Qur’an & Genetics
On Giant Chromosomes in the Qur`an
Ahmad Shammazadeh
Topics:
1.
Which Chromosomes
are called Giant Chromosomes?
2.
What interested
me toconduct a research on Giant Chromosomes?
3.
Why and how the
Almighty God has guided us to study the Giant
Chromosomes?
4.
The situation
and importance of Giant Chromosomes in modern Genetics.
5.
Is it possible
that Giant Chromosomes have brought life to Earth?
*****
Which chromosomes are called Giant Chromosomes?
The 23rd pair
of human chromosomes is the sexual Chromosome and the 22 remaining pairs are called
Autosomal Chromosomes. Eight pairs(from no. 1 to no. 8) of them, are Giant
Chromosomes. These 8 pairs of chromosomes are very important for human life, because
every giant chromosome is made up of about 181 million letters that make up the
human genetic code.
ENDOMITOSIS AND ENDOREDUPLICATION
Nagl et al. (1985) described polytene chromosomes as giant chromosomes
produced by changes in the mitotic cycle during the interphase stage. In such a
modified nuclear cycle, the chromatin duplicates its DNA content during the G1
and S stages, but, instead of passing to the G2 stage, the nucleus initiates a
new G1 phase, thus starting a new cycle of chromatin duplication. This type of
cycle was first described in 1939 by Geitler, as occurring in the somatic cells
of the insect Gerrislateralis (Painter and Reindorp, 1939; D''''''''''''Amato,
1964), and was named the endomitotic cycle because it develops within the
nuclear envelop without either achromatic spindle formation or nuclear or
cellular division (Nagl, 1970a; Brodsky and Uryvaeva, 1985). The term
endomitosis is, however, generally used to describe the formation of both
polyploid and polytene nuclei (q.v. Nagl, 1974). Nagl (1978, 1981, 1987) has
suggested the term endocycle rather than endomitosis, and D''''''''''''Amato
(1984) has adopted the term endomitotic and endoreduplication to distinguish
between those that produce polyploid and polytene nuclei, respectively.
The endomitotic cycle (endomitosis) starts with a normal prophase
(endoprophase), after which the chromosome contracts further (endometaphase),
their sister chromatids separate from each other (endoanaphase) and decondense
to assume the interphase nuclear structure, resulting in polyploid cells, with
double the chromosome number (endopolyploidy) at the end of each cycle. The
essential difference between endomitosis and the normal cell cycle is the
absence of nuclear membrane dissolution in endomitosis, with the whole cycle
occurring inside the nucleus. Such cycles have been observed in the anther
tapetum of some angiosperm species, as in some Passiflora species and in
Papaverrhoeas( Figure 1a).
The endoreduplication cycle differs from endomitosis because it results
in polytene cells (cells with many identical paired chromatids). In the
endoreduplication cycle, the chromatid number is duplicated, but they do not
segregate, and after various endoreduplication cycles, larger and thicker
chromosomes are produced, called polytenics. In the endoreduplication cycle,
the condensation and decondensation stages are not evident (DAmato 1984, 1989),
except in some cells where it is possible to see the chromocenter dispersion
phase, known as the Z-phase (Nagl, 1970b, 1972; Cavallini et al., 1981). (Plant polytene
chromosome, Gianna Maria Griz Carvalheira). *
*The
full paper can be found in the final page.
*****
What interested me to conduct a research on Giant
Chromosomes?
When reading
the Qur`an during my teens, I encountered the sixth verse of surah Zumar and the
eleventh verse of surah Shura. In these verses The Almighty God explains the human
embryonic stages, and the word “An’aam” is used in this verse, which means cattle
such as camel, sheep, cow etc. The use of the word “An’aam” made me think that possibly almighty God did
not mean the normal cattle, but possibly another type of creatures.
I went through many
translations and interpretations of these Qur’anic verses, but they all
considered “An’aam” to be normal cattle .None used another meaning, and because
cattle does not fit to these verses, interpreters and translators have made up
a translation to adjust the text!
When I was forty, a schematic shape
of a pair of chromosomes in the Encyclopedia Britannica caught my eyes.The
shape showed that it has two short arms as hands, two long arms as legs, and a
central part(centromere) as original body, exactly as cattle(An’aam!). On
that day I felt very happy because I finally found the original meaning of “An’aam”
in those verses, after such a long time!
Why
and how The Almighty God Has guided us to know the Giant Chromosomes?
By this
discovery, only fifty percent of the problem or understanding of the verses was
solved, because in the 6th verse of surah Zomar, it mentions eight pairs
of An’aam, meanwhile human chromosomes are 23 pairs. This, of course is an
important point! Because if The Almighty God had told us that the 23 pairs of An’aam,
everybody in today`s time, would immediately realize, that “An’aam” is
chromosomes, without any use for human life!
But the Almighty God by mentioning
eight pairs of An’aam, invited us to know what these 8 pairs of An’aam are, and
encouraged us to think about them, to conduct research on them, to find about
their characteristics, and use the results in our lives.
When The Almighty
God describes Himself proudly as the highest at the top and the in end of the verses
would not like to tell us about such insignificant matters which is written in
the interpretations and translations of Qur’an!
Therefore, while
He describes Himself in the verse as “flourisher of the universe” on the top of the verse, and “there is nothing
like Him; and He is the All-Hearer and the All-Seer”, in the end of the verse,
of course, He would like to announce us certainly a very important matter!
