Chapter 12 - Gene Regulation

Motif o o the largest in mammals the zinc ion of each

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Unformatted text preview: mmals The zinc ion of each finger is held in place by 2 cysteines and 2 histidines Helix-loop-Helix Motif o o o Has 2 alpha-helical segments separated by a loop HLH domain often preceded by a stretch of highly basic amino acids (basic HLH or bHLH) positively charged amino acids contact DNA which determines sequence specificity bHLH proteins always occur as dimmers, or heterodimers (encoded by different genes) Leucine Zipper Motif o o o o leucines occur every 7th amino acid along a stretch of alpha helix alpha helix turns every 3.5 resudues so leucines all face the same directions two of these alpha helices can zip together to form a coiled coil dimers basic amino acids on one side of leucine-containing helix recognise DNA Regulating Transcription o TATA box is part of eukaryotic core promoter determines where transcription starts 3 o o Other promoter regions help regulate the frequency of transcription because of proximity to start of a gene, they are referred to as proximal promoter elements Alternative promoter allow some genes to be transcribed at more than one site PEPCK gene o PEPCK gene (phosphoenolpyruvate carboxykinase) glucogenesis pathway converts pyruvate to glucose core promoter is where initiation complex assembles Regulating Transcription o o o o o o o o o Researchers use the following techniques to find DNA sequences involved in regulation: deletion mapping, DNA footprinting, genome-wide location analysis Genome wide location analysis allows simultaneous monitoring of all the sites within the genome that carry a particular activity The goal of genome wide location analysis is to identify all the sites in the genome bound by a particular transcription factor under a given set of conditions Deletion mapping make DNA with dleletions in different region towards the 5 end of transcription start site (to the left) monitor transcription DNA footprinting bound transcription factors protect DNA from digestion by nucleases isolate chromatin from cells, digest with nucleases and identify the protected areas Expression of most genes is also regulated by even more distant DNA elements Enhancers are DNA elements that stimulate transcription can be located very far upstream from the regulated gene and can be moved or flipped without losing its function Enhancers are restricted to a given promoter by insulators Coactivators serve as intermediates for transcription factors, and are divided into 2 classes those that interact with transcription machinery and those that alter chromatin structure by modifiying histones to regulate transcription (using histone acetyltransferases, HATS and chromatin remodelling complexes) Coactivators o o Those that interact with the transcription machinery recruit and interact with transcription machinery such as GTFs (general transcription factors, like TFIID or RNA polymerase Those that alter chromatin structure modifiying histones to regulate transcription incorporate DNA into nucleosomes (wrapped around histones) impede access to DNA inhibits initiation and elongation of transcription Altering Chromatin Structure o o Nucleosomes have an N terminal tail that can be convalently modified modification impact chromatin structure and function (example: methylation of H3 causes transcriptional silencing) Acetylation of histone residues prevents chromatin from forming compact structures maintains euchrom...
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