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Genomics Theory > Lecture 14: Epigenomics > Flashcards

Lecture 14: Epigenomics Flashcards

1
Q

Define EPIGENETICS

A
  1. Epigenetics is the study of CHANGES in the REGULATION OF GENE ACTIVITY and expression that are NOT DEPENDENT ON GENE DNA SEQUENCES.
    • Often refers to the study of single genes or sets of genes.
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2
Q

Epigenetics studies factors that cause:

A

STABLE & HERITABLE, yet REVERSIBLE, changes in the way genes are expressed WITHOUT changing their original DNA sequence.

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3
Q

Epigenetic changes are made

A

Epigenetic changes are made by ADDING OR SUBTRACTING various CHEMICAL TAGS on DNA nucleotides and histones.

➔ DNA methylation, acetylation, & phosphorylation.

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4
Q

DEFINE Epigenomics

A

Epigenomics refers to more GLOBAL ANALYSES of epigenetic changes across the ENTIRE GENOME

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5
Q

DNA packaging into chromatin…

HOW IS CHROMOSOME MADE?

A

DNA + PROTEIN (CHROMATIN) = CHROMOSOMES

DIAGRAM IN SLIDE 4

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6
Q

Epigenetic regulatory mechanisms control gene
expression across cell types

A

ZYGOTE TO

  • nerve cells
  • RBC
  • Smooth muscle cell
  • fat (adipose) cells
  • intestinal epithelial cells
  • Striated muscle cells
  • bone tissue with OSTEOCYTES
  • Loose connective tissue with fibroblasts

DIAGRAM IN SLIDE 5

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7
Q

Epigenetics & phenotype DIAGRAM

A

SLIDE 6 NEED TO UNDERSTAND VEN DIAGRAMS

  1. GENETICS =
    SNP
    MUTATIONS

GENETICS + EPIGENETICS = uRNA, ncRNA

EPIGENETICS
- CpG
methylation
- histone modification

Environment
= nutrition, drugs, toxins and pathogens

IMPORTANT DRAW

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8
Q

Altering chromatin structure DIAGARMS

A

SLIDE 7

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9
Q

Altering chromatin structure :

‘At least three different processes can alter gene transcription through changes in chromatin’

A
  1. modification of histone proteins
  2. chromatin remodelling
  3. DNA methylation
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10
Q

What are Histones? = 3

A
  1. Nucleosomes arranged as an octamer of histone proteins with PROTUDING N-TERMINAL ENDS.
      1. 147 bp of coiled DNA wrapped around the histones.
      1. Two each of the four core histones H2A, H2B, H3 and H4
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11
Q

What is Histone H1?

A

Histone H1, the linker protein, is bound to DNA between nucleosomes.

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12
Q

Histones DIAGRAM

A

IMPORTANT ON SLIDE 8

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13
Q

What is Histone CODE?

A

THE PATTERN OF HISTONE MODIFICATIONS
- ‘the histone code’ - can determine HOW HISTONES BEHAVE.

THEY DEFINE THE CHROMATIN STATE.

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14
Q

Understanding Histone modifications and Histone code:

4

A
  1. The pattern of histone modifications - the histone code - can determine how histones behave. They define
    the chromatin state.

➢ These MODIFICATIONS ARE ‘POST-TRANSLATIONAL MODIFICATIONS’

  1. ➢ Many histone tags work together to
    control histones. These include:
  2. o Acetyl
  3. o Phosphate
  4. o Methyl
  5. o Ubiquitin

3 ➢ MODIFICATION of the HISTONE TAILS ACT AS ‘EPIGENETIC MARKS’ THAT CONTROL THE ‘EXPRESSION OR REPLICATION OF CHROMOSOMAL REGIONS’
- ‘read by transcriptional factors’

4 ➢ The ‘epigenetic marks’ in the histones are HERITABLE.

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15
Q

Many histone tags work together to control histones.

These include: 4

A
  1. Acetyl
  2. Phosphate
  3. Methyl
  4. Ubiquitin

DIAGRAM ON SLIDE 9

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16
Q

UNDERSTANDING ‘Active’ & ‘repressive’ histone marks = 2

A

1 ➢ DIFFERENT amino acids CONSTITUTING HISTONE TAILS are represented along with theDIFFERENT COVALENT MODIFICATION SPECIFIC OF EACH RESIDUE.

2 ➢ ‘Active marks’ are represented in the UPPER SECTION, and ‘repressive marks’ in the LOWER SECTION.

