Download 3` Untranslated Regions

2 Corinthians 13:1-3
1 This will be my third visit to you. “Every
matter must be established by the testimony
of two or three witnesses.”
2 I already gave you a warning when I was
with you the second time. I now repeat it
while absent: On my return I will not spare
those who sinned earlier or any of the others,
3 since you are demanding proof that Christ is
speaking through me. He is not weak in
dealing with you, but is powerful among you.
Repetition and
Organization of
DNA Sequences
Timothy G. Standish, Ph. D.
Abstract
When Darwinism and intelligent design make the
same prediction and this prediction goes against
interpretation of data, proponents of Darwinism
may step back from the predictions arising from
their worldview, then attempt to say that data
interpreted to go against both intelligent design
and Darwinism disproves ID while ignoring the
fact that if, the interpretation of the data is true, it
also calls into question Darwinism.
Junk DNA provides an interesting case history of
this phenomenon.
Background
During the late 1960s papers began to
appear that showed eukaryotic DNA
contained large amounts of repetitive
DNA that did not appear to code for
proteins (i.e., Britten and Kohne, 1968).
By the early 1970s, the term Junk DNA
had been coined to refer to this noncoding DNA (i.e., Ohno, 1972).
Evidence
Conservation of protein (and DNA)
sequences is commonly interpreted to
indicate functionality
Significant variation in non-coding DNA is
evident between relatively closely related
species and even within species (i.e., Zeyl and
Green, 1992).
Mutation of some non-coding DNA does not
produce significant changes in phenotype
(Nei, 1987).
What is Junk DNA?
“Junk DNA” is DNA that does not code for
proteins; this is the definition that we will use.
The meaning of “junk DNA” has become restricted
significantly in recent years as the functionality of
much of what was once considered junk has
become obvious. Most modern genetics texts avoid
the term. Even when junk DNA is mentioned, it
may be given significantly different definitions.
For example, Lodish et al. (1995) called it “Extra
DNA for which no function has been found.”
Types of Junk DNA
Nine different types of DNA were
listed as junk DNA by Nowak (1994)
These nine types can be grouped into
three larger groups:
1Repetitive DNA sequences
2Untranslated parts of RNA transcripts
(pre-mRNA)
3Other non-coding sequences
Repetitive DNA
Repeated sequences seem too short to code for
proteins and are not known to be transcribed.
Five major classes of repetitive DNA:
1 Satellites - Up to 105 tandem repeated short DNA
sequences, concentrated in heterochromatin at the ends
(Telomeres) and centers (Kinetochore) of chromosomes.
2 Minisatellites - Similar to satellites, but found in clusters
of fewer repeats, scattered throughout the genome
3 Microsatellites - Shorter still than minisatellites.
4 and 5 Short (300 bp) and Long (up to 7,000 bp)
Interspersed Elements (SINEs and LINEs) - Units of
DNA found distributed throughout the genome
Untranslated Parts of mRNA
Not all of the pre-mRNA transcribed from
DNA actually codes for the protein. These
non-coding parts are never translated.
Three non-coding parts of eukaryotic mRNA:
1 5' untranslated region
2 Introns - Segments of DNA that are transcribed
into RNA, but are removed from the RNA
transcript before the RNA leaves the nucleus as
mRNA
3 3' untranslated region
A “Simple” Eukaryotic Gene
Transcription
Start Site
5’ Untranslated Region
Introns
5’
Exon 1 Int. 1
Promoter/
Control Region
Exon 2
3’ Untranslated Region
3’
Int. 2 Exon 3
Exons
RNA Transcript
Terminator
Sequence
Other Non-coding Sequences
Pseudogenes - DNA that resembles functional
genes, but is not known to produce functional
proteins. Two types:
1 Unprocessed pseudogenes
2 Processed pseudogenes
Heterogeneous Nuclear RNA - A mixture of
RNAs of varying lengths found in the nucleus.
Approximately 25 % of the hnRNA is pre-mRNA
that is being processed, the source and role of the
remainder is unknown.
Problems With Junk DNA
Junk DNA makes up a significant
portion of total genomic DNA in many
eukaryotes.
97 % of human DNA is “junk”
If this DNA is functionless, this
phenomenon presents interpretation
problems for both naturalism and
intelligent design.
The Problem for ID
It is hard to imagine a designer creating so
elegantly and efficiently at higher levels, but
leaving a lot of junk at the DNA level.
This calls into question the intelligent-design
argument that organisms are so complex and
efficient that they must be the result of design
rather than the result of random events.
Darwinists have eagerly proclaimed junk DNA to
be molecular debris left behind in the genome as
organisms have changed over time - The
potsherds of evolution.