„خَلَقَكُم مِّن
نَّفْسٍ وَاحِدَةٍ ثُمَّ جَعَلَ مِنْهَا زَوْجَهَا وَأَنزَلَ لَكُم مِّنَ
الْأَنْعَامِ ثَمَانِيَةَ أَزْوَاجٍ ۚ يَخْلُقُكُمْ فِي بُطُونِ أُمَّهَاتِكُمْ
خَلْقًا مِّن بَعْدِ خَلْقٍ فِي ظُلُمَاتٍ ثَلَاثٍ ۚ ذَٰلِكُمُ اللَّهُ رَبُّكُمْ
لَهُ الْمُلْكُ ۖ لَا إِلَٰهَ إِلَّا هُوَ ۖ فَأَنَّىٰ تُصْرَفُونَ(Zumar :6)
„
„فَاطِرُ السَّمَاوَاتِ وَالْأَرْضِ ۚ جَعَلَ
لَكُم مِّنْ أَنفُسِكُمْ أَزْوَاجًا وَمِنَ الْأَنْعَامِ أَزْوَاجًا ۖ
يَذْرَؤُكُمْ فِيهِ ۚ لَيْسَ كَمِثْلِهِ شَيْءٌ ۖ وَهُوَ السَّمِيعُ الْبَصِيرُ(Shura :11)”
Below, are the
various translations of the above verses:
Traditional and
old-fashioned translation (from King Fahad complex for the printing of the Holy
Qur’an),
·
“He created you(all) from a single person(Adam) then made from him his
wife [havva(Eve)]. And He has sent down for you of cattle eight pairs(of the
sheep, two, male and female, of the goats, two, male and female, of the oxen,
two, male and female, and of the camel, two, male and female). He creates you
in the wombs of your mothers: creation after creation in three veils of
darkness “ (Zumar verse 6)
·
“The creator of the heavens and the earth. He has made for you mates
from yourselves, and for the cattle(also) mates. By this means He
creates you(in the wombs)” (Shura verse 11)
Modern translation (by Ali
QuliQarai- Printed by Islamic college for advanced studies- London)
·
“ He created you from a single soul, then made from it its mate, and He
has sent down for you eight mates of the cattle. He creates you in the wombs of
your mothers, creation after creation, in a threefold darkness” (Zumar verse 6)
·
“The originator of the heavens and the earth, He made for you mates from
your own selves, and mates of the cattle, by which means He multiplies
you” (Shura verse 11)
My translation
·
He created you from unique soul. Then organized of it its mate, and He
sent down for you eight pairs of An’aam. He creates you in the wombs of your
mothers, a creation after another creation in three stages of darkness.(Zumar
verse 6)
·
“The flourisher of the universe, organized for you of yourselves mates
and of An’aam pairs, He reduplicates you in it(An’aam) there is nothing like Him; and He is the All-Hearer
and the All-Seer” (Shura verse 11)
Notes:
-
In the 11th verse of surah Shura The Almighty God is clearly
explaining the merging process of sexual chromosomes of man(X&Y) and of
woman(X&X), and reduplication human embryo by this combined pair chromosome, and the perfected and completed creation
and prolongation of mankind, which He is proud of it.
-
Not only these two translations but all translations of Qur’an in every
language has omitted the statement “He reduplicates you in it”, because
translators can not understand the meaning of An’aam, then, they add the
phrase “by this means” to complete the translation.
-
In the Qur`anic vocabulary, the heavens and the earth means the
universe
-
“He sent down for you eight pairs of An’aam”. This statement is
translated correctly in all translations, but none ask how God has sent us
eight pairs of cattle from the heaven and why?
On the other hand, it is against
scientific achievements!
-
In the traditional translations, translators would like to explain the
eight pairs of cattle, but all of them explain only four pairs of cattle! As
you can see in the first translation.
The situation and importance of Giant Chromosomes in modern
Genetics.
From the “Plant Polytene Chromosome”, which is a brief
history of Giant Chromosomes with 80 reference articles, I understood the
researches which have been conducted on Giant Chromosomes, considered them as
Polytene Chromosomes. In this way, I knew why the title of Giant chromosomes
could rarely be found on the net.
I also found the following
information on the net. It shows Giant Chromosomes play an important role in
therapy of many diseases. I underline the most important achievements below:
Scientists Analyze Chromosomes 2 and 4
NHGRI-Supported Researchers Discover Largest "Gene Deserts"; Find New Clues to Ancestral Chromosome Fusion Event
BETHESDA, Md., Wed., April 6,
2005 - A detailed analysis of chromosomes 2 and 4 has detected the largest
"gene deserts" known in the human genome and uncovered more evidence
that human chromosome 2 arose from the fusion of two ancestral ape chromosomes,
researchers supported by the National Human Genome Research Institute (NHGRI),
part of the National Institutes of Health (NIH), reported today.
In a study published in the April 7 issue of the
journal Nature, a multi-institution team, led by Washington University
School of Medicine in St Louis, described its analysis of the high quality,
reference sequence of chromosomes 2 and 4. The sequencing work on the
chromosomes was carried out as part of the Human Genome Project at Washington
University; Broad Institute of MIT, Cambridge, Mass.; Stanford DNA Sequencing
and Technology Development Center, Stanford, Calif.; Welcome Trust Sanger
Institute, Hinxton, England; National Yang-Ming University, Taipei, Taiwan;
Genoscope, Evry, France; Baylor College of Medicine, Houston; University of
Washington Multi mega base Sequencing Center, Seattle; U.S. Department of
Energy (DOE) Joint Genome Institute, Walnut Creek, Calif.; and Roswell Park
Cancer Institute, Buffalo, N.Y.
"This analysis is an impressive achievement that
will deepen our understanding of the human genome and speed the discovery of
genes related to human health and disease. In addition, these findings provide
exciting new insights into the structure and evolution of mammalian
genomes," said Francis S. Collins, M.D., Ph.D., director of NHGRI, which
led the U.S. component of the Human Genome Project along with the DOE.
