Short interspersed repeat sequences SINEs

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. 

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). 

RFLP(s), Restriction Fragment Length Polymorphism(s) see, Sequence Compositional Complexity sd, standard deviation SINE(s), Short Interspersed Repeat(s)... 

Several publications describe assays for genomic animal DNA. Analysis of short interspersed nuclear elements (SINEs) allows specific detection of DNA from many species, including cattle, horse, pig, deer, and dog. SINEs are repeated, unblocked, and dispersed throughout the genome sequences. They represent retroposons (included in the genome transcripts of intracellular RNA) and constitute more than 20% of the genome of humans and other mammals. Unique sequences could be identified for every species and used for the development of a species-specific PCR assay (Walker et al., 2003). For this application the laboratory has to prepare its own control samples with the DNA extracted from reference samples. 

There are four types of transposon-derived repeating sequences, of which three transpose through RNA intermediates and one transposes directly as DNA (the last one is considered below). We have already identified the LINEs. The second set is called short interspersed elements (SINEs), of which the Alus are the only active members that exist in the human genome. 

Short interspersed sequences (SINES). Much of the reiterated DNA is present in repeated segments... 

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