Extra reading Flashcards

1
Q

What is dosage compensation?

A

Process by which organisms equalise the expression from the X chromosome in males and females

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2
Q

What is X inactivation? (2)

A
  • 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
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3
Q

What is Xic? (2)

A
  • The X inactivation centre
  • Cis-acting master switch locus for initiation of X inactivation
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4
Q

What are the components of the Xic? (4)

A
  • Xist
  • Tsix
  • Rex1
  • Rnf12
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5
Q

What is the function of Xist? (2)

A
  • 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
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6
Q

What is the function of Tsix? (2)

A
  • Complementary to Xist RNA
  • Expression of one inactivates the other
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7
Q

How does Xist cause X inactivation?

A

The first chromosome to accumulate above a threshold amount of Xist is the one that is inactivated

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8
Q

What is the function of Rnf12? (3)

A
  • Ubiquitin ligase encoded by Xic locus
  • Degrades Rex1
  • More Rnf12 production means more Xist production and less Tsix production
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9
Q

What is the function of Rex1? (2)

A
  • Autosomally derived protein
  • Transcriptional repressor of Xist RNA
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10
Q

How is X inactivation propagated and maintained beyond the Xic? (3)

A
  • 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
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11
Q

What are the events which follow Xist inactivation of the X chromosome? (10)

A
  • 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
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12
Q

How is dosage compensation achieved in mammals? (2)

A
  • 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
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13
Q

What is the function of piRNA?

A

Cleaves products of transposons in germ cells

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14
Q

What causes fragile X syndrome? (3)

A
  • 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
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15
Q

What is the nature of FMRP?

A

miRNA binding protein

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16
Q

How is FMRP involved in axon outgrowth? (2)

A
  • FMRP interacts with miR-125a-bound RISC complex which translationally inhibits Map1 and Calm1
  • Causes inhibition of axon outgrowth
17
Q

How is FMRP involved in synapse stabilisation? (4)

A
  • 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
18
Q

What are the main functions of long ncRNAs? (4)

A
  • Gene regulation in cis
  • Scaffolding of nucleoprotein complexes
  • Decoys
  • Silencing of mRNA by forming double stranded complexes with mRNAs (antisense like miRNAs)
19
Q

What are examples of scaffolding long ncRNAs?

A

roX1 and roX2

20
Q

What is HOTAIR?

A

Antisense RNA complex within the Hox C complex

21
Q

What are the features of HOTAIR antisense RNA? (3)

A
  • Forms a multi stem loop structure
  • 5’ portion binds PRC2 (methylates H3K27)
  • 3’ portion binds LSD1 (DEmethylates H3K4me3)
22
Q

What is the action of PRC2 complex?

A

Methylates H3K27

23
Q

What is LSD1? (2)

A
  • Histone demethylase
  • Demethylates H3K4me3
24
Q

What is the function of HOTAIR? (2)

A
  • Binds PRC2 and LSD1
  • Switches target loci from transcriptionally active (H3K4 methylated) to inactive (H3K27 methylated)
25
Q

What are decoy long ncRNAs? (2)

A
  • Bind to proteins to inhibit their action
  • E.g. growth arrest-specific transcript 5 (Gas5)
26
Q

What is the action of Gas5? (3)

A
  • 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
27
Q

How does ChIP work? (5)

A
  • 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
28
Q

How is the distribution of histone modifications and specific chromatin proteins in chromatin studied?

A

Chromatin immunoprecipitation (ChIP)

29
Q

What goes on with Rex1? (3)

A
  • 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