Chromosome 4 has long been of interest to the medical
community because it holds the gene for Huntington's disease, polycystic kidney
disease, a form of muscular dystrophy and a variety of other inherited
disorders. Chromosome 2 is noteworthy for being the second largest human
chromosome, trailing only chromosome 1 in size. It is also home to the gene
with the longest known, protein-coding sequence - a 280,000 base pair gene that
codes for a muscle protein, called titin, which is 33,000 amino acids long.
One of the central goals of the effort to analyze the
human genome is the identification of all genes, which are generally defined as
stretches of DNA that code for particular proteins. The new analysis confirmed
the existence of 1,346 protein-coding genes on chromosome 2 and 796
protein-coding genes on chromosome 4.
As part of their examination of chromosome 4, the
researchers found what are believed to be the largest "gene deserts"
yet discovered in the human genome sequence. These regions of the genome are
called gene deserts because they are devoid of any protein-coding genes.
However, researchers suspect such regions are important to human biology
because they have been conserved throughout the evolution of mammals and birds,
and work is now underway to figure out their exact functions.
Humans have 23 pairs of chromosomes - one less pair
than chimpanzees, gorillas, orangutans and other great apes. For more than two
decades, researchers have thought human chromosome 2 was produced as the result
of the fusion of two mid-sized ape chromosomes and a Seattle group located the
fusion site in 2002.
In the latest analysis, researchers searched the
chromosome's DNA sequence for the relics of the center (centromere) of the ape
chromosome that was inactivated upon fusion with the other ape chromosome. They
subsequently identified a 36,000 base pair stretch of DNA sequence that likely
marks the precise location of the inactivate centromere. That tract is
characterized by a type of DNA duplication, known as alpha satellite repeats,
that is a hallmark of centromeres. In addition, the tract is flanked by an
unusual abundance of another type of DNA duplication, called a segmental
duplication.
"These data raise the possibility of a new tool
for studying genome evolution. We may be able to find other chromosomes that
have disappeared over the course of time by searching other mammals' DNA for
similar patterns of duplication," said Richard K. Wilson, Ph.D., director
of the Washington University School of Medicine's Genome Sequencing Center and
senior author of the study.
In another intriguing finding, the researchers
identified a messenger RNA (mRNA) transcript from a gene on chromosome 2 that
possibly may produce a protein unique to humans and chimps. Scientists have
tentative evidence that the gene may be used to make a protein in the brain and
the testes. The team also identified "hypervariable" regions in which
genes contain variations that may lead to the production of altered proteins
unique to humans. The functions of the altered proteins are not known, and
researchers emphasized that their findings still require "cautious
evaluation."
In October 2004, the International Human Genome
Sequencing Consortium published its scientific description of the finished
human genome sequence in Nature. Detailed annotations and analyses have
already been published for chromosomes 5, 6, 7, 9, 10, 13, 14, 16, 19, 20, 21,
22, X and Y. Publications describing the remaining chromosomes are forthcoming.
The sequence of chromosomes 2 and 4, as well as the
rest of the human genome sequence, can be accessed through the following public
databases:
GenBank (www.ncbi.nih.gov/Genbank) at NIH's National
Center for Biotechnology Information (NCBI); the UCSC Genome Browser (www.genome.ucsc.edu) at the University of
California at Santa Cruz; the Ensembl Genome Browser (www.ensembl.org) at the Wellcome Trust Sanger
Institute and the EMBL-European Bioinformatics Institute; the DNA Data Bank of
Japan (www.ddbj.nig.ac.jp);
and EMBL-Bank (www.ebi.ac.uk/embl/index.html) at EMBL's
Nucleotide Sequence Database.
NHGRI is one of the 27 institutes and centers at NIH,
an agency of the Department of Health and Human Services. The NHGRI Division of
Extramural Research supports grants for research and for training and career
development at sites nationwide. Additional information about NHGRI can be
found at www.genome.gov.
For more information, contact:Geoff Spencer, NHGRI
(301) 402-0911- spencerg@mail.nih.gov
******
Human genome hits halfway mark
Human chromosomes: Cracking the human code has been a
bit like painting a picture.Four years after publishing a draft of the human
genetic sequence, researchers have hit the halfway mark in producing the
"gold standard" version.
They have just published a detailed run-down of a 12th
chromosome - known as chromosome five - which means there are just 12 left to
complete.
Chromosome five is the largest so far, with 923
recorded genes, of which 66 are involved in human disease.
The chromosome, which was sequenced by US scientists,
is detailed in Nature.
It is the second of
three chromosomes that the Department of Energy Joint Genome Institute (JGI)
has finalised in collaboration with colleagues at the Stanford Human Genome
Center (SHGC)
Code breakers
Cracking the human code has been a bit like painting a
picture. First comes a rough sketch followed by a slightly fuller version
before, finally, the minute detail is added.
When the draft version of the human genome was
unveiled in June 2000, 97% of the "book of life" had been
read. Then, last year, scientists announced the decoding was almost 100%
complete.
Now, several institutions around the world have
divided up the 24 humanchromosomes - the cellular structures into which DNA is
wound - and are going through them with a fine-tooth comb for a final time, to
fill gaps and correct errors.
This extremely
accurate sequence will be a powerful tool for scientists trying to understand
human disease.
Spencer Abraham, Secretary of Energy
They are, as it were, dotting the I's and crossing the
T's and giving the whole sequence a thorough spell-check.
"It
is about getting everything in the right order," commented Dr Tim Hubbard,
of the Human Genetics group at the Sanger Institute in Cambridge, UK.
"In the draft version there were
100,000 gaps in the whole genome. It was a small percentage of the sequence,
but it meant you were uncertain about the order of the pieces.
