Repeated sequences roles

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

Kaneda S, Takeishi K, Ayusawa D et al. Role in translation of a triple tandemly repeated sequence in the 5 -untranslated region of human thymidylate synthase mRNA. Nucleic Acids Res 1987 15 1259-1270. 

Once a sequence amplification event occurs, the nature of any selection on the copies is important. In many (or even most) cases, it appears that the majority of repeated DNA sequences represent pseudogenes, which mutate at a neutral rate of evolution.8 Along with amplification dynamics, the possible removal of repeated sequences must also be considered. Removal does not seem to play a major role with the interspersed repeated DNA elements,8,29 30 but it is likely to be important in tandemly repeated satellite elements. Other mechanisms might also alter evolution of parts of a repeated DNA sequence. For instance, human Alu family copies are initially rich in CpG dinucleotides. These sites appear to be approximately 10-fold more subject to mutation than other sites in the genome,19,31... 

The function of many of the subunits is not known. The core subunits, RBPl through RBP3, seem to play a role similar to their homologues in prokaryotic RNA polymerase. Five of them are present in all three RNA polymerases. RPBl has a repeated sequence of PTSPSYS in the C-terminal domain (CTD), which, as the name applies, is found at the G-terminal region of the protein. Threonine, serine, and tyrosine are all substrates for phosphorylation, which is important in the control of transcription initiation. 

Is intermediate DNA transcribed The majority of experiments that demonstrate DNA/RNA homology have been done under conditions that will only allow repeated sequences to hybridize. Many studies indicate that RNA sequences are transcribed from repetitive DNA both during development (Denis, 1966 GliSin et al., 1966 Whiteley et al., 1966 Church and McCarthy, 1967a, b Davidson et al., 1968 Hennig, 1968) and in differentiated adult cells (McCarthy and Hoyer, 1964 Paul and Gilmour, 1968). However, many of these RNA sequences are retained in the nucleus (Shearer and McCarthy, 1967 McCarthy et al., 1969), so their functional role is uncertain. We will return to this point in a later section. 

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