Repetitive DNA

237 Pages·2012·6.775 MB·English

by  M.A. Garrido-Ramos, M. Schmid

Repetitive DNA
Genome Dynamics
Vol. 7
Series Editor
Michael Schmid
Würzburg
Repetitive DNA
Volume Editor
Manuel A. Garrido-Ramos
Granada
26 figures, 11 in color, and 1 table, 2012
Basel · Freiburg · Paris · London · New York · New Delhi · Bangkok ·
Beijing · Tokyo · Kuala Lumpur · Singapore · Sydney
Dr. Manuel A. Garrido-Ramos
Departamento de Genética
Facultad de Ciencias
Universidad de Granada
Avda. Fuentenueva s/n
18071 Granada (Spain)
Library of Congress Cataloging-in-Publication Data
Repetitive DNA / volume editor, Manuel A. Garrido-Ramos.
p. ; cm. -- (Genome dynamics, ISSN 1660-9263 ; v. 7)
Includes bibliographical references and index.
ISBN 978-3-318-02149-3 (hard cover : alk. paper) -- ISBN 978-3-318-02150-9
(e-ISBN)
I. Garrido-Ramos, Manuel A. II. Series: Genome dynamics ; v. 7. 1660-9263.
[DNLM: 1. DNA--genetics. 2. Repetitive Sequences, Nucleic Acid. 3.
Genomics--methods. W1 GE336DK v.7 2012 / QU 58.5]

614.5'81--dc23
2012014216
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ISSN 1660–9263
e-ISSN 1662–3797
ISBN 978–3–318–02149–3
e-ISBN 978–3–318–02150–9
Contents
VII Editorial
Schmid, M. (Würzburg)
VIII Preface
Garrido-Ramos, M.A. (Granada)
1 The Repetitive DNA Content of Eukaryotic Genomes
López-Flores, I.; Garrido-Ramos, M.A. (Granada)
29 Telomere Dynamics in Mammals
Silvestre, D.C.; Londoño-Vallejo, A. (Paris)
46 Drosophila Telomeres: an Example of Co-Evolution with Transposable Elements
Silva-Sousa, R.; López-Panadès, E.; Casacuberta, E. (Barcelona)
68 The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes
Tollis, M.; Boissinot, S. (Flushing, N.Y./New York, N.Y.)
92 SINEs as Driving Forces in Genome Evolution
Schmitz, J. (Münster)
108 Unstable Microsatellite Repeats Facilitate Rapid Evolution of Coding and
Regulatory Sequences
Jansen, A. (Heverlee/Leuven); Gemayel, R.; Verstrepen, K.J. (Heverlee)
126 Satellite DNA Evolution
Plohl, M.; Meštrović, N.; Mravinac, B. (Zagreb)
153 Satellite DNA-Mediated Effects on Genome Regulation
Pezer, Ž.; Brajković, J. (Zagreb); Feliciello, I. (Zagreb/Napoli); Ugarković, Đ. (Zagreb)
170 The Birth-and-Death Evolution of Multigene Families Revisited
Eirín-López, J.M. (A Coruña); Rebordinos, L. (Cádiz); Rooney, A.P. (Peoria, Ill.);
Rozas, J. (Barcelona)
197 Chromosomal Distribution and Evolution of Repetitive DNAs in Fish
Cioffi, M.B.; Bertollo, L.A.C. (São Carlos)
222 Author Index
223 Abbreviations
226 Latin Species Names
228 Subject Index
V
Section Title
Editorial
As has been clearly stated by the former Series Editor of Genome Dynamics, Jean-
Nicolas Volff, this book series aims to provide readers with an up- to- date overview
on genome structure and diversity. Therefore, it is a great pleasure to introduce vol-
ume 7 entitled ‘Repetitive DNA’. The existence of repetitive DNAs in the genomes of
eukaryotes was first recognized in 1961 by Kit [1] and Sueoka [2] by virtue of their
unique buoyant density in DNA density gradient centrifugation using caesium chlo-
ride or caesium sulphate. During the following 50 years, molecular biology revealed
an astonishing richness of diverse reiterated DNA classes, such as transposon- derived
sequences, inactive retroposed copies of cellular genes, simple sequence repeats, seg-
mental duplications, and large blocks of tandemly repeated sequences [3]. The impor-
tance of repetitive DNAs is underlined by the simple fact that repeated sequences
account for more than half of the human genome.
The initial idea to this book was born during a visit at the University of Granada
(Spain) where Manuel A. Garrido- Ramos of the Department of Genetics convinc-
ingly exposed the need of reviewing more recent research on these fascinating classes
of DNA. He has done a remarkable job in selecting and coordinating authorities in
the field to write ten chapters covering a wide range of subjects. I express my grati-
tude to him and all the authors for all the time they invested. The constant support of
Thomas Karger with this timely book series is again highly appreciated.
