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THE HUMAN NUCLEAR GENOME
know that protein-coding genes are not the sole repository of heritable traits and
that the situation is extremely more complicated involving RNA-coding genes and
epigenetic control.
2.
RNA-coding genes.
RNA-coding genes produce active RNAs that can profoundly
alter normal gene expression and hence produce an altered trait or disease.
3.
Epigenetic control.
Epigenetic control involves chemical modification of DNA
(e.g., methylation) and chemical modification of histones (e.g., acetylation, phos-
phorylation, and addition of ubiquitin) both of which can profoundly alter nor-
mal gene expression and hence produce an altered trait or disease.
A. SIZE. The size of protein-coding genes varies considerably from the 1.7-kb insulin gene
S
45 kb low density lipoprotein (LDL) receptor gene S 2400 kb dystrophin gene.
B. EXON–INTRON ORGANIZATION
1.
Exons (expression sequences)
are coding regions of a gene with an average size
of
200 bp.
2.
Introns (intervening sequences)
are noncoding regions of a gene with a huge
variation in size.
C. REPETITIVE DNA SEQUENCES. Repetitive DNA sequences may be found in both
exons and introns.
D. CLASSIC GENE FAMILY. A classic gene family is a group of genes that exhibit a high
degree of sequence homology over most of the gene length.
E.
GENE SUPERFAMILY. A gene superfamily is a group of genes that exhibit a low degree
of sequence homology over most of the gene length. However, there is relatedness
in the protein function and structure. Examples of gene superfamilies include the
immunoglobulin superfamily, globin superfamily, and the G-protein receptor super-
family.
F.
ORGANIZATION OF GENES IN GENE FAMILIES
1.
Cluster.
Genes can be organized as a tandem repeated array with close cluster-
ing (where the genes are controlled by a single expression control locus) and com-
pound clustering (where related and unrelated genes are clustered) all on a single
chromosome.
2.
Dispersed.
Genes can be organized in a dispersed fashion at two or more differ-
ent chromosome locations all on a single chromosome.
3.
Multiple clusters.
Genes can be organized in multiple clusters at various chro-
mosome locations and on different chromosomes.
G. UNPROCESSED PSEUDOGENES, TRUNCATED GENES, INTERNAL GENE FRAG-
MENTS. In humans, there is strong selection pressure to maintain the sequence of im-
portant genes. So, to propagate evolutionary changes, there is a need for gene duplica-
tion. The surplus duplicated genes can diverge rapidly, acquire mutations, and either
degenerate into nonfunctional pseudogenes or mutate to produce a functional protein
that is evolutionary advantageous. As a result of this process, families of protein-coding
genes are frequently characterized by the presence of the following:
1.
Unprocessed pseudogenes
which are defective copies of genes that are not tran-
scribed into mRNA
2.
Truncated genes
which are portions of genes lacking 5
or 3 ends
3.
Internal gene fragments
which are internal portions of genes
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24
CHAPTER 4
H. PROCESSED PSEUDOGENES
1.
Processed pseudogenes are transcribed into mRNA, converted to cDNA by reverse
transcriptase, and then the cDNA is integrated into a chromosome.
2.
Processed pseudogenes are typically not expressed as proteins because they lack a
promoter sequence.
I.
RETROGENES
1.
Retrogenes are processed pseudogenes where the cDNA integrates into a chromo-
some near a promoter sequence by chance. If this happens, then a processed
pseudogene will express protein.
2.
If selection pressure ensures the continued expression of a processed pseudogene,
then the processed pseudogene is considered a retrogene.
A. RIBOSOMAL RNA (rRNA) GENES
1.
There are
200 copies of rRNA genes which encode for rRNAs that are compo-
nents of ribosomes used in protein synthesis.
2.
The 200 copies of rRNA genes are located in the nucleolus which consists of por-
tions of five pairs of chromosomes (i.e., 13, 14, 15, 21, and 22) that contain the
200 copies of rRNA genes.
3.
The rRNA genes are arranged in clusters called nucleolar organizers and within
the nucleolar organizers the genes are arranged in a tandem series.
B. TRANSFER RNA (tRNA) GENES
1.
There are 497 tRNA genes which encode for tRNAs that are used in protein syn-
thesis.
C. SMALL NUCLEAR RNA (snRNA) GENES
1.
There are
80 snRNA genes which encode for snRNAs that are components of
the major GU-AG spliceosome and minor AU-AC spliceosome used in RNA splic-
ing during protein synthesis.
