Current Genomics

ISSN: 1389-2029

Current Genomics
Volume 9, Number 3, May 2008

Contents


Haploinsufficiency of DNA Damage Response Genes and their Potential Influence in Human Genomic Disorders Pp. 137-146
M. O’Driscoll
[Abstract]


Drosophila Lethal Giant Larvae Neoplastic Mutant as a Genetic Tool for Cancer Modeling Pp. 147-154
F. Froldi, M. Ziosi, G. Tomba, F. Parisi, F. Garoia, A. Pession and D. Grifoni
[Abstract]


Simulation of Genomes: A Review Pp. 155-159
A. Carvajal-Rodríguez
[Abstract]


Molecular Mechanisms of Inherited Arrhythmias Pp. 160-168
C.M. Wolf and C.I. Berul
[Abstract]


Genome Analysis of Food Grade Lactic Acid-Producing Bacteria: From Basics to Applications Pp. 169-183
B. Mayo, D. van Sinderen and M. Ventura
[Abstract]


A Survey of Chloroplast Protein Kinases and Phosphatases in Arabidopsis thaliana Pp. 184-190
I. Schliebner, M. Pribil, J. Zühlke, A. Dietzmann and D. Leister
[Abstract]


Analysis of the Fragile X Trinucleotide Repeat in Basques: Association of Premutation and Intermediate Sizes, Anchoring AGGs and Linked Microsatellites with Unstable Alleles Pp. 191-199
M.I. Arrieta, J.M. Ramírez, M. Télez, P. Flores, B. Criado, M. Barasoain, I. Huerta and A.J. González
[Abstract]


Oncogenomic Approaches in Exploring Gain of Function of Mutant p53 Pp. 200-207
S. Donzelli, F. Biagioni, F. Fausti, S. Strano, G. Fontemaggi and G. Blandino
[Abstract]


Modeling the Genetic Control of HIV-1 Dynamics After Highly Active Antiretroviral Therapy Pp. 208-211
C-X. Ma, Y. Li and R. Wu
[Abstract]




Abstracts


[Back to top]
Haploinsufficiency of DNA Damage Response Genes and their Potential Influence in Human Genomic Disorders
M. O’Driscoll

Genomic disorders are a clinically diverse group of conditions caused by gain, loss or re-orientation of a genomic region containing dosage-sensitive genes. One class of genomic disorder is caused by hemizygous deletions resulting in haploinsufficiency of a single or, more usually, several genes. For example, the heterozygous contiguous gene deletion on chromosome 22q11.2 causing DiGeorge syndrome involves at least 20-30 genes. Determining how the copy number variation (CNV) affects human variation and contributes to the aetiology and progression of various genomic disorders represents important questions for the future. Here, I will discuss the functional significance of one form of CNV, haploinsufficiency (i.e. loss of a gene copy), of DNA damage response components and its association with certain genomic disorders. There is increasing evidence that haploinsufficiency for certain genes encoding key players in the cells response to DNA damage, particularly those of the Ataxia Telangiectasia and Rad3-related (ATR)-pathway, has a functional impact. I will review this evidence and present examples of some well known clinically similar genomic disorders that have recently been shown to be defective in the ATR-dependent DNA damage response. Finally, I will discuss the potential implications of a haploinsufficiency-induced defective DNA damage response for the clinical management of certain human genomic disorders.


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Drosophila Lethal Giant Larvae Neoplastic Mutant as a Genetic Tool for Cancer Modeling
F. Froldi, M. Ziosi, G. Tomba, F. Parisi, F. Garoia, A. Pession and D. Grifoni

Drosophila lethal giant larvae (lgl) is a tumour suppressor gene whose function in establishing apical-basal cell polarity as well as in exerting proliferation control in epithelial tissues is conserved between flies and mammals. Individuals bearing lgl null mutations show a gradual loss of tissue architecture and an extended larval life in which cell proliferation never ceases and no differentiation occurs, resulting in prepupal lethality. When tissues from those individuals are transplanted into adult normal recipients, a subset of cells, possibly the cancer stem units, are again able to proliferate and give rise to metastases which migrate to distant sites killing the host. This phenotype closely resembles that of mammalian epithelial cancers, in which loss of cell polarity is one of the hallmarks of a malignant, metastatic behaviour associated with poor prognosis. Lgl protein shares with its human counterpart Human giant larvae-1 (Hugl-1) significant stretches of sequence similarity that we demonstrated to translate into a complete functional conservation, pointing out a role in cell proliferation control and tumorigenesis also for the human homologue. The functional conservation and the power of fly genetics, that allows the researcher to manipulate the fly genome at a level of precision that exceeds that of any other multicellular genetic system, make this Drosophila mutant a very suitable model in which to investigate the mechanisms underlying epithelial tumour formation, progression and metastatisation. In this review, we will summarise the results obtained in these later years using this model for the study of cancer biology. Moreover, we will discuss how recent advances in developmental genetics techniques have succeeded in enhancing the similarities between fly and human tumorigenesis, giving Drosophila a pivotal role in the study of such a complex genetic disease.


