Further
Reading
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Gene Silencing and Inactivation
By: Brad Bullock
April 22nd, 2005 bama.ua.
pdf
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Genetics
nature.com |
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Primer on
Molecular
Genetics primer.pdf
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Genomic Medicine — A Primer
Alan E. Guttmacher, M.D., and Francis S. Collins, M.D., Ph.D.
NEJM
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GLOSSARY
Amino acids: peptide building blocks of
proteins.
Bases: a building block of DNA and RNA. There are five different
bases or nucl: Adenine, Thymine, Guanine, Cytosine (ATGC).
DNA stands for Deoxyribonucleic acid. It's a double-stranded chemical instruction manual for
cell structure and everything a cell does: grow, divide, even when and how to die.
RNA stands for Ribonucleic acid. RNA are single- stranded chemical instructions double-stranded, messenger RNA
(mRNA) carries single pages of instructions out of the nucleus to places they're needed throughout the cell. RNAi
stands for RNA interference
 TOPIC
SEARCH
Google Scholar Polypeptides: chains of amino acids. Proteins are made up of several or many polypeptides.
Proteins: Molecules that make up the unique cell structure
(skin, heart, long, immune cell) and carry out activities throughout the body,
such as pumping blood (heart cells), to migration (immune
cells).
encoded protein: the recipe for protein as contained in
messenger RNA (mRNA).
Ribosomes are message centers throughout the cell where the information from DNA arrives in the form of messenger RNA.
Here the RNA message gets translated into a form the ribosome can understand and tells it which protein building blocks it needs and in what order to assemble them. SNPs
(polymorphisms) (markers of biologic diversity)
... "the DNA sequences of two unrelated humans
vary at millions of bases. ... we are each thus
heterozygous at about 3 million bases. Many efforts are
currently under way, ... to catalogue these variants,
commonly referred to as "single-nucleotide polymorphisms"
(SNPs), and to correlate these specific genotypic
variations with specific phenotypic variations relevant
to health.
Some SNP–phenotype correlations occur as a direct
result of the influence of the SNP on health. More
commonly, however, the SNP is merely a marker of
biologic diversity that happens to correlate with
health because of its proximity to the genetic factor that
is actually the cause." NEJM
Transcription
is the process where messenger RNA information is obtained from DNA
information. Translation is the
process where messenger RNA information is interpreted in the
Ribosome and used to assemble the end product - the unique proteins
that determine cellular activity.
Resources:
postmodern.com
Methylation can cause the over- or under- expression of genes
DNA methylation - is a hallmark of
cancer. Specifically, it is the addition of a methyl group to specific
cytosines (the components of DNA) that regulates gene activity.
Tumor
suppressor gene methylation in follicular lymphoma: a comprehensive
review
http://bit.ly/4Eih9o
One analogy for methylation is that of a car
with an ignition that is filled with a glue (methyl). The
ignition (the gene) cannot be turned off so the car runs continuously.
Scientists
are looking for agents that can turn off or inhibit the undesirable
methylation (remove the glue that is specific to the tumor
promoting, or tumor silencing, genes).
In summary, malignant behavior (loss of growth control or inability to die) can
be caused by damaged genes (i.e., translocations) and also by
methylation which alters which genes are turned on or off.
Hypermethylation
can cause oncogenes to produce
proteins that cause malignant behavior.
Hypomethylation
can quiet genes that normally
suppress cancer (tumor suppressor genes).
In this modification, methyl (CH3) groups are
added to the DNA of specific genes within the cell at specific
sites. These groups sit on the DNA and block certain proteins from
binding. In this way, the DNA methylation could be stopping the cell
from operating normally, Teitell said.
"By silencing cellular genes, this type of
modification is damaging a cell's ability to sense its environment
and may be causing it to grow uncontrollably," Teitell said.
unisci.com
Chromatin Remodeling - Protein fibers called histones that interact with DNA. Drugs that inhibit histone
deacetylases, for example, may activate tumor suppressor
genes.