"It
is important for doing experiments to have the complete sequence - to have no
gaps at all."
********
Giant chromosome
According to researchers at the JGI and SHGC,
the landmark chromosome five is a genetic behemoth, containing key disease
genes and a wealth of information about how humans evolved.
"This extremely accurate sequence
will be a powerful tool for scientists trying to understand human
disease," said US Secretary of Energy, Spencer Abraham.
DNA IN HUMAN CELLS
The double-stranded DNA molecule is held together by
chemical components called basesAdenine (A) bonds with thymine (T); cytosine(C)
bonds with guanine (G)
These letters form the "code of life".
There are estimated to be about 2.9 billion base-pairs in the human genome
wound into 24 distinct bundles, or chromosomes
Written in the DNA are about 30,000 genes, which human
cells use as starting templates to make proteins. These sophisticated molecules
build and maintain our bodies.
The giant chromosome is made up of 180.9 million
letters - A's, T's, G's and C's
that make up the genetic code.
Of the 923 genes that sit on chromosome five, 66
are known to be link to disease when they go wrong. Another 14 diseases seem to
be connected to chromosome five genes, but they have not been linked to
specific genes yet.
Having a detailed
picture of chromosome five will be an immense help to researchers investigating
these illnesses.
"It is very useful
to have a base sequence which you can then compare individuals to," Dr
Hubbard told BBC News Online.
"Then you can look for key
differences between people that do have the disease and people that don't have
the disease."
Another feature of chromosome five will pique the
interest of scientists studying the difference between humans and chimpanzees.
Despite great similarities between the genomes of the
two species, there are some key structural variations.
In particular, one large section of chromosome five is
flipped backwards in humans compared with chimps.
Such an inversion makes it impossible for the two
chromosomes to pair up during reproduction, which could have driven a wedge
between the evolving ancestral populations.
'Junk'
DNA
It is not just the genes in chromosome five that the
scientists are interested in. Volumes of genetic materiallie in between the
genes, which for a long time were dismissed as "junk" by researchers.
But on closer inspection, it seems this judgement was
premature. The fact that sequences of junk were conserved for hundreds of
generations suggests they have a function worth holding on to.
"Important genetic motifs gleaned from vast
stretches of non-coding sequence have been found on chromosome five," said
Eddy Rubin, JGI's director.
"Comparative
studies conducted by our scientists of the vast gene desert... have shown these
regions, conserved across many mammals, actually have a powerful regulatory
influence."
Over the next few months, the remaining 12 human
chromosomes should be completed to a final gold standard of accuracy.
Dr. Hubbard concluded: "Severalgroups are working on the remaining chromosomes - tidying them up - and they should all be complete by the end of the year."
Is it possible that Giant Chromosomes
have brought life to Earth?
As I have stated , the sixth
verse of surah Ana`m states that “God sent down for you eight pairs of An`am ”,
as God is using the word “sent
down”, He is possibly
telling us that the primary source
of life have arrived from interstellar space to Earth in eight pairs of
chromosomes ,this also
confirms modern scientific theories which state that the primary elements of
life have been brought to Earth by comets.
It had been previously expected
that the “Rosetta” research satellite in 2014 will have scientific achievements
for us, but it seems that researchers have not still achieved a desired result.
Because so far I have been unable to find the results of the mission.
Finally, we can also ask the question, are Giant
Chromosomes responsible for turning the primitive man to the modern man? and if
the answer is yes, then will this make Darwin`s evolutionary school in the context
of anthropology crumble.
Note:
The complete
Persian/Farsi text of this article(13 pages), since 2006
has been published in some of the famous Iranian Qur’anic websites under the
title of: چهارپایان
ویژه قرآنی
March 2015- Ahmad Shammazadeh- hmdshmzdeh@gmail.com
Attached paper:
Plant
Polytene Chromosome
Gianna Maria GrizCarvalheira
Laboratَrio de Citogenética Vegetal, ءrea de Genética, Departamento de Biologia, UFRPE,
52171-030 Recife, PE, Brasil. E-mail: carva@elogica.com.br
INTRODUCTION
Polytene chromosomes are structures found in highly specialized tissues
in some animal and plant species, which are amplified through successive cycles
of endoreduplication, finally producing several copies of each chromosome. For
this reason, they have been very important in elucidating chromosome fine
structure and physiology, especially in diptera.
In plants, polytene chromosomes have been observed in only a few
species, and seemed to be restricted to ovary and immature seed tissues, e.g.,
in Phaseoluscoccineus and P. vulgaris (Nagl, 1981), until relatively recently,
when they were observed in the cells of the anther tapetum of Vignaunguiculata
(Guerra and Carvalheira, 1994) and of some Phaseolus species (Carvalheira and
Guerra, 1994). With the discovery of the polytenics in tapetum tissue, it was
observed that in many other species of various angiosperm families the tapetal
cells also display polytene, polyploid or both types of nuclei. In some species
of Phaseolus and Vigna the polytenics are more clearly defined and, therefore,
better suited to the study of this type of chromatin organization. It is,
however, important to differentiate between the nuclear cycles that result in
polyploid nuclei and those that produce polytene nuclei, because these two
terms of the nuclear types are often used indiscriminately in the literature.
In this paper some aspects of the occurrence of plant polytenes will be
summarized along with the structure and function of these chromosomes.
