Download Genetic regulation of eukaryotes

Gene regulation in eukaryotes
Table of content
0. Introduction
0-1. The importance of genetic regulation
0-2. Regulatory levels
I. Regulation of transcription
I-1. Chromatin regulation
I-2. Interactions between cis- and trans-regulatory elements
I-2.1. Structure of a gene
I-2.2. Promoters
I-2.3. Enhancers and silencers
I-2.4. The pre-initiation complex
I-2.5. Transcription factors
I-2.6. Types of gene expression
I-2.7. cell communication-induced gene expression
I-2.8. Steroid hormone activation
I-2.9. Interferon- activation
I-2.10. Cell type-specific gene expression
I-2.11. Interactions among gene expressions
I-2.12. Evolution of genetic regulation
II. Regulation after transcription
II-1. Posttranscriptional regulation
II-1.1. mRNA processing
II-1.2. Splicing
II-1.3. Capping
II-1.4. Polyadenylation
II-1.4. mRNA editing
II.1.5. Alternative gene usage
II-1.6. mRNA transport
II-1.7. mRNA localization
II-1.8. mRNA stability
II-2. Regulation of translation
II-3. Posttranslational regulation
II-3.1. Protein degradation
II-3.2. Protein processing and modification
III. Regulatory RNAs
III-1. Micro RNAs
III-2. Overlapping RNAs
III-3. RNA interference
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0. Introduction (0. + 1. slides)
0-1. The importance of genetic regulation
Gene expression has become a key issue in biology in the past couple of years. There are
several reasons for this. Our curiosity to understand the processes (1) controlling the
formation of an adult human from a single cell; (2) controlling the operation of adult body; (3)
and resulting in the amazing variability observable in human population and in other animals.
Understanding genetic regulation is basically important in future medicine: in diagnosis and
cure of illness, and in general, in individual-based healthcare. The technological development
has enabled us by now to accurately analyze both the expression of individual genes and
simultaneously a huge number of genes (functional genomics*: DNA chips* and protein
chips*). The other reason for the present day popularity of gene expression is based on two
novel scientific discoveries. One of the discoveries includes the (1) regulatory RNAs* (noncoding RNAs). According to the traditional view, the exclusive function of RNAs is to
convey information from DNA to proteins. However, it turned out that RNAs operate not only
as mediators in the flow of genetic information but they also regulate the manifestation of this
information. To be more specific, it appears that a great portion of genes are under the control
of various types of regulatory RNAs. (2) It also turned out that the various anatomical
structures and physiological processes are determined by specific genetic modules, termed
gene networks* composed of functionally-linked genes, and not by individual genes.
The importance of genetic regulation is indicated that in 2006 both in Chemistry and
Physiology or Medicine the Nobel Price was awarded in this issue.
0-2. Regulatory levels (1. + 2. slides)
Transcription
mRNA processing
mRNA transport
mRNA localization
mRNA stability
post-transcriptional regulation
Translation
Protein degradation
Protein processing and modification
post-translational regulation
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I. Regulation of transcription
1. Chromatin* regulation (3. slide)
- DNA methylation
- Acetylation
- Histone-repulsing sequences
2. Interactions between cis- and trans- regulatory elements
● cis-elements:
promoters, enhancers and silencers
● trans-elements: RNA polymerase, transcription factors and co-factors
I-1. Regulation of chromatin (4. slide)
Regulation of histone – DNA binding allows the establishment of different chromatin states
leading to distinct ‘readouts’ of the genetic information, such as gene activation or gene
silencing. The acetylation of histone proteins removes positive charges, thereby reducing the
affinity between histones and DNA, which makes it easier for RNA polymerase and
transcription factors to find access to regulatory sequences and to activate transcription from
them. Methylation of histones and DNA sequences leads to the opposite effect than that of
acetylation. Methylation of histones results in a stronger binding to DNA. Methylation of
DNA sequences has been shown to result in the silencing of gene expression in certain cells.