D. SMALL NUCLEOLAR RNA (snoRNA) GENES
1.
The snoRNA genes encode for snoRNAs that direct site-specific base modifica-
tions (2
-O-ribose methylation and pseudouridylation) in rRNA.
2.
There are two large clusters of snoRNA genes found on chromosome 15q which
are paternally imprinted, expressed in the brain and may play a role in the Prader-
Willi syndrome.
E.
REGULATORY RNA GENES
1.
The regulatory RNA genes encode for RNAs that are similar to mRNA.
2.
The SRA-1 (steroid receptor activator) RNA gene encodes for SRA-1 RNA that
functions as a coactivator of several steroid receptors.
3.
The XIST gene encodes for XIST RNA that functions in X chromosome inactivation.
F.
MICRO RNA (miRNA) OR SMALL INTERFERING RNA (siRNA) GENES
1.
There are
250 miRNA or siRNA genes which encode for miRNAs or siRNAs
that block the expression of other genes.
G. ANTISENSE RNA GENES
1.
There are
1600 antisense RNA genes which encode for antisense RNA that binds
to mRNA and physically blocks translation.
H. RIBOSWITCH GENES
1.
Riboswitch genes encode for riboswitch RNAs
which bind to a target molecule,
change shape, and then switch on protein synthesis.
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25
THE HUMAN NUCLEAR GENOME
There are two main mechanisms of epigenetic control which
include
A. CHEMICAL MODIFICATION OF DNA
1.
DNA can be chemically modified by methylation of cytosine nucleotides per-
formed by methylating enzymes.
2.
An increased methylation of a DNA segment will make that DNA segment less
likely to be transcribed into RNA, and hence any genes in that DNA segment will
be silenced (i.e., c methylation of DNA
silenced genes).
3.
The mechanism that determines which DNA segments are methylated is unknown.
4.
DNA methylation plays a crucial role in the epigenetic phenomenon called
genomic imprinting.
a.
Genomic imprinting is the differential expression of alleles depending on
whether the allele is on the paternal chromosome or the maternal chromo-
some.
b.
When a gene is imprinted, only the allele on the paternal chromosome is
expressed, whereas the allele on the maternal chromosome is silenced (or visa
versa).
c.
During male and female gametogenesis, male and female chromosomes must
acquire some sort of imprint that signals the difference between paternal and
maternal alleles.
d.
The role of genomic imprinting is highlighted by several rare diseases like
Prader-Willi syndrome, Angelman syndrome, Beckwith-Wiedemann syndrome,
and hydatidiform moles that show abnormal DNA methylation patterns.
B. CHEMICAL MODIFICATION OF HISTONES
1.
Histone proteins can be chemically modified by acetylation, methylation, phos-
phorylation, or addition of ubiquitin (all of which are sometimes called epige-
netic marks or epigenetic tags).
2.
An increased acetylation of histone proteins will make a DNA segment more likely
to be transcribed into RNA and hence any genes in that DNA segment will be
expressed (i.e., c acetylation of histones
expressed genes).
3.
The mechanism that determines the location and combination of epigenetic tags is
unknown.
A. SATELLITE DNA
1.
Satellite DNA is composed of very large-sized blocks (100 kb S several Mb) of
tandem-repeated noncoding DNA.
2.
Large-scale variable number tandem repeat (VNTR) polymorphisms
are typi-
cally found in satellite DNA.
3.
The function of satellite DNA is not known.
B. MINISATELLITE DNA
1.
Minisatellite DNA is composed of moderately sized blocks (0.1 kb S 20 kb) of
tandem-repeated noncoding DNA.
2.
Simple VNTR polymorphisms
are typically found in minisatellite DNA.
3.
Types of minisatellite DNA include
a.
Hypervariable minisatellite DNA consists of a 9–64-bp repeat unit and is
found near the telomere and other chromosomal locations. Hypervariable min-
isatellite DNA is a “hotspot” for genetic recombination, is used as a genetic
marker, and is used in DNA fingerprinting.
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CHAPTER 4
b.
Telomeric DNA consists of a 6-bp repeat unit and is found at the end of all
chromosomes. Telomeric DNA allows the replication of linear DNA of the lag-
ging strand during chromosome replication.
C. MICROSATELLITE DNA (SIMPLE SEQUENCE REPEAT OR SHORT TANDEM
REPEATS)
1.
