Stress and Aging Pp. 1-10
[Abstract] [Full text article]
Validating Computer Programs
for Functional Genomics in Gene Regulatory Regions Pp. 11-27.
[Abstract] [Full text article]
The Origin, Development and Present Status
of the Concept of the Gene: A Short Historical Account of the Discoverieså Pp. 29-40
Petter Portin
[Abstract] [Full text article]
DNA
Methylation and Breast Cancer Pp. 41-58
1T. Ferguson
and S. J. Nass
[Abstract] [Full text article]
Mammalian Homologues of the Drosophila melanogaster flightless I
Gene Involved in Early Development
Pp. 59-70
H. D. Campbell, I. G. Young, and K. I.
Matthaei
[Abstract] [Full text article]
Chromosomal Abnormalities,
Cancer and Mouse Models: The Critical Role of Translocation-Associated Genes in
Human Cancer Pp. 71-80
I. Sánchez-García
[Abstract] [Full text article]
The CMT1A-REP Binary Repeat:
from Disease Causing Genomic Re-arrangements to a Role in Gene Evolution Pp. 81-90
M. L.
Kennerson, N. T. Nassif, and G. A. Nicholson
[Abstract]
The Human Aquaporin Gene
Family Pp.
91-102
Baoxue Yang
[Abstract] [Full text article]
Current Gene Therapy
Strategies for Colorectal Cancer Pp.
103-115
Rachel
Hargest
[Abstract] [Full text article]
[Back to top] Stress and
Aging
Ken-ichi Isobe
This review focuses on the stress responses and host defense systems, which affect the aging process. Various kinds of external stresses such as heat shock, UV, X-ray, drugs, infection or internal stresses such as reactive oxygen species (ROS) generated by metabolism induce damages to nucleic acids and proteins. Several long-lived mutants have been established in C. elegans, all of which are resistant to environmental stresses. In humans, individuals with Werner’s syndrome show early senescence. The affected gene was cloned and found to be one of DNA helicase, which may work as a repair enzyme following DNA injurious stress. DNA-damaging stresses such as alkylating agents, UV or radiation induce p53 protein expression. Enhanced expression of the p53 protein promotes DNA repair, cell-cycle arrest or apoptosis. The development and aging of the immune system were accelerated in p53-deficient mice. The defects of the repair system induce premature aging, and longevity may depend on the strength of the defense system. Senescent human diploid fibroblasts (HDL) contain elevated amounts of the cyclin-dependent kinase inhibitor p21WAF1 (p21), which has been shown to induce cell-cycle arrest. It has been shown recently that the histone deacetylase inhibitors, sodium butyrate and trichostatin A, induce a cellular senescence-like phenotype in NIH3T3 cells or HDL and enhance p21 promoter activity. We suffer from oxidative stress under normal physiological conditions. It was to counteract such oxidative stresses that mammals developed a defense system. The major enzymes to catalyze oxygen radicals are SOD, catalase and glutathion peroxidase. The expression of Mn-SOD was shown to be induced by infectious stress. We favor the hypothesis that longevity may depend on the strength of these defense systems.
[Back
to top] Validating
Computer Programs for Functional Genomics in Gene Regulatory Regions
L. Florea,
M. Li, C. Riemer, B. Giardine, W. Miller R. Hardison
In the field of functional genomics, many computer programs are being implemented to find DNA sequences that are candidates for coding proteins, regulating gene expression or playing some other important role. Many such programs have adjustable parameters whose chosen values dramatically affect the output. Attempts to optimize such parameter settings involve establishing an appropriate reference data set and evaluating the results obtained with the programs over a reasonable range of parameter values varied in small intervals. Within the context of automated searches for candidate gene regulatory regions in mammals and bacteria, we discuss problems and progress in (i) building such reference data sets, and (ii) defining appropriate cost functions..
[Back
to top] The
Origin, Development and Present Status of the Concept of the Gene: A Short
Historical Account of the Discoverieså
Petter
Portin
The classical view of the gene prevailing during the
1910Æs and 1930Æs comprehended the gene as the indivisible unit of genetic
transmission, genetic recombination, gene mutation and gene function. The
discovery of intragenic recombination in the early 1940Æs led to the neoclassical
concept of the gene, which prevailed until the 1970Æs. In this view the gene
or cistron, as it was now called, was divided into its constituent parts, the mutons and recons materially identified
as nucleotides. Each cistron was believed to be responsible for the synthesis
of one single mRNA and concurrently for one single polypeptide. The discoveries
of DNA technology, beginning in the early 1970Æs, have led to the second revolution
in the concept of the gene in which none of the classical or neoclassical
criteria for the definition of the gene hold strictly true. These are the
discoveries concerning gene repetition and overlapping, movable genes, complex
promoters, multiple polyadenylation sites, polyprotein genes, editing of the
primary transcript and gene nesting. Thus, despite the fact that our comprehension
of the structure and organization of the genetic material has greatly increased,
we are left with a rather abstract, open and general concept of the gene.
