| Current Genomics
ISSN: 1389-2029
Current Genomics
Volume 6, Number 7, November 2005
Contents
Epigenomics - Genome Wide Modifications of Cytosine and New Dimensions in Our Understanding of Differentiation
and Disease Pp.491
L.E. Coverdale and C.C. Martin
[Abstract]
Genes Induced by Reovirus Infection Have a Distinct
Modular Cis-Regulatory Architecture Pp.501
R. Lapadat, R.L. DeBiasi, G.L. Johnson, K.L. Tyler and I.
Shah
[Abstract]
Fragile X Mental Retardation Protein: Many Partners
and Multiple Targets for a Promiscuous Function Pp.515
E.W. Khandjian, E. Bechara, L. Davidovic and B. Bardoni
[Abstract]
Long Range Regulatory Sequences Delimited by Progressive
Deletions of a Mouse Nkx2-5-GFP-BAC Clone: A New Approach
to Identify Distal Gene Regulators in Evolutionarily Conserved
Non-Coding Sequences Pp.523
X. Chi, R.J. Schwartz, S. Mukherjee and P.K. Chatterjee
[Abstract]
PC9, A New Actor in Autosomal Dominant Hypercholesterolemia
Pp.535
D. Allard, M. Abifadel, J.-P. Rabès and M. Varret
[Abstract]
Approaching Inherited Disease on a Genomic Scale
Pp.545
J. Freudenberg, Y.-H. Fu and L.J. Ptácek
[Abstract]
Two Strategies to Identify Genes Underlying Complex
Diseases Pp.551
S.-F. Lei, S. Wu, V. Dvornyk and H.-W. Deng
[Abstract]
Origin and Expansion of Trinucleotide Repeats and
Neurological Disorders Pp.563
P. Gandhi, Z. Khan, P. Bhadoria, R. Gupta, N.K. Saha and
P.S. Bisen
[Abstract]
Abstracts
[Back to top]
Epigenomics - Genome Wide Modifications of Cytosine
and New Dimensions in Our Understanding of Differentiation
and Disease
L.E. Coverdale and C.C. Martin
The term epigenetics defines the heritable changes in gene
expression that occur through changes in the chromatin structure,
rather than changes in the DNA sequence. The methylation of
cytosines (m5C) in CpG dinucleotides (DNA methylation) and
the modification of histones are fundamental epigenetic mechanisms
that regulate eukaryotic gene expression. In general, increases
in DNA methylation are associated with gene silencing whereas
decreases in DNA methylation are often associated with gene
expression. As a result, DNA modification provides an additional
level of genetic information by incorporating a fifth nucleotide
into the genetic code. Epigenetic regulation has been shown
to be important in cellular differentiation, embryonic development,
and when abnormal – carcinogenesis and disease. Until
recently studies investigating epigenetic modifications of
DNA were restricted to looking at specific gene loci. High
throughput genomic methods such large scale bisulphate sequencing,
restriction landmark genome scanning (RLGS), CpG island microarrays
and mass spectroscopy methods have now been developed that
allow researchers to assay levels of DNA methylation and chromatin
structure over wide areas of the genome or the entire genome
– the epigenome or methylome. This new area of research
has been termed epigenomics, and its aim is to describe the
complete set of DNA methyation modifications within a cell.
Comparative studies are presently being conducted in order
to understand epigenomic differences in a number of systems.
These included epigenome comparisons between undifferentiated
and differentiated embryonic cells, cancerous and non-cancerous
cell types, and cells exposed to varying environmental parameters.
Studying global changes in DNA methylation has the potential
to identify early indicators of carcinogenesis or biomarkers
for conditions that alter the normal epigenomic status within
an organism.
[Back to top]
Genes Induced by Reovirus Infection Have a Distinct
Modular
Cis-Regulatory Architecture
R. Lapadat, R.L. DeBiasi, G.L. Johnson, K.L. Tyler and
I. Shah
The availability of complete genomes and global gene expression
profiling has greatly facilitated analysis of complex genetic
regulatory systems. We describe the use of a bioinformatics
strategy for analyzing the cis-regulatory design
of genes diferentially regulated during viral infection of
a target cell. The large-scale transcriptional activity of
human embryonic kidney (HEK293) cells to reovirus (serotype
3 Abney) infection was measured using the Affymetrix HU-95Av2
gene array. Comparing the 2000 base pairs of 5’ upstream
sequence for the most differentially expressed genes revealed
highly preserved sequence regions, which we call “modules”.