ENDOMITOSIS AND ENDOREDUPLICATION
Nagl et al. (1985) described polytene chromosomes as giant chromosomes
produced by changes in the mitotic cycle during the interphase stage. In such a
modified nuclear cycle, the chromatin duplicates its DNA content during the G1
and S stages, but, instead of passing to the G2 stage, the nucleus initiates a
new G1 phase, thus starting a new cycle of chromatin duplication. This type of
cycle was first described in 1939 by Geitler, as occurring in the somatic cells
of the insect Gerrislateralis (Painter and Reindorp, 1939; D''''''''''''Amato,
1964), and was named the endomitotic cycle because it develops within the
nuclear envelop without either achromatic spindle formation or nuclear or
cellular division (Nagl, 1970a; Brodsky and Uryvaeva, 1985). The term
endomitosis is, however, generally used to describe the formation of both
polyploid and polytene nuclei (q.v. Nagl, 1974). Nagl (1978, 1981, 1987) has
suggested the term endocycle rather than endomitosis, and D''''''''''''Amato
(1984) has adopted the term endomitotic and endoreduplication to distinguish
between those that produce polyploid and polytene nuclei, respectively.
The endomitotic cycle (endomitosis) starts with a normal prophase
(endoprophase), after which the chromosome contracts further (endometaphase),
their sister chromatids separate from each other (endoanaphase) and decondense
to assume the interphase nuclear structure, resulting in polyploid cells, with
double the chromosome number (endopolyploidy) at the end of each cycle. The
essential difference between endomitosis and the normal cell cycle is the
absence of nuclear membrane dissolution in endomitosis, with the whole cycle
occurring inside the nucleus. Such cycles have been observed in the anther
tapetum of some angiosperm species, as in some Passiflora species and in
Papaverrhoeas( Figure 1a ).
The endoreduplication cycle differs from endomitosis because it results
in polytene cells (cells with many identical paired chromatids). In the
endoreduplication cycle, the chromatid number is duplicated, but they do not
segregate, and after various endoreduplication cycles, larger and thicker
chromosomes are produced, called polytenics. In the endoreduplication cycle,
the condensation and decondensation stages are not evident (DAmato 1984, 1989),
except in some cells where it is possible to see the chromocenter dispersion
phase, known as the Z-phase (Nagl, 1970b, 1972; Cavallini et al., 1981).
Depending on the behavior of the sister chromatids, polytene nuclei can
be divided into two structural types. The first, and most well studied, are the
chromosomes of the larval cells of Drosophila, Chironomidae and other diptera
(Ashburner, 1970; Brodsky and Uryvaeva, 1985). These polytenics are
characterized by numerous transverse bands along their linear axis, produced by
the exact pairing of sister chromatids and the intimate association of their
chromomeres (Ashburner, 1970). The somatic pairing of homologous chromosomes
gives the false impression that there has been a decrease in chromosome number,
because each nucleus appears to contain the haploid number of giant
chromosomes.
The other structural type of polytene nuclei also has the grouping of
sister chromatid bundles resulting from several endoreduplication cycles, but
in this case is characterized by the lack of any intimate pairing of the
chromatids ( Figure 1b ). This nucleus type is observed more frequently,
typical examples being found in the gianttrophoblast cells of mammals (Nagl,
1985), the trophocit cells of many insects (Painter and Reindorp, 1939), some
ovary tissues during the development of many angiosperms (Corsi et al., 1973;
Nagl, 1976) and in the anther tapetum of some plant species
(D''''''''''''Amato, 1984; Guerra and Carvalheira, 1994; Carvalheira and
Guerra, 1994, 1998). In these nuclei, which can be recognized both by the large
size of their chromocenters and by the diploid number of polytene chromosomes,
the chromosome number does not appear to be reduced as in polytene-type nuclei.
Another peculiar giant chromosome type, which likewise does not present somatic
pairing, has been found in some ciliates (e.g., Stylonychiamytilus) that have a
macronucleus with polytene chromosomes and a diploid micronucleus (Ammermann,
1971; Ammermann et al., 1974). The polytenics of these ciliates display band and
interband patterns (also seen in Drosophila), but the macronucleus
disintegrates after its development while the micronucleus remains active.
It is interesting to note that the endocycles are not processes of cell
multiplication but are associated with cell differentiation and seem to be
genetically controlled, with both endopolyploidy and polyteny leading to cell
specialization in certain tissues. These nuclei have generally been observed in
ephemeral tissues made up of only a few cells with intense metabolic activity,
the main function of which is to provide nutritional support to vital organs
during certain periods of development (e.g., the larval salivary glands of
insects, the mammalian trophoblasts and the embryo suspensor cells of
angiosperms). In such tissues, the cytoplasmatic volume and nuclei DNA content
of the cells are increased by endomitosis or endoreduplication cycles (Nagl,
1974, 1985; Nagl et al., 1985).
OCCURRENCEOF POLYTENE CHROMOSOMES
Polytene nuclei were first observed in the larval salivary glands of
Chironomidae, by Balbiani in 1881, but only at the beginning of the 1930s did
Heitz and Bauer & Painter, independently and simultaneously, rediscover
these enormous nuclei in the Malpighian tubules of Bibiohortulanus and in the larval
salivary glands of Drosophila melanogaster, respectively (Ashburner, 1970). A
few years later, Koltzoff, in 1934, and Bauer, in 1935, proposed the term
polytenics for the giant chromosomes observed in these nuclei (Ashburner,
1970); polytene cells have since been described in many species (Nagl, 1978;
Brodsky and Uryvaeva, 1985; Carvalheira and Guerra, 1998).
