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Current
Genomics
ISSN: 1389-2029
Current Genomics
Volume 6, Number 8, December 2005
Contents
Mini Hot Topic
Genomic Platforms for “evo-devo”
Guest Editor: Ralf J. Sommer
Editorial Pp. 569-570
Closing the Gap: Comparative Approaches to Studying
Insect Development in the Red Flour Beetle Tribolium castaneum
and Other Short and Intermediate Germ Insects
Pp. 571-578
T.D. Shippy and S.J. Brown
[Abstract]
Harnessing Caenorhabditis Genomics for
Evolutionary Developmental Biology Pp. 579-588
E.S. Haag and D. Pilgrim
[Abstract]
General Articles
Puzzles of the Human Genome: Why Do We Need Our Introns?
Pp. 589-595
L. Fedorova and A. Fedorov
[Abstract]
The Neurotrophic and Antiangiogenic Functions of PEDF:
A Reflection of its Variable Phosphorylation States
Pp. 597-607
G. Maik-Rachline and R. Seger
[Abstract]
Genes Involved in Apoptosis Regulation: Implications
for Cancer Therapy Pp. 609-611
S. Fulda and K.-M. Debatin
[Abstract]
Tyrosine Kinase Receptors Signaling Revealed by Global
Expression Profiles: Implications for Cancer Biology
Pp. 613-618
R.M. Melillo and M. Santoro
[Abstract]
Complex Transcription Mechanisms in Mammalian Genomes
– The Transcriptome of FANTOM3 Pp. 619-625
S. Katayama and Y. Hayashizaki
[Abstract]
Abstracts
[Back to top]
Editorial
Genomic Platforms for “evo-devo”
Much of the knowledge in modern biology is based on studies
of a handful of model organisms, such as the mouse Mus
musculus, the fruit fly Drosophila melanogaster,
the worm Caenorhabditis elegans and the weed Arabidopsis
thaliana [1]. In the last 10 years genomic resources
have revolutionized research in these organisms and provided
precise knowledge of the molecular mechanisms governing fundamental
biological processes: The genome sequence, expression profiling,
large-scale RNA interference and yeast-two hybrid screens
moved biology into the “-omics”-era.
However, these fascinating developments have to be placed
into an evolutionary perspective: All established model organisms
represent just one of many species in a given taxa. For example,
D. melanogaster is one of more than 1000 Drosophila
species and one of more than one million insects [2]. Similarly,
C. elegans is a nematode, but there are an estimated
1-10 million of these mostly very tiny and inconspicuous organisms
[3]. Also, these organisms do not represent the tree of life
in a comprehensive way. Molecular phylogeny suggests that
insects and nematodes, i.e. D. melanogaster and C.
elegans, represent closely related taxa and belong to
a group called Ecdysozoa [4]. At the same time, the other
major branch of the invertebrates, the so-called Lophotrochozoans
including the molluscs and annelids, is not represented by
any model organism at all. A closer look at the phylogeny
reveals yet another problem. Within their groups, model organisms
often belong to highly derived taxa. For example, Drosophila
is a dipteran fly, C. elegans a rhabditid nematode and both
do not represent all of the typical ancestral characters of
insects and nematodes, respectively. Many interesting questions
result from these evolutionary and phylogenetic considerations:
How representative are the selected model organisms? Is what
we find in D. melanogaster true for all other Drosophila
species, or even for all insects? Can we use our knowledge
about the model organisms to reconstruct the evolutionary
history of insects, nematodes or mammals? And finally, what
can we learn about humans when we study vertebrate or even
invertebrate models?
In the late 80th and early 90th, evolutionary
developmental biology was born as a new discipline in developmental
biology. “Evo-devo”, as it is often called, tries
to provide answers to these questions and aims for a developmental
understanding of the evolution of form, morphology and biological
diversity. The idea is simple: Turn away from the well-known
model organisms and study organisms that look similar, but
nonetheless different. With the wealth of Drosophila
knowledge at hand, look into beetles and butterflies. Compare
developmental patterning as known in C. elegans with
other nematode species. Compare the mouse with other mammals,
Xenopus with other frogs and the zebrafish with Medaka. Take
the Arabidopsis data and look into other weeds, trees
and non-flowering plants. Although there was a lot of skepticism
initially, evolutionary developmental biology has passed the
test of time and many exciting research projects are under
way [5].