Some genes and gene clusters are bracketed by so called nucleosomes repulsing sequences,
such as matrix attachment region (MAR), locus control region (LCR) and scaffold-associated
region (SAR) sequences. These sequences have been shown to inhibit chromatin condensation
via their repulsive effects on the nucleosomes, thereby allowing transcription from the DNA
stretches they bracket
I-2. Interactions between cis- and trans- regulatory elements
Cis-element: they are found on he same DNA strand as the gene
Trans-element: they are located in the cytoplasm
I-2.1. structure of a gene (5. slide)
A gene is composed of transcribed and regulatory regions. The transcribed region consists of
non-coding (5’-UTR and 3’-UTR; untranslated regions) and coding region. In a strict sense,
only the exons (encoding amino acid sequences) are called as coding regions. The parts of
regulatory regions are the promoters, enhancers (facilitates transcription) and silencers (inhibit
transcription). Introns are 11 times longer than exons on average, while non-coding exons (5’UTR and 3’-UTR) have the same size as the coding ones.
I-2.2. Promoters (6. slide)
Transcriptional regulation is by far the most important mode for the control of eukaryotic
gene expression. The cis-regulatory sequences involve regulatory DNA motives, which are
recognized by specific transcription factors. Basal promoter elements termed TATA boxes are
located between 20 and 30 bases upstream of the transcriptional start site of eukaryotic genes.
Proximal promoter elements, such as the CAAT box and GC box, reside within 40 to 250
bases upstream of the transcriptional start site. The various “boxes” are so called consensus
sequences meaning that that they do not or only slightly vary even across large evolutionary
distances.
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I-2.3. Enhancers and silencers (7. slide)
The enhancer/silencer regulatory sequences are predominantly located upstream of the genes,
though some elements may occur downstream or within the introns. Enhancer sequences can
reside up to hundreds of thousands of base pairs from the coding region. The regulatory
sequences of an average gene reside within 10.000 base pairs. The number and type of
regulatory elements vary with each gene. The borders of genes are determined by the insulator
sequences, whose function is to restrict the effect of regulatory sequences to the gene they
control and isolate.
I-2.4. The pre-initiation complex (8. slide)
The pre-initiation complex facilitates the binding of RNA polymerase II to the promoter, and
thus the transcription. The RNA polymerase is composed of 12 subunits. RNA polymerase
binding the promoter has to be preceded by the attachment of several transcription factors to
the promoter or to the polymerase itself. The pre-initiation complex can only initiate a basal
expression level from a specific gene.
I-2.5. Transcription factors (9. slide)
Trans-regulatory factors of transcription, which exert direct regulatory effects on the gene
expression, include RNA polymerases, transcription factors and accessory factors. They can
directly bind to the DNA or to another transcription factor. Approximately 5-10 percent of
total gene content encodes transcription factors in higher-order organism, including human.
The different classes of eukaryotic RNAs are transcribed by three distinct polymerases. The
most complex controls are those that regulate the expressions of RNA polymerase IItranscribed mRNAs. Numerous proteins, such as TFIIA, B, C, D (TF = transcription factor)
interact with the TATA-box in a direct or indirect manner. The protein identified as C/EBP
binds to the CAAT-box element, and the SP1 protein binds to the GC-box. Several types of
transcription factors are responsible for the recognition of more distant enhancer elements.
The various cell types each express characteristic combinations of transcription factors, and
this comprising the major mechanism ensuring tissue-specific gene expression. Transcription
factors bind DNA either as homodimers or as heterodimers, with a variety of partners, with
distinct consequences for transcription. Further, the activities of transcription factors depend
on the presence or absence of cofactors, and on post-translational modifications, including
phosphorylation, acetylation and glycosylation. An additional means of transcription
regulation is the alternative usage of promoters, which enforces the alternative use of exons
and can result in a variety of tissue-specific isoforms.
I-2.6. Types of gene expression (10. slide)
1. Constitutive (continuous) – e.g. housekeeping genes
2. Induced
2a. nutrition material-induced: glucose in liver cell, (E.coli: lac operon)
2b. stress: heat shock, osmotic shock (salt)
2c. Cell-communication-induced: hormones, growths factors
2d. Developmentally regulated
I-2.7. Cell communication-induced gene expression (11. slide)
Cells more often communicate with each other by means of signal molecules. A signal
molecule can bind to a receptor inducing a strictly regulated cascade of biochemical events,
called signal transduction. Alternatively, signal molecules can enter the cell and exert their
effects in the cytoplasm or in the nucleus. There are three basic types of them. They can be
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transcription factors, thus they directly influence gene expression by binding an enhancer
sequence on he DNA (it is rare), or they can bind to a transcription factor, or to an other
factor, which exert its effect on a transcription factor through multiple steps. The intracellular
binding partner of a signal molecule is also called receptor.