.
[Back
to top] DNA Methylation and Breast Cancer
A.T.
Ferguson and S. J. Nass
Traditionally, scientists have focused on structural changes in DNA sequences, such as mutations and deletions, as the cause for altered patterns of gene expression in human cancer. However, a recent explosion of studies indicates that epigenetic changes can be equally important in controlling gene expression. For example, global changes in DNA methylation occur during the progression of breast cancer. These changes include hypomethylation and hypermethylation of chromosomal regions and specific genes that are implicated in the genesis of breast cancer. As an example, we will pay particular attention to two genes, estrogen and progesterone receptor, which have long been associated with breast cancer initiation and progression. Identifying and characterizing these epigenetic modifications may lead to improvements in early detection, prognosis and design of novel therapies for a disease that is one of the leading causes of cancer death among women. This review will describe the changes in DNA methylation that have been identified in breast cancer thus far, and their functional consequences, including gene silencing, uncontrolled cell growth, genomic instability and hypermutability. Further, we will discuss the clinical ramifications of these findings.
[Back
to top] Mammalian
Homologues of the Drosophila melanogaster
flightless I Gene Involved in Early Development
H. D. Campbell, I. G. Young, and K. I. Matthaei
The many obvious differences
between simple and more complex multicellular organisms mask the extraordinarily
high degree of conservation of the basic life processes and the proteins involved
in them. The evolutionary conservation of many essential genes allows knowledge
gained from mutational studies in simpler organisms to be used to identify
the corresponding genes in mammals. The function of mammalian homologues can
then be investigated by gene targeting in mice. Early development in the fruitfly
Drosophila melanogaster
is far more accessible to investigation than corresponding mammalian processes
and many interesting genes involved in early development in this organism
have been identified and isolated. Embryos carrying null alleles of the Drosophila melanogaster flightless
I (fliI) gene exhibit only partial
cellularization and gastrulation fails. Weak alleles of fliI result in adult flies lacking flight
ability and exhibiting abnormal indirect flight muscle ultrastructure. The
fliI gene was positionally cloned
and the predicted protein of 1256 amino acids found to contain leucine-rich-repeat
(LRR) and gelsolin-like domains. Homologues of fliI have subsequently been cloned from
C. elegans, human (FLII) and mouse (Fliih)
via PCR. FLII maps to 17p11.2, into
a region affected in Smith-Magenis syndrome and in childhood primitive neuroectodermal
tumours. The gelsolin domain interacts with G-actin in a Ca2+-independent
manner, and has F-actin binding and severing activities. FLAP1 and FLAP2,
novel ligands for the LRR domain detected in the yeast two-hybrid system,
are derived from related mammalian genes. FLAP2 has been independently reported
as an HIV-1 TAR RNA binding protein and as a transcriptional repressor. The
LRR has been shown to interact with Ras both in vitro, and in vivo in yeast.
Genomics-based studies on fliI and
its homologues have opened up their involvement in a novel pathway of cytoskeletal
regulation which appears to play an essential role in early development.
[Back to top]
Chromosomal Abnormalities,
Cancer and Mouse Models: The Critical Role of Translocation-Associated Genes
in Human Cancer
I. Sánchez-García
Cancer
results from subversion of the processes that control the normal growth, location
and mortality of cells. This loss of normal control mechanisms arises from
the acquisition of mutations in three broad categories of genes: proto-oncogenes,
tumor suppressor genes and DNA repair enzymes. Proto-oncogene activation may
occur by mutation, gene amplification or DNA rearrangement. Chromosomal translocations
entail the generation of gene fusions in both haematopoietic and solid mesenquimal
tumors. Despite the successful identification of these specific and consistent
genetic events, the nature of the intimate association between the gene fusion
and the resulting phenotype is pending to understand. The application of transgenic
methods to the study of these cancer-associated gene fusions have provided
insights into their in vivo functions and suggested mechanisms
by which lineage selection may be achieved. Herein these studies are reviewed
to illustrate how manipulation of their loci in the mouse have contributed
to current understanding in unique and unexpected ways.
