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Post-Transcriptional Regulation - Coggle Diagram
Post-Transcriptional Regulation
X-Chromosome Inactivation/Regulatory RNA's
In XX individuals, one X chromosome must be repressed
it doesn't have to be repressed all the way and people have varying levels of X-chromosome expression
the process of silencing an x-chromosome is called dosage compensation
Dosage Compensation Mechanism
1) XIST RNA is contained in XIC locus. XIST is transcribed by Pol II (capping, splicing, polyadenylation n all!) but never leaves the nucleus
2) XIST coats chromosome that produced it
can be visualized at this point un situ hybridization
3) XIST recruits macroH2A
4) macroH2A is methylated by DNA methylase
5) HDAC is recruited
6) Deacetylation overcomes insulators and silences the x-chromosome
Lots of macroH2A = Barr Bodies
Why isn't x-inactivation considered imprinting?
The silenced chromosome is chosen at random whereas imprinting is specific to one parent
since inactivation is random, all female mammals are mosaics of x-chromosome expression with x-chromosomes from each side of the family
When does x-inactivation happen?
XIST is expressed at the 2-4 cell stage
inactivation happens at 32-64 cell stage
Riboswitches
Intro
generally located in 5' UTR
usually in bacteria
usually regulate basic metabolism
aptamer - a molecule that metabolites bind to after being bound by riboswitches, changes/downregulates 5' UTR
Two most studied mechanisms
attenuation - formation of a transcriptional terminator upon ligand binding/ in the absence of a ligand
RBS accessibility regulation
TPP RIboswitch
thiamine - vitamin B1
TPP turn translation on/off depending on thiamine levels
Mechanisms
Inhibition - high levels of B1
TPP binds to aptamer in 5'UTR to prevent translation
Activation - low levels of B1
Alternative structure in 5' UTR allows ribosome access to RBS (shine-delgarno) and translation occurs
Only riboswitch found all across the tree of life
glmS mRNA
makes GlmS enzyme
RXN: F-6-P + Glu -> Glucosamine-6-P + L-Glu
Mechanism - lots of glucosamine-6-P
1) Riboswitch inactive but GlmS is still made
2) GlmS produces glucosamine-6-P until it reaches excess
3) Excess glucosamine-6-P binds to glmS riboswitch leading to self-cleavage
4) GlmS mRNA is rapidly degraded
5) GlmS enzyme levels fall
tRNA Riboswitch (Riboswitch Example 3) - Attenuation?
Occurs in uncharged tRNA's and allows transcription
Attenuation occurs when charged tRNA binds and the RNAP terminator hairpin is formed
uncharged tRNA serves as a signal for low levels of specific amino acids
This was amino acids are only made as they are needed
RNAi
miRNA
Intro
regulatory RNA's that are expressed as long dsDNA
Mostly expressed from Pol II
produce small active RNA's
21-23 nucleotides long
Mechanism
1) Pol II transcribes precursor into nucleus
called pri-miRNA
2) Drosha partially processes miRNA down to 60-70 nt
called pre-miRNA
3) pre-miRNA is exported to cytoplasm and loaded into RISC
RISC - multisubunit protein complex, stands for RNA-Induced Silencing Complex
includes a ribonuclease called Dicer
Dicer chops pre-miRNA into 21-23nt pieces
includes a helicase that denatures non-target dsRNA
includes Argonaute
an endonuclease
4) Pairing of miRNA and mRNA leads to two possible outcomes
If good match, Argonaute cleaves RNA. Target mRNA is degraded by exonucleases
If bad match, only translation of mRNA is repressed. Degradation happens at normal time
siRNA
Intro
artificially made
gene-specific knockdowns
designed as dsRNA or small hairpin RNA (shRNA)
produce small active RNA
21-23 nucleotides
Mechanism
1) dsRNA is introduced into cytoplasm via infection and bound by RISC
2) Dicer chops siRNA into 21-23nt pieces
3) short dsRNA separated by helicase. RISC keeps RNA guide with complimentary siRNA that's complimentary to target mRNA
4) Pairing of siRNA and mRNA leads to two possible outcomes
If good match, Argonaute cleaves RNA. Target mRNA is degraded by exonucleases
If bad match, only translation of mRNA is repressed. Degradation happens at normal time
Intro
RNAi - a phenomenon in which dsDNA prevents translation
also referred to as transcriptional silencing (DIFFERENT from gene silencing)
Three possible outcomes
target mRNA degraded
target mRNA is translationally inhibited
gene is silenced via chromatin changes
Signal Transduction Pathways
How cells send signals to transcription factors
Generic Mechanism
1) Small molecule (hormone/metabolite) or a protein binds to a membrane-bound receptor (can be inside or outside of the cell)
2) The small molecule/protein is sensed because the signal receptor has a conformational change
process is called receptor dimerization
3) transcription is stimulated by signal accumulation
Commonly work through phosphorylation cascades
Examples
JAK-STAT pathway
MAP Kinase pathway
Post-Transcriptional Regulation 101
Post-Transcriptional Regulation - mRNA's are only activated when they are needed
Examples
Riboswitches
Phosphorylation
Pre-assembly of ribosomes at start codon
mRNA storage
Regulation of mRNA stability
Regulation of mRNA circularization
RNAi