Michael Schmid
Würzburg, March 2012
References
1 Kit S: Equilibrium sedimentation in density gradi- 3 Platzer M: The upcoming genome and its upcoming
ents of DNA preparations from animal tissues. dynamics; in Volff J- N (ed): Vertebrate Genomes,
J Mol Biol 1961;3:711– 716. Genome Dynamics Vol 2. Basel, Switzerland, Karger
2 Sueoka N: Variation and heterogeneity of base com- Publishers, 2006, pp 1– 16.
position of deoxyribonucleic acids: a compilation of
old and new data. J Mol Biol 1961;3:31– 40.
VII
Preface
The seventh volume of Genome Dynamics is dedicated to ‘Repetitive DNA’. Eukaryotic
genomes are composed of a plethora of different types of DNA sequences repeated
from a few to hundreds of thousands times, either dispersed or arranged in tan-
dem. The experimental data compiled by the new molecular techniques associated
with the completion of genome projects has led to changes in our understanding of
the structural features, functional implications and evolutionary dynamics of these
repetitive DNA sequences. These recent developments have opened new insights into
the knowledge of mechanisms involved in gene expression, organization, and evolu-
tion of multigene families, the fraction of the eukaryotic repetitive DNA which has
an undisputedly clear function. Also, we have a comprehensive view today on the
structure and functionality of telomeres and centromeres, both composed of repeti-
tive DNA sequences. Additionally, these advances have shed light on the most abun-
dant fraction of repetitive DNA, composed of microsatellite DNA, satellite DNA and,
above all, transposable elements. Though not long ago these genomic elements were
thought to accumulate as junk or, alternatively, as genomic parasites proliferating for
their own benefit, today this early view is changing in most cases. Thus, microsatel-
lite DNAs might facilitate an organism’s evolvability, satellite DNA transcripts might
participate in heterochromatin formation as well as in modulation of gene expres-
sion. Also, today there is no doubt about the significant role of mobile elements in
shaping the structure and evolution of genes and genomes, generating genetic inno-
vations and regulating gene expression. The present volume offers a timely update of
recent developments in the repetitive DNA research, including the study of multigene
families, centromeres, telomeres, microsatellite DNA, satellite DNA, and transpos-
able elements.
I would like to thank all authors who have contributed to this volume with their
excellent review articles and the referees for their invaluable efforts. I also want to
express my gratitude to the Series Editor Dr. Michael Schmid and his team as well as
to Karger Publishers for their outstanding assistance during the preparation of this
volume.
Manuel A. Garrido- Ramos
Granada, March 2012
VIII
Garrido- Ramos MA (ed): Repetitive DNA.
Genome Dyn. Basel, Karger, 2012, vol 7, pp 1–28
The Repetitive DNA Content of Eukaryotic
Genomes
I. López- Flores (cid:2) M.A. Garrido- Ramos
Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
Abstract
Eukaryotic genomes are composed of both unique and repetitive DNA sequences. These latter
form families of different classes that may be organized in tandem or may be dispersed within
genomes with a moderate to high degree of repetitiveness. The repetitive DNA fraction may rep-
resent a high proportion of a particular genome due to correlation between genome size and
abundance of repetitive sequences, which would explain the differences in genomic DNA con-
tents of different species. In this review, we analyze repetitive DNA diversity and abundance as
well as its impact on genome structure, function, and evolution.
Copyright © 2012 S. Karger AG, Basel
The Repetitive Fraction of Eukaryotic Genomes
Pioneering work by Britten and Kohne [1] revealed that in addition to unique
sequences the eukaryotic genomes contain large quantities of repetitive DNA, clas-
sified into moderately or highly repetitive sequences according to their degree of
repetitiveness. Later, the repetitive DNA sequences were grouped according to
other criteria such as their organization (tandemly arrayed or dispersed) or their
functional role. Although repetitive DNA sequences include several types of RNA
or protein- coding sequences, most of the repetitive part of the genome was earlier
considered ‘junk DNA’ with no known function. Today, with many genomes com-
pletely sequenced and the background research of more than 40 years, we have ample
information on the significance of the repetitive DNA within eukaryotic genomes
and concepts are changing. Figure 1 shows a classification of the several types of
repetitive DNA according to an organizational criterion, which has been followed in
this review. Among tandem repetitive DNA, there are moderately repetitive DNAs,
such as ribosomal RNA (rRNA) and protein- coding gene families or short tandem
telomeric repeats, as well as highly repetitive non- coding microsatellite and satellite
DNAs, including centromeric DNA. Among dispersed repeats, transposable elements
(TEs) such as DNA transposons and retrotransposons (mainly long terminal repeat
(LTR) retrotransposons and long interspersed elements, LINEs) stand out, consti-
tuting a fraction of highly repetitive DNA as a whole. In addition, genomes contain
retrotransposed sequences such as short interspersed elements (SINEs; moderately
to highly repetitive DNA), retrogenes and retropseudogenes, as well as several gene
families composed of dispersed members (moderately repetitive DNA). In addition,
many genomes are characterized by segmental duplications (SDs), duplicated DNA
fragments greater than 1 kb, with both dispersed and tandem organization.
