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42 Cards in this Set
- Front
- Back
Levels of gene expression control |
transcriptional, mRNA processing, translational, post-translational |
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transcriptional factor regulations: |
presence of DNA motif in promoter, promoter accessibility, abundance of transcription factor, activity of TFs |
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Signal transduction |
the process of sensing external stimuli and conveying the information to intracellular targets to effect a response |
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HSF1 |
trimerizes inresponse to proteotoxic stress, binds to heat shock elements (HSE) present as enhancers in promoters of heat shockprotein genes. Trimerization is repressed in non-stressed cells by intra-molecular interactions |
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Steroid hormones |
lipid soluble steroid hormones pass through plasma membrane and bind intracellular hormone receptors, whichenter the nucleus and bind to hormone response elements (HRE) present as enhancers in hormone regulated genes. Fat soluble |
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Peptide hormones |
extracellular peptide hormones bind to membrane bound receptors, which activates asignal transduction cascade (usually involving protein phosphorylation) that leads to TF activation. Water soluble |
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Basal promoter elements |
(TATA, GC, CAAT box) bind general (TBP) and basal transcription factors (NF1, Sp1) and and recruit RNA polymerase II. Enhancers bind activatingTF providing gene specific regulation of expression. |
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Enhancers |
(i) act over large distances (ii) orientationindependent (iii) position independent (upstream, downstream of start site or within introns). |
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Promoters |
(i) function in short distances (ii) immediately upstream of initiation site. (iii) Position dependant, non functional if moved (iii) orientation dependant |
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Transcription factors |
modular proteins with domains required forDNA binding and transcriptional activation (some also contain dimerization or ligand binding domains). |
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DNA binding domain (DBD) |
for attachment to DNApromoter/enhancer elements |
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Transcriptionalactivation domain(TAD), |
for binding other proteins requiredfor transcriptional activation |
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DNA binding motifs |
zinc finger motif, helix-turn-helix motif |
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Dimerization motifs |
leucine zipper, helix-loop-helix. |
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Reporter Plasmids |
sequential or targeted deletions toidentify promoter sequences required for transcriptional regulation |
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Gel mobility shift assay |
radioactive DNAprobe containing binding site for TF mixed with cell extract and separated on non-denaturing gel. DNA probe bound to TFis shifted in mobility during separation. Technique will demonstrate the presence of a TF with the ability to bind the DNAprobe in the cell extract |
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ChromatinImmuno-Precipitation |
(ChIP) demonstrate binding of TF (or other DNA-binding protein) to specific chromatin location in vivo. Cells treated with formaldehyde to cross-link proteins and DNA.DNA sheared and mixed with antibody (Ab) to specific TF. DNA/TF/Ab complexes purified, proteins removed andsequence of isolated DNA determined by sequencing or hybridization (ChiP-chip). |
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Epigenetic |
regulation of gene expression by changes in chromatin structure (heritable but reversible). |
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Heterochromotin |
ensely packed transcriptionally inner, generally inactive |
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Euchromotin |
loosely packed transcriptionally active |
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Position-effectvariegation |
occurs when a gene is transferred from euchromatic region to heterochromaticregion (or vice versa) resulting in altered gene expression. Drosophila mottled eye: inversion of X chromosome segmentmoving the white gene into a heterochromatic region in some eye facets but not others. |
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Two kinds of Chromatin remodelling |
Thealteration of nucleosomes in preparation for transcription HATs and SWI/SNF |
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HAT, histoneacetyl transferases |
acetylate histone lysine residues resulting inloosening of DNA-nucleosome interaction - more open chromatin facilitates TF binding and transcriptional activation.HDACs (histone deacetylases) remove acetyl groups resulting in chromatin compaction. Acetylation = more transcription |
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SWI/SNF(matingtype switching/sucrose non-fermenting ATPases): |
shifts nucleosomesalong DNA to clear promoter regions for TF binding. |
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DNA methyl transferases (DMNT) |
attach methyl groups to cytosine residues inCpG dinucleotides to create C5-methylcytosine. Methylation of gene promoters (CpG islands) recruits chromatinmodifying proteins resulting in chromatin compaction and inhibition of gene expression |
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Imprinted genes |
methylation pattern of a gene is determined by its parental origin. Igf2 gene is methylated in female germ line but notmale germ line. Only the copy inherited from the father is transcriptionally active. |
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Inactivation of whole chromosome |
dosage compensation of genes on X chromosome. mammals (XX/XY):in females one of the X chromosomes is inactivated. Drosophila (XX/XY): in males the X chromosome is hyperactivated.C. elgans (XX/XO): in hermaphrodites both of the X chromosomes are hypoactivated. |
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Alternate splicing of mRNA |
primary mRNA transcript can be processed to include or exclude different exon such that the various mature mRNAs can be translated into proteins with different functions |
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Cytoplasmiccontrol of mRNA stability |
PABP1/eIF-4E mediated circularization prevents mRNA decay, deadenylation allows binding ofdeadenylating enzyme to destabilizing sequence AUUUA in the 3’UTR of short-lived mRNAs. Long lived have CCUCC sequence |
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MicroRNAs |
Post-Transcriptional regulation synthesized as pre-miRNA with ds hairpin structure, Drosha removes ends producing pre-miRNAthat is exported to cytoplasm, Dicer removes hairpin loop to produce short 22 nucleotide dsRNA, associates with AGO2protein to form the RNA-Induced Silencing Complex (RISC), strands are unwound, one is destroyed, the other (guide)base pairs with complementary sequence in specific mRNA 3’UTR resulting in silencing (translational inhibition or mRNAdegradation) |
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SiRNAs vs MiRNAs |
Made from same process SiRNAs: maintain integrity of genome, defence against transposon, MiRNAs: regulate gene expression |
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molecular chaperone proteins |
bind to exposed hydrophobic domains onunfolded proteins and prevent aggregation. Assist in protein folding and intercellular transport. Deliver irreversiblydamaged proteins to the ubiquitin-proteasome system (UPS). Regulate proteostasis |
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Proteasome-mediated proteolysis |
Damaged and short-lived proteins areubiquitinated and delivered to the proteasome for destruction. |
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What is the name of the promotor localized DNA sequence that binds ti hormone-receptor complexes to activate gene expression? |
HREs (Hormone response Element) |
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What it the name of the process by which membrane bound receptor protein activation leads to changes in gene expression? |
signal transduction |
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Basal promoter elements contain binding sites for both ____and____, ,which are required for the recruitment of _____to the basal promotor |
basal transcription factors, general transcription factors, RNA polymerase II |
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Small RNAs that result from exogenous sources of dsRNA (e.g. virus) and are involved in gene silencing are called |
siRNAs (short interfering RNAs) |
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Small RNAs encoded by a cell that are involved in gene silencing though partial hybridization of target sequences are called |
microRNAs |
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What is the name of the process in which abnormal gene expression occurs due to the movement of a gene from a euchromatic to heterochromatic region of the chromosome/? |
Position-effect variegation |
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A group of chromatin remodelling factors that transfer acetyl groups to specific lysine residues of histone proteins are called |
HATs (Histone acetyl trangerases) |
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CpG islands re often found in promotor regions and can be modified by _____enzymes which add a ____ group to _______ residues causing transcriptional repression |
DNMTs (DNA methyl transferases), methyl, 5-methylctosine |
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What is the name of the process by which the expression of a gene is determined by its parental origin and what type of base modification is responsible for this? |
Process = Gene imprinting Base modification = methylation |