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Simulation of Genomes: A Review
A. Carvajal-Rodríguez

There is an increasing role of population genetics in human genetic research linking empirical observations with hypotheses about sequence variation due to historical and evolutionary causes. In addition, the data sets are increasing in size, with genome-wide data becoming a common place in many empirical studies. As far as more information is available, it becomes clear that simplest hypotheses are not consistent with data. Simulations will provide the key tool to contrast complex hypotheses on real data by generating simulated data under the hypothetical historical and evolutionary conditions that we want to contrast. Undoubtedly, developing tools for simulating large sequences that at the same time allow simulate natural selection, recombination and complex demography patterns will be of great interest in order to better understanding the trace left on the DNA by different interacting evolutionary forces. Simulation tools will be also essential to evaluate the sampling properties of any statistics used on genome-wide association studies and to compare performance of methods applied at genome-wide scales. Several recent simulation tools have been developed. Here, we review some of the currently existing simulators which allow for efficient simulation of large sequences on complex evolutionary scenarios. In addition, we will point out future directions in this field which are already a key part of the current research in evolutionary biology and it seems that it will be a primary tool in the future research of genome and postgenomic biology.


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Molecular Mechanisms of Inherited Arrhythmias
C.M. Wolf and C.I. Berul

Inherited arrhythmias and conduction system diseases are known causes of sudden cardiac death and are responsible for significant mortality and morbidity in patients with congenital heart disease and electrical disorders. Knowledge derived from human genetics and studies in animal models have led to the discovery of multiple molecular defects responsible for arrhythmogenesis. This review summarizes the molecular basis of inherited arrhythmias in structurally normal and altered hearts.

On the cellular and molecular levels, minor disturbances can provoke severe arrhythmias. Ion channels are responsible for the initiation and propagation of the action potential within the cardiomyocyte. Structural heart diseases, such as hypertrophic or dilated cardiomyopathies, increase the likelihood of cardiac electrical abnormalities. Ion channels can also be up or down-regulated in congenital heart disease, altering action potential cellular properties and therefore triggering arrhythmias. Conduction velocities may be inhomogeneously altered if connexin function, density or distribution changes.

Another important group of electrophysiologic diseases is the heterogeneous category of inherited arrhythmias in the structurally normal heart, with a propensity to sudden cardiac death. There have been many recent relevant discoveries that help explain the molecular and functional mechanisms of long QT syndrome, Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia, and other electrical myopathies. Identification of molecular pathways allows the identification of new therapeutic targets, for both disease palliation and cure. As more disease-causing mutations are identified and genotypic-phenotypic correlation is defined, families can be screened prior to symptom-onset and patients may potentially be treated in a genotype-specific manner, opening the doors of cardiac electrophysiology to the emerging field of pharmacogenomics.


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Genome Analysis of Food Grade Lactic Acid-Producing Bacteria: From Basics to Applications
B. Mayo, D. van Sinderen and M. Ventura

Whole-genome sequencing has revolutionized and accelerated scientific research that aims to study the genetics, biochemistry and molecular biology of bacteria. Lactic acid-producing bacteria, which include lactic acid bacteria (LAB) and bifidobacteria, are typically Gram-positive, catalase-negative organisms, which occupy a wide range of natural plant- and animal-associated environments. LAB species are frequently involved in the transformation of perishable raw materials into more stable, pleasant, palatable and safe fermented food products. LAB and bifidobacteria are also found among the resident microbiota of the gastrointestinal and/or genitourinary tracts of vertebrates, where they are believed to exert health-promoting effects. At present, the genomes of more than 20 LAB and bifidobacterial species have been completely sequenced. Their genome content reflects its specific metabolism, physiology, biosynthetic capabilities, and adaptability to varying conditions and environments. The typical LAB/bifidobacterial genome is relatively small (from 1.7 to 3.3 Mb) and thus harbors a limited assortment of genes (from around 1,600 to over 3,000). These small genomes code for a broad array of transporters for efficient carbon and nitrogen assimilation from the nutritionally-rich niches they usually inhabit, and specify a rather limited range of biosynthetic and degrading capabilities. The variation in the number of genes suggests that the genome evolution of each of these bacterial groups involved the processes of extensive gene loss from their particular ancestor, diversification of certain common biological activities through gene duplication, and acquisition of key functions via horizontal gene transfer. The availability of genome sequences is expected to revolutionize the exploitation of the metabolic potential of LAB and bifidobacteria, improving their use in bioprocessing and their utilization in biotechnological and health-related applications.