Gene Families
Gene families are groups of paralogous genes, typically exhibiting related sequences
and functions. A gene family is produced when a single gene is copied one or more
times by a gene- duplication event, such as whole- genome duplication (ancient poly-
ploidy is common in plant lineages and is considered a key factor in eukaryote evo-
lution) and SD (see below). Over time, duplications may occur several times and
produce many copies of a particular gene. Family sizes range from 2 members up
to several hundred [2]. Depending on their organization, gene families are classified
into dispersed and tandem gene families. Dispersed genes include for example the
families of olfactory receptor genes from mammals (forming the largest known mul-
tigene family in the human genome: 802 genes, 388 potentially functional and 414
apparent pseudogenes), the MADS box genes, the fatty acid- binding protein genes or
the tRNA genes (see [3] for references). Among tandem gene families, some examples
are globins, histones, and rRNA genes.
Ribosomal RNA genes (rDNA) are probably the best- known example of a mul-
tigene family. rRNA plays a vital role in protein synthesis, as it constitutes the main
structural and the catalytic component of the ribosomes. In most eukaryotes, rDNA
consists of tandemly arrayed repeat units, containing 3 of the 4 genes encoding nuclear
rRNA, located in the nucleolar organizer region (NOR) on 1 or more chromosomes.
Each repeat unit contains the 28S large subunit, the 18S small subunit, the 5.8S gene,
as well as 2 external transcribed spacers (ETS) and 2 internal transcribed spacers
(ITS1 and ITS2) and a large non- transcribed spacer (NTS). Thus, the nuclear rRNA
genes are typically arranged as a 5(cid:3)- ETS- 18S- ITS1- 5.8S- ITS2- 28S- ETS- 3(cid:3) transcrip-
tion unit, organized in tandem repeats and separated by the NTS. The ETS plus
the NTS constitute the intergenic spacer (IGS). This is known as the major rDNA
family. The number of repeat units varies between eukaryotes, from 39 to 19,300
in animals and from 150 to 26,000 in plants [4]. The different components forming
rDNA are known to evolve generally at different rates. The 18S rDNA is among the
slowest- evolving genes found in living organisms, contrary to the spacers, which
are rapidly evolving sequences (they are not the subject to selective constraints)
2 López- Flores · Garrido- Ramos
with the NTS evolving faster than the ITSs and ETSs [2]. The 28S rRNA gene also
evolves relatively slowly. The evolution of the rRNA gene complex at varying rates
has different phylogenetic utilities. The 18S and 28S rRNA genes allow the inference
of phylogenetic history across a broad taxonomic range, whereas the spacers can
be useful in determining relationships between closely related species, sometimes
intraspecific relationships, and at times have been suitable for population studies.
Nucleotide sequences of spacers are very similar among repeats of the same species
but differ greatly between species. The model of concerted evolution should explain
this observation in which the individual repeats do not evolve independently (see
below). Instead, the molecular drive force tends to homogenize repeated sequences
within genomes and among the genomes of an entire species, leading to divergence
between species [5]. However, nucleotide sequences of the rRNA coding regions are
almost identical between closely related species, and they are similar even among
distantly related species. This similarity should be maintained by strong purifying
selection that operates for the coding regions. Thus, we can explain the entire set of
observations concerning the rRNA gene family in terms of mutation, homogeniza-
tion, and purifying selection [3]. The fourth rRNA gene is the gene encoding 5S
rRNA, which forms another family known as the minor rDNA family, which com-
prises tandem repetitions of the gene separated by an NTS. In most eukaryotes, the
5S rRNA genes are found at another location of the nuclear genome, although e.g. in
sturgeons, the 2 rDNA families are in the same chromosome pair and in some species
of protozoa, fungi, and algae the 5S ribosomal genes are located between the 28S and
the 18S genes (within the IGS) [6]. The 5S rRNA genes were also believed to undergo
concerted evolution. However, it has been found recently that the 5S genes located
at different loci might evolve by the birth- and- death evolution model. This model
predicts that new genes in a family are formed by gene duplication (diversification),
and some of these duplicate genes specialize (differentiate) and are maintained in
the genome for a long period of time, while others are inactivated or deleted in dif-
ferent species (pseudogenization) [3]. In this sense, Freire et al. [7] found that the 5S
genes of mussels showed a mixed mechanism, involving the generation of genetic
diversity through birth- and- death, followed by a process of local homogenization
resulting from concerted evolution in order to maintain the genetic identities of the
different 5S genes.
Histone genes provide another widely known example of tandemly arrayed genes.
Histones are highly conserved eukaryotic proteins that have a crucial role in the func-
tion and formation of the nucleosome. There are 5 major histone genes – H1, H2A,
H2B, H3, and H4 – which are separated from each other by non- coding IGSs. Each
major histone gene includes some minor variant forms. Some variants originate from
changes in only a few amino acids (for example mouse H3.1 and H3.2 differ only in
1 amino acid), while other variants originate from changes affecting larger portions
of the protein (e.g. mouse H3.1/H3.2 and H3.3) [8, 9]. The number of histone genes
varies between species. For example, the yeast Saccharomyces cerevisiae has 2 copies
Repetitive DNA in Eukaryotes 3