The idea is simple, that´s true. However, the practical
realization proves rather complicated, as there are many technical
challenges to be faced. In many model organisms, modern research
is based on genetic analysis (Drosophila, C. elegans)
or gene knockout approaches (mouse), tools that are simply
not available in most non-model organisms. Stable DNA-mediated
transformation is standard in Drosophila, C. elegans,
Arabidopsis and the mouse, but is still a problem
in most non-model organisms. And finally, there is no genome
sequence and there are no genome-dependent “-omics”
approaches available in non-model species.
But there is light at the end of the tunnel. Whole genome
sequencing projects are ongoing for many non-model organisms,
including some of the species that have been selected by the
“evo-devo” researchers (http://www.nhgri.nih.gov/12511858).
Similarly, as research communities are growing, important
methods are being developed that help functional studies getting
off the ground. Two review articles in this issue of Current
Genomics cover two prominent animal taxa that are of
great interest for evolutionary developmental biology [6,
7]. The review by Shippy and Brown summarizes insect segmentation
with a focus on the red flour beetle Tribolium castaneum
[6]. Whereas Drosophila has a long germ band with
basically all segments of the animal developing simultaneously,
Tribolium and most other insects have a so-called
short or intermediate germ band; that is, segments develop
consecutively over longer time periods. Haag and Pilgrim discuss
the evolution of sex determination in nematodes primarily
by comparing C. elegans with its relatives Caenorhabditis
briggsae and Caenorhabditis remanei [7].
C. elegans and C. briggsae show a mode of reproduction
that is very unusual for nematodes, they are self-fertilizing
hermaphrodites. Such animals are modified females that generate
a limited number of sperm early in development before they
switch to female development for the rest of their life. In
the laboratory, C. elegans can be kept in the absence
of males simply by self-fertilization. Most nematodes however,
such as C. remanei, are “gonochoristic”
with equal numbers of males and females.
The genomes of T. castaneum and the two Caenorhabditis
species have recently been sequenced and provide a new incentive
for evo-devo researchers in these areas. Shippy and Brown,
as well as Haag and Pilgrim, demonstrate how the genome sequence
and precise information about the gene content of these organisms
can be used to study the evolution of insect segmentation
and the mode of nematode reproduction and sex determination.
They highlight the potential of functional approaches and
show how genomic platforms could provide a new start in the
field of evolutionary developmental biology.
As non-model organisms arrive in the post-genome era, large-scale
whole genome approaches will not be restricted to evolutionary
developmental biology. Many interesting molecular problems
can be tackled in the long run, from the evolution of repetitive
elements and transposons to synteny and genome organization.
Genomes are continuously subjected to modification. Therefore,
the comparison of more closely related species will provide
important insight into genome dynamics and the underlying
mechanisms. With several eukaryotic genomes in hand and several
additional ones to come soon an evolutionary framework is
in reach for many areas of biology, from development and physiology
all the way to genome dynamics itself. The data is there we
just have to use it.
References
[1] Wolpert, L. Principles of development. Oxford
University Press, New York 2002.
[2] Powell, J.R. Progress and prospects in evolutionary
biology: The Drosophila Model. Oxford University Press,
New York 1997.
[3] Blaxter, M. Caenorhabditis elegans is a nematode. Science
1998, 282: 2041-2045.
[4] Aguinaldo, A.A., et al. Evidence for a clade
of nematodes, arthropods and other moulting animals. Nature
1997, 387: 489-493.
[5] Rudel, D., Sommer, R.J. The evolution of developmental
mechanisms. Dev. Biol. 2003, 264:
15-37.
[6] Shippy, T.D., Brown, S.J. Closing the gap: Comparative
approaches to studying insect development in the red flour
beetle Tribolium castaneum and other short and intermediate
germ insects. Current Genomics, 2005,
6: 571-578.
[7] Haag, E.S., Pilgrim, D. Harnessing Caenorhabditis genomics
for evolutionary developmental biology. Current Genomics,
2005, 6: 579-588.
