Long interspersed repeat sequences

All of the mammalian transposable elements that have been characterized to date seem to be the result of transpositions that proceeded through an RNA intermediate. This process is known as retrotransposition or retroposition. Three classes of these retrotransposable elements are known in mammals (1) SINEs, or short interspersed repeated sequences such as the human Alu family and rodent Bl (2) LINEs, or long interspersed repeated sequences such as LI in a variety of mammalian species and (3) retrovirus-like elements, such as THE 1 in humans and mys and IAP in rodents. Retrovirus-like elements have long terminal repeats (LTRs) that often surround two open reading frames (ORFs) like those of retroviruses, but they lack the ability to leave one cell and enter another. LINEs also have two ORFs, but have no LTRs. SINEs have no LTRs and no ORFs. Transposition of all of these elements must involve reverse transcription of the RNA intermediate in some cases the required reverse transcriptase is apparently encoded by the element itself. 

There are several large classes of DNA sequences which are not translated, including those for structural RNAs [ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs)], pseudogenes, and repetitive DNAs [e.g., short and long interspersed repeated sequences (SINES and LINES)]. Ribosomal... 

Repetitive sequences are also defined by the number of base pairs in each repeated segment. Sequences that have from 100 to 500 bp are referred to as SINES (short interspersed repeated sequences) and sequences that have several thousand base pairs are referred to as LINES (long interspersed repeated sequences.) Thus, repetitive DNA sequences can be described both by the length of the segment and the degree to which it is repeated. 

The moderately repetitive sequences, which are defined as being present in numbers of less than 10 copies per haploid genome, are not clustered but are interspersed with unique sequences. In many cases, these long interspersed repeats are transcribed by RNA polymerase II and contain caps indistinguishable from those on mRNA. 

Fig. 10. The structure of mouse DNA containing the integrated mouse mammary tumour provirus. The integrated viral DNA can be present in many copies. The provirus contains two long terminal repeat sequences, LTR, only one of which (left) is shown in detail here. Each LTR contains sequences termed U3, R and U5 (for details, see Ref. 67). Interspersed between the LTRs are the genes named gag, pol and env, encoding viral coat proteins, reverse transcriptase and envelope proteins, respectively. The glucocorticoid-binding sequence is represented by the black box, and the transcriptional initiation area is indicated by the hatched box.

Additional analysis of DNA sequences in the human genome has revealed that large blocks of human genes are filled with repeated elements, including long interspersed repetitive elements (LINEs) and short interspersed repetitive elements (SINEs). Short interspersed repetitive elements such as Alu sequences are often used as target sequences for DNA fingerprinting. 

Studies of overall genome composition based on reassociation kinetics (Simpson et ai, 1982 Cox et ai, 1990 Marx et a/., 2000) and analysis of fully sequenced bacterial artificial chromosome (BAC) clones from the 5. mansoni genome project show that platyhelminth genomes contain abundant highly and moderately repetitive sequence (Fig. 2.1). Much of the repetitive DNA comprises two classes of integrated mobile elements class I elements, which include long terminal repeat (LTR) retrotransposons and retroviruses, non-LTR retro-transposons and short interspersed nuclear elements (SINES) and transpose via an RNA intermediate, and class II elements (trans-posons), which transpose as DNA (Brindley et ai, 2003). Additionally, small dispersed or tandemly repeated sequences are common. A wide variety of these sequences have been isolated and characterized from a variety of taxa (Table 2.4). 

Second, it is important to consider whether a clone library will be representative of a particular repeated sequence. Besides the genetic factors, above, unusual patterns of restriction sites in some repeated sequences may influence their relative abundance in a library. This would be more likely for a tandemly repeated sequence or a very long repeated sequence than for short, interspersed repeated DNA sequences. Traditional A or plasmid libraries would be sufficient for most studies, but in certain situations it might be necessary to resort to DNA libraries of randomly frag-... 

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