Higher-order patterns of modules, called “supermodules”,
were significantly over-represented in the 5’ upstream
regions of transcriptionally responsive genes. These supermodules
contain binding sites for multiple transcription factors and
tend to define the role of genes in processes associated with
reovirus infection. The supermodular design encodes a cis-regulatory
logic for transducing upstream signaling for the control of
expression of genes involved in similar biological processes.
In the case of reovirus infection, these processes recapitulate
the integrated response of cells including signal transduction,
transcriptional regulation, cell cycle control, and apoptosis.
The computational strategies described for analyzing gene
expression data to discover cis-regulatory features
and associating them with pathological processes represents
a novel approach to studying the interaction of a pathogen
with its target cells.
[Back to top]
Fragile X Mental Retardation Protein: Many Partners
and Multiple Targets for a Promiscuous Function
E.W. Khandjian, E. Bechara, L. Davidovic and B. Bardoni
Fragile X syndrome is the most common inherited form of mental
retardation and is due to the silencing of FMR1 gene
coding for the FMRP protein. FMRP is an RNA binding protein
endowed with Nuclear Localization and Nuclear Export Signals
and is associated with actively translating polysomes as part
of mRNP complexes. During the past years, efforts from many
laboratories to unravel the function of this protein, resulted
in the identification of several proteins (mostly RNA-binding)
and few hundred of mRNAs that are targeted by FMRP. The puzzle
illustrating the FMRP role depicts a protein implicated in
different steps of mRNA metabolism. However, its precise mechanism
of action is not still understood and the specificity of its
function is probably dependent on RNA and/or proteins that
interact and associate with it.
[Back to top]
Long Range Regulatory Sequences Delimited by Progressive
Deletions of a Mouse Nkx2-5-GFP-BAC Clone: A New Approach
to Identify Distal Gene Regulators in Evolutionarily Conserved
Non-Coding Sequences
X. Chi, R.J. Schwartz, S. Mukherjee and P.K. Chatterjee
Many genes important during early development in vertebrates
are regulated by sequences located at large distances from
the protein coding region. Clues to the location of these
long-range gene-regulatory elements can be obtained from comparing
genomic sequences of evolutionarily distant species such as
the mouse and human. However, identifying them functionally
remains a major challenge. Analysis of distal regulatory sequences
is important not only for a complete understanding of regulation
of the gene in specific tissues, but also for exploring mechanisms
and possible therapeutic strategies for diseases linked to
variations in those sequences. Polymorphisms existing in far
away regu-latory sequences that are linked statistically to
a disease can be associated with a gene only when such sequences
are functionally implicated in regulating the expression of
that gene. The mechanistic pathway that connects the disease
to the malfunction of the gene can then be identified, and
possible therapeutic interventions explored. A strategy that
uses transgenic mice developed with a GFP-reporter gene tagged
BAC clone to functionally identify such long-range regula-tory
sequences in the cardiac specific Nkx2-5 gene is illustrated.
A combinatorial approach using the full length Nkx2-5 GFP-BAC
and several of its truncations, chosen on the basis of cross-species
genomic sequence alignment of highly conserved non-coding
DNA, as transgenes helped delimit the boundaries of transcriptional
regulation to sequences 27 kb upstream of the Nkx2-5 gene.
Identifying sequences involved in the regulation of genes
distant to them are discussed in view of their potential for
exploring mechanistic pathways for disease and possible therapeutic
interventions.
[Back to top]
PC9, A New Actor in Autosomal Dominant Hypercholesterolemia
D. Allard, M. Abifadel, J.-P. Rabès and M. Varret
First named Narc-1 (Neural apoptosis regulated convertase
1), PC9 is the ninth member of the family of proprotein convertases.
This newly identified human subtilase contributes to cholesterol
homeostasis and mutations in its gene, PCSK9 (Proprotein
Convertase Subtilisin/Kexin type 9), are responsible for Autosomal
Dominant Hypercholesterolemia. This is the first example of
a dominant disease associated with a defect in a member of
the convertase family. Hypercholesterolemia is a main risk
factor of atherosclerosis and its vascular complications.
In the general population, about 1 person out of 20 presents
high plasma LDL-cholesterol. In particular, familial forms
with autosomal dominant transmission affect about 1 person
out of 500. Until recently, mutations in only two genes were
associated with the disease: the LDLR gene encoding
a transmembrane receptor implicated in endocytosis and degradation
of circulating LDL, and the APOB gene encoding the
main ligand of this receptor present at LDL surface. Pathophysiology
of these two main forms of the disease has been extensively
studied and is well understood. In 1999, two teams simultaneously
published hypercholesterolemic families presenting neither
LDLR nor APOB defects and, in 2003, a third
major gene involved in Autosomal Dominant Hypercholesterolemia,
PCSK9, was identified. To date, no substrate of PC9 has
been found except itself. The purpose of the present review
is to compile all reported data and current knowledge on PC9
and hypotheses of its role in cholesterol homeostasis and
in pathophysiology of hypercholesterolemia.