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17
Q

Active & repressive histone marks

A

DIAGRAM ON SLIDE 10

18
Q

UNDERSTANDING HISTONE ACETYLATION: 6

A

1 ➢ DNA is negatively charged, whilst HISTONES are POSITIVELY CHARGED.

  1. ➢ Acetylation of histones occur in the LYSINE RESIDUES OF HISTONE TAILS
  2. ➔ NEUTRALISES
    the POSITIVE LYSINE CHARGE
  3. ➔’DECREASES HISTONE AFFINITY FOR DNA’
  4. ➔ DNA ‘less tightly wound’
  5. ➔ PERMITS TRANSCRIPTION.
19
Q

Acetylated lysine residues VS Deacetylated lysine residues

A

➢ Acetylated lysine residues ➔ transcriptional activation (gene expression).

➢ Deacetylated lysine residues ➔ transcription repression (gene silencing).

20
Q

Histone acetylation: HISTONE ACETYLASE AND HISTONE DEACETYLASE

A
  1. ➢ Histone acetylase (HAT) & histone deacetylase (HDAC) enzymes add/remove acetyl groups,
    respectively.
21
Q

HYPERACETYLATION?

A

➢ Histones near active genes are hyperacetylated

22
Q

Understanding DNA methylation: 6

A
  1. ➢ Best understood example of EPIGENETIC GENE REGULATION.
  2. ➢ Most genes have ‘GC RICH AREAS’ of DNA in their promoter regions: ‘CpG islands.’
  3. ➢ ‘METHYLATION of C’ residues within the CpG islands leads to GENE SILENCING/REPRESSION.
  4. Covalent addition of a methyl group at the 5-carbon of the cytosine ring ➔ 5-
    methylcytosine (5mC).
  5. Methylation prevents binding of transcription factors and leads to condensed chromatin
    ➔ transcription repressed ➔ gene silencing
  6. ➢ Demethylation ➔ EXPANDED CHROMATIN➔ TRANSCRIPTION PERMITTED.
23
Q

DNA Methylation diagram

A

slide 12…important

24
Q

DNA Methylation Continued… why is it essential? explain 4

A

➢ DNA methylation is essential for the NORMAL CONTROL OF GENE EXPRESSION IN DEVELOPMENT.

2 ➢ ~ 1.5% of human DNA is 5-methylcytosine.

3 ➢ IN SOMATIC CELLS, 5mC is almost exclusively in CpG sites.

…..4. EXCEPTION IS EMBRYONIC STEM CELLS

25
Q

Addition of methyl groups is controlled by a family of enzymes called EXPLAIN -3

A
  1. ➢ Addition of methyl groups is controlled by a family of enzymes called DNA methyltransferases
    (DNMTs).

…..2…. 3 DNMTs required for ESTABLISHMENT & MAINTIENCE E of methylation patterns: DNMT1, DNMT3a & DNMT3b.

…..3…. 2 other DNMTs may have MORE SPECIALISED but RELATED FUNCTIONS: DNMT2 and DNMT3L.

26
Q

The role of DNA methyltransferases in DNA methylation = 5

A
  1. ➢ ‘DNMT3a & 3b’ seem to mediate establishment of new or ‘de novo’ DNA METHYLATION PATTERNS.
  2. ➢ ‘DNMT1’ appears responsible for the MAINTENANCE of
    established patterns of DNA methylation.

….3… It follows the replication fork adding methylation
marks to newly synthesized DNA = MAINTENANCE DNA METHYLATION.

…..4…HEMIMETHYLATED DNA carries the information which nucleotide on the new strand should be methylated.

  1. ➢ DNMT3b may assist DNMT1 in maintaining normal gene hypermethylation in diseased cells (e.g. cancer cells).
27
Q

The role of DNA methyltransferases in DNA methylation… DIAGRAMS

A

2 ON SLIDE 14

28
Q

UNDERSTANDING

‘Methylation of DNA is reversible: DNA Demethylation’. = 4

A
  1. ➢ DNA DEMETHYLATION, the removal of methyl group – important for epigenetic reprogramming
  2. ➢ Demethylation is catalyzed by TEN-ELEVEN TRANSLOCATION -TET - FAMILY OF 5mC HYDROXYLASES
  3. include TET1, TET2 & TET3.
  4. ➢ Promote DNA demethylation by binding to CpG rich regions to PREVENT UNWANTED METHYLTRANSFERASE ACTIVITY, and by CONVERTING 5mC to C via hydroxylase activity
29
Q

