Some Aspects of Chromosome Structure and Functions

238 Pages·2002·25.147 MB·English

by  J. T. Epplen, A. Epplen-Haupt (auth.), R. C. Sobit, G. Obe, R. S. Athwal (eds.)

Some Aspects of
Chromosome Structure
and Functions
Some Aspects of
Chromosome Structure
and Functions
Edited by
R.C. Sobti
Department of Biotechnology
Panj ab University, Chandigarh, India
G.Obe
Institute of Genetics
University of Essen, Universitaetsstrasse 5,
D-45117, Essen, Gennany
R.S. Athwal
Department of Pathology and Laboratory Medicine
Fels Institute for Cancer Research and Molecular Biology
Temple University School of Medicine Philadelphia, USA
Kluwer Academic Publishers
BOSTON DORDRECHT LONDON
,
Narosa Publishing House
DELHI CHENNAI MUMBAI KOLKATA
A c.1.P. catalogue record for the book is available from the Library of Congress
ISBN 0-7923-7057-0
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Copyright © 2002, Narosa Publishing House, New Delhi, India
No part of the material protected by this copyright notice may be reproduced or utilized in
any form or by any means, electronic or mechanical, including photocopying, recording or
by any information storage and retrieval system, without written permission from the
copyright owner.
Dedicated to
Dr. Adayapalam T. Natarajan
Professor Emeritus, Leiden University
Leiden, The Netherlands
in recognition of his contributions to the
fields of Cytogenetics, Radiation Genetics
and Environmental Mutagenesis
Preface
It was at the end of the 19th century that a Swiss biologist, Karl Nageli first proposed the existence
of hereditary organelles that carried information from parent to offspring. Ensuing decades experienced
vigorous studies that led to the development of discovery that chromosomes are indeed the carriers
of genetic information.
Subsequent studies, especially by Morgan and Bridges, established unequivocally the chromosome
theory of inheritance.
Today, the structure of chromosome is well established. At the physical level, eukaryotic chromosomes
are composed of a single, linear, double helix of DNA. The elementary helical structure involves
nucleosomes, comprised of histones around which the DNA is wrapped. A hierarchy of higher order
helical structures of chromosomal architecture may possibly be responsible for the regulation of gene
expression.
The localized condensations of DNA constitute chromomeres. Uncoiled structures sometimes
extending from chromomeres, which form loops, is the result of discontinuities in the regular coiling
of the DNA in the chromosome.
The focus of the current investigations in this area is on the molecular architecture of the chromosomes,
where many aspects are still in process of being unravelled. A total of three billion nucleotide pairs,
which correspond to approximately 30,000-50,000 genes, exist in human genome. A draft of the
sequence of the nucleotides for the major part of the human genome is now available in the genome
databases. The sets of nucleotide sequences in the DNA coding for a specific function, constitute the
genes. A gene comprised of a defined number of nucleotides arranged in specific order thus is the unit
of inheritance.
Abnormalities at both physical as well as molecular levels in DNA are the cause of many human
diseases. Physical abnormalities in chromosome structure and number like polyploidy, aneuploidy
etc. are known to result in various syndromes e.g., trisomy of chromosome 21 results in Down's
syndrome, monosomy of X chromosome is present in Turner's syndrome. Similarly, many other
syndromes with numerical chromosomal abnormality exist. At the molecular level, the irregularities
in nucleotide sequence or loss or gain of a nucleotide in the DNA structure is also implicated in
causing many diseases. The alterations of single nucleotides have been identified as etiological
factors of a number of human diseases. Dreadful diseases such as cystic fibrosis, Xeroderma pigmentosa,
Sickle cell anaemia and Graves disease etc. are a few amongst many such diseases. Even cancers Hke
retinoblastoma, cervix, cob-rectum, and of other organs are a result of mutational activation of
normal proto-oncogenes into abnormal oncogenes. The proto-oncogenes and anti-oncogenes liable to
mutational activation and causing cancer include myc, ras, src, p53, yes, abl,fes, erh-B,jins, rvs, mas,
sis, int-2, myb,fos, met, etc.
