A novel rat genomic simple repeat DNA with RNA-homology shows triplex (H-DNA)-like structure and tissue-specific RNA expression.
Mammalian genome contains a wide variety of repetitive DNA sequences of relatively unknown function. We report a novel 227 bp simple repeat DNA (3.3 DNA) with a d{(GA)7A(AG)7} dinucleotide mirror repeat from the rat (Rattus norvegicus) genome. 3.3 DNA showed 75-85% homology with several eukaryotic mRNAs due to (GA/CU)n dinucleotide repeats by nBlast search and a dispersed distribution in the rat genome by Southern blot hybridization with [32P]3.3 DNA. The d{(GA)7A(AG)7} mirror repeat formed a triplex (H-DNA)-like structure in vitro. Two large RNAs of 9.1 and 7.5 kb were detected by [32P]3.3 DNA in rat brain by Northern blot hybridization indicating expression of such simple sequence repeats at RNA level in vivo. Further, several cDNAs were isolated from a rat cDNA library by [32P]3.3 DNA probe. Three such cDNAs showed tissue-specific RNA expression in rat. pRT 4.1 cDNA showed strong expression of a 2.39 kb RNA in brain and spleen, pRT 5.5 cDNA showed strong expression of a 2.8 kb RNA in brain and a 3.9 kb RNA in lungs, and pRT 11.4 cDNA showed weak expression of a 2.4 kb RNA in lungs. Thus, genomic simple sequence repeats containing d(GA/CT)n dinucleotides are transcriptionally expressed and regulated in rat tissues. Such d(GA/CT)n dinucleotide repeats may form structural elements (e.g., triplex) which may be sites for functional regulation of genomic coding sequences as well as RNAs. This may be a general function of such transcriptionally active simple sequence repeats widely dispersed in mammalian genome.
Dey
Indranil
I
Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi-110067, India.
Rath
Pramod C
PC
D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D004247:DNA / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D005260:Female; D016678:Genome; D009690:Nucleic Acid Conformation; D009928:Organ Specificity; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D051381:Rats; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D018076:DNA, Complementary; C051802:triplex DNA; D012313:RNA; D004247:DNA