In plants, the first giant nuclei were observed by Osterwalder in 1898,
in the enormous antipodal cells (antipodes) of the embryo sac of Aconitum (Nagl,
1981). However, as with the discovery of the giant cells of Chironomidae, the
antipodal nuclei were largely forgotten for about 60 years. Only in 1956 did
Tschermack-Woess and collaborators, during a reappraisal of the genus Aconitum
genus and other plant species, recognize that the chromosomes observed in the
antipodes were polytenics (Nagl, 1981). Unlike Drosophila polytene chromosomes,
which present numerous bands and interbands, plant polytenics have a granular
and fibril structure with no distinct bands (see Figure 1 ). This structure
probably occurs because of the absence of intimate synapsis between the sister
chromatids. It is also believed that the chromocenter dispersion phase (Z
phase) has some influence on the morphology of plant polytenics, as it results
in a slight separation of these chromatids (Nagl, 1970a). However, Nagl (1969a)
has reported that in Phaseolus vulgaris the structure of polytene chromosomes
of embryo suspensor cells seems to be altered when these cells are submitted to
low temperatures, becoming partly compacted and forming bands similar to those
seen in Drosophila. Such results have not been observed again, remaining the
only report of plant polytenics with bands and interbands.
Since the discovery of the polytene nuclei in antipodes, many other
tissues composed of polytene cells have also been described ( Table I ). It is
interesting to note that, until very recently, the cells with polytene
chromosomes seemed to be limited to ovary tissues (antipodal cells, synergids,
endosperm and embryo suspensor cells); however, polytenics have now been
observed in anther hair, glandular hair and anther tapetal cells ( Table I ).
Polyteny can also be induced in vitro and it has been found that the
meristematic tissues of root tips and the cotyledon cells of some plant species
are able to form polytene chromosomes when submitted to specific treatments,
including high temperatures (Shang and Wang, 1991) or an appropriate amount of
certain growth regulators (mainly auxin and cytocinin) in the medium (Marks and
Davies, 1979; Therman and Murashige, 1984).
POLYTENE CHROMOSOMES OF EMBRYO SUSPENSOR
The most widely studied plant tissues with polytene cells is the
Phaseolus embryo suspensor tissue. This tissue is found in the developing ovary
of several angiosperm species (Esau, 1974). In P. coccineus and P. vulgaris,
the suspensor is composed of about 200 cells, distributed between the basal and
junction regions. The basal region is formed of about 20 giantmononucleate
cells with a high level of polytenization, and with the DNA content of some
cells being up to 8.192 C (Brady, 1973a,b). The junction region is composed of
about 180 cells linking the basal region to the embryo proper. This last region
possesses polyploid cells and/or cells with low polyteny level (Brady and
Clutter, 1974).
The embryo suspensor provides nutritional support for the immature
embryo, supplying proteins or synthesizing the substances necessary for embryo
development (Schulz and Jensen, 1969). The underdevelopment of the cell wall of
suspensor cells and their other structural characteristics indicate their
secretory function in transporting nutrients through their membranes to the
embryo (Nagl, 1974; Cionini, 1987). Analyses of the growth regulator level and
transcription activity indicate that the suspensor tissue may play an important
role during embryo ontogenesis, and seems to have a function in the synthesis
of phytohormones needed for embryo development (Walbot et al., 1972; Clutter et
al., 1974; Alpi et al., 1975; Cionini et al., 1976; Lorenzi et al., 1978).
The basal cells of the embryo suspensor tissue of P. coccineus display
22 polytene chromosomes that are up to 30 times larger than the mitotic ones
(Nagl, 1974), the 11 chromosome pairs having been identified earlier by their
heteropycnosis pattern (Nagl, 1967). All mitotic chromosomes present
heterochromatic centromeric bands and some weak interstitial and terminal ones
(Schweizer and Ambros, 1979). Staining with the fluorochromes CMA and DAPI has
revealed that most of these bands are CMA+, although unlike mitotic bands they
contain a small amount of DAPI+ heterochromatin (Schweizer, 1976). The
difference observed in the fluorescent pattern has been attributed to the
better structural resolution of the giant chromosomes.
In situ hybridization experiments, with isotopic (q.v. Schumann et al.,
1990) and non-isotopic markers (q.v. Nenno et al., 1994), have contributed
considerably to the characterization of polytenics. These techniques have
permitted both the location of many of their DNA sequences and the study of
their replication cycle (Brady and Clutter, 1974). For example, the
cytolocalization of the ribosomal genes in P. coccineus has been demonstrated
by the use of RNAr-H3, revealing RNA puff activity both in satellite pairs and
in the heterochromatin of chromosome pairs, without satellites (Avanzi et al.,
1971, 1972; Durante et al., 1977). Isotopic techniques have also made it
possible to observe the extra nucleoli associated with the telomeres of the
polytenics without satellites, suggesting the existence of amplification in
this region (Nagl, 1973). Actually, the extra DNA synthesis in the polytenics
of the Phaseolus suspensor occurs at the beginning of embryogenesis and not
simultaneously with the endoreduplication cycles (Avanzi et al., 1970). Such
gene amplification can occur both in the ribosomal cistrons and other regions
of the genome and involves some polytene chromosome chromatids (Cremonini and
Cionini, 1977). Some of these amplified regions are released from the
polytenics to form micronucleoli. According to Avanzi et al. (1971), the
micronucleoli are composed of a spherical mass of ribonucleoprotein covered by
a layer of DNA. These micronucleoli seem to be associated with the intense
metabolism of the suspensor basal cells (Nagl, 1973).
With advances in the fluorescence in situ hybridization technique
(FISH), several other sequences have been located in plant polytene chromosomes.
The first genic sequence hybridized in polytenics was that of the phaseolin
group (Schumann et al., 1990; Nenno et al., 1993, 1994). This gene encodes the
main seed storage protein of Phaseolus species. In these papers, it was
demonstrated that the phaseolin gene seems to be located in chromosome 7 of P.
coccineus. Another gene that has been located in the polytenics of P. vulgaris
is the PGIP gene which encodes for polygalacturonase-inhibiting protein, a cell
wall protein that specifically inhibits fungal endopolygalacturonases that are
important during the early stages of plant pathogenesis. The PGIP gene has been
located in a single region of the pericentromeric heterochromatin of the
chromosome pair X, next to the euchromatin (Frediani et al., 1993).
