Term
| What is the function of UAS binding |
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Definition
| to bring the activation domain into proximity of the promoter |
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Term
| Descripe Gal4p activation domain |
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Definition
| They are acidic with high levels of aspartic and glutamic acid. They also have key hydrophobic residues. These residues are though to form adhesive surface for protein interaction. The activation domain function is regulated recruitment of proteins important for transcription. |
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Term
| Immobilized template assays. |
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Definition
Have beads with DNA bound that contain promoter.
Add transcription factor
Add various proteins that bind DNA(TFII, polI)
Washaway unbound proteins.
Add NTPs and allow transcription to proceed.
Analyze transcripts by primer extension. |
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Term
| What needs Gal4-AH to bind |
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Definition
TFIIB requires it and everything after depends on TFIIB binding.
Only TFIID can bind without it. |
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Term
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Definition
| second site mutation is within the same gene as the first mutation. |
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Term
| Intergenic(extragenic) suppressors |
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Definition
| The second mutation is in another gene. Mutation can help restore the binding ability between the Two proteins |
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Term
| Activator bypass eperiment |
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Definition
Gal11P is a point mutation in Gal11 subunit. Creates a surface that just happens to bind to the Gal4 DNA binding-dimerization domain.
Gal11P is an intergenic suppressor mutation.
This mutation allows the normally non-activating Gal4P DNA binding domain to recruit the holoenzyme complex and activate transcription |
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Term
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Definition
Spt-Ada-Gcn5-acetyltransferage. Helps facilitate the binding of TBP to natural promoters (a coactivator, saga does not bind to DNA, but is held near promoters by protein protein interactions). Saga also contains the Gcn5 protein, a histone acetyltransferase.
Required for induction of the GAL genes upon switching cells to galactose. Spt3p and Spt20p are subunits of the saga complex |
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Term
| chromatin immunoprecipitation |
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Definition
ChIP- a powerful method to determine the sites along a chromosome where interaction with specific proteins occurs within living cells.
Add formaldehyde. Creates covalent crosslinks between proteins and DNA.
Prepare cell lysate and sonicate to break chromatin into smaller pieces.
Add antibody that specifically binds to the protein of interest.
Antibody-protein-DNA complexes are bound to protein- A beads to precipitate.
The DNA sequence associated with the protein comes along for the ride. This allows preparation of a DNA sample enriched in the DNA sequences associated with the protein. |
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Term
| what is the order of factor binding at the GAL1 promoter upon induction of transcription |
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Definition
Gal4p occupancy increases first
then saga/TBP
then polII |
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Term
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Definition
| A saga protein with HAT activity that may locally acetylate histones and promote RNA polII binding. Its not required at GAL1 but is required for normal transcription of other saga regulated genes. |
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Term
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Definition
DNA sequences
orientation independent
act at long distances
contain several binding sites for multiple transcrription factors
associated with DNase I HS sites
Have specific binding sites transcription factors that are only produced in that cell. |
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Term
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Definition
liver specific protein
only transcribed in hepatocytes
enhancer has binding sites for AP1 and HNF4
Promoter has sites for HNF1 and HNF3
Without HNF1 and HNF3 the enhancer cannot activate transcription |
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Term
| when does Beta globin take over in humans |
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Definition
| about 10 weeks after birth |
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Term
| What confers high levels of transcription |
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Definition
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Term
| Developmental specificity |
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Definition
| determined by stage specific transcription factors mainly bound to the promoter |
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Term
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Definition
| determined by transcription factors bound both at promoters and LCR |
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Term
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Definition
human erythroleukemia cells
transcribe globin genes. |
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Term
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Definition
| chromosomal deletion that removes most of LCR from one copy of chromosome 11. They get no transcription of globin mRNA from that chromosome so they are thalassemic. |
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Term
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Definition
| non homologous end joining. will insert DNA into recipients chromosome.Happens in Metazoan. Alternative to homologous recombination. Often get multiple copies at the same site. |
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Term
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Definition
| erythroid kruppel-like factor, required for beta globin transcription, but not for gamma or sima. binds to CCACACCCT |
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Term
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Definition
| the first erythroid specific transcription factor identified, required for erythroid cell maturation. binds to WGATAR, which is overrepresented in the globin locus. |
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Term
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Definition
| Determines what protein is binding to the specific sequence by using a column. |
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Term
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Definition
| clone the promoter and enhancer regions adjacent to a reporter gene. You can then measure the reporter gene. after transforming the plasmid into cells |
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Term
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Definition
| a reporter gene. Reacts with substrates luciferin and ATP to emit visible light, measure in light detection instrument called a luminometer. |
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Term
| HSV thymidine kinase gene |
