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Genetics Lecture No. 17.docx

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Biology 2581B
Jim Karagiannis

Genetics Lecture No. 17: Eukaryotic Gene Regulation Wednesday March 13 , 2013h Complexities In Eukaryotic Gene Regulation: -Different cell types display vastly different morphologies, functions, and behaviours. Though fibroblasts (secrete components of ECM for the formation of connective tissue) and neurons (process information) are very different cells, they both possess the same underlying genetic material. The phenotypic differences of the cells can be partly explained by gene regulation. In the cloning of Dolly the sheep, a fibroblast cell was taken from an adult sheep and its nuclear material was then transferred into an enucleated egg cell, where they fuse together. That fibroblast was able to direct the formation of a fully functional normal sheep. All the information required to create a fully functional sheep is present in any particular cell type. Differences in different eukaryotic cell types have to do with how that information is used in a process called differential expression. Differing Regulation (Differential Expression) Of Genes: -Genes are regulated differently across tissues (gene expression is different for different sets of genes in different tissues), across time (gene expression is different for different sets of genes at different parts of the cell cycle), and during development (gene expression is different for different sets of genes at different stages of eukaryotic development). Eukaryotes & Gene Expression: -Eukaryotes are developmentally complex, multicellular systems that need to coordinate gene expression in various tissues, at various times in the cell cycle or development, and in response to external signals. Eukaryotes have a much larger genome than prokaryotes and organize their genetic material (using histones) into nucleosomes and chromatin (prokaryotes have DNA in the form of chromatin alone). Human Genome = 3 x 10 base-pairs E. Coli = 4 x 10 base-pairs Regular Protein Recognition Site = 12 base-pairs How unique is that cis-acting sequence? 4 = 16, 000, 000 different possible configurations For E. Coli = 4 x 10 * 2 (cis-acting sequences on both strands) / 16 000 000 = 0.5 Therefore not very probable to have a cis-acting sequence by chance. For Humans = 3 x 10 * 2 (cis-acting sequences on both strands) / 16 000 000 = 375 Therefore highly probable to have many cis-acting sequences by chance. -Eukaryotes can have up to 700 times more DNA and 10 times more genes than a typical prokaryote. The problem with this is that it is more difficult for eukaryotes to achieve specificity in regulation. This issue is resolved through higher affinity binding of proteins to DNA and through the control of gene expression requiring the presence or absence of a particular combination of proteins (combinatorial control). The Three RNA Polymerases In Eukaryotes: -There are three RNA polymerases in eukaryotes: RNA Polymerase I (transcribes tandem repeats of rRNA genes), RNA Polymerase II (transcribes protein-encoding mRNA and microRNA genes), and RNA Polymerase III (transcribes tRNA and 5S rRNA genes). Each protein-encoding gene has a complex and unique set of cis-regulatory regions (some nearby, some up to tens of thousands of nucleotides away) that influence the ability of RNA pol II to initiate transcription. Recall that gene expression in eukaryotes involves transcription and mRNA processing in the nucleus, then translation and modifications in the cytoplasm in order to produce an active protein. The Role Of Chromatin In Eukaryotic Transcription: -Eukaryotes organize their genetic material into nucleosomes and chromatin, where the tight packaging of DNA and the associated histones act as a barrier to transcription. The DNA must unwrap and the histones (negative regulator to transcription) must be moved to allow transcription. DNA molecules containing a promoter and an associated gene can be purified away from chromatin proteins in vitro. The addition of basal factors and RNA polymerase to this purified (naked) DNA induces high levels of transcription. Within the eukaryotic nucleus, DNA is present within chromatin. Promoter regions are generally sequestered within the nucleosome and only rarely bind to basal factors and RNA polymerase. Thus, the chromatin structure maintains basal transcription at very low levels. Chromatin remodelling can expose the promoter region. Remodelling proteins cause specific nucleosomes to unravel in specific cells at specific times during differentiation or development. These exposed promoter regions more readily bind basal factors. As chromatin makes promoter sequences less accessible to RNA pol II, mechanisms affecting chromatin structure are critical to gene regulation in eukaryotes, but not prokaryotes. Cis- & Trans-Acting Elements In Prokaryotes Vs. Eukaryotes: -Prokaryotes have cis-acting elements (positive regulatory sequences e.g. where CRP binds, promoters, operators) and trans-acting elements (RNA polymerase, activator proteins, repressor proteins). Eukaryotes have cis-acting elements (enhancers, core promoters, silencers, insulators) and trans-acting elements (RNA polymerase II, basal factors, activator proteins, repressor proteins). Cis-acting regulatory elements are regions of the DNA sequence that lie nearby on the same DNA molecule as the gene they control. Promoter elements typically lie directly adjacent to the gene that they control. Enhancers that regulate expression can sometimes lay
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