Transcript regulatory transcription factors

Eukaryotic
Gene Regulation
(CHAPTER 15- Brooker Text)
October 23 & 25, 2007
Bio 184
Dr. Tom Peavy
Eukaryotic Gene Regulation
Transcriptional Regulation:
• Regulatory transcription factors may activate or inhibit
• Compaction level of chromatin influences transcription
• DNA methylation (usually) inhibits transcription
(note: prokaryotes use DNA methylation but rather for
protection from invasive organisms and replication)
• RNA processing to mRNA (e.g. alternative splicing)
REGULATORY TRANSCRIPTION FACTORS
There are two main types
– General transcription factors
• Required for the binding of the RNA pol to the core
promoter and its progression to the elongation stage
• Are necessary for basal transcription
– Regulatory transcription factors
• Serve to regulate the rate of transcription of nearby
genes
• They influence the ability of RNA pol to begin
transcription of a particular gene
• Regulatory transcription factors recognize
cis regulatory elements located near the
core promoter
• The binding of these proteins to these
elements, affects the transcription of an
associated gene
activators bind enhancers
repressors bind silencers
Regulation of Regulatory
Transcription Factors
• There are three common ways that the function of
regulatory transcription factors can be affected
– 1. Binding of an effector molecule
– 2. Protein-protein interactions
– 3. Covalent modification
The transcription factor
can now bind to DNA
Formation of
homodimers and
heterodimers
Figure 15.5
CHANGES IN
CHROMATIN STRUCTURE
• Changes in chromatin structure can involve
changes in the structure of DNA and/or changes in
chromosomal compaction
• These changes include
–
–
–
–
1.
2.
3.
4.
Gene amplification
Gene rearrangement
DNA methylation
Chromatin compaction
Uncommon ways to regulate
gene expression
Common ways to regulate
gene expression
Chromatin Structure
• The three-dimensional packing of chromatin is an important parameter
affecting gene expression
• Chromatin is a very dynamic structure that can alternate between two
conformations
– Closed conformation
• Chromatin is very tightly packed
• Transcription may be difficult or impossible
– Open conformation
• Chromatin is highly extended
• Transcription can take place
• Variations in the degree of chromatin packing occur in eukaryotic
chromosomes during interphase
– During gene activation, tightly packed chromatin must be converted to
an open conformation in order for transcription to occur
DNA Methylation
(or DNA methylase)
CH3
Only one strand is
methylated
CH3
Both strands are
methylated
CH3
Figure 15.15
• DNA methylation usually inhibits the transcription of
eukaryotic genes
– Especially when it occurs in the vicinity of the promoter
• In vertebrates and plants, many genes contain
CpG islands near their promoters (not common
in yeast and Drosophila)
– These CpG islands are 1,000 to 2,000 nucleotides long
– In housekeeping genes
• The CpG islands are unmethylated
• Genes tend to be expressed in most cell types
– In tissue-specific genes
• The expression of these genes may be silenced by the
methylation of CpG islands
Figure 15.16 Transcriptional silencing via methylation
Transcriptional
activator binds to
unmethylated DNA
This would inhibit the
initiation of transcription
Can also cause conformational changes of chromatin
Stability of mRNA
• The stability of eukaryotic mRNA varies considerably
– Several minutes to several days
• The stability of mRNA can be regulated so that its
half-life is shortened or lengthened
– This will greatly influence the mRNA concentration
• And consequently gene expression
• Factors that can affect mRNA stability include
– 1. Length of the polyA tail
– 2. Destabilizing elements (e.g. AU-rich elements)
Initiation Factors and the Rate of
Translation
• Modulation of translation initiation factors is widely
used to control fundamental cellular processes
• Under certain conditions, it is advantageous for a
cell to stop synthesizing proteins
– Viral infection
• So that the virus cannot manufacture viral proteins
– Starvation
• So that the cell conserves resources
Transmission of DNA
By Mitosis
(CHAPTER 3- Brooker Text)
BIO 184
Dr. Tom Peavy
Mitosis
Eukaryotic cells that are
destined to divide progress
through a series of stages
known as the cell cycle
Synthesis
Gap 1
Gap 2
Figure 3.6 (b)
• Mitosis is subdivided into five phases
– Prophase
– Prometaphase
– Metaphase
– Anaphase
– Telophase
• Chromosomes are
decondensed
• By the end of this
phase, the
chromosomes have
already replicated
– But the six pairs of
sister chromatids are
not seen until prophase
• The centrosome
divides
• Nuclear envelope
dissociates into
smaller vesicles
• Centrosomes
separate to
opposite poles
• The mitotic spindle
apparatus is formed
– Composed of
mircotubules (MTs)
• Spindle fibers interact
with the sister chromatids
• Kinetochore microtubules
grow from the two poles
– If they make contact with a
kinetochore, the sister
chromatid is “captured”
– If not, the microtubule
depolymerizes and retracts
to the centrosome
• The two kinetochores on
a pair of sister chromatids
are attached to
kinetochore MTs on
opposite poles
• Pairs of sister
chromatids align
themselves along a
plane called the
metaphase plate
• Each pair of
chromatids is
attached to both
poles by kinetochore
microtubules
• The connection holding
the sister chromatids
together is broken
• Each chromatid, now an
individual chromosome,
is linked to only one pole
• As anaphase proceeds
– Kinetochore MTs shorten
• Chromosomes move to
opposite poles
• Chromosomes reach
their respective poles
and decondense
• Nuclear membrane
reforms to form two
separate nuclei
• In most cases,
mitosis is quickly
followed by
cytokinesis
Meiosis &
Chromosomal Theory
(CHAPTER 3- Brooker Text)
MEIOSIS
• Like mitosis, meiosis begins after a cell has
progressed through interphase of the cell cycle
• Unlike mitosis, meiosis involves two successive
divisions
– These are termed Meiosis I and II
– Each of these is subdivided into
•
•
•
•
•
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
Figure 3.12
Spindle apparatus complete
Chromatids attached via
kinetochore microtubules
• Bivalents are organized
along the metaphase plate
– Pairs of sister chromatids are
aligned in a double row, rather
than a single row (as in
mitosis)
• The arrangement is random
with regards to the (blue and
red) homologues
– Furthermore
• A pair of sister chromatids is
linked to one of the poles
• And the homologous pair is
linked to the opposite pole
Figure 3.13
The two pairs of sister chromatids
separate from each other
However, the connection that
holds sister chromatids together
does not break
Sister chromatids reach their
respective poles and decondense
Nuclear envelope reforms to produce
two separate nuclei