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A Survey of Chloroplast Protein Kinases and Phosphatases in Arabidopsis thaliana
I. Schliebner, M. Pribil, J. Zühlke, A. Dietzmann and D. Leister

Protein phosphorylation is a major mode of regulation of metabolism, gene expression and cell architecture. In chloroplasts, reversible phosphorylation of proteins is known to regulate a number of prominent processes, for instance photosynthesis, gene expression and starch metabolism. The complements of the involved chloroplast protein kinases (cpPKs) and phosphatases (cpPPs) are largely unknown, except 6 proteins (4 cpPKs and 2 cpPPs) which have been experimentally identified so far. We employed combinations of programs predicting N-terminal chloroplast transit peptides (cTPs) to identify 45 tentative cpPKs and 21 tentative cpPPs. However, test sets of 9 tentative cpPKs and 13 tentative cpPPs contain only 2 and 7 genuine cpPKs and cpPPs, respectively, based on experimental subcellular localization of their N-termini fused to the reporter protein RFP. Taken together, the set of enzymes known to be involved in the reversible phosphorylation of chloroplast proteins in A. thaliana comprises altogether now 6 cpPKs and 9 cpPPs, the function of which needs to be determined in future by functional genomics approaches. This includes the calcium-regulated PK CIPK13 which we found to be located in the chloroplast, indicating that calcium-dependent signal transduction pathways also operate in this organelle.


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Analysis of the Fragile X Trinucleotide Repeat in Basques: Association of Premutation and Intermediate Sizes, Anchoring AGGs and Linked Microsatellites with Unstable Alleles
M.I. Arrieta, J.M. Ramírez, M. Télez, P. Flores, B. Criado, M. Barasoain, I. Huerta and A.J. González

Fragile X Syndrome (FXS) is associated with an unstable CGG repeat sequence in the 5’ untranslated region in the first exon of the FMR1 gene which resides at chromosome position Xq27.3 and is coincident with the fragile site FRAXA. The CGG sequence is polymorphic with respect to size and purity of the repeat. Interpopulation variation in the polymorphism of the FMR1 gene and consequently, in the predisposition to FXS due to the prevalence of certain unstable alleles has been observed. Spanish Basque population is distributed among narrow valleys in northeastern Spain with little migration between them until recently. This characteristic may have had an effect on allelic frequency distributions. We had previously reported preliminary data on the existence of FMR1 allele differences between two Basque valleys (Markina and Arratia). In the present work we extended the study to Uribe, Gernika, Durango, Goierri and Larraun, another five isolated valleys enclosing the whole area within the Spanish Basque region. We analyzed the prevalence of FMR1 premutated and intermediate/grey zone alleles. With the aim to complete the previous investigation about the stability of the Fragile X CGG repeat in Basque valleys, we also analyzed the existence of potentially unstable alleles, not only in relation with size and purity of CGG repeat but also in relation with DXS548 and FRAXAC1 haplotypes implicated in repeat instability. The data show that differences in allele frequencies as well as in the distribution of the mutational pathways previously identified are present among Basques. The data also suggest that compared with the analyzed Basque valleys, Gernika had increased frequency of susceptibility to instability alleles, although the prevalence of premutation and intermediate/grey zone alleles in all the analyzed valleys was lower than that reported in Caucasian populations.


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Oncogenomic Approaches in Exploring Gain of Function of Mutant p53
S. Donzelli, F. Biagioni, F. Fausti, S. Strano, G. Fontemaggi and G. Blandino

Cancer is caused by the spatial and temporal accumulation of alterations in the genome of a given cell. This leads to the deregulation of key signalling pathways that play a pivotal role in the control of cell proliferation and cell fate. The p53 tumor suppressor gene is the most frequent target in genetic alterations in human cancers. The primary selective advantage of such mutations is the elimination of cellular wild type p53 activity. In addition, many evidences in vitro and in vivo have demonstrated that at least certain mutant forms of p53 may possess a gain of function, whereby they contribute positively to cancer progression. The fine mapping and deciphering of specific cancer phenotypes is taking advantage of molecular-profiling studies based on genome-wide approaches. Currently, high-throughput methods such as arraybased comparative genomic hybridization (CGH array), single nucleotide polymorphism array (SNP array), expression arrays and ChIP-on-chip arrays are available to study mutant p53-associated alterations in human cancers. Here we will mainly focus on the integration of the results raised through oncogenomic platforms that aim to shed light on the molecular mechanisms underlying mutant p53 gain of function activities and to provide useful information on the molecular stratification of tumor patients.


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Modeling the Genetic Control of HIV-1 Dynamics After Highly Active Antiretroviral Therapy
C-X. Ma, Y. Li and R. Wu

The progression of HIV disease has been markedly slowed by the use of highly active antiretroviral therapy (HAART). However, substantial genetic variation was observed to occur among different people in the decay rate of viral loads caused by HAART. The characterization of specific genes involved in HIV dynamics is central to design personalized drugs for the prevention of this disease, but usually cannot be addressed by experimental methods alone rather than require the help of mathematical and statistical methods. A novel statistical model has been recently developed to detect genetic variants that are responsible for the shape of HAART-induced viral decay curves. This model was employed to an HIV/AIDS trial, which led to the identification of a major genetic determinant that triggers an effect on HIV dynamics. This detected major genetic determinant also affects several clinically important parameters, such as half-lives of infected cells and HIV eradication times.