Term
| how do you discover whether a cis element is necessary or not for transcription? |
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Definition
| make mutations and/or deletions & see which sequence prevents transcription (or prevents repression of transcription if you're messing with a down-regulator) |
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Term
| how do you discover whether something is sufficient for transcription? |
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Definition
| move cis element into a gene that is not normally transcribed & see if you can induce transcription |
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Term
| where do you find the core promoter? |
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Definition
| cis element very close to the start site of the gene |
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Term
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Definition
| position RNA polymerase at the transcription start site so that it is poised to initiate transcription at the right place with the right "friends" that enable it to do so |
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Term
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Definition
| amplify the signal of transcription |
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Term
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Definition
| dampens the signal of transcription |
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Term
| what proteins do enhancers & silencers bind to do their jobs? |
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Definition
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Term
| how were distal enhancers found? |
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Definition
| they did ChIP (chromatin immunoprecipitate) & found out that transcription factor that binds very far away is necessary for transcription --> then co-IP that transcription factor & figure out which part of the DNA sequence they bind to (discovered that these sequences are found very far away from transcription start site) |
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Term
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Definition
| trans-acting factors that every gene uses |
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Term
| do genes have specific trans-acting factors? |
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Definition
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Term
| RNA polymerase is made up of ______ enzymes |
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Definition
|
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Term
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Definition
| active binding site where it does its stuff |
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Term
| GTFII works with ______ to do transcription |
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Definition
|
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Term
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Definition
| TATA binding protein subunit |
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Term
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Definition
| sticks its nose into the active site of the RNA polymerase & helps position the active site near the transcription start site |
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Term
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Definition
| binds near B & D & stabilizes them |
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Term
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Definition
| recruits H to the complex |
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Term
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Definition
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Term
| 5 possible roles for transcription factors |
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Definition
1. bind DNA
2. scaffolding proteins
3. enzymes
4. remodelers
5. co-activators |
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Term
| 2 possible results of PTM modifications that can happen on histones |
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Definition
1. make binding sites for transcription factors
2. weaken nucleosomes |
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Term
| Why are there many more unique scaffolding & DNA binding proteins than there are co-activators? |
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Definition
| they need to be more specific |
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Term
| 3 major types of histones |
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Definition
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Term
| why are tails on the histones what are modified by modifying transcription factors? |
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Definition
| accessible outside of the nucleosome |
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Term
| is DNA available for transcription while in the nucleosome formation? |
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Definition
|
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Term
| what is the implication that transcription factors can be "friendly"? |
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Definition
| you can get a bunch binding within a very short stretch of nucleotides (only 50!) |
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Term
| layout of nucleosomes along the DNA |
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Definition
| about 147 base pairs of DNA wrapped around histone (forming the nucleosome) followed by 50-80 base pairs between that nucleosome & the next one |
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Term
| what is the highly structured order of nucleosomes along the DNA? |
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Definition
| package together in solenoids with nucleosome-free regions between them |
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Term
| how do you get transcription cis elements that are so far away to come together? |
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Definition
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Term
| how does the cell know which nucleosome to remove? |
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Definition
| what is unique is the DNA sequence being hidden |
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Term
| pioneer transcription factors |
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Definition
| bind to DNA on surface of nucleosome & recruit remodelers/histone modifiers |
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Term
| what is the protein that forms a ring around the two DNA strands in the loop to help stabilize it to bring the various enhancers together? |
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Definition
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Term
| _______ attaches to double-stranded DNA but reads single-stranded DNA |
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Definition
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