<0.05). The cutoff values for gene grouping were described in the Methods section. The mean densities of the antisense L1s within a gene and the 30 kb upstream and downstream regions are selectively depicted below the corresponding histogram (see legend to Fig. 3).

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