(CHAPTER 15- Brooker Text) October 23 & 25, 2007 Bio 184 Dr. Tom Peavy 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

Figure 15.5 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. Gene amplification 2. Gene rearrangement 3. DNA methylation 4. 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

Only one strand is methylated Both strands are methylated DNA Methylation CH3 (or DNA methylase) Only one strand is methylated CH3 Both strands are methylated 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

(CHAPTER 3- Brooker Text) Transmission of DNA By Mitosis (CHAPTER 3- Brooker Text) BIO 184 Dr. Tom Peavy

Mitosis Synthesis Gap 1 Gap 2 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

(CHAPTER 3- Brooker Text) 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 Figure 3.12

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