The investigations on the role of chromosomes in causing diseases have made medical genetics as
one of the frontier fields in research. The advent of molecular genetics has further revolutionised
research. Genetic screening, especially at pre- and neo-natal stages, has significantly contributed to
the prevention of human suffering. The scope and versatility of new techniques has made it possible
to test ideas previously open only to speculation.
viii Preface
With exception to newborn and some carrier screening, most genetic testing is performed in
university laboratories, with medical geneticists often conveying the results directly to family members.
But in recent years, there has been a strong trend towards physician performing diagnostic tests.
Moreover, scientists, employed by commercial firms are trying to develop simple tests, to identify
disease-causing alleles, which people will be able to perform at home.
Another scientific program of recent origin is that of Gene Mapping-Human Genome Project.
The human genome contains an estimated 50,000 genes which encode information in DNA. These
genes are distributed among 23 pairs of chromosomes. Although most of these genes have been
assigned to specific chromosomal location, but only a few genetic diseases out of about 4000, have
been understood at molecular level.
This volume was planned to compile the data on various aspects of structure and functions of
chromosomes investigated iu laboratories around the world. This volume is specially dedicated to
honor Professor A.T. Natarajan, a distinguished cytogeneticist, who has dedicated his life to unravel
structural mysteries of chromosomes.
R.c. SOBTI
G.0BE
R.S. ATHWAL
Contents
Preface
Vll
1. Aspects of Tandemly Organized, Repetitive Sequences in
Chromosomal DNA 1
1. T. Epplen and A. Epplen-Haupt
2. Mapping and Organization of Highly-Repeated Sequences by Means of
Fluorescence in situ Hybridization Against Synaptonemal Complex-
Associated Chromatin of Rye 11
N. Cunado, 1. Barrios and 1 L. Santos
3. Some Insights on the Mechanism of in situ DNA Digestion by Restriction
Enzymes and on Fluorochrome Banding: Case of the Argentata group 17
Julio Cesar Pieczarka and Margarete Sune Mattevi
4. Structural Differences of Chromosomes in Plants Detected by Fluorescence
in situ Hybridization Using Probes of rDNA, Arabidopsis-type
Telomere Sequence Repeats and pCrT7-4 27
Katsuhiko Kondo, Norikazu Tagashira, Magdy Hussein Abd El-Twab,
Yoshikazu Hoshi, Goro Kokubugata, Yoshito Honda and
Kyaw Kyaw Khaung
5. Planococcus citri (Homoptera, Coccoidea): A Paradigmatic Case of
Chromosome Structure as an Epigenetic Way to Control Gene Expression 37
Marina Ferraro
6. Cytogenetic and Molecular Analysis of Heterochromatic Areas in the
Holocentric Chromosomes of Different Aphid Species 47
Gian Carlo Manicardi, Mauro Mandrioli, Davide Bizzaro and
Umberto Bianchi
7. Translocation Frequencies for X and Y Chromosomes Predicted by
Computer Simulations of Nuclear Structure 57
G. Kreth, P. Edelmann, Ch. Munkel, 1. Langowski and C. Cremer
8. Evolution of DNA Repair Mechanisms 73
Bernd Kaina, Klaus Becker, Thomas Grombacher and Gunter Obe
9. Cytogenetics of Lepidopteran Insects 89
VL. Sharma and R.C. Sobti
10. Chromosome Structure in Fishes 103
Claudio Oliveira, Jonathan M. Wright and Fausto Foresti
x Contents
11. A Review of Chromosome Banding in Fishes 109
OP. Sharma, N.K. Tripathi and K.K. Sharma
12. Chromosomes in Birds 123
v.L. Sharma and R.C. Sobti
13. Chromosomal Analysis in Human Population Monitoring 133
G. Wolf and H. Fender
14. Genotoxic Investigations on Occupationally Exposed Cattle Yard Workers 149
1.S. Yadav and v.K. Kaushik
15. Telomeres, Telomerase and Cancer 157