The FISH technique as applied in polytene chromosomes has also been a
useful tool to study gene evolution. Nagl (1991) hybridized telomeric DNA and
the aromatase gene sequence (both from human genome) in P. coccineus and P.
vulgaris polytenics. The results showed that these sequences also hybridize
with plant chromosomes, supporting the hypothesis of the evolutionary
conservation of important coding or non-encoding sequences throughout living
organisms.
POLYTENE CHROMOSOMES OF ANTHER TAPETUM
Polytene chromosomes are also observed in other plant tissues, of which
the anther tapetum tissue has made valuable contributions to the understanding
of polytenics in angiosperms. This tissue is widely conserved, being found in
groups ranging from bryophytes to angiosperms (Pacini and Franchi, 1993).
The tapetum is the innermost layer of the anther wall in close contact
with the pollen grains ( Figure 1c ). It is generally composed of a simple
layer of cells, characterized by the presence of dense cytoplasm and quite a
well-developed nucleus (Echlin, 1971). During the differentiation of the
tapetum, the cells increase both their cytoplasmatic and nuclear volume and
then undergo autolysis and degenerate (Mascarenhas, 1990). The
tapetum''''''''''''s function seems to be related to the maturation of pollen
grain, with biochemical and cytological studies demonstrating the intense
metabolic activity in its cells at the end of the tetrad stage and during exine
formation (Rowley, 1993).
Until recently, most of the information on the nuclear development of
the tapetal cells has come from studies of anther ontogenesis, based on
histological analyses by optical or electronic microscopy. Cytological analyses
in tapetum were done mainly by Cooper (1933), Brown (1949), Oksala and Therman
(1977), Franceschi and Horner (1979), and D''''''''''''Amato (1984, 1989).
However, cytogenetical analysis of the tapetal cells of Vigna species has
revealed that this tissue can present very peculiar characteristics (Guerra and
Carvalheira, 1994). Anther tapetum cells are characterized by the presence of
endomitotic or endoreduplication cycles (Cooper, 1933; D''''''''''''Amato,
1984, 1989; Malallah et al, 1996). In species where the tapetum layer is
composed of mononucleate cells, the increase in DNA content is generally a
consequence of several endoreduplication cycles, while in species with bi- or
multinucleate cells in the tapetum it is the endomitotic cycle which is
responsible. In spite of the endoreduplication cycle producing mononucleate cells,
tapetalbinucleate cells with polytene nuclei have sometimes been observed
(Carvalheira and Guerra, 1994).
In general, at the beginning of meiosis, the tapetal cells are
mononucleate and diploid. During the tapetal differentiation, three cellular
types can be observed, i.e. multinucleate cells, with more than one diploid
nucleus (Malallah et al., 1996), mononucleate cells, with a single polyploid
nuclei (Carvalheira, G.M.G. and Guerra, M., unpublished data), and mono- or
binucleate cells, with one or two polytene nuclei (Carvalheira and Guerra,
1994). In each of these cases, the DNA content per cell is often increased,
suggesting that this tissue needs several copies of most genes to supply
specific substances for exine development and consequent pollen grain
maturation.
The increase in the ploidy level is probably caused either by
suppression of anaphase movement (producing a dumbbell-shaped polyploid
interphase nucleus) or by the occurrence of endomitotic cycles (DAmato, 1989),
while the increase in the number of nuclei per cell is due to the occurrence of
one or more mitosis cycles without cytokinesis, resulting in multinucleate
cells. Polytene nuclei, on the other hand, are formed through the
endoreduplication cycles, and could remain in the interphase stage until the S
phase, or progress to the prophase stage and return to a new G1 phase (Guerra
and Carvalheira, 1994).
Analysis of both ploidy level and nuclear structures in tapetal cells in
genera of several subfamilies has revealed that their chromatin structure may
be constant at the genus level. In the family Scrophulariaceae, for example,
some species of the genera Pedicularis and Melampyrum have tapetal cells with
tetraploid nuclei, in the post-meiotic period. On the other hand, in this same
family, the genera Odontetis, Euphrasia and Bellardia have nuclei with enormous
chromocenters, but with the same ploidy level (Greilhuber, 1974).
Like the other plant tissue with polytene chromosomes, anther tapetum
cells can display polytenics that vary in structure and morphology from species
to species (q.v. Nagl, 1974, 1981; Carvalheira and Guerra, 1994, 1998). For
example, polytene nuclei in the antipodes of Papaverrhoeas were classified by
Nagl (1981) into four different types, i.e., nuclei with chromocenters
associated with radial chromatin bundles; decondensed nuclei with isolated
chromatin fibers; nuclei with condensed chromatin, and nuclei with polytenics
proper. Similar variation was found in suspensor cells of Phaseolus embryos,
where the polytenics sometimes had granular or fibril form, depending on the
degree of contraction in the interchromomeres (Nagl, 1978).
According to Carvalheira and Guerra (1998), the chromatin structure of
the polytene nuclei in tapetal cells may basically be divided into three
different types:
1. Individualized polytene chromosomes whose chromatin bundles are
heteropycnotic in the proximal region and dispersed in the distal region (
Figure 1d ), characteristic of Phaseoluscoccineus, P. vulgaris (Carvalheira and
Guerra, 1994), Vignaunguiculata (Guerra and Carvalheira, 1994; Carvalheira and
Guerra; 1998), V. umbellata, V. radiata (Carvalheira and Guerra, 1998),
Lathyrus and Sesbaniamarginata.
