Extra reading Flashcards
What is dosage compensation?
Process by which organisms equalise the expression from the X chromosome in males and females
What is X inactivation? (2)
- Inactivation of an X chromosome in any cell in early female embryo is random and permanent
- Means that female mammals are mosaic for X inactivation
What is Xic? (2)
- The X inactivation centre
- Cis-acting master switch locus for initiation of X inactivation
What are the components of the Xic? (4)
- Xist
- Tsix
- Rex1
- Rnf12
What is the function of Xist? (2)
- Non-coding RNA which decorates the entire length of the X chromosome from which it is transcribed
- Prevention of diffusion to the other X chromosome is not understood
What is the function of Tsix? (2)
- Complementary to Xist RNA
- Expression of one inactivates the other
How does Xist cause X inactivation?
The first chromosome to accumulate above a threshold amount of Xist is the one that is inactivated
What is the function of Rnf12? (3)
- Ubiquitin ligase encoded by Xic locus
- Degrades Rex1
- More Rnf12 production means more Xist production and less Tsix production
What is the function of Rex1? (2)
- Autosomally derived protein
- Transcriptional repressor of Xist RNA
How is X inactivation propagated and maintained beyond the Xic? (3)
- YY1 transcription factor binds to Xist RNA
- Triggers further accumulation of YY1 binding to Xist with hnRNPU RNA binding protein
- Complex spreads along the chromosome to allow decoration with Xist
What are the events which follow Xist inactivation of the X chromosome? (10)
- Xist decorates the inactive X
- Core histone acetylation is decreased
- Core histone H3K4 methylation is decreased
- Core histone H3K27 methylation is increased (polycomb)
- Core histone H2A ubiquitination of lysine 119 is increased (H2AK119Ub)
- PRC2 and PRC1 binding is increased
- H3K9 methylation is increased
- HP1alpha binding is increased
- CpG DNA methylation is increased
- All causes condensation of inactive X into the Barr body which can’t be transcribed
How is dosage compensation achieved in mammals? (2)
- Xist RNA decorates the X from which it is transcribed and recruits YY1 and hnRNPU
- 1 X is silenced by decreasing H3K4 methylation and histone acetylation and promoting H3K27 and H3K9 methylation , polycomb complex, HP1alpha recruitment and DNA methylation
What is the function of piRNA?
Cleaves products of transposons in germ cells
What causes fragile X syndrome? (3)
- CGG trinucleotide expansion in the FMR1 gene suppresses its expression and reduces abundance of the fragile X mental retardation protein (FMRP)
- FMRP regulates neuronal connectivity and plasticity
- Causes mental impairment and autism in humans
What is the nature of FMRP?
miRNA binding protein
How is FMRP involved in axon outgrowth? (2)
- FMRP interacts with miR-125a-bound RISC complex which translationally inhibits Map1 and Calm1
- Causes inhibition of axon outgrowth
How is FMRP involved in synapse stabilisation? (4)
- FMRP-miR125a RISC binds to PSD-95 mRNA to inhibit translation
- PSD-95 is expressed in post-synaptic neurons which stabilises glutamate receptors
- Glutamate stimulation causes disassembly of FMRP-miR125a RISC on PSD-95 mRNA via phosphorylation of FMRP
- Allows PSD-95 expression and synapse stabilisation
What are the main functions of long ncRNAs? (4)
- Gene regulation in cis
- Scaffolding of nucleoprotein complexes
- Decoys
- Silencing of mRNA by forming double stranded complexes with mRNAs (antisense like miRNAs)
What are examples of scaffolding long ncRNAs?
roX1 and roX2
What is HOTAIR?
Antisense RNA complex within the Hox C complex
What are the features of HOTAIR antisense RNA? (3)
- Forms a multi stem loop structure
- 5’ portion binds PRC2 (methylates H3K27)
- 3’ portion binds LSD1 (DEmethylates H3K4me3)
What is the action of PRC2 complex?
Methylates H3K27
What is LSD1? (2)
- Histone demethylase
- Demethylates H3K4me3
What is the function of HOTAIR? (2)
- Binds PRC2 and LSD1
- Switches target loci from transcriptionally active (H3K4 methylated) to inactive (H3K27 methylated)
What are decoy long ncRNAs? (2)
- Bind to proteins to inhibit their action
- E.g. growth arrest-specific transcript 5 (Gas5)
What is the action of Gas5? (3)
- Gas5 binds to and inhibits GR so it can no longer enter the nucleus and bind to target genes to cause upregulation of energy metabolism
- When cells enter growth arrest they need to conserve energy rather than utilise
- Gas5 decoy causes energy conservation as an adaptive response to starvation/metabolic restriction
How does ChIP work? (5)
- Cross link DNA and chromatin proteins with formaldehyde
- Fragment chromatin by sonication/shearing
- Immunoprecipitation of chromatin fragments containing protein/histone modification of interest
- Remove crosslinks, amplify fragments by PCR, library preparation and fragment sequencing
- Map fragments to reference genome to identify the DNA sequences that are associated with the protein/histone modification of interest
How is the distribution of histone modifications and specific chromatin proteins in chromatin studied?
Chromatin immunoprecipitation (ChIP)
What goes on with Rex1? (3)
- Rex1 is a DEDDh exonuclease, distinct from the exosome but synthetic lethal with Rrp6 (yeast screens)
- Involved in tRNA maturation
- Normally localised in nucleus but in cytoplasm under stress conditions which impacts tRNA availability therefore changes which genes are transcribed under stress conditions
