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genomics > The epigenome > Flashcards

The epigenome Flashcards

1
Q

Genome

A

complete set of genetic material in a cell (DNA sequence in a single full set of chromosomes)

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2
Q

First level of DNA packing

A

nucleosomes

- histone proteins bound to DNA

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3
Q

Chromatin

A

organisation of DNA in nucleosomes:

> Euchromatin: gene-rich, transcriptionally active, dispersed appearance (nucleosomes are far apart), unique DNA sequences = compartment A

> Heterochromatin: gene-poor, less transcriptionally active, condensed appearance, repetitive DNA sequences = compartment B

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4
Q

Packing Solution of Genome

A
  • Nucleosomes are wound up to form 30nm fibres
  • Fibres are then wound up further with scaffold proteins to generate higher-order structures
  • Chromosomes are the most densely packed form of genomic DNA
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5
Q

Epigenome

A

the sum total of changes in the genome that do not occur in the primary DNA sequence which affect gene expression

*epigenetic change results in a change in phenotype but not in genotype

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6
Q

Types of epigenetic mechanisms

A

DNA methylation
Histone modification
X-inactivation
Genomic imprinting

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7
Q

What is DNA methylation?

A

DNA methylation is the addition of methyl groups (-CH3) in the 5’ position of a cytosine

  • catalysed by DNA methyltransferase enzymes
  • requires S-Adenosyl methionine to provide the methyl group
  • doesn’t happen at every cytosine in DNA
  • occurs in CpG dinucleotides in differentiated cells
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8
Q

Enzyme which catalyses DNA methylation

A

DNA methyltransferase

-DNMT1, DNMT3a, DNMT3b

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9
Q

What provides the methyl group for DNA methylation?

A

S-Adenosyl Methionine (SAM)

-becomes S-Adenosyl Homocysteine (SAH) due to loss of methyl group

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10
Q

How does DNA methylation affect gene expression?

A

turns transcription off by preventing the binding of transcription factors

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11
Q

What is DNA demethylation?

A

removal of the methyl group, converting the nucleotide back to cytosine via a number of intermediates (not directly back to cytosine):

  • 5-hydroxymethylcytosine
  • 5-formylcytosine
  • 5-carboxycytosine
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12
Q

What is histone modification?

A

addition of chemical groups to histone proteins

Examples:

  • acetylation
  • methylation
  • phosphorylation
  • ubiquitination
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13
Q

How are histone modifications named?

A

Modifications are named based on the histone it affects, the amino acid and the actual modification.

For example, a modification called H3K4Me3 means that it is a modification on Histone 3, the Lysine at position 4 and is tri-methylated.

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14
Q

What are the enzymes that add modifications to histone tails called?

A

WRITERS

Histone acetyltransferase (HAT1)
Histone methyltransferase (EHMT1)
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15
Q

What are the enzymes that remove modifications to histone tails called?

A

ERASERS

Histone Deacetylase (HDAC1)
Histone Demethylase (KDM1)
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16
Q

Enzymes which bind to histone modifications and alter gene activity and protein production are known as..

A

READERS

Bromodomain and Extra-terminal (BET) proteins- BRD2

Chromodomain proteins -CBX1

17
Q

Effects of histone modification

A

Histone acetylation at Lysine residues relaxes chromatin structure, making it more accessible for transcription factors

Histone methylation is more complex and can repress or activate transcription depending on where it occurs

Histone modifications can occur concurrently and so their effects can interact or modify each other

18
Q

What is X-inactivation?

A

inactivation of one of the two X chromosomes in every somatic cell in females

19
Q

Importance of X inactivation

A

ensures that every somatic cell in all humans has the same number of active copies of every gene (because Y chromosome in males has virtually no genes)

20
Q

Steps of X inactivation

A
  • The Xist gene is transcribed as a long non-coding RNA (lncRNA) in the X-inactivation centre (Xic) and binds all over the X-chromosome to regulate gene expression
  • Histone acetylation is removed and histone and DNA methylation occurs to inactivate that chromosome
  • Inactive X-chromosome is heterochromatic and is referred to as Barr body
21
Q

How to prevent other X chromosome from inactivating?

A

You don’t want both X chromosomes to be inactive and so one chromosome transcribes Tsix gene in the opposite direction from a reverse sequence long noncoding RNA and antagonises Xist RNA to keep one X active.

22
Q

What is genomic imprinting?

A

Genomic imprinting refers to selective expression of a gene depending on whether it was inherited from the male parent or the female parent.

23
Q

Where are imprinted genes found?

A

in clusters in autosomes

24
Q

What is imprinting mediated by?

A

imprinting control regions (ICRs), which silence genes near them using DNA methylation and histone methylation

  • one parental copy is silenced by DNA methylation catalysed by DNMT3s and histone methylation leading to inactivation
  • long noncoding RNAs (lncRNAs) are essential to the process (like X-inactivation)
  • imprinting patterns are reset during gamete formation
25
Q

Pharmacoepigenetics

A

studies the underlying epigenetic patterns that lead to variation in an individual’s response to medical treatment.

26
Q

What is the pharmacoepigenetics field split into?

A

Two areas:

  • Epigenetic regulation of genes
  • Epigenetic effect of drugs
27
Q

Cancer epigenetics

A

Global DNA methylation is altered in tumour cells

  • Hypermethylation of tumour suppressor genes (reducing gene expression)
  • Hypomethylation of tumour activating genes (increasing gene expression and favouring cancer formation)
28
Q

Epigenetic enzymes in tumour cells

A

epigenetic enzymes are often mutated in tumour cells:

  • DNMT3a and TET1/2
  • Histone Acetyltransferases
  • Histone Methyltransferases
  • Histone Kinases
  • Histone Readers (acetyl/methyl/phosphoryl)
  • Histone Demethylases
29
Q

Pharmaco Epigenetic drugs in cancer treatment

A

DNA Methyltransferase Inhibitors

  • 5-Azacytidine (Vidaza)
  • Treatment of Myelodysplastic syndrome

Histone Deacetylase Inhibitors

  • Romidepsin (Istodax)
  • Treatment of Cutaneous T-cell Lymphoma

genomics (20 decks)

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