R. C. Sobti, Jaspreet Kochar, N. Capalash and S. Sharma
16. Chromosomal Radiosensitivity as an Indicator of Genetic Predisposition to
Breast Cancer 167
Ram Parshad and Katherine K. Sanford
17. Molecular Genetics of Gastrointestinal Tract Cancers 177
R.c. Sobti, Jaspreet Kochar, Neena Capalash, Kamana
Parashar, S. Sharma, A. Joshi, K. Singh and D. Bhasin
18. Molecular Pathogenesis of Lung Cancer 193
R.c. Sobti, S. Sharma, A.K. Janmeja and S.K. Jindal
19. Bladder Cancer: Genetic and Epidemiological Factors Involved in
its Genesis 207
R.C. Sobti, Adnan Issa AL-Badran, Khadijeh Onsori and S.K. Sharma
20. Molecular Genetics of Prostate Cancer 225
R. C. Sobti, Khadijeh Onsory, Adnan [ssa AL-Badran,
S.K. Sharma and Harsh Mohan
INDEX 237
Some Aspects of Chromosome Structure and Functions
R.C. Sobti et al (Eds)
Copyright © 2002, Narosa Publishing House, New Delhi, India
1. Aspects of Tandemly Organized, Repetitive
Sequences in Chromosomal DNA
J.T. Epplen! and A. Epplen-Haupt
Molecular Human Genetics, Ruhr-University, 44780 Bochum, Germany
Abstract: Most tandemly reiterated DNA sequences have not yet revealed their intrinsic properties
and secrets, although these elements are abundant and ubiquitously interspersed in most genomes.
Some characteristics of these repeats are discussed herein with special emphasis on the chromosomal
interaction and medical aspects.
Key words: DNA binding proteins; repetitive DNA elements; trinucleotide diseases.
1. Introduction
The knowledge on sequences from chromosomal DNA has expanded immensely in recent years,
refining also our ideas on genetic complexities. For virtually all of the approximately 40,000 genes
in the human genome, at least partial sequence data are available today, providing the basis for further
functional analyses also on the protein level. It remains still somewhat obscure, however, why coding
sequences represent only a minor fraction of eukaryotic chromosomes e.g., about 3% of the entire
human genome. Repetitive sequences comprise - 50% of this genomic "desert" (Ohno, 1972) and
have attracted some interest due to their striking features, perhaps reflecting structural meaning in
chromosomes. Repetitive DNA has long been regarded as a characteristic feature of eukaryotic
chromosomes, but these elements have also been detected in more and more prokaryotes (Hancock,
1996) with the exception of Escherichia coli. Functional meaning of these sequences has not been
proven beyond doubt and, therefore, it has generally been questioned, except for some special
repetitive genes e.g., the rRNA gene batteries some of which contain several hundred copies in
tandem arrays at several loci (Lewin 1980). Studies on the evolution of repetitive sequences, on their
possible functions in recombination mechanisms and gene expression as well as recent findings on
their roles in certain human diseases, on protein binding and specific DNA secondary structures point
to biological relevance of at least some members of this class of sequences~nevertheless a
comprehensive theory on the biological meaning of repetitive elements remains to be established.
Here we cover the large group of repetitive sequences comprising different basic motifs in tandem
arrays. A comprehensive and broadly accepted classification scheme is basically derived from the
lengths of their repetition units (see Tautz, 1993). The names of the different subclasses were chosen
unsystematically - following the initial designation of the so-called satellite DNA. These 'satellites'
to the bulk of other genomic DNA were described historically first in the early era of space enthusiasm
more than 3 decades ago -and they were named without knowledge of their exact sequence composition.