Straw Gods
This argument is based on assumptions
about the way the designer/God must be
God is God and He can create in any way
He wants. If He wants to create organisms
with lots of unnecessary DNA, then He
can do that if He wants
In other words, God can’t be defined,
then, based on a faulty definition, argued
against on the basis of that definition
Darwinists Jumped on the Data
Dawkins (1993) and Orgel and Crick proposed that
successful genes are selfish in that they “care” only about
perpetuation of their own sequence. Thus repetitive DNA
represents successful selfish genes.
Brosius and Gould (1992) suggested nomenclature
assuming junk DNA was once functional DNA, currently
functionless, and is raw material for future functional genes.
Walter Gilbert and others (Gilbert and Glynias, 1993; Dorit
and Gilbert, 1991; Dorit et al., 1990) suggested exons are
the nuts and bolts of evolution while introns are the space
between them. Thus, to make a functional protein, standard
parts can be used, just as we use standard nuts, bolts and
other parts to make a bridge or bicycle
The Problem for Darwinists
Darwinism predicts at least some degree of
efficiency as natural selection should select against
less “fit” or efficient members of a population.
Only the most efficient organisms would be
expected to survive in a selective environment.
The large amount of junk DNA in some
eukaryote’s genomes seems very inefficient.
One would think that a trend would be evident in
organisms going from less to more efficient use of
DNA. In fact, if junk DNA really is junk, then the
trend is almost the opposite with the most primitive
organisms having the least junk DNA.
Changes in the Quantity of DNA
The amount of non-coding DNA can vary
significantly between closely related
organisms (i.e., salamanders) indicating that
changes in non-coding DNA is an easy
evolutionary step.
If change is easy, why are those with more
than the average not less fit?
If DNA is junk, it would be an added burden,
but the burden might not be significant, thus
change would be neutral in terms of fitness
Do Changes in Junk DNA
Quantity Impact Fitness?
Making DNA requires significant input of energy as
dNTPs, along with production of enzymes to
produce and maintain the DNA. Factor all that into
the human average of 75 trillion cells 6 x 109
bp/nucleus and the cost seems significant.
Unneeded DNA presents a danger to the cell.
Mutations could result in the production of junk RNA wasting
resources and potentially interfering with production of needed
RNAs and consequently proteins.
Junk proteins could be made that would waste cell resources at
best, or, at worst, may alter the activity of other proteins
Non-coding DNA has a
Significant Impact
Sessions and Larson (1987) showed that in
salamanders larger amounts of genomic DNA
correlates with slower development
Meagher and Costich (1996) showed
significant negative correlation between junk
DNA content and calyx diameter in S. latifolia
Petrov and Hartl (1998) have shown that, at
least in Drosophila species, functionless DNA
is rapidly lost
Evidence for Functionality in
Non-coding DNA
As early as 1981 (Shulman et al., 1981) statistical methods
were published for obtaining coding sequences out of the
morass of noncoding DNA.
More recently neural networks have been used to locate
protein coding regions (Uberbacher and Mural, 1991).
Searls (1992, 1997) suggested that DNA exhibits all the
characteristics of a language, including a grammar.
Mantegna et al. (1994) applied a method for studying
languages (Zipf approach) to DNA sequences and suggested
“noncoding regions of DNA may carry biological
information.” (This has not gone unchallenged; see
Konopka and Martindale, 1995.)
Roles of Non-coding DNA
Expressed as RNA
Introns - May contain genes expressed independently of
the exons they fall between.
Many introns code for small nuclear RNAs (snoRNAs).
These accumulate in the nucleolus, and may play a role in
ribosome assembly. Thus the introns cut out of pre-mRNA
may play a role in producing, or regulating production of
machinery to translate the mRNA’s code
3' Untranslated Regions - Play an important role in
regulating some genes (Wickens and Takayama, 1994).