I-2.8. Steroid hormone activation (12. slide)
The glucocorticoid receptors are located in the cytoplasm in an inactive state (hsp29 chaperon
performs inhibition). Steroid hormone binding dislocates hsp29, and results in the formation
of a dimeric (two-subunit) molecule, which in turn, enter to the nucleus, bind to its response
DNA element (GRE: glucocorticoid response element) and activate transcription from the
linked gene.
I-2.9. Interferon- activation (13. slide)
Interferon (IFN)-γ binding to its receptor induces JAK kinase activation, which in turn results
in the phosphorylation of STAT-1 transcription factor. As a result, activated STAT-1
forms a dimeric molecule, enter to nucleus and induce transcription from genes harboring the
appropriate response elements (alternative terms: recognition sequences, motives, consensus
sequences).
I-2.10. Cell type-specific gene expression (14. slide)
Although, almost all of our cells comprise the same genetic content, there are a huge number
of cell type, and each type of cells expresses different genes. The question is how it is
possible. The various cell types developed by means of differentiation. The genetic basis of
differentiation is the formation of different chromatin pattern (varying histone binding to the
DNA) in different tissues. The histone binding pattern determines the type of transcription
factors expressed in a cell, and the transcription factors decide whether the expression of a
particular gene is On or OFF. Normally, several transcription factors and co-factors are
required for the control of a gene. If one of them is missing, there is no transcription. Further,
even though, the appropriate transcription factors are present in a cell, no gene expression is
induced if the regulatory region of the target gene is blocked by histones.
I-2.11. Interactions among gene expressions (15. slide)
A particular physiological process is controlled by functionally linked groups of genes, which
is called gene network. These gene directly or indirectly interact with each other. There can be
various results of the interactions. An extreme situation is when the changing of expression of
s ingle gene alters the expression of all members of the gene cluster. Naturally, it is not a
realistic situation, especially in embryogenesis, since the expression of various genes can
occur at different time (upward and downward genes). Another extremity is when alteration if
gene expression is buffered by other genes. In ontogenesis, this effect is called robustness, and
its function is to protect ontogenetic pathways from environmental and genetic perturbances.
I-2.12. Evolution of genetic regulation (16-17b. slides)
Certain genes of higher-order organisms are more complex than the same in lower-order
organisms. It means that the particular gene is composed of more functional domain in
complex organism than in primitive ones. However, these alterations occur in only large
evolutionary distances involving only a few gene. Much more frequent situation is that the
same gene has the same function id distantly related species. There is not a big difference in
the number of genes between human, fruit fly and C. elegans (a worm). Several
developmental genes can be replaced between fruit fly and mouse without exerting observable
changes (anatomical, behavioral, etc.). Thus, animals have the same toolkits (genes) with the
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same function, what varies is the operation of genes in different species. Hat is, genes are
expressed differently (different amount, space and time) in various organisms. The striping of
zebra is a good example form the timing of gene expression. The number of stripes in the
three zebra species is determined by the starting of striping during the embryogenesis. An
example for the spatial alteration of gene expression is the loss of the legs of snakes. The
Hoxc-6 and Hox-8 genes of snakes are expressed in the same segments of the snakes, which
results in the development of vertebrates instead of legs.
II. Regulation after transcription
II-1. Posttranscriptional regulation
II-1.1. mRNA processing (18. slide)
The vast majority of eukaryotic mRNAs are subject to post-transcriptional processing. A
typical pre-mRNA (it is a form of heteronuclear RNA coding for an mRNA) is composed of
the following parts. Exon becomes the part of mRNA, while the introns are removed by
splicing. The upstream non-coding sequence of the first exon is termed 5’-UTR (untranslated
region) or leader sequence. The codon AUG coding for methionine is the translation start site
of the mRNA. The downstream non-coding region of the last exon is termed trailer (or 3’UTR). The poly-adenylation signal is located at the downstream region of the 3’-UTR.
