Table II.2 Different classes of annotated repetitive genome components

(amplified from (Shapiro and Sternberg 2005))

Structural class

Structural or functional characteristics

Oligonucleotide motif

4 – 50 bp; protein binding or recognition sites

Homopolymeric tract

Repeats of a single nucleotide (N)n

Variable nucleotide tandem repeats (VNTR)

Repeats of dinucleotides and longer sequences <100 bp that may vary in number in the tandem array: (NN…N) n   (Csink and Henikoff 1998; Lindstedt 2005)

Composite elements

Composed of two or more oligonucleotide motifs, sometimes with non-specific spacer sequences; examples include palindromic operators, promoters, enhancers and silencers, replication origins, site-specific recombination sequences.

Tandem array microsatellites or simple sequence repeats (SSR)

Head-to-tail repeats of small sequence elements from 2-6 nucleotides in length; subject to frequent changes in repeat number and length; in genetic loci, expression levels tend to go down with increased microsatellite length. (Bagshaw, Pitt et al. 2008; Subirana and Messeguer 2008; Usdin 2008)

Tandem array satellites

Repeats of larger elements, typically 100-200 bp in length; satellite arrays typically contain thousands of copies; often found at centromeres. (Sharma and Raina 2005; Palomeque and Lorite 2008; Plohl, Luchetti et al. 2008; Tomilin 2008; Adega, Guedes-Pinto et al. 2009; Despons, Baret et al. 2010; Wang, Zhang et al. 2010)

Terminal inverted repeat (TIR) DNA transposons

DNA-based mobile genetic elements flanked by inverted terminal repeat sequences of <50 bp; may encode proteins needed for transposition; vary in length from several hundred to several thousand base pairs (Bergman and Quesneville 2007; Kapitonov and Jurka 2008; Moschetti, Chlamydas et al. 2008; Roberts, Chandler et al. 2008; Pritham 2009)

Foldback (FB) DNA transposons

DNA transposons with extensive (many kb) inverted repeats at each end (Casals, Caceres et al. 2005; Marzo, Puig et al. 2008)

Rolling circle DNA transposons (helitrons)

DNA transposons that insert from a circular intermediate by rolling circle replication; can generate tandem arrays (Zhou, Froschauer et al. 2006; Hollister and Gaut 2007; Kapitonov and Jurka 2007; Rousseau, Loot et al. 2007; Rousseau, Loot et al. 2008; Du, Fefelova et al. 2009; Yang and Bennetzen 2009)

Long terminal repeat (LTR) retrotransposons

Retroviruses and non-viral mobile elements flanked by direct terminal repeats of several hundred base pairs; insert at new locations following reverse transcription from an RNA copy into duplex DNA (Rho, Choi et al. 2007; Novikova 2009)

Long interspersed nucleotide element (LINE) retrotransposons

Mobile elements several kb in length with no terminal repeats; encode proteins involved in retrotransposition from a PolII-transcribed RNA copy by target-primed reverse transcription (Dewannieux and Heidmann 2005; Ohshima and Okada 2005; Ding, Lin et al. 2006)

Short interspersed nucleotide element (SINE)  retrotransposons

Mobile elements, a few hundred base pairs in length with no terminal repeats; do not encode proteins (mobilised by LINE products from a PolIII-transcribed RNA copy) (Dewannieux and Heidmann 2005; Jurka, Kohany et al. 2005; Ohshima and Okada 2005; Wallace, Wagstaff et al. 2008)





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