Ralf J. Sommer
Max-Planck Institute for Developmental Biology
Department for Evolutionary Biology
Spemannstrasse 37, D-72076 Tübingen
Germany
E-mail: ralf.sommer@tuebingen.mpg.de
[Back to top]
Closing the Gap: Comparative Approaches to Studying
Insect Development in the Red Flour Beetle Tribolium castaneum
and Other Short and Intermediate Germ Insects
T.D. Shippy and S.J. Brown
The homeotic gene studies of Ed Lewis [1] and the embryonic
patterning studies of Christiane Nüsslein-Volhard and
Eric Wieschaus [2-4] are landmarks of insect developmental
genetics that continue to inspire the work of developmental
geneticists today. The genes they discovered were subsequently
shown to be evolutionarily conserved and are now considered
to be basic components of the genetic toolkit that is deployed
during development in virtually all metazoans, albeit with
specific roles that vary between animal groups. Their systematic
approach, which combined the power of genetics with molecular
and experimental biology, established Drosophila as a premier
model organism for developmental studies. Pioneering work
in the field of evo-devo (evolution of development) extended
the Drosophila studies to other insect and arthropod groups
to determine the extent to which these genes and their regulatory
networks have general applications to insect development or
reflect the unique phylogenetic history of the Diptera. The
systematic approach that has been so successful in Drosophila
has been applied in other insects that are amenable to genetic
manipulation, perhaps most successfully in the genetic analysis
of homeotic genes in the red flour beetle, Tribolium casta-neum.
However, most non-drosophilid insects are difficult to rear
in the lab or are not candidates for facile genetic analysis.
As a result, comparative studies are often limited to inferring
function from the expression patterns of candidate genes.
There is hope, however, of narrowing the gap in technical
sophistication that separates Drosophila from other insects.
Recently, the reverse genetics technique of RNA interference
(RNAi) has made it possible to determine gene function even
in the absence of mutants. Moreover, the genomic sequence
of several insects, including Tribolium, will soon be available.
Here we review recent advances in the study of insect development
made possible by RNAi analysis, which have whetted our appetites
for the large-scale comparative genomic approaches that will
soon be possible.
[Back to top]
Harnessing Caenorhabditis Genomics for Evolutionary
Developmental Biology
E.S. Haag and D. Pilgrim
The genome sequence of the nematode C. elegans transformed
the study of this important research organism in countless
ways. In this paper, we outline the equally great impact it
has had on evolutionary developmental biology, with an emphasis
on sex determination. Sex determination is a compelling area
for comparative studies in Caenorhabditis for two
reasons. First, striking differences in reproductive mode
(gonochorism vs. androdioecy) are seen even between
sister species, and these depend at some level on changes
in the regulation of sex determination. Second, as an early
and continually active area of C. elegans research,
many molecular mechanisms are known that suggest hypotheses
about how these reproductive modes differ from each other.
Testing these hypotheses has required development of genomic
resources for several non-elegans species of Caenorhabditis.
Much progress has been made on this front, and several other
major projects are currently underway. With these tools in
hand, both reverse genetic approaches (RNA interference, cross-species
transformation, gene knockouts) and forward genetic screens
can be employed in multiple species in the genus. While much
remains to be learned, some major surprises have already emerged.
One is that the molecular evolution of interacting sex-determining
proteins is characterized by rapid compensatory evolution.
Another is that outwardly similar hermaphroditic species of
Caenorhabditis may have gained this important reproductive
adaptation in parallel via distinct germline modifications
of the ancestral sex determination pathway. These results
provide insights into how nematode mating systems evolve,
and important context in which to refine our understanding
of the C. elegans model whose characterization made
it all possible.
[Back to top]
Puzzles of the Human Genome: Why Do We Need Our Introns?
L. Fedorova and A. Fedorov
Ninety five percent of human genomic DNA does not code for
proteins or functional RNA molecules, and is frequently referred
to as “junk” or “selfish” DNA. The
vast majority of this noncoding DNA has no documented role
in the cell. However, according to recent analyses, three
quarters of the human genome is transcriptionally active.
We discuss whether the expression of non-coding genomic sequences
is valuable for the cell or if it is a second-hand “junk”
because of the incompleteness in transcriptional machinery
organization and functioning. Introns constitute a major fraction
of the noncoding DNA, representing over 40% of mammalian genomes.
They are ambivalent elements that cause several problems and
at the same time bring benefits to their host cells. There
is a strong correspondence between the average length of introns
and the size of the genome. Here we review the latest summary
statistics on human introns, the evolution of introns in mammals,
and the distribution of genes that encode functional RNAs
within introns. We also suggest that splicing is an important
filter for organisms with large genomes, serving to distinguish
between functional mRNAs and arbitrary RNA transcripts generated
from random loci.