II-1.2. Splicing (19. – 20. slides)
Splicing is a modification of genetic information after transcription, in which introns are
removed and exons are joined. Splicing is an essential process in eukaryotic pre-mRNA
processing that must precede translation. The so-called spliceosomal introns are spliced by the
spliceosome*, by means of a large RNA-protein complex composed of five small nuclear
ribonucleoproteins (snRNPs (pronounced "snurps") and many accessory proteins. The splice
donor site (contains a GU consensus sequence) is located at the 5’-end-, while splice acceptor
site (contains a AG consensus sequence) at the 3’-end exon/intron boundary.
Functions of introns:
1. Alternative splicing: more than one proteins can be produced form the same RNA.
2. It contains regulatory regions
3. Most of them are junks, that is, it does not perform any useful function neither for the gene,
cell, or the organism. The genome simply is not able to get rid of them.
4. Introns have structural roles
II-1.3. Capping (21. slide)
Post-transcriptional processing of the 5' end of the RNA product of DNA transcription comes
in the form of a process called capping. At the end of transcription, the 5' end of the RNA
transcript contains a free triphosphate group since it was the first incorporated nucleotide in
the chain. The capping process replaces the triphosphate group with another structure called
the "cap", which is 7-methyl guanozine. The cap is added by the enzyme guanyl transferase.
This enzyme catalyzes the reaction between the 5' end of the RNA transcript and a guanine
triphosphate (GTP) molecule. In the case of alternative capping, depending on cell type, cap is
formed at different position of the mRNA. Alternative capping is a relative rare form of posttranscriptional regulation.
Functions of capping:
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1. Protection against exonucleases
2. Needed for the binding of ribosomes
II-1.4. Polyadenylation (22. slide)
Polyadenylation is the covalent linkage of a polyadenylyl moiety to a mRNA molecule. In
eukaryotic organisms, polyadenylation is the mechanism by which most mRNA molecules are
terminated at their 3' ends. The poly A tail aids in mRNA stability by protecting it from
exonucleases. Polyadenylation is also important for export of the mRNA from the nucleus,
and for translation. Polyadenylation occurs during and immediately after transcription of
DNA into RNA in the nucleus. After transcription has been terminated, the mRNA chain is
cleaved through the action of an endonuclease complex associated with RNA polymerase.
The cleavage site is characterized by the presence of the base sequence AAUAAA near the
cleavage site. After the mRNA has been cleaved, 50 to 250 adenosine residues are added to
the free 3' end at the cleavage site. This reaction is catalyzed by polyadenylate polymerase.
Polyadenylation signal, cleavage site and site of polyA addition are distinct, but located close
to each other.
Functions:
1. Protection against exonucleases
2. Determination of life time
II-1.4. mRNA editing (23. slide)
RNA editing is a co- or post-transcriptional mechanism which alters the content of the
mRNA. For example, in mammalian apolipoprotein mRNA one CU transition (substitution
editing) by cytidine deaminase changes the CAA codon of the mRNA to UAA stop codon.
This results in the generation of a truncated yet functional transcript in the intestine. In
glutamate receptor expressing in several neuron types, the glutamate receptor mRNA is
modified by RNA editing to contain different amino acid composition, which result in altered
functioning of the resulting receptor protein. RNA editing occurs rarely in nature
II.1.5. Alternative gene usage (24. – 26. slides)
Alternative promoter usage means that a gene can be transcribed from various promoters in
different tissues, resulting in proteins with varying length or with varying amino acid
sequences if alternative splicing also occurs. Alternative polyadenylation results polypeptides
with various length and exon content if it is coupled with alternative splicing. Approximately
60% of human genes encodes at least two splice variants.
II-1.6. mRNA transport (27. slide)
Eukaryotic mRNAs must leave the nucleus in order to be translated into proteins. Mature
mRNAs exit through the nuclear pores, but the underlying mechanisms are not fully
understood. A large portion of unprocessed transcripts never leave the nucleus and are
degraded.
II-1.7. mRNA localization (28. slide)
Protein traveling to the appropriate organelles is directed by the signal peptides locating on
the N-terminal of proteins. Another possibility for pass a certain protein to the desired
organelle is based on mRNA targeting. Some mRNAs contain a zip code on the 5’ termini,
which contains information for the subcellular targeting of mRNA.
