Interspersed genome-wide repeats

By recent estimates, approximately 45% of the human genome is composed of repetitive sequences (repeated sequences of nucleotides). Although their significance is not understood, several types of repetitive sequences have been identified and investigated. There are two general classes tandem repeats and interspersed genome-wide repeats. Each is briefly described. 

As their name implies, interspersed genome-wide repeats are repetitive sequences that are scattered around the genome. Most of these sequences are the result of transposition (Section 18.1), a mechanism whereby certain DNA sequences can be duplicated and move within the genome. Transposable DNA elements, referred to as transposons, excise themselves and then insert at another site. More commonly, however, transposition mechanisms involve an RNA transcript intermediate. These latter DNA elements are called RNA transposons or retrotransposons. The most abundant retrotransposon in humans is the Alu sequence. Alu sequences, whose lengths are about 280 bp, are present in about 500,000 copies. The function of Alu sequences and other retrotransposons is unknown. It is suspected that they are molecular parasites whose primary purpose is their own propagation. 

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). 

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