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42 Cards in this Set

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Levels of gene expression control

transcriptional, mRNA processing, translational, post-translational

transcriptional factor regulations:

presence of DNA motif in promoter, promoter accessibility, abundance of transcription factor, activity of TFs

Signal transduction

the process of sensing external stimuli and conveying the information to intracellular targets to effect a response

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

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

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

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.

Enhancers

(i) act over large distances (ii) orientationindependent (iii) position independent (upstream, downstream of start site or within introns).

Promoters

(i) function in short distances (ii) immediately upstream of initiation site. (iii) Position dependant, non functional if moved (iii) orientation dependant

Transcription factors

modular proteins with domains required forDNA binding and transcriptional activation (some also contain dimerization or ligand binding domains).

DNA binding domain (DBD)

for attachment to DNApromoter/enhancer elements

Transcriptionalactivation domain(TAD),

for binding other proteins requiredfor transcriptional activation

DNA binding motifs

zinc finger motif, helix-turn-helix motif

Dimerization motifs

leucine zipper, helix-loop-helix.

Reporter Plasmids

sequential or targeted deletions toidentify promoter sequences required for transcriptional regulation

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

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).

Epigenetic

regulation of gene expression by changes in chromatin structure (heritable but reversible).

Heterochromotin

ensely packed transcriptionally inner, generally inactive

Euchromotin

loosely packed transcriptionally active

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.

Two kinds of Chromatin remodelling

Thealteration of nucleosomes in preparation for transcription


HATs and SWI/SNF

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

SWI/SNF(matingtype switching/sucrose non-fermenting ATPases):

shifts nucleosomesalong DNA to clear promoter regions for TF binding.

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

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.

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.

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

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

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)

SiRNAs vs MiRNAs

Made from same process


SiRNAs: maintain integrity of genome, defence against transposon,




MiRNAs: regulate gene expression

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

Proteasome-mediated proteolysis

Damaged and short-lived proteins areubiquitinated and delivered to the proteasome for destruction.

What is the name of the promotor localized DNA sequence that binds ti hormone-receptor complexes to activate gene expression?

HREs (Hormone response Element)

What it the name of the process by which membrane bound receptor protein activation leads to changes in gene expression?

signal transduction

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

Small RNAs that result from exogenous sources of dsRNA (e.g. virus) and are involved in gene silencing are called

siRNAs (short interfering RNAs)

Small RNAs encoded by a cell that are involved in gene silencing though partial hybridization of target sequences are called

microRNAs

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

A group of chromatin remodelling factors that transfer acetyl groups to specific lysine residues of histone proteins are called

HATs (Histone acetyl trangerases)

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

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