II-1.8. mRNA stability (29. slide)
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The stability of mRNAs can vary to a great extent, which may change in response to
regulatory signals. The following sequences and processes affect the mRNA half-life: AUrich elements, secondary structure, deadenylation of the poly(A) tail, 5’ de-capping and
fragment degradation.
II-2. Regulation of translation (30. slide)
Translation can be regulated at every steps. The most important control point is the translation
initiation.
II-3. Posttranslational regulation
II-3.1. Protein degradation (31. slide)
Protein degradation in eukaryotes requires a protein cofactor called ubiquitin*, which, by
binding to the proteins, identifies them for degradation by proteolytic enzymes. Specific
amino acids at the N-termini of proteins determine the rate of ubiquitin binding and thus the
stability of proteins.
II-3.2. Protein processing and modification (32. slide)
Protein degradation in eukaryotes requires a protein cofactor called ubiquitin*, which, by
binding to the proteins, identifies them for degradation by proteolytic enzymes. Specific
amino acids at the N-termini of proteins determine the rate of ubiquitin binding and thus the
stability of proteins.
III. Regulatory RNAs
Although RNAs are best known for their roles in translating genetic information into proteins,
the analyses of data on genomic sequences indicate the hitherto considerably underestimated
importance of regulatory (noncoding) RNAs, including antisense RNAs* micro (mi)RNAs*
and small interfering (si)RNAs*.
Types of RNAs (33. slide)
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RNA
s
Non-coding RNA
Coding RNA
Transcription RNA
mRNA
tRNA
messenger
transfer
rRNA
ribosomal
Regulatory RNA
siRNA
aoRN
miRN
small interfering
micro
antisense overlapping
snRNA
snoRNA
small nuclear
small nucleolar
III-1. Micro RNAs (34. - 35. slides)
A continuously increasing number of miRNAs have been described in the genomes of several
multicellular organisms. MicroRNA genes yield RNA transcripts that are processed into short
single-stranded segments, which then double over on themselves to form hairpin structures. It
has been proposed that they act as components of protein/RNA complexes. A miRNA can
both pair exactly with a mRNA and cause its degradation via RNA interference* (RNAi; see
bellow) or it can pair partially with a message and shut off translation. Recent studies
involving computational approaches suggest that the human genome may encode well over
1500 different miRNAs; the number known is rising rapidly. MicroRNAs are promiscuous
transactivators, i.e. a single RNA is assumed to regulate the expression of several genes. It is
hypothesized that up to one-third of human genes are regulated by these small RNAs. A
miRNA is a form of single-stranded (ss)RNS which is typically 20-25 nucleotides long. The
miRNAs are transcribed from DNA, but are not translated into protein. The DNA sequence
that codes for a miRNA gene is longer than the miRNA. This DNA sequence includes the
miRNA sequence and an approximate reverse complement. When this DNA sequence is
transcribed into a single-stranded RNA molecule, the miRNA sequence and its reversecomplement base pair to form a double stranded RNA hairpin loop; this forms a primary
miRNA structure (pri-miRNA). Drosha, a nuclear enzyme, cleaves the base of the hairpin to
form pre-miRNA. The pre-miRNA molecule is then actively transported out of the nucleus
into the cytoplasm. The Dicer enzyme then cuts 20-25 nucleotides from the base of the
hairpin to release the mature miRNA. The function of miRNAs appears to be in gene
regulation. For that purpose, a miRNA is complementary to a part of one or more mRNAs,
usually at a site in the 3’-UTR (untranslated region). The annealing of the miRNA to the
mRNA inhibits protein translation. In some cases, the formation of the double-stranded RNA
through the binding of the miRNA triggers the degradation of the mRNA transcript through a
process similar to RNAi, though in other cases it is believed that the miRNA complex blocks
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the protein translation machinery or otherwise prevents protein translation without causing the
mRNA to be degraded.
III-2. Overlapping RNAs (36. - 37. slides)
Natural cis-encoded antisense RNAs are endogenous transcripts that are transcribed from the
opposite strand of the same genomic locus as the sense RNA and have a region of perfect
overlap with the sense transcripts. Very surprising novel data suggest that at least 30-40% of
genes are under the control of cis-antisense RNAs. The binding of mRNAs and antisense
transcripts can sterically block translation from mRNA or, alternatively, it may trigger the
RNA interference pathway, which eventually leads to the degradation of mRNA.