Heterogeneous nuclear RNA - Only speculation is
possible, but with the discovery of ribozymes and RNAi it
is possible these RNAs are playing an important role
Roles of Non-coding DNA
Satellite DNA:
– Attachment sites of spindle fibers during cell division
– Telomeres protect the ends of chromosomes
Mini and Microsatellites - Defects are associated
with some types of cancer, Huntington’s disease
and fragile-X disease
– May serve as sites for homologous recombination with
the Alu SINE
– A and T boxes resembling A-rich microsatellites are
found associated with the nuclear scaffold
– The AGAT minisatellite has a demonstrated function in
regulation
Conclusions
Less and less non-coding DNA looks like junk
Some classes of non-coding DNA remain
problematic, particularly Pseudogenes
Discovery of important functions for non-coding
DNA calls into question any support the idea of
junk DNA provides Darwinism
Proponents of ID must be cautious in accepting the
interpretation put on data by Darwinists
Darwinists need to consider the predictions made
by their own theory before interpreting data to
discredit ID when the interpretation is equally
problematic in the context of natural selection
The Globin Gene Family
Globin genes code for the
a
b
protein portion of hemoglobin
In adults, hemoglobin is made
Fe
up of an iron containing heme
molecule surrounded by 4
globin proteins: 2 a globins
b
a
and 2 b globins
During development, different globin genes are
expressed which alter the oxygen affinity of
embryonic and fetal hemoglobin
Model For Evolution Of The
Globin Gene Family
Ancestral
Globin gene
Duplication
Mutation
a
b
Transposition
Chromosome 16
a
z
z
Embryo
b
Duplication and Mutation
e
g
Duplication and Mutation
Gg
a2 a1 yq
e
Ag
a
yz ya2 ya1
Fetus and
Adult
Embryo
Fetus
Chromosome 11
b
yb
d
b
Adult
Pseudo genes (y) resemble genes, but may lack introns and, along with other
differences typically have stop codons that come soon after the start codons.
Eukaryotic mRNA
5’ Untranslated Region
5’ G
Exon 1 Exon 2
3’ Untranslated Region
Exon 3
AAAAA
3’
Protein Coding Region
5’ Cap
3’ Poly A Tail
RNA processing achieves three things:
Removal of introns
Addition of a 5’ cap
Addition of a 3’ tail
This signals the mRNA is ready to move out of the
nucleus and may control its lifespan in the
cytoplasm
“Junk” DNA
It is common for only a small portion of a
eukaryotic cell’s DNA to code for proteins
In humans, only about 3 % of DNA actually
codes for the about 100,000 proteins produced by
human cells
Non-coding DNA was once called “junk” DNA
as it was thought to be the molecular debris left
over from the process of evolution
We now know that much non-coding DNA is
involved in important functions like regulating
expression and maintaining the integrity of
chromosomes
Eukaryotes Have Large
Complex Genomes
The human genome is about 3 x 109 base
pairs or ≈ 1 m of DNA
That’s a lot more than a typical bacterial
genome
E. coli has 4.3 x 106 bases in its genome
Because humans are diploid, each nucleus
contains 6 x 109 base pairs or ≈ 2 m of DNA
That is a lot to pack into a little nucleus!
Only a Subset of Genes is
Expressed at any Given Time
It takes lots of energy to express genes
Thus it would be wasteful to express all
genes all the time
By differential expression of genes, cells
can respond to changes in the environment
Differential expression, allows cells to
specialize in multicelled organisms.
Differential expression also allows
organisms to develop over time.
Eukaryotic DNA Must be
Packaged
Eukaryotic DNA exhibits many levels of
packaging
The fundamental unit is the nucleosome,
DNA wound around histone proteins
Nucleosomes arrange themselves together
to form higher and higher levels of
packaging.
Highly Packaged DNA Cannot
be Expressed
The most highly packaged form of DNA is
“heterochromatin”
Heterochromatin cannot be transcribed,
therefore expression of genes is prevented
Chromosome puffs on some insect
chomosomes illustrate where active gene
expression is going on
Logical Expression Control Points
Increasing cost
DNA packaging
Transcription
RNA processing
mRNA export
mRNA masking/unmasking
and/or modification
mRNA degradation
Translation
Protein modification
Protein transport
Protein degradation
The logical
place to
control
expression is
before the
gene is
transcribed
A “Simple” Eukaryotic Gene
Transcription
Start Site
5’
5’ Untranslated Region
Introns
Exon 1 Int. 1
Promoter/
Control Region
3’ Untranslated Region
Exon 2
3’
Int. 2 Exon 3
Exons
RNA Transcript
Terminator
Sequence
Enhancers
DNA
Many bases
5’
3’
Enhancer
5’
Promoter
TF
Transcribed Region
3’
TF
5’
TF TF RNA
RNA
Pol.
Pol.
5’
RNA
3’
Eukaryotic mRNA
5’ Untranslated Region
5’ G
Exon 1 Exon 2
3’ Untranslated Region
Exon 3
AAAAA
3’
Protein Coding Region
5’ Cap
3’ Poly A Tail
RNA processing achieves three things:
Removal of introns
Addition of a 5’ cap
Addition of a 3’ tail
This signals the mRNA is ready to move out of the
nucleus and may control its lifespan in the
cytoplasm