[Back to top]
Approaching Inherited Disease on a Genomic Scale
J. Freudenberg, Y.-H. Fu and L.J. Ptácek
We review current approaches that can extend our understanding
of monogenic disease towards complex disease. Recent studies
showed that currently established disease genes differ in
their protein size, tissue specificity and the phylogenetic
distribution of homologs. These characteristics can be explained
by the fact that monogenic disease mutations must be sufficiently
deleterious to produce a clearly recognizable phenotype, but
also must not be lethal in an early embryonic stage. On the
other hand, deletion of each gene in the human genome must
be evolutionarily disadvan-tageous. For most genes, this disadvantage
might manifest as an increased susceptibility to complex disease.
Accord-ingly, mildly deleterious variants can be observed
in a wide spectrum of genes. The phenotypic manifestation
of these mildly deleterious variants might depend on somatic
mutations, which cause the breakdown of compensating mecha-nisms
in individual cells. At present, association studies are the
most promising strategy for mapping complex disease phenotypes.
However, these are restricted to the identification of common
disease variants and often provide only mar-ginally convincing
statistical evidence. Novel computational strategies, which
take prior biological knowledge into ac-count, therefore might
play a major role in the design and interpretation of large-scale
association studies.
[Back to top]
Two Strategies to Identify Genes Underlying Complex
Diseases
S.-F. Lei, S. Wu, V. Dvornyk and H.-W. Deng
Dissecting the genetic basis of complex diseases remains
one of great challenges in human genetics, because these diseases
have polygenic determinations and involve multiple gene-gene
and gene-environmental interactions. Definite conclusions
about finding genes underlying complex diseases need substantial
evidence from three levels of gene function. The traditional
strategy of gene identification is to determine putative susceptibility
genes on the DNA level, and then to find related association
between susceptibility genes and complex diseases on the RNA
and protein levels. However, with rapid development of technologies
of proteomics and microarrays, a new high-throughput strategy
backward from protein to RNA and further to DNA becomes available
for gene discovery. This strategy can systemically test gene
expression, analyze co-expressed genes or regulatory network,
and detect the effects of environmental factors on the onset
and development of complex diseases. Here we attempt to outline
these two strategies using obesity as an example of a complex
disease, and to compare their advantages and disadvantages.
In conclusion, we suggest that these two strategies may complement
each other and thus help to uncover a more comprehensively
and more completely multi-faceted spectrum of genetic determination
for complex diseases.
[Back to top]
Origin and Expansion of Trinucleotide Repeats and
Neurological Disorders
P. Gandhi, Z. Khan, P. Bhadoria, R. Gupta, N.K. Saha and
P.S. Bisen
Unstable expansions of trinucleotide repeats (TNRs) are
associated with a growing number of neurological disorders
(at least 14), including HD (Huntington’s disease),
fragile X-syndrome, MD (Myotonic dystrophy) and Freidreich’s
ataxia. These disorders are often characterized by a tendency
of certain pathological alleles to further expand due to biases
in the parental origin of mutations, at times, leading to
the most severe forms. TNR expression involves changes in
the repeat tract length, threshold value, secondary structure
formation, interruptions, mismatch repair mechanism, genes
and their involved sequences, the product thereof and anticipation.
The interactions of each of these factors with the others
influence manifestations of the disease. The exact cellular
events and/or mechanism of varied expression in all the neurological
diseases with similar repeats have not yet been clearly understood.
A correlation between trinucleotide expansion, chromosomal
fragile sites and neurological diseases has, however, been
established. This review deals with the involvement of TNRs
in neurological disorders with respect to the type of repeat,
level of normal, premutation and expansion of repeats, chromosomal
locus and the involved genes along with clinical implications.
Possible answers to two basic questions regarding the mechanisms
of involvement of repeat expansions and interrelationships
between such expansions and fragile sites have been provided
based on the available experimental data. Detection of trinucleotide
repeat expansion and fragile genetic sites could be among
the excellent parameters for screening and diagnosis of human
neurodegenerative disorders. An insight into the mechanisms
involved may help the clinicians to develop suitable treatments. |
