MoBio Interspersed Repeats Chapter 3

Interspersed repeats are repeated DNA sequences located at dispersed regions in a genome. They are also known as mobile elements or transposable elements. As discussed in Chapter 8 Section D, a stretch of DNA sequence may be copied to a different location through DNA recombination. After many generations, such sequence (the repeat unit) could spread over various regions. Mobile elements were first discovered by Barbara McClintock in 1940s from the studies of corn. Subsequently, they were found in all kinds of organisms. In mammals, the most common mobile elements are LINEs and SINEs.

Table 3-G-1. Examples of mobile elements.



LINEs stands for Long Interspersed Nuclear Elements. Its basic organization is shown below.


Figure 3-G-2. Basic organization of LINEs. ORF1 and ORF2 are open reading frames. The protein product of ORF1 is called p40, with unknown function. ORF2 encodes a reverse transcriptase which is necessary for copying the element to other locations. The red color regions on both ends are direct repeats. All mobile elements contain direct repeats whose origin is explained in Chapter 8.


Figure 3-G-3. Comparison between direct repeats and inverted repeats. Direct repeats have the same sequence along a given direction. Inverted repeats have complementary sequences along opposite directions.

The most common LINEs in humans is the L1 family. A human genome contains about 60,000 to 100,1000 L1 elements.


"SINEs" stands for Short Interspersed Nuclear Elements. Its length is about 300 bp. In humans, the most abundant SINEs is the Alu family. A human genome contains about 700,000 to 1,000,000 Alu sites. Although most LINEs and SINEs are located in extragenic regions, some of them are located in introns. For example, the human retinoblastoma gene (RB gene) is as long as 180 kb, consisting of 27 exons. Its introns contains many Alu and a few L1 elemtns.