Introduction

Repetitive elements or repeats are sequences present in multiple copies in the genome but, unlike multigene families, they do not have any clear function in the host. Low-copy repeats generated by large-scale genomic duplications represent a class by themselves, and are discussed in Chapter 5.

From: Genomic Disorders: The Genomic Basis of Disease Edited by: J. R. Lupski and P. Stankiewicz © Humana Press, Totowa, NJ

Table 1

Repetitive Elements in the Human Genome

Type/class Superfamily Further division1 Family Genome (%)b

Tandem Satellites Approx 20?

repeats Telomeric and subtelomeric repeats <0.01

Microsatellites and minisatellites 1.4

Interspersed DNA Mariner/Tc1 11 families 2.8

repeats transposons hAT 14 families 2.4

PiggyBac 1 families 0.02

MuDr 2 families 0.03

Harbinger HARBI1 gene — P Single-copy genes —

Non-LTR L1 LINE L1 17

retrotransposons SINE Alu 10.5

Retropseudogenes — 0.1-0.3c

CR1 LINE L2 3.1

L3 0.31

SINE MIR 1

MIR3 0.29

LTR retro- Copia (HERVs) Class I >90 families 2.5 transposons (gamma retroviruses)

Class II 11 families 0.5 (beta retroviruses)

Class III >30 families 6 (spumaviruses)

Gypsy Single-copy genes —

This table shows the basic division of human repetitive elements. See refs. 3,6,123,128, and Repbase update (4).

aFor non-LTR transposons, we also included dependent nonautonomous elements (SINEs, retropseudogenes).

bThe numbers represent the proportion of detectable repeats in the sequenced genome. Centromeric and heterochromatic satellites are underrepresented in the sequenced regions, but based on reassociation studies the proportion is estimated to be approx 20%.

Depending on the detection method.

In general, repetitive elements are divided into tandem repeats and interspersed repeats (Table 1). Tandem repeats are head-to-tail repetitions of the same sequence motif. Interspersed repeats are active or inactive copies of TEs dispersed throughout the genome. Repetitive elements can be grouped into sets of similar copies, called families or subfamilies. Families of TEs that encode enzymes necessary for their replication are termed autonomous. Nonautono-mous elements do not encode all necessary proteins, and their replication (amplification) depends on proteins provided by the autonomous elements. Nonautonomous elements can, thus, be viewed as parasitic elements competing for replication machinery with the autonomous copies. Amplification of both autonomous and nonautonomous elements depends also on additional factors provided by the host cell.

Based on their replication strategy, interspersed repeats are broadly divided into DNA transposons and retrotransposons. The DNA transposons amplify using the host DNA repli cation machinery, and their transcripts serve solely as mRNAs participating in translation of transposon-encoded proteins involved in the transposon insertions and excisions. The retrotransposons replicate via an RNA intermediate and, thus, their transcripts serve both as mRNAs for protein translation and as templates for DNA synthesis. Before integration into the genome, retrotransposon RNA must be copied into cDNA using RNA-dependent DNA polymerase, also known as reverse transcriptase (RT) (1,2).

Recognizable copies of all repetitive elements constitute approx 50% of the human genome (3). During the course of the human genome sequencing, more than 600 repeat families and subfamilies have been discovered. All are systematically organized in Repbase Update (RU) (http://www.girinst.org/Repbase_Update.html) (4).

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