MBMB 451A Section One - Fall 2006
Chromatin and TranscriptionCofactor or Coactivator 1. work with DNA specific transcription factors to make them more effective - examples A. TFIID B. yeast mediator - contains 20 polypeptides binds to the CTD of RNA polymerase II C. CBP/p300 works with CREB protein D. TRAPS - steroid receptor protein cofactor E. OCA-B with Oct 1 protein F. SAGA complex - contains Ada proteins (adaptor protein) one of which is also known as Gcn5 works with acidic activators such as Gal4 protein or Gal4-VP16 2. Several of these proteins modify chromatin acetylation of histone tails A. TAFII 250 acetylates histones B. Gcn5 is one of the first characterized histone acetyl transferases (HAT) Gaining Access to the DNA - Large multi-subunit protein complexes alter the state of chromatin figure 21.16 (Genes VII) 1. ATP-dependent chromatin remodeling machines a. they contain a DNA dependent or nucleosome dependent ATPase subunit i. the ATPase activity is essential point mutations in the ATPase domain knocks out the chromatin remodeling activity ii. other subunits are also associated with the ATPase subunit that make up the complete complex (range in number from 1-10) iii. some of these other subunits are actin related proteins called ARPs iv. there is also sequence similarity between several of the other subunits which are indications of a conserved core functional complex . b. they alter the structure of the nucleosome i. the nucleosomal DNA is made more accessible for binding to transcription factors figure 21.17 (Genes VII) ii. changes can also be observed by measuring access to cutting by restriction endonucleases iii. changes have also been observed in DNA supercoiling suggesting a change in the path of DNA around the nucleosome iv. electron microscopy studies have suggested a reduction on the amount of DNA wrapped in the remodeled nucleosome c. sliding of the nucleosome on DNA can also be observed i. changes in electrophoretic mobility is observed ii. MNase mapping also shows changes in translational positioning 2. Different classes of chromatin remodeling complexes a. SWI/SNF or SWI-SNF like complexes required for activation of a small subset of genes found in humans, flies, and yeast at least two different forms of the complex in yeast or humans in yeast it has 11or 15 subunits total complex is 2 Megadaltons in size b. ISWI or imitation SWI complexes -its DNA dependent ATPase subunit is similar to the ATPase subunit of SWI/SNF -has the distniguishing protein domain called SANT -smaller complexes: they have only 1-4 subunits -more abundant and play a more global role -are involved in transcriptional repression - there are three distinct ISWI complexes in flies and yeast c. Mi-2 or CHD complexes -these chromatin remodeling complexes are associated with histone deacetylases (HDAC) - see below for more info - ATPase subunit has sequence homology to the ATPase subunit of SWI/SNF belongs to the Swi2 superfamily, but makes up its own subfamily d. INO80 complex -involved in DNA repair -has DNA helicase activity associated with the complex e. SWR1 complex -promotes the exchange of H2A from the nucleosome -brings in the H2A variant called H2AZ 3. These complexes can be recruited to specific chromatin sites by a. transcriptional activators such as SWI/SNF by Gal4, Gcn5 and the glucocorticoid receptor protein b. repressors such as the ISWI complex from yeast called ISW2 by the Ume6 repressor protein 4. Histone acetyltransferases (HATs) a. cytoplasmic HATs (Type B) i. acetylate newly synthesized H3 and H4 histones before depositing on to DNA ii. after binding to DNA the acetyl groups are removed b. nuclear HATs (Type A) i. have been found to be required for gene activation ii. part of TFIID has HAT activity (TAFII250) iii. these HAT proteins are usually large multi-subunit complexes two classes: the GNAT and MYST families iv. are often targeted to specific regions through protein-protein interactions with promoter-specific transcription factors bound to their response elements figure 21.19 and 21.20 (Genes VII) example is recuitment of the SAGA complex by Gal4 c. HATs are associated with or recruited by transcription activators d. The histone deacetylases or HDACs are associated with corepressor and inhibit transcription 5. Histone methyltransferases a. methylation of lysine or arginine b. methylation helps proteins containing chromodomains bind to nucleosome c. some of the proteins that contain chromodomains are know to help form heterochromatin example is heterochromatin protein 1 or HP1 d. competition between acetylation and methylation
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Last updated on September 14, 2006 .
