VOL. 1, No. 1, January 2005

J. C. Biro and N. Baroukh [2005] Med Hypotheses Res 2: 303-313.

Prediction of Genome-Wide Associative Regulatory
Role of Short and Long Interspersed Nucleotide
Elements (SINE and LINE)

J. C. Biro* and N. Baroukh

Karolinska Institute, Stockholm, Sweden (J.C.B.) and Genome Sciences Department,
Lawrence Berkeley National Laboratory, Berkeley, CA, USA (N.B.)

Abstract. Repetitive elements represent the same or similar biological information
many thousands times dispersed in the genome. This property makes them simultaneously
suitable for associative regulation of the entire genome. Alu elements (SINE) often exonize,
becoming transcribed as part of a larger gene, and the resulting mRNA is complementary
to the genomic DNA at ~1.4 million sites. LINE retro-transposons are able to move and
leave a signature at thousands of different genes. Many of them have multiple
transcriptions factor (TF) binding sites and probably function as promoters, which indicate
that some of the single TFs might activate large clusters of previously dedicated genes.
Simple repeats have low information content, but still enough to influence quantitative
parameters of biological regulation.
  Special attention has been paid to a LINE element, called NAD (next to the APOA
conserved domain) located in the human APOA1/C3/A4/A5 gene cluster and highly
conserved, even in the mouse genome. NAD shows all necessary bioinformatical signatures
of a promoter and is represented at 260 places in the human genome, but non-functional in
transgenic mice. We interpret these results in favor of existence of species-specific,
conditional promoters (in contrast to the conventional cis-regulatory elements).

*Address all correspondence to: Dr. J. C. Biro, 88 Howard, No. 1205, San Francisco, 94195
CA, USA. E-Mail:

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