Illustration of
mRNA transcription
- Click to enlarge
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Bad Recipe
There
appears to be three components of malignant cell behavior, which may
be targeted by therapy:
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Genomic
- mutations in DNA, which provides the recipe for proteins
that determine cell behavior.
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Transcription
- "The instructions stored within DNA are read and
processed by a cell in two steps: transcription and
translation." This step in cell division can be targeted
by therapy.
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Epigenetic - non-DNA-related participants in malignant behavior, such as DNA methylation - regulating which genes (tumor promoters / repressors) are turned on or off.
We might say that the genomic event (DNA mutation) happens first , but the downstream activities (transcriptional and epigenetic) are required to carry out the bad recipe ... resulting in the abnormal growth and survival behavior of a cancer.
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About
Genes and DNA
 Here
we provide basic terms to help you to understand how genes and gene
expression contributes to cancer, and how recent insights may lead to
new drugs that target the underlying causes of malignancy.
DNA
stands for Deoxyribonucleic acid. It is the "instruction manual"
for the manufacture of cell proteins that determine cell structure
and activity, including growth and survival.
DNA exists in all cells except mature erythrocytes.
The DNA "manual" contains thousands of pages called genes.
DNA is made up of bases (nucleotides) that are arranged in a specific sequence. The specificity of the sequence accounts for the production of a specific protein.
Gene function, which
determines how cells grow and survive, may be altered by either a
change (a mutation) in the sequence of the DNA or a change in
epigenetic programming of a gene -- like the "chapters of the
book" that are read (excessively) or not read.
Genes contain
the instructions or recipes for the assembly of unique
proteins. Some of these proteins are related to cell growth
and survival.
RNA:
In order for DNA to produce a protein, an intermediate step is required.
... In this step, DNA is transcribed into
RNA. The sequence of mRNA that encodes a protein is oriented in only one direction, which is known as the "sense" orientation.
Oncogenes
are mutated and/or over-expressed versions of normal genes
that can cause a cell to lose growth restraints, fail to
differentiate (mature to a next stage), or prevent the cell from initiating
the programmed cell death process called apoptosis. Some
oncogenes turn on other genes that can promote malignant behavior. Tumor
suppressor genes are genes that protect cells from
becoming a cancer. They may put the brakes on accelerated growth, or initiate
cell death when DNA damage is detected. Therefore, the low expression of tumor suppression genes can lead to
cancer. Epigenetic
refers to the regulation of gene expression - how,
when, where, how much, that is not due to DNA mutations.
Two key areas of epigenetic control
are
Chromatin Remodeling
and
DNA
Methylation (see Sidebar for details)
It is possible to reverse aberrant gene
expression (such as genes that drive proliferation (oncogenes) or
genes that fail to detect and stop malignancy (tumor suppressor
genes).
Several epigenetic drugs targeting the DNA methylation and histone
deacetylation enzymes have been tested in clinical trials; some have
recently been approved. Targeted
therapeutics may be designed to offset the over-expression of oncogenes, or
the silencing of tumor suppressor genes ... that is, treatments
can influence epigenetic regulation
of cells.
* "Over expression of some genes may be responsible for some forms of cancer;
gene silencing and inactivation techniques could be a cure for these diseases."
bama.ua.edu
pdf
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Antisense RNA experiments lead to the discovery of
RNAi. |
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RNA Interference
[RNAi] - post-transcriptional gene silencing.
"The antisense approach to gene silencing involves injecting an organism with RNA sequence complementary to mRNA transcribed from a target gene. The antisense RNA and sense mRNA hybridize and block translation and the production of an encoded protein. The presence of dsRNA duplex led to what we now recognize as an RNA interference effect."
Source miami.edu
Details on RNAi macalester.edu |
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Gene
silencing is any method of interfering with transcription
or translation of a gene and the protein it produces.* |
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Gene
inactivation is any method that modifies the DNA or
proteins around the DNA that prevents transcription * of DNA
into RNA and thus the encoded protein.