2. Polytene nuclei with chromocenters associated with the chromatin
bundles ( Figure 1e ), found in most of the species analyzed, including
Arachishypogeae, Caesalpineaechinata, Clitoriacajanifolia, Crotalaria retusa,
in three Habenaria species, Luffacylindrica, Macroptiliumpeduncularis, two
Phaseolus species (Carvalheira and Guerra, 1994), Pithecellobiumdulce,
Pisumsativum, Sophoratomentosa, Tropaeolummajus and Zomicarpariedeliana.
3. Polytene nuclei with chromocenters unassociated with chromatin
bundles ( Figure 1f ), a less frequent type, characteristic of Genipaamericana,
Indigoferahirsuta, Lupinuspolyphyllus, Vignavexillata (Carvalheira and Guerra,
1998) and Vicia sp.
Of these three types of chromatin organization, only the first is ideal
for karyological analyses. The polytenics of this group is generally
individualized and condensed. This type of chromatin organization has allowed
good chromosome spreads to be obtained, facilitating the chromosome counting.
In most Phaseolus and Vigna species analyzed that had this type of
organization, it was possible to observe all 22 chromosomes of the karyotype
(q.v. Guerra and Carvalheira, 1994; Carvalheira and Guerra, 1994).
Although this type of chromatin organization seems to be ideal for
karyological analyses, these polytene chromosomes are somewhat smaller than
those observed in the embryo suspensor of Phaseolus or those of some other
genera (compare Figure 1b and d ). The largest polytenics of the anther tapetal
cells (observed in Vignaunguiculata) are about 3.5 times bigger than the
mitotic ones (Guerra and Carvalheira, 1994). The difference in size observed
between polytenics of the embryo suspensor and anther tapetum is probably
related to the number of endoreduplicated cells present in each of these
tissues. As was mentioned previously, only a few basal cells undergo many
endoreduplication cycles in the embryo suspensor tissue (Nagl, 1981), while in
the anther tapetum hundreds of cells undergo this process. The low level of
chromatin endoreduplication associated with a large number of cells seems to satisfy
the metabolic necessities of both the anther tapetum and microspores. On the
other hand, in the giant cell of the embryo suspensor, many endoreduplication
cycles seem to be necessary to maintain the perfect functional and nutritional
stage of the embryo, most of whose nutrients are supplied by the suspensor
cell.
Although the polytenics of the anther tapetum are reduced in size, they
have helped in the cytolocalization of DNA sequences. The first in situ
hybridization in tapetalpolytenics has revealed interesting data different from
that which was observed in the polytene chromosomes of the embryo suspensor
(Guerra and Kenton, 1996). As stated earlier, after in situ hybridization with
the human telomere DNA probe, Nagl (1991) observed that the embryo suspensor
polytenics of Phaseolus show a group of dots or compact bands at the telomeres.
However, when synthetic telomere oligomers were hybridized with
tapetumpolytenics in an amphidiploid hybrid of Phaseolus, the oligo was
preferentially located at, or close to, the chromocenters. These fluorescent
areas were distributed randomly in the nuclear area, although association with
the nuclear boundary was never observed (Guerra and Kenton, 1996). This may
suggest that, at least in some aspects, the basic molecular organization of
diploid nuclei in the anther tapetum is not completely conserved after the
endoreduplication cycles. In fact, the loss of telomere association with the
nuclear membrane has been documented in some special chromosome types, such as
pigeon lampbrush chromosomes (Solovei and Macgregor, 1995) and Dipterapolytenic
chromosomes (Agar and Sedat, 1983). In plant polytene nuclei, however, this
loss of telomeric association with the nuclear envelope was reported for the
first time in anther tapetumpolytenics (Guerra and Kenton, 1996).
These chromosomes have also helped in the identification of the 45S
ribosomal sites in Phaseoluscoccineus and Vignaunguiculata (Guerra et al.,
1996), and 5S sites, in V. radiata and V. unguiculata (Carvalheira et al.,
1998). In P. coccineus, six ribosomal sites were observed in tapetal cells, as
has been reported previously (see Avanzi et al., 1972; Durante et al., 1977).
Surprisingly, however, ten ribosomal sites were observed in V.
unguiculatatapetumpolytenics (Guerra et al., 1996), instead of one or two pairs
as earlier reported (Frahm-Leliveld, 1965; Barone and Saccardo, 1990; Galasso
et al., 1992). The large number of ribosomal sites observed in V. unguiculata
when compared with Phaseolus has suggested that this increase in ribosomal
sites may have been initiated by genetic mechanisms, such as gene conversion.
According to Guerra et al. (1996), the variation in the number of rDNA sites
observed between species of related taxa could be due to the differential amplification
and fixation of rDNA sequences at different chromosomal sites. On the other
hand, four 5S ribosomal sites were observed in V. radiata and V. unguiculata
(Carvalheira et al., 1998), confirming the previous reports for V. unguiculata
(Galasso et al., 1995), although these reports were first published for V.
radiata.
In conclusion, although the polytenics of the anther tapetum are smaller
than those in suspensor cells, both the large number of polytene cells in this
tissue and their structural polytene morphology make these chromosomes more
convenient for the study of plant polyteny and chromosome organization. Guerra
and Carvalheira (1994) and Carvalheira and Guerra (1994, 1998) have suggested
that such chromosomes present cycles of diffuse and condensed stages. The
change from diffuse to condensed stage seems to depend on the endoreduplication
level, genetic background and environmental factors. All these observations
suggest that bundled polytene chromosomes of plants, at least in tapetal cells,
are most probably the consequence of advanced endoreduplication cycles
resulting in prophase or prophase-like chromosomes that may still be able to
perform some DNA and RNA synthesis (Brady and Clutter, 1974; Cionini et al,
1982).