[Back
to top] The CMT1A-REP
Binary Repeat: from Disease Causing Genomic Re-arrangements to a Role in Gene
Evolution
M. L. Kennerson,
N. T. Nassif, and G. A. Nicholson
The CMT1A-REP binary repeat consists of two homologous regions of DNA, a proximal CMT1A-REP element and a distal CMT1A-REP element, that flank a 1.5 Mb DNA segment on chromosome 17p11.2-p12. Misalignment between sequences within the two elements of this binary repeat during homologous recombination causes two inherited peripheral neuropathies, Charcot-Marie-Tooth type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP). Despite contributing to the instability of this region of chromosome 17, CMT1A-REP is maintained as a binary repeat in chimpanzees and all human populations of different ethnic origin. Two genes mapping wholly, or partially, within the binary repeat have been recently identified. The distal CMT1A-REP element is known to lie within the COX10 gene and a duplicated ‘pseudo’ exon of this gene is present in the proximal CMT1A-REP element. A second gene, C17ORF1A, localises partially within the proximal CMT1A-REP element. This gene includes the duplicated COX10 exon and part of the flanking intronic sequences within its coding region. The sequences derived from the COX10 gene form part of the open reading frame and 3’ untranslated region of C17ORF1A by the utilisation of the opposite DNA strand to that used in the COX10 gene. The antisense nature of C17ORF1A raises the possibility of C17ORF1A acting as a down regulator of the COX10 gene. This review will highlight the unique features of this disease-causing repeat and its role in the formation of a previously undescribed gene that appears to be present only in humans and primates.
.[Back
to top] The Human Aquaporin Gene Family
Baoxue Yang
Aquaporin (AQP) water channel proteins are responsible for osmotically driven water transport across cell membranes of mammalian tissues, lower animals and plants. Recently, the cDNAs encoding ten mammalian AQPs with widely different tissue expression patterns have been cloned. This article reviews the recent progress in molecular cloning, gene organization, chromosomal localization and mutations of human AQPs. Sequence and genomic structure analyses indicate that the AQP gene family contains at least three subgroup. AQPs 0, 1, 2, 4, 5 and 6 have 40-50 % amino acid homology and their genes contain 4 exons. AQPs 3, 7 and 9 belong to distinct subfamily that contains 6 exons and functions as transporters of small neutral solutes as well as water. AQP8 belongs to the third subgroup with unique exon-intron boundaries. Mutations in AQP2 cause human nephrogenic diabetes insipidus (NDI). The understanding of AQP genetics is important in studying the pathogenesis of diseases related AQP disorders and finding new targets for therapy.
[Back to top] Current Gene Therapy Strategies for Colorectal Cancer
Rachel
Hargest
Colorectal cancer is one of the commonest cancers worldwide and despite improvements in surgery, radiotherapy and chemotherapy the overall five year survival is around 50%. Therefore, novel treatments need to be developed in order to add to the therapeutic armamentarium. Gene therapy is a promising new modality of treatment which can be used in combination with existing therapies. Current gene therapy strategies usually involve the use of interventional genetic techniques to enhance the immunological response to a tumour or to deliver cytotoxic agents to tumour cells. Such strategies can be used alone or in combination and are being explored in a number of clinical trials. More recently, attempts to correct some of the underlying genetic abnormalities in various cancers have been made. The genetic changes which lead to the development of colorectal cancer are well described and, therefore, may be amenable to correction. Replacement of tumour suppressor genes such as p53 has been shown to reverse phenotypic changes in animal models and has been licensed for human use in clinical trials. This technique appears to be safe in the small number of patients treated, thus far and several tumour responses have been demonstrated. Prophylactic treatment with tumour suppressor genes for individuals at high risk of developing colorectal cancer, such as those with familial adenomatous polyposis, may prove beneficial in preventing or delaying the onset of malignant change. The search for safer and more efficient gene delivery vectors continues since traditional adenovirus, retrovirus and plasmids are beset by problems of safety or efficiency. The ultimate gene delivery vector is likely to be a human artificial chromosome which would allow delivery of a large number of genes together with their controlling sequences. Colorectal cancer is a disease which can be attacked by a number of genetic mechanisms in order to kill tumour cells directly, prevent further growth and enhance the anti-tumour immune response. Clinical protocols need to move from the stage of small clinical trials to mass application and it is likely that improved gene delivery vectors will be necessary in order for this to occur.