Microsatellite DNA is composed of small-sized blocks (1–6 bp) of tandem-repeated
noncoding DNA. The most common microsatellite in humans is a (CA)
n
repeat
where n
10–100.
2.
The length of microsatellite DNA is highly variable from person to person, but the
length of microsatellite DNA is constant in each person. Consequently, microsatel-
lite DNA can be used as a molecular marker in determining paternity and popula-
tion genetic studies.
3.
Microsatellite instability
refers to a condition whereby microsatellite DNA is ab-
normally lengthened or shortened due to defects in the DNA repair process.
4.
Microsatellite instability is a hallmark feature in hereditary nonpolyposis colorec-
tal cancer (HNPCC or Warthin-Lynch syndrome). All HNPCC tumors show mi-
crosatellite DNA throughout the entire genome that has abnormally lengthened or
shortened. This microsatellite instability is caused by mutations in genes for DNA
mismatch repair enzymes (Mlh1, Msh2, and Msh6).
D. TRANSPOSONS (TRANSPOSABLE ELEMENTS; “JUMPING GENES”). Transposons
are composed of interspersed repetitive noncoding DNA that make up an incredible
45% of the human nuclear genome. Transposons are mobile DNA sequences that jump
from one place in the genome to another (called transposition).
1.
Types of transposons
a.
Short interspersed nuclear elements (SINEs). SINEs (
100–400 bps) have
been very successful in colonizing the human genome. SINEs are generally
transcriptionally active only under stressful situations whereby SINE RNAs
promote protein synthesis under stress. The Alu repeat (280 bp) is a SINE that
is the most abundant sequence in the human genome. When Alu repeats are
located within genes, they are confined to introns and other untranslated
regions.
b.
Long interspersed nuclear elements (LINEs). LINE 1 (
6.1 kb) is the most
important human transposon in that it is still actively transposing (jumping)
and occasionally causes disease by disrupting important functioning genes.
LINE 1 accounts for almost all the reverse transcriptase activity in the human
genome and allows for the retrotransposition and the creation of processed
pseudogenes and retrogenes.
c.
Long terminal repeat (LTR) transposons. LTR transposons are retrovirus-like
elements which are flanked by long terminal repeats (LTRs) that contain tran-
scriptional regulatory elements. The endogenous retroviral sequences (ERV)
are LTR transposons that contain the gag gene and pol gene which encode for
a protease, reverse transcriptase, RNAase H, and integrase.
d.
DNA transposons. DNA transposons contain terminal inverted repeats and
encode for the enzyme transposase which is used in transposition. Most DNA
transposons in humans are no longer active (i.e., they do not jump) and there-
fore are considered transposon fossils.
2.
Mechanism of transposition.
Transposable elements jump either as double-
stranded DNA using conservative transposition or through an RNA intermediate
using retrotransposition.
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27
THE HUMAN NUCLEAR GENOME
a.
Conservative transposition (Figure
4-2). In conservative transposition,
the transposon (T) located on a host
chromosome jumps as double-stranded
DNA. Transposase (encoded in the
DNA of the transposon) cuts the
transposable element at a site marked
by inverted repeat DNA sequences.
The transposon is inserted into a new
location on a target chromosome.
And the host chromosome undergoes
DNA repair. This mechanism is simi-
lar to the mechanism that a DNA
virus uses in its life cycle to transform
host DNA.
b.
Retrotransposition (Figure 4-3). In
retrotransposition, the transposon
(T) undergoes transcription which
produces an RNA copy that encodes
a reverse transcriptase (RT) enzyme.
The reverse transcriptase makes a
double-stranded DNA copy of the
transposon from the RNA copy. The
transposon is inserted into a new lo-
cation on a target chromosome using
the enzyme integrase. This mecha-
nism is similar to the mechanism that
an RNA virus (retrovirus) uses in its
life cycle to transform host DNA.
● Figure 4-2 Conservative Transposition.
● Figure 4-3 Retrotransposition.
● Figure 4-4 Mutation at Former Site.
Mutation
Host
chromosome
Host chromosome
3.
Transposons and genetic variability.
The main purpose of transposons is to af-
fect the genetic variability of the organism. Transposons can do this in several ways:
a.
Mutation at the former site of the
transposon (Figure 4-4). After the
transposon (T) is cut out of its site in
the host chromosome by trans-
posase, the host chromosome under-
goes DNA repair. A mutation (X)
may arise at the repair site.
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