Term
| The five main regulatory levels of gene expression |
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Definition
| Genome, transcription, RNA processing and export, translation, posttranslational events |
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Term
| translational control -- give an example |
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Definition
| examples include control of gene expression by RNAi and microRNAs |
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Term
| Genome and control of gene expression |
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Definition
| For chromatin: Includes control over gene amplification/deletion (rare), DNA rearrangements (rare), DNA methylation, chromatin decondensation and condensation, histone modifications (ex: methylation, acetylation), changes in HMG proteins |
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Definition
| CHECK WHAT THIS MEANS AND WHAT IT DOES FOR GENE EXPRESSION IN CONTEXT OF GENOME |
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Definition
| CHECK WHAT THIS MEANS AND WHAT IT DOES FOR GENE EXPRESSION IN CONTEXT OF GENOME |
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Term
| transcription and control of gene expression |
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Definition
| For genes available for expression: Transcription -- controlled by transcription factors |
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Definition
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Term
| RNA processing and nuclear export -- control of gene expression |
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Definition
| For primary RNA transcript (pre-mRNA): RNA splicing and other processing events; for mRNA in nucleus: transport of mRNA to cytoplasm |
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Term
| Translation and control of gene expression |
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Definition
| For mRNA in cytosol: mRNA degradation; alternatively: Translation (polypeptide synthesis): includes targeting of some newly forming polypeptides to the ER, plus control of translation by initiation factors and translational repressors, including microRNAs |
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Term
| Posttranslational control of gene expression |
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Definition
| For polypeptide product in cytosol or ER: includes protein folding and assembly, possibly polypeptide cleavage, possible modification, possible import into organelles. For functional proteins: includes possible protein degradation |
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Term
| What is RNAi (RNA interference) based on? |
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Definition
| Based on the ability of small RNAs to trigger mRNA degradation; mRNAs can be controlled by a class of small RNA molecules that inhibit their expression via sequence complementarity |
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Term
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Definition
| a cytoplasmic ribonuclease that cleaves double stranded RNA into short fragments about 21-22 bp long --> result is siRNAs (small interfering RNAs) |
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Term
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Definition
| the fragments that result after Dicer cleaves double-stranded RNA into short fragments about 21-22 bp long |
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Term
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Definition
| RNA-induced silencing complex |
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Term
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Definition
| the result of siRNAs combining with a group of proteins to form an inhibitor of gene expression called RISC (RNA-induced silencing complex) --> in this case, RISC is called siRISC |
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Term
| What is the function of the passenger strand of siRNA? |
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Definition
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Term
| What is the function of the guide strand of siRNA? |
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Definition
| Binds the siRISC to a target mRNA by complementary base pairing |
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Term
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Definition
| If siRNA is exactly complementary to the target mRNA, the enzyme Slicer cleaves the target mRNA |
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Term
| What happens if complementarity is only partial between siRNA and target mRNA? |
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Definition
| Translation of mRNA is inhibited; mRNA isn't degraded |
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Term
| RDRP -- what is it? where is it found? what does it do? |
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Definition
| Plants and C. elegans have RDRP (RNA-dependent RNA polymerase) which can make dsRNA (double stranded RNA) using mRNA as a template, amplifying the effect of RNAi (RNA interference) |
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Term
| Petunia example, slide 13 -- explain how RNAi and RDRP combine to lead to destruction of mRNA |
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Definition
-transformation of wild-type petunia with a transgene encoding a pigment-producing protein can lead to a loss of pigment (white areas) due to RNAi
-What happens: extra copies of the gene result in a very high level of mRNA encoding the pigment-producing enzyme, which activates RDRP. RDRP makes dsRNA that initiates RNAi, leading to destruction of this mRNA |
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Term
| Primary microRNAs (pri-mRNAs) |
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Definition
| Initial form of miRNAs -- pri-mRNAs are longer molecules that fold into hairpin loops |
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Term
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Definition
| cleaves pri-mRNAs into smaller hairpins called precursor miRNAs or pre-miRNAs |
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Term
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Definition
| after pre-miRNAs are exported to the cytoplasm, Dicer cleaves them to form a miRNA |
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Term
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Definition
| formed by miRNA being added to additional proteins; miRISC inhibits expression of mRNAs containing sequences complementary to the miRNA |
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Term
| What does miRISC degrade or not degrade? |
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Definition
| -mRNAs with fully complementary sequences are degraded by miRISC; mRNAs with partially complementary sequences are translationally inhibited |
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Term
| True or false - several miRNAs can target the same mRNA |
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Definition
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Term
| What is one important role of miRNAs? |
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Definition
| miRNAs play important roles in embryonic development |
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Term
| How is cancer related to miRNA? |
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Definition
| cancer cells produce excessive amounts of some miRNAs and insufficient amounts of others |
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Term
| How can miRNA act as an oncogene? |
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Definition
Example: miR-17-92 inhibits translation of PTEN, a phosphatase that inhibits PI3K-Akt signaling pathways. Overproduction of this miRNA leads to constitutive activation of the PI3K-Akt signaling pathway and consequent enhancement of cell proliferation.
Similarly: miR-155 and miR-21 inhibit expression of two genes involved in DNA mismatch repair (HSH2 and MLH1); their overexpression can cause inability to carry out DNA repair. |
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Term
| How can miRNA act as a tumor suppressor? |
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Definition
-the miR-15a/miR-16-1 cluster is often deleted in certain forms of leukemia; one of the functions of these miRNAs is to inhibit Bcl-2, a protein that inhibits apoptosis
-Too little miR-15a/miR-16-1 leads to lack of inhibition of Bcl-2 and thus to inability of the cell to carry out apoptosis when needed
-miR-29 works in a similar way (regulates expression of an anti-apoptotic protein similar to Bcl-2)
-let-7 regulates expression of RAS oncogenes |
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Term
| How can miRNAs influence histone modifications? |
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Definition
-miR-101 is frequently deleted in prostate cancer; this miRNA normally inhibits synthesis of EZH2, a protein that catalyzes histone methylation
-loss of miR-101 is therefore associated with increased histone methylation and silencing of some tumor suppressor genes |
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Term
| RNAi knockdown -- what is it? |
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Definition
| RNAi is very actively used in research to selectively silence genes of interest (THIS is RNAi knockdown) |
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Term
| Uses of siRNAs in research and therapeutics? |
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Definition
-RNAi knockdown
-RNAi may be used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process
-RNAi is also a promising therapeutic approach, especially for orphan diseases for which no treatment currently exists
-several RNAi drugs are in clinical development to treat a variety of diseases, but none are approved yet
-ex: using RNAi to lower cholesterol levels; this would provide an alternative to statins (drugs that lower cholesterol levels by inhibiting the enzyme that synthesizes cholesterol) |
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Term
| What is the biggest problem in developing RNAi therapeutics? |
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Definition
| RNAi delivery -- RNA is charge and so it can't cross the cell membrane; RNA is also unstable as it is degraded by RNAses |
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Term
| What are some solutions to the problem of RNAi therapeutic delivery? |
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Definition
-using artificial backbones/modifications to stabilize siRNAs
-developing new methods for targeted delivery of siRNAs to the target tissue (liposomes, nanoparticles, etc.) |
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Term
| name some RNAi delivery options |
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Definition
DO WE NEED TO KNOW THIS?
-naked siRNA (not very effective), cholesterol conjugated siRNA, aptamer conjugated siRNA, liposome formulated siRNA, antibody-protamine complexed siRNA |
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