The so-called micro satellites or simple repeats (short tandem repeats) harbor the shortest basic motifs
and the lowest degree of complexity. Their motifs range from 1-6 basepairs (bp) in length with 5 to
approximately 100 perfect tandem copies at each locus. Simple repeat loci are scattered throughout
2
EpPLEN AND EpPLEN-HAUPT
the human genome in about 104_105 copies of the elements with mono- and di-nucleotide motifs and
in lower numbers of those with longer motifs. Microsatellites with the most abundant motif (GT)!
(CA) are found in 50,000 to 100,000 copies, a number exceeding even the number of genes in the
human genome (Nadir et al., 1996). The distribution pattern of simple repetitive sequences is more
or less even: one such element is located within 10 kilo bases (kb) on average, also within transcriptional
units in the 3'- and 5'- untranslated regions of protein-coding mRNAs. In addition to microsatellites,
minisatellites (Jeffreys et ai., 1985) have sometimes also been named 'variable number of tandem
repeats' (VNTR).
The repetitive units of minisatellites are 9 to approximately 100 bp long. Two to several hundred
copies exist per locus. For each locus the basic units show varying sequence similarities to different
core sequences. Thus, larger minisatellite units are practically never completely homogenous: the
repetitive motifs exhibit sequence variability within one locus. In the human genome, many thousands
of minisatellites with different repetitive units are interspersed with practically all other DNA elements,
but they are often clustered in subtelomeric chromosomal regions (Royle et al., 1988). This observation
led to speculations about a possible function of mini satellites in the pairing of chromosomes during
meiosis or in recombination events. Analysis of crossovers adjacent to a GC-rich mini satellite, which
is known to mutate by conversion and crossover within the repeat array, revealed a recombination
hotspot centered upstream of the locus. Allele-specific cosuppression of crossovers and repeat instability
suggests that the hotspot is responsible for driving repeat turnover and thus that minisatellites might
evolve as by-products of localized meiotic recombination in the human genome (Jeffreys et al.,
1998). Both, micro- and minisatellites exhibit a high degree of polymorphism. The number of repetitive
units at a given locus can be polymorphic to hypervariable between individuals in a population.
Generally, minisatellites are by far more polymorphic than microsatellites and can have extremely
large numbers of different alleles (Pena et ai., 1995). This hypervariability is also due to the slight
variations in the sequence make-up of the individual repeat unit.
Classical satellites represent the longest category of tandemly organized repetitive DNA. Originally,
they were identified in buoyant density gradients (Skinner, 1977). In these gradients, the main band
comprises the bulk of genomic DNA. Several additional minor bands of differing density arise due
to their different GC-content. Satellites consist of large areas of highly repetitive DNA. With DNA
sequencing methodology growing more efficient, satellites have been recognized as consisting of
quite heterogenous sequence entities. Their GC-content (and resulting specific density) does not
necessarily have to differ from the rest of the genome, leading to the designation as 'cryptic' satellite
sequences (Tautz, 1993). Satellites often contain millions of tandem repeats with short motifs. The
more perfect the tandem repeats are organized in a satellite, the less amenable is this DNA block to
complete sequence analysis. Classical satellites have repetitive units of up to 100 or even 1000 bp.
The degree of sequence redundancy amounts to up to 107 copies at each locus. In general, there are
only one or a few satellites per genome, and no more than one (or two) per chromosome. Satellites
are mostly located in heterochromatic regions e.g., at the centromeres or on the sex chromosomes
(Jones and Singh 1981; Therkelsen et al., 1997).
Repetitive elements other than tandemly organized structures are not detailed here except for their
relationships to the former. Interspersed repetitive sequences are situated as single, isolated copies of
a repetitive motif in between other (in some cases repetitive) sequences. Short and long interspersed
nucleotide elements [SINES and LINES (Singer, 1982)] are d°ef ined according to their lengths of less
or more than 500 bp. Each of these types cover about 5-1 % of the human genome. Origin and
development appear to result from mobilization and (random) insertion mechanisms -comparable to
(retro-) transposition of retroviruses. Alu elements are the most abundant sequences among the