Download Eukaryotic Genomes

Eukaryotic Genomes
CHAPTER 19
Structural Levels of DNA
• a single linear DNA double helix averages about 4 cm
in length
• DNA associates with proteins that condense it so it
will fit in the nucleus
• DNA-protein complex = chromatin
▫ chromatin looks like “beads on a string” when unfolded
 “beads” = nucleosomes made up of histones (proteins)
“string” = DNA
 http://www.youtube.com/watch?v=9kQpYdCnU14&feature=relmfu
 http://www.youtube.com/watch?v=gbSIBhFwQ4s&feature=relmfu
• chromatin fiber (30 nm)
▫ created by interactions
between adjacent nucleosomes
and the linker DNA
• chromatin fiber (300 nm)
▫ created when the 30 nm
chromatin fiber forms loops
called looped domains
attached to a protein scaffold
made of nonhistones
• chromosome
▫ forms when the 300 nm
chromatin fiber folds on itself
Regulation of Chromatin Structure
• compactness of chromatin helps regulate gene
expression
▫ heterochromatin – highly compact so it is
inaccessible to transcription enzymes
▫ euchromatin – less compact allowing
transcription enzymes access to DNA
• chemical modifications that can alter chromatin
compactness:
▫ histone acetylation (-COCH3) neutralizes the
histones so they no longer bind to neighboring
nucleosomes causing chromatin to have a looser
structure
DNA Methylation
• addition of methyl groups to DNA bases (usually
cytosine) inactivate DNA
• methylation patterns can be passed on
• after DNA replication, methylation enzymes correctly
methylate the daughter strand
• accounts for genomic imprinting in mammals –
expression of either the maternal or paternal allele of
certain genes during development
• (NOTE: inheritance of chromatin modifications that
do not involve a change in the DNA sequence is called
epigenetic inheritance)
• http://www.youtube.com/watch?NR=1&v=dfdnf1Wpg
0E&feature=endscreen
Cell Differentiation
• process of cell specialization (form &
function) during the development of
an organism
• differences in cell types results from
differential gene expression
• several control points at which gene
expression can be regulated (turned
on/off, accelerated, slowed down)
▫ most commonly regulated at
transcription in response to an
extracellular signal
Regulation of Transcription Initiation
• general transcription factors – proteins that form a
transcription initiation complex on the promoter
sequence (ex: TATA box) allowing RNA polymerase to
begin transcription
• control elements – segments of noncoding DNA that
help regulate transcription by binding certain proteins
▫ proximal control elements
▫ distal control elements (enhancers) - interact with specific
transcription factors:
 activators –stimulate transcription by binding to enhancers
 repressors - inhibit transcription by binding directly to
enhancers or by blocking activator binding to enhancers or
other transcription machinery
1.
activators bind to enhancer
with 3-binding sites
2. a DNA-bending protein
brings the bound activators
closer to the promoter
3. activators bind to general
transcription factors &
mediator proteins, helping
them to form a functional
transcription initiation
complex
•
activators can also promote histone acetylation & repressors can
promote histone deacetylation
Cell Type-Specific Transcription
• the # of different genes far
exceeds the # of different
control elements; therefore,
the particular combination of
control elements is what is
important in controlling
transcription along with the
available activators in the cell
Co-expressed Genes
• most co-expressed genes are found scattered
over different chromosomes
• to coordinate their gene expression, each gene is
regulated by the same control elements & these
control elements are activated by the same
chemical signals
Post-Transcriptional Regulation
• alternative RNA-splicing: regulatory proteins specific to
a cell type control intron-exon choices, thereby
producing different mRNA molecules from the same
primary transcript
• methods of mRNA degradation:
▫ enzymatic shortening of the poly-A tail triggers
the removal of the 5′ cap which is followed by the
digestion of the mRNA by nucleases
▫ nucleotide sequences in the untranslated region at
the 3′ end regulate the length of time an mRNA
remains intact
▫ microRNAs (miRNAs) – small RNA molecules
that bind to complementary sequences on mRNA
causing degradation by associated proteins;
miRNAs may also block translation
▫ RNA interference (RNAi) pathway – involve small
interfering RNAs (siRNAs) that function in the
same way as miRNAs
• initiation of translation:
▫ can be blocked by regulatory proteins that bind to
specific sequences or structures within the
untranslated region at the 5’ end of the mRNA &
prevent the attachment of ribosomes
▫ translation will not begin if the poly-A tails are not
long enough
▫ “global” control – activation or inactivation of one
or more of the protein factors required to initiate
translation
• protein processing & degradation:
▫ regulation of the modification or transporting of a
protein
▫ ubiquitin-tagged proteins are degraded by
proteasomes
Genes Associated With Cancer
• proto-oncogenes = normal cellular genes that code for
proteins that stimulate normal cell growth & division
▫ can be converted to oncogenes (cancer-causing genes) by:
 translocation – proto-oncogene ends up near an active
promoter or vice versa
 amplification – increases # of proto-oncogenes in cell
 point mutations in a promoter, enhancer, or the coding
region itself
• tumor-suppressor genes = encode proteins that help
prevent uncontrolled cell growth
▫ mutations that decrease the normal activity of these genes
may contribute to the onset of cancer
Example: ras gene & p53 gene
• ras gene is a proto-oncogene
▫ it encodes a G protein that, in response to growth
factors, triggers a cell signaling pathway that
synthesizes a cell cycle stimulating protein
▫ mutations in this gene can lead to the production of a
hyperactive G protein that continuously triggers this
pathway even when growth factors are absent
• p53 gene is a tumor-suppressor gene
▫ it promotes the synthesis of cell cycle inhibiting
proteins
▫ a mutation that knocks out this gene can lead to
excessive cell growth & cancer
Model of Cancer Development
• changes that must occur at the DNA level for a cell
to become fully cancerous:
▫ appearance of at least one oncogene
▫ mutation or loss of several tumor-suppressor
genes
 in most cases mutations must knock out both
alleles to block tumor suppression
Tumor Viruses
• can transform cells into cancer cells through the
integration of viral nucleic acid into host cell
DNA
▫ retroviruses may donate an oncogene to the cell
▫ integrated viral DNA may disrupt a tumorsuppressor gene or convert a proto-oncogene to an
oncogene
• produce proteins that inactivate p53 and other
tumor-suppressor proteins
Predisposition to Cancer
• an individual inheriting an oncogene or a
mutant allele of a tumor-suppressor gene is one
step closer to accumulating the necessary
mutations for cancer to develop
▫ (ex) breast cancer genes: BRCA1 or BRCA2
 a woman who inherits one mutant BRCA1 allele has
a 60% chance of developing breast cancer before the
age of 50
Eukaryotic vs. Prokaryotic Genomes
Eukaryotes
Prokaryotes
• larger genome but fewer genes
in a given length of DNA
• more noncoding DNA (10,000
times as much as prokaryotes )
• most of the DNA does not
encode protein or RNA
• genes contain introns so they
are much longer than
prokaryotic genes
• smaller genome but more
genes in a given length of DNA
• less noncoding DNA
• most of the DNA codes for
protein, tRNA, or rRNA
• genes are not interrupted by
introns
Human Genome
• 98.5% does not code for
proteins, rRNAs, or tRNAs
▫ 24% is gene-related
regulatory sequences and
introns
▫ 44% is repetitive DNA made
up of transposable elements
& related sequences
Transposable Elements
• two types:
▫ transposons – move within a
genome by means of a DNA
intermediate
 can move by “cut-and-paste”
or “copy-and-paste”
▫ retrotransposons – move
within a genome by means of
an RNA intermediate
 always leave a copy at the
original site because they are
initially transcribed into an
RNA intermediate
 to be inserted at another
site, the RNA intermediate
must be converted back to
DNA by reverse
transcriptase
Other Types of Repetitive DNA
• probably arose by mistakes that occurred during DNA
replication or recombination
• accounts for about 15% of the human genome
• about 1/3 of this consists of large-segment duplications
(10,000-300,000 base-pairs)
▫ long stretches of DNA that have been copied from one
chromosomal location to another
• remaining 2/3 is simple sequence DNA – copies of
tandemly repeated short sequences like GTTAC
▫ most is located at chromosomal telomeres and
centromeres indicating it has a structural role
Gene-Related DNA
• consists of coding & noncoding DNA
• constitutes about 25% of the human genome
• about ½ of the total coding DNA consists of solitary
genes
• remaining ½ occurs in multigene families = collections
of identical or similar genes
▫ (ex) identical gene family = rRNA
 allows for quick production of millions of ribosomes
▫ (ex) non-identical families = α-globin and β-globin
Evolution of Genomes
• extra sets of chromosomes can arise from:
▫ errors during meiosis
 polyploidy – extra sets of genes
 mutations can accumulate in the extra sets of genes
 unequal crossing-over
 can result in one chromosome with a deletion and
another with a duplication
▫ errors during DNA replication
 slippage
 occurs when DNA template shifts with respect to the
new complementary strand resulting in a region of the
DNA not be copied or being copied twice
• rearrangement of existing DNA sequences by:
▫ exon duplication
▫ exon shuffling
 mixing & matching of different exons either within a
gene or between two nonallelic genes owing to errors
in meiotic recombination
• transposable elements:
▫ can promote recombination
▫ disrupt cellular genes or control elements
▫ carry entire genes or individual exons to new
locations
Evolution of Globin Genes
• all the α-globin and β-globin genes likely evolved
from one common ancestral globin gene
▫ the ancestral globin gene duplicated and diverged into
α-globin and β-globin ancestral genes
▫ the ancestral α-globin and β-globin genes later
duplicated several times and their copies diverged into
the current family genes
▫ the divergences undoubtedly arose from accumulated
mutations
▫ some of the gene duplications and subsequent
divergences are also suspected to have produced new
genes with novel, yet related functions