[Back to top]
The Neurotrophic and Antiangiogenic Functions of PEDF:
A Reflection of its Variable Phosphorylation States
G. Maik-Rachline and R. Seger
The pigment epithelium-derived factor (PEDF) is a non-inhibitory
serpin, which is expressed mainly in the eye, but was also
reported to be present in the adult human brain, spinal cord
and plasma. It is characterized as a neurotrophic/neuroprotective
factor and one of the most potent natural inhibitors of angiogenesis
in the eye, where it plays a physiological regulatory role
in retinal angiogenesis. In this review we describe the expression,
structure-function relationships, biological activities and
regulation of PEDF. In addition, we emphasize our recent findings
on the role of extracellular phosphorylation in PEDF activity,
and show that the neurotrophic and antiangiogenic functions
of PEDF are highly influenced by its phosphorylation state.
Hence, phosphorylation of PEDF may be one of the modes that
determine its specific physiological outcome.
[Back to top]
Genes Involved in Apoptosis Regulation: Implications
for Cancer Therapy
S. Fulda and K.-M. Debatin
Apoptosis, the cell’s intrinsic death program, plays
an important role in the regulation of tissue homeostasis.
Also, killing of cancer cells by various cytotoxic approaches
such as anticancer drugs, γ-irradiation,
suicide genes or immunotherapy, is predominantly mediated
through induction of apoptosis in target cells. Understanding
the molecular events that regulate apoptosis and how tumor
cells evade apoptotic deletion have provided a paradigm to
link cancer genetics and response to cancer therapy. Thus,
insights into the mechanisms regulating drug-induced apoptosis
provide rational targets for novel therapeutic interventions.
[Back to top]
Tyrosine Kinase Receptors Signaling Revealed by Global
Expression Profiles: Implications for Cancer Biology
R.M. Melillo and M. Santoro
Increasing numbers of human diseases involve mutations, misexpression
or malfunctioning of receptor protein tyrosine kinases (RTK).
In particular, human cancers are often characterized by altered
RTK function, due to different genetic causes. Identification
of the gene expression program triggered by (RTKs) is essential
to clarify the molecular basis of their biological activities.
Intracellular signals of RTKs are initiated by specific tyrosines
which, when auto-phosphorylated, recruit signal transducers.
How the activation of different signaling pathways is translated
into a certain pattern of gene expression is currently unknown.
Recently, scientists have tried to answer this question applying
DNA microarrays technology using wild-type and mutant RTKs
transiently stimulated with their cognate growth factors.
The transcriptional response to chronic stimulation of cells
upon ectopic expression of oncogenic RTKs has also been investigated
through DNA microarrays. The results obtained recently in
this field, with their possible implication in cancer development
and their impact on cancer diagnosis and treatment will be
discussed.
[Back to top]
Complex Transcription Mechanisms in Mammalian Genomes
– The Transcriptome of FANTOM3
S. Katayama and Y. Hayashizaki
Systematic analysis of a biological system requires elucidation
of its components. However, genome sequencing is only the
first step; any analysis of transcription control and further
functional genomics require the identification of all transcribed
transcripts. FANTOM is the international consortium for the
“functional annotation of mouse” or the “functional
annotation of mammals”, and produces data for analyzing
the human and mouse transcriptome. To gain a substantial overview,
FANTOM3, which is our latest milestone, has provided not only
additional mouse full-length cDNAs, but also four datasets
using new or familiar technologies; 1) 102,801 fully-sequenced
and annotated cDNAs, derived from 237 full-length cDNA libraries;
2) 722,642 5’-ESTs and 1,578,613 3’-ESTs; 3) 7,151,511
mapped CAGE tags from 145 mouse libraries and 3,106,472 CAGE
tags mapped from 24 human libraries, for identifying not only
the precise start sites of transcription, but also relative
expression and promoter usage; 4) 118,594 GIS and 968,201
GSC mapped ditags from four GIS and four GSC libraries for
identifying the precise transcribed regions. Mapping of these
transcripts drew the outline of the complex antisense transcription
network on the genome, and many putative noncoding transcripts
were shown to participate in such sense-antisense paring.
Both sense and antisense transcripts tended to be co-expressed,
and some transcripts influenced the copy number of the opposite
transcript. Several previous studies using different cDNA
synthesizing methods or microarray tiling experiments achieved
the same results in other species, showing that the complex
transcription and regulation by antisense transcription is
a common feature in higher eukaryote genomes. |
