(CHAPTER 15- Brooker Text)

October 23 & 25, 2007Bio 184

Dr. Tom Peavy

Eukaryotic

Gene Regulation

Eukaryotic Gene 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)

Transcriptional Regulation:

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

• 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 enhancersrepressors bind silencers

• 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

Regulation of Regulatory Transcription Factors

Figure 15.5

The transcription factor can now bind to DNA

Formation of homodimers and

heterodimers

• Changes in chromatin structure can involve changes in the structure of DNA and/or changes in chromosomal compaction

• These changes include– 1. Gene amplification– 2. Gene rearrangement– 3. DNA methylation– 4. Chromatin compaction

CHANGES IN CHROMATIN STRUCTURE

Uncommon ways to regulate gene expression

Common ways to regulate gene expression

• 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

Chromatin Structure

Figure 15.15

(or DNA methylase) CH3

CH3

CH3

Only one strand is methylated

Both strands are methylated

DNA Methylation

• 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

Transcriptional silencing via methylationFigure 15.16

Transcriptional activator binds to

unmethylated DNA

This would inhibit the initiation of transcription

Can also cause conformational changes of chromatin

• 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)

Stability of mRNA

• 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

Initiation Factors and the Rate of Translation

(CHAPTER 3- Brooker Text)

Transmission of DNA

By Mitosis

BIO 184Dr. Tom Peavy

MitosisEukaryotic cells that are destined to divide progress through a series of stages known as the cell cycle

Gap 1 Gap 2

Synthesis

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

(CHAPTER 3- Brooker Text)

Meiosis &

Chromosomal Theory

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 completeChromatids 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 poleFigure 3.13

The two pairs of sister chromatids separate from each otherHowever, the connection that holds sister chromatids together does not break

Sister chromatids reach their respective poles and decondenseNuclear envelope reforms to produce two separate nuclei