III-3. RNA interference (38. - 39. slides)
RNA interference (RNAi) is a mechanism in molecular biology where the presence of certain
fragments of double-stranded RNA (dsRNA) interferes with the expression of a particular
gene. RNAi appears to be a highly potent and specific process which is actively carried out by
special mechanisms in the cell, known as the RNA interference machinery. While the
complete details of how it works are still unknown, it appears that the machinery, once it finds
a double-stranded RNA molecule, cuts it up, separates the two strands, and then proceeds to
destroy other single-stranded RNA molecules that are complementary to one of those
segments. dsRNAs direct the creation of small interfering RNAs (siRNAs*) which target
RNA-degrading enzymes (RNAses) to destroy transcripts complementary to the siRNAs. The
genetic information of many viruses is held in the form of double-stranded RNA, so it is
likely that the RNA interference machinery evolved as a defense against these viruses. The
machinery is however also used by the cell itself to regulate gene activity: certain parts of the
genome are transcribed into microRNAs, short RNA molecules that fold back on themselves
in a hairpin shape to create a double strand. When the RNA interference machinery detects
these double strands, it will also destroy all mRNAs that match the microRNA, thus
preventing their translation and lowering the activity of many other genes. RNAi has been
linked to various cellular processes, including the formation of centromeric structure and gene
regulation, through microRNAs and heterochromatin formation. The effectiveness of RNAi
lies in two processes: (1) Cleavage of mRNA by the RISC complex; (2) amplification of the
original signal by RNA-dependent RNA polymerase by utilizing mRNA as a template and the
complementary strand of siRNAs as a primer for the amplification step in the first part shows
that transcription and translation, and the second part presents the mechanism of RNA
interference.
Together: DICER forms siRNAs from double-stranded RNA molecules. The fate of siRNAs
can be as follows. 1. The siRNA bind to RISC, and after being single stranded, it lads the
RISC to the target mRNA, where the RISC cut the mRNA at a single point, which is followed
by the degradation of mRNA by Razes. 2. The single stranded siRNS detaches (or not
attaches to) from the RISC, and binds directly to the mRNA. This binding is recognized by an
RNA-dependent RNA polymerase, which utilizes the siRNA as a primer and the mRNA as a
template for the synthesis of second RNA strand. The newly formed double-stranded RNA
will serve as a substrate for DICER, which will create new and new siRNAs. This
amplification step make RNA interference so effective. RNA interference participate in gene
expression regulation as an antiviral defense mechanism.
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Role in the medicine The double stranded (ds)RNAs that trigger RNAi may be usable as
drugs. Another speculative use of dsRNA is in the repression of essential genes in eukaryotic
human pathogens or viruses that are dissimilar from any human genes; this would be
analogous to how existing drugs work. RNAi interferes with the translation process of gene
expression and appears not to interact with the DNA itself. Proponents of therapies based on
RNAi suggest that the lack of interaction with DNA may alleviate some patients' concerns
about alteration of their DNA (as practiced in gene therapy), and suggest that this method of
treatment would likely be no more feared than taking any prescription drug. For this reason
RNAi and therapies based on RNAi have attracted much interest in the pharmaceutical and
biotech industries.
Glossary
Chromatin is the complex of DNA and protein found inside the nuclei of eukaryotic cells.
The major proteins involved in chromatin are histone proteins, although many other
chromosomal proteins have prominent roles too. The functions of chromatin are to package
DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and
meiosis, and to serve as a mechanism to control expression. Changes in chromatin structure
are affected mainly by methylation (DNA and proteins) and acetylation (proteins). Chromatin
is easily visualized by staining, hence its name, which literally means colored material.
Simplistically, there are three levels of chromatin organization: 1. DNA wrapping around
nucleosomes - The "beads on a string" structure. 2. A 30 nm condensed chromatin fiber
consisting of nucleosome arrays in their most compact form. 3. Higher level DNA packaging
into the metaphase chromosome.
DNA chips: Scientists use DNA microarrays to measure the expression levels of large
numbers of genes simultaneously.
Epigenetic inheritance: the same genetic content can determine more than one phenotype as
a result of, for example, maternal effects.