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Molecular Biology is the path from DNA (recipe) to proteins
that carry out activity
| DNA
> |
RNA
> |
>
Protein |
| Original
instruction manual |
Transcribed
page of the manual |
End
product |
| Alphabet
( blocks) of information: |
Alphabet
(blocks) of information:
|
Assembled
sequence of amino acids |
| Double
stranded information |
Single
stranded information |
Functioning
product. Information on how protein is made is not possible at
this point |
| Error
detection and repair |
No
error protection or repair |
No
error protection or repair |
| Location:
within the nucleus |
Location:
transcribed outside nucleus to areas of cells where it
can be translated into assembly of proteins |
Location:
varied cell locations |
| Cancer:
a mutation in the DNA - one, or more, of the four letters of the DNA is replaced by another letter, or due to deletion or insertion of one or more letters, in one or more DNA
regions |
Cancer:
the transcription and translation of mutated areas of DNA |
Cancer:
abnormal amounts or types of protein that causes loss of
growth control or prolonged survival of the cells - malignant
behavior |
Regarding
polymorphisms
Polymorphisms
are normal variations in DNA sequence between individuals. There are about 60,000 polymorphisms in human genome
But why does it matter to patients?
A big reason for the variable toxicity and efficacy of drugs
is that we are
not the same .... on a genetic level. Our cells may
produce different
enzymes and amounts based on normal genetic variations
(polymorphisms) ... the recipes for cellular proteins. Enzymes,
for example, that degrade, or fail to degrade, a given drug
can increase toxicity or limit efficacy.
Vincristine for example: The variable half life of
vincristine accounts for
the toxicity it can produce when the body does not degrade it
fast enough.
Anyhow, it's possible to identify the polymorphisms that
influence drug
metabolism so that we can give the "right drug, at the
right dose, to the
right patients."
More on the subject: "Genetic variations in
the response to drugs can cause measurable differences in
clinical endpoints such as rates of cure, morbidity, side
effects, and death. Data in this category demonstrate that
genetic variability in the context of a drug effect
significantly changes medical outcomes. These data sets are
different from pharmacodynamics data sets, which may show a
difference that is not sufficiently significant to alter
practice or policy." pharmgkb.org
See also ncbi.nlm.nih.gov
11937185t
Related Terms
DNA methylation - is a hallmark of
cancer. Specifically, it is the addition of a methyl group to specific
cytosines (the components of DNA) that regulates gene activity.
Epigenetics
- In biology,
the term epigenetics refers to changes in phenotype
(appearance) or gene
expression caused by mechanisms other than changes in the
underlying DNA
sequence, hence the name epi- (Greek: over; above) -genetics.
(Wikipedia)
Pharmacodynamics the
study of the relationships between the concentration of a drug
at its site(s) of action and the magnitude of the biological
or physiological effect that is achieved.
Pharmacokinetics - the
study of the bodily absorption, distribution, metabolism and
excretion of drugs.
Drug - A chemical or
biological substance used in the diagnosis,
treatment, or prevention of a disease or phenotype, or as a
component of a
medication.
Molecular assay - an
experiment in which the characteristics of a molecule (or
ensemble of molecules) are measured.
Cellular Assay - an
experiment in which the response or characteristics of a cell
(or population of cells) is measured.
Genotype - is the
internally coded, heritable information carried by the
organism. Variation in genotype represents differences in
sequence within a species, such as SNPs, the location or the
number of
repeats, deletions, or critical splice sites.
Phenotype - the
observable properties of an organism produced by the
interaction of the genotype with the environment. For
pharmacogenetics, the "environment" is often defined
as exposure to a drug, although it may include other variables
as well.
Transcription factors - "The normal growth,
development and function of an organism requires precise and
coordinated control of gene expression. A major part of this
control is exerted by regulating messenger RNA (mRNA)
production and involves complex interactions between an array
of transcriptionally active proteins and specific regulatory
DNA sequences." ncbi.nlm.nih.gov |
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