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Definition
| used in gene knockout. gets killed by gancyclovir. used to enrich the homologous recombinants. |
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Term
| Cromosome conformation capture analysis |
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Definition
| used to detect loops. Use formaldehyde to seal the bonds between DNA and protein. Then use restriction enzymes. then use proximity ligation and analyze with PCR. Sequences that were thousands of base pairs apart in the chromosome are now ligated together only a few hundred base pairs apart |
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Term
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Definition
| active chromosome hub- the spatial clustering of active genes and their regulatory elements. |
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Term
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Definition
| additional regulatory elements that prevent mis regulation of genes in eukaryotes. prevent regulatory elements of one domain from influencing promoters in a different domain. |
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Term
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Definition
| insulator protein that binds HS4 site. In chickens. not involved in barrier activity |
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Term
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Definition
| demarcrates the boundary between euchromatin and heterochromatin in chickens. |
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Term
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Definition
| actively transcribed genes are associated with hyperacetylation of histones H3 and H4 and methylation of H3 lys 4, while the condensed heterochromatic and non-transcribed region are hypoactelylated and methylated at h3 lys 9 |
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Term
| benefits of the yeast mating type |
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Definition
| cells with the same genotype give rise to cells with different phenotypes. |
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Term
| Heterochromatic gene silencing |
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Definition
| differs from simple repression in that larger regions of a chromosome, not just an individual promoter are repressed. |
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Term
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Definition
| changes in gene expression patterns that are heritable but do not involve changes in the DNA sequence of the genes involved. |
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Term
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Definition
| position effect variegation- the same gene in genetically identical cells can have different expression patterns. Due to heterogeneous patterns of chromatin structure and modification. |
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Term
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Definition
| expressed in all cell types- activator of a-cell specific genes |
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Term
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Definition
| very basic with lysine and arganine residues. high transcription is likely due to acetylation of histones. |
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Term
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Definition
| histone methyl transferase |
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Term
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Definition
| origin recognition complex- normally involved in initiation of DNA replication, but when bound to silencer DNA acts as an initiator of silencing. a complex of six proteins |
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Term
| Rap1p and Abf1P. multifuntion proteins can act as transcriptional activators at some promoters, but are repressors at the HM loci |
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Definition
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Term
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Definition
| mutation in the silencer DNA sequence that inhibit the binding of ORC, Rap1-, or Abf1- to the silencer sequence |
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Term
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Definition
| silent information regulators. required for propagation of the silenced chromatin. |
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Term
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Definition
| required for full silencing of HMR and HML. Sir1 mutants consist of 80% silenenced cells and 20% derepressed |
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Term
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Definition
| an NAD dependent histone deacetylase. removes acetyl groups from histones, preferentially at lysine 16 of histone H4. Sir2-like proteins are consereved from bacteria to mammals. Has additional roles in cellular aging |
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Term
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Definition
| seem to coat the silenced region by binding to histone tails. Sir3p is known to bind more strongly to deactylated histones. sir proteins are also known to bind each other. |
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Term
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Definition
| histone acetyltransferaces believed to counteract sir2p function |
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Term
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Definition
| bind to acetylated histone tails and help prevent inappropriate spreading of silencing. At HMR, mutation of BDF1 or YTA7 genes lead to spread of silencing |
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Term
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Definition
| required to keep the mating type genes repressed. localized to the heterochromatic region. binds to the histone H3 tail only when the tail is methylated at lysine 9. H3 lys 9 is localized to the exact same chromomal region as swi6. Contains a chromodomain, which is a protein domain that binds to methylated lysines. |
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Term
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Definition
| when its methylated it is excluded from the silencing regions |
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Term
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Definition
| ubiquitylates histone H2b at lysine 123 |
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Term
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Definition
| methylates histone H3 at lysine 4 |
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Term
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Definition
| methyl-CpG binding protien. binds methylated DNA. includes histone deacetylases. promotes condensation so repression |
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Term
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Definition
| a form of epigenetic regulation that regulates transcription of a homologous pair of alleles based on which parent the gene was inherited from. |
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Term
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Definition
| insulin like growth factor2. Only paternal gets expressed. required for prenatal growth. the genomic thing causes methylation of insulator. this means that CTCF cant bind. |
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