Exon shuffling: gaining novel domains of proteins by acquiring a new exon from another
gene located at other part of the genome during evolution.
Forward genetics: The experimental procedure that begins with a random mutation and a
subsequent search for the altered phenotype and the mutant gene responsible for this
phenotype.
Functional genomics uses high-throughput techniques like DNA microarrays* and
proteomics* to describe the function and interactions of genes. These techniques allow the
analysis of the expression level of a huge number of gene at the same time.
Gene expression is a multi-step process that begins with transcription, followed by post
transcriptional modification and translation.
Gene networks are genetic modules composed of functionally-linked genes, which determine
the development and operation of particular traits, physiological processes or behaviors.
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The genome of an organism is the whole hereditary information of an organism that is
encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the noncoding sequences.
Genomics is the study of an organism's/species’ genome.
A knockout animal is a genetically engineered animal (usually mouse) one or more of whose
genes have been made inoperable. Knockout is a route to learning about a gene that has been
sequenced (revealing the order of bases) but has an unknown or incompletely known function.
Phenotype: anything that is part of the observable structure, function or behavior of an
organism
Protein chips (= protein microarrays) are measurement devices used in biomedical
applications to determine the presence and/or amount (referred to as quantitation) of proteins
in biological samples.
Proteome The entirety of proteins in existence in an organism. Most importantly, while the
genome* is a rather constant entity, the proteome differs from cell to cell and is constantly
changing through its biochemical interactions with the genome and the environment.
Proteomics is the large-scale study of proteins (simultaneous analysis of a large number of
proteins). This term was coined to make an analogy with genomics*, and while it is often
viewed as the "next step", proteomics is much more complicated than genomics.
Regulatory RNAs A commonly used synonym is non-coding RNA, RNA molecules that
function without being translated into proteins. Their functions include regulation of gene
expression at the levels of transcription (chromatin modification) and translation.
Reverse genetics The experimental approach that begins with a cloned segment of DNA,
followed by the insertion of this DNA to the host genome. The foreign DNA can serve both a
transgene, which is over-expressed in the host animal, or it can serve to knock out an
endogenous gene of the host. The aim of reverse genetics to find altered phenotype resulted
by the genetic manipulation.
Ribonuclease (RNase) is an enzyme that catalyzes the breakdown of RNA into smaller
components.
Signal transduction: is any process by which a cell converts one kind of signal or stimulus
into another. Processes referred to as signal transduction often involves a sequence of
biochemical reactions inside the cell, which are carried out by enzymes and other proteins
linked through second messengers.
Silent codon positions. The genetic code is redundant, which means that in most cases more
than one codon determines a single amino acids. Those base replacements, which do not
result in the change of amino acids are called as silent changes. Those positions of codons
(generally third ones), which contain the replaceable bases are called silent codon positions.
Small interfering RNA (siRNA), are a class of 20-25 nucleotide-long RNA molecules that
interfere with the expression of genes. They are naturally produced as part of the RNA
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interference (RNAi) pathway by the enzyme Dicer. They can also be exogenously
(artificially) introduced by investigators to bring about downregulation of a particular gene.
SiRNA's have a well defined structure. Briefly, this is a short (usually 21-nucleotide) doublestrand of RNA (dsRNA) with 2-nucleotide overhangs on either end, including a 5' phosphate
group and a 3' hydroxy (-OH) group.
Spliceosome is a complex of RNA and many protein subunits that remove the non-coding
introns from unprocessed mRNA. The RNAs that spliceosomes consist of are named U1, U2,
U4, U5, and U6, and participate in several RNA-RNA and RNA-protein interactions.
Transcription factor: a protein that binds DNA at a specific promoter and enhancer or other
transcription factors, and thereby directly controls transcription. Transcription factors can be
selectively activated or deactivated by other proteins, often as the final step in signal
transduction*.
Transgenic organism: An organism that has integrated foreign DNA into its germ line as a
result of the experimental introduction of DNA. Recombinant DNA techniques are commonly
used to produce a transgenic organism.
Ubiquitin is a 76 residue polypeptide that can be conjugated to specific proteins by members
of a complex family of enzyme cascade systems, whereby signaling that the particular protein
is destined for degradation.
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