Term
| What is the proximal promoters structure? |
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Definition
| A promoter around 80-120bp away from the core promoter, which has both activator and repressor binding sites. Has a CCAAT box that is bound by CTF and NF1 factors ( CCAAT TF and Nuclear factor 1) and C/EBO (CCAAT enhancer binding proteins). |
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Term
| What is a SP1 site in relation to proximal promoters? |
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Definition
| A factor that binds with CpG islands - has 3 zinc fingers for specificity |
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Term
| What do yeast genes have instead of enhancers? |
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Definition
| Upstream activation sequences (300-500bp) away from promoter |
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Term
| How far away from the core promoter can enhancers be? |
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Definition
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Term
| What sort of structure do enhancers have and what does this mean> |
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Definition
| Modular organsation - contain binding sites for multiple reactions - different combination can regulate expression |
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Term
| How is the human immunoglobulin kappa light chain gene enhancer regulated? |
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Definition
| The variable region is encoded by distant DNA sequences which are brought together during B cell development via somatic recombination. There are around 300 DNA sequences for variable genes that can all undergo recombination events - generating antibody diversity |
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Term
| What are super enhancers and what to they typically activate? |
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Definition
| clusters of several enhancers that activate gene expression at a higher level than regular enhancers - typically regulate key genes that determine cell type |
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Term
| What are LCRs and what do they do? |
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Definition
| Locus control regions - control families of genes - override other factors and are typically evolved in development |
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Term
| What are DNA hypersensitivity sites believed to correspond too? |
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Definition
| Areas where the DNA is accesible to interacting proteins |
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Term
| When do co-activators bind? |
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Definition
| When transcription activator proteins (enhancers) bind to DNA |
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Term
| How is the 'finger' formed in the zinc finger binding domain/ |
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Definition
| The cys and his residues interact with the zinc |
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Term
| What does the zinc finger bind DNA in? |
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Definition
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Term
| Where do helix-turn-helix domains bind DNA and what is their structure? |
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Definition
| Major groove, two alpha helices, one slightly longer, linked by a turn - forms a homodimer |
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Term
| How can Id proteins prevent HTH binding? |
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Definition
| By forming heterodimers with proteins with HTH domains - preventing them forming homodimers |
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Term
| How does a bZip domain bind DNA? |
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Definition
| dimerise at the basic region before binding DNA as a helix - recognises sites with double symmetry |
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Term
| How do transcriptional activators tend to bind DNA? |
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Definition
| mediated by DNA binding domain within the amino acid sequence. Can also identify positive or negative charges -known as acidic or negative activation domains. There are also specific binding domains such as SP1, Ap1 or OCT2 |
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