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Genomics > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

Definition of epigenetics

A

Study of heritable changes in gene function that occur without a change in DNA base sequence

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2
Q

Definition of imprinted genes

A

Genes that are only expressed from either the maternal/paternal allele

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3
Q

Definition of parthenogenote

A

Both sets of nuclear material in an egg cell is from females

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4
Q

Definitions of androgenote

A

Both sets of nuclear material in an egg cell is from males

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5
Q

Definition of uniparental disomy

A

2 copies of a chromosome come from the same parent

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6
Q

Definition of continuous gene syndromes

A

Clinical phenotype caused by a deletion/duplication of many genes in close proximity

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7
Q

Describe the functions and properties of epigenetics

A
  • Stable in cell division in somatic cells
  • Markers reset in germ cells and early embryos
  • Pluripotent cells <=epigenetics=> differentiated cells
  • Imprinting
  • X inactivation
  • Control of transposons
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8
Q

What are the pros and cons of transposons

A

Needed for variation

If inserted into genes => can be harmful

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9
Q

What are the 3 genetic factors that contribute to disease

A

Genetics
Phenotypes
Epigenetics

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10
Q

Describe the epigenetic mechanism

A

Interact with transcription factors to regulate gene expression patterns
Underly embryonic development, differentiation and identity

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11
Q

Describe the properties and function of CpG dinucleotides

  • what is a CpG dinucleotide
  • how does it contribute to epigenetics
  • where are they found
A

5’ Cytosine + phosphodiester bond + Guanine 3’

Methylation of cytosine => repression of gene expression

Often found in CpG dinucleotides

  • unmethylated at promotors => allow for transcription
  • methylated promoters in germline somatic cells => differentiation

CpG is methylated in the rest of the genome and not common compared to other nucleotides

In development, move between unmethylated <=> methylated in gene bodies

Can be found within gene sequences (iGpG)

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12
Q

Describe how histone proteins are modified

A

Chemical tags bind to histone proteins (arginine, lysine)

tags indicate whether gene is expressed/not expressed

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13
Q

Describe the 3 outcomes of genomic imprinting in reproduction

  • biparental
  • parthenogenote
  • androgenote
A

Each gamete has the genes but different genes are expressed

Fertilised biparental

  • viable embryo
  • normal sized placenta

Parthogenote
-large embryo
-small placenta
=>ovarian teratoma as a result of hyperdifferentiation

Androgenote

  • small embryo
  • huge placenta
  • hydatidiform mole forms as a result of trophoblastic hyperplasia
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14
Q

Describe uniparental disomies in imprinting disorders

-what are the associated symptoms generally

A

2 copies of a chromosome come from the same parent

generally associated with

  • growth failure
  • dwarfism
  • neonatal diabetes
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15
Q

Describe Angelman syndrome

  • who and what is inherited
  • cause
  • symptoms
A

Deletion/mutation (imprinting/genetic) transmitted from mother but received from father which is silent

Results from deleted/mutated maternally expressed genes

Cheerful, mental retardation

UPD more common due to higher rates of maternal non disjunction

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16
Q

Describe Prader Willi syndrome

  • who and what is inherited
  • cause
  • symptoms
A

Deletion/mutation (imprinting) transmitted from father but received from mother which is silent

Results from deletion/imprinting mutated paternally expressed genes

Central obesity, always hungry

17
Q

What is a potential treatment for Angelman Syndrome

A

No cure but activating the silenced allele => ameliorated associated symptoms

18
Q

Describe the cause of Beckwith-Weidmann

-what can lead to an increased incidence

A

Deregulation of inherited genes from epimutations

Increased incidence in IVF

19
Q

Describe the cause of Silver Russell

A

Maternal UPD instead of 1 chromosome from each parent

20
Q

Describe the cause of Transient Neonatal Diabetes Mellitus

A

Genetic mutation=> epimutation

-Affects maintenance of imprinted DNA methylation in development

21
Q

Describe the 3 epigenetic gene players and examples

  • writers
  • readers
  • erasers

Where are the genes that code for these players
What happens when mutations occur in these regions

A

Writers

  • introduce chemical modifications onto DNA and histone
  • histone methyl and acetyltransferase

readers

  • identify and interpret modifications
  • bromo and chromodomains

Erasers

  • remove chemical tags
  • histone demethyl and deacetylases

All coded for by genes in DNA
Any mutations in these regions => different pathologies, can be Mendelian

22
Q

Describe the relationship between twins and epigenetics

How does this arise

A

Increased MZ disconcordance for common diseases due to environmental/epigenetics

  • Identical DNA sequences
  • Differences in intrauterine and postnatal environments
23
Q

What is the ENCODE project

-what does it aim to do

A

Aims to catalogue regulatory elements that affect epigenomes
-study epigenomic signatures of cells grown in culture

Linked epigenomic data to corresponding genetic info => reference epigenome
-representation of how epigenomic elements regulate gene expression in human body

24
Q

Describe the outcomes of ENCODE

A

identify

  • non traditional disease causing mutations
  • long range enhancer mutations and mutations in gene deserts from GWAS
  • inform on disease mechanisms => potential treatment modalities
25
Q

Describe the link between cancer and epigenetics

A

Hypomethylation/loss of imprinting => tumour formation

Epigenetic mechanisms change accessibility of chromatin to transcriptional regulation locally/globally via DNA/nucleosome arrangement modifications

Epigenetic gene regulation collaborates with genetic alterations => cancer

26
Q

What are the 3 classifications of epigenetic modifiers and their effects

A

DNA modifications
Histone modification
Chromatin modelling

Contributes to all stages of cancer
+50% of cancers involve chromatin organisation
Melanoma = 92% affected have 1+ EM mutation

27
Q

What are the potential targets in cancer therapy

What are examples of drugs

A

Methylation is the only flexible genomic parameter that can alter genome function under environmental influence

Genomes of many cancers are hypermethylated => silence regulatory genes (tumour suppressors)
-demethylating drugs (azacytidine, decitabine)

Histone deacetylase inhibitors (HDAC)
-combination of 5AzaC + HDAC as epigenetic factors work together

Histone methyltransferases (EH22) have antitumour effects

Genomics (17 decks)

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