TET proteins function in: 3

A
  1. Transcriptional activation & repression (TET1),
  2. Tumour suppression (TET2), &
  3. DNA methylation reprogramming processes (TET3)
30
Q

Hyper- and Hypo-methylation Of DNA: consequences…

‘Too little methylation =hypo-methylation’ = 4

A
  1. Too little methylation =hypo-methylation
  2. ➢ more active transcription.
  3. ➢ “turns on” genes promoting cell growth.
  4. ➢ chromosome instability (highly active DNA is more likely to be duplicated, deleted, & moved).
31
Q

Methylation of DNA is reversible: DNA Demethylation DIAGRAM

A

ON SLIDE 15

32
Q

Hyper- and Hypo-methylation 0f DNA: consequences

‘Too much methylation = hyper-methylation’ = 5

A
  1. Too much methylation = hyper-methylation
  2. ➢ less active transcription.
  3. ➢ “turn off” genes that keep cell growth in check.
  4. ➢ “turn off” genes that repair damaged DNA.
  5. ➢ “turn off” genes that initiate programmed cell death.
33
Q

Hyper- and Hypo methylation 0f DNA: consequences

A

DIAGRAM ON SLIDE 16

34
Q

Changes in DNA methylation during development - GRAPH

A

ON SLIDE OF 17

35
Q

Changes in DNA methylation during development: 6

A
  1. erasure of parental epigenetic settings
  2. ‘de novo’ methylation and establishment of imprinting marks
  3. Demethylation in early embryo
  4. ‘de novo’ methylation in trophoblast lineages
  5. ‘de novo’ methylation in somatic cells
  6. maintenance methylation

Primordial germ cells (PGCs)
SPERM
EGG
FERTILISED OOCYTE
BLASTOCYST
SOMATIC CELLS
PLACENTA YOLK, SAC
ADULT
PGCs

36
Q

Epigenetic Inheritance: 4

A
  1. ➢ When the ZYGOTE is FORMED MANY EPIGENETIC TAGS ARE REMOVED from the CHROMOSOMES OF THE PARENTS.
  2. ➢ ButSOME EPIGENETIC TAGS REMAIN and can be PASSED DOWN TO FUTURE GENERATIONS:
    - ‘EPIGENETIC INHERITANCE’
  3. ➢ Epigenetic inheritance describes HERITABLE ALTERATIONS IN WHICH THE DNA SEQUENCE ITSELF IS UNCHANGED
  4. ➢ PARENTS EXPERIENCE, MANIFESTED IN THE FORM OF ‘EPIGENETIC TAGS’
    passed down to future generations
37
Q

Who are identical twins and how are they same or different? = 3

A
  1. ➢ Identical twins are from the SAME ZYGOTE, so they BEGIN LIFE with the
    SAME GENETIC INFORMATION, including
    epigenetic tags.
  2. ➢ WHILST INFANTS, they experience the SAME OR VERY SIMILAR ENVIRONMENTS, so
    there is LITTLE VARIATION IN THE EPIGENOME.

3 ➢ However OVER TIME the twins’ ENVIRONMENTS will DIVERGE, resulting in
INDIVIDUAL EPIGENETIC TAGS TO FORM FOR EACH TWIN.

38
Q

Identical twins - WHY DO THEY LOOK DIFFERENT WHEN THEY ARE OLDER? = 3

A

1 ➢ The DIFFERENCE in the twins’ EPIGENOMES
is what makes them BECOME DIFFERENT WHEN THEY ARE OLDER.

  1. ➢ The EPIGENETIC TAGS can have SUCH AN EFFECT ON THE TWINS THAT ONE CAN DEVELOP A DISEASE WHILE THE OTHER DOES NOT.
  2. ➢ When this situation occurs, RESEARCHERS WILL TRY TO PINPOINT THE ENVIRONMENTAL FACTORS THAT ARE RESPONSIBLE FOR THE DISEASE.
39
Q

Identical twins – differences over time

A

➢ Comparative genomic hybridisation onto metaphase chromosomes for methylated DNA:

  • The 3 year old twins have a similar DNA methylation distribution
  • The 50 year old twins show abundant changes (hypermethylation and hypomethylation events = green & red signals).
40
Q

Identical twins – differences over time

A

Diagram on slide 20

41
Q

Environmental factors can control epigenetically controlled development:

Queen versus worker bee = 4

A
  1. ➢ Larvae that develop into worker bees and queen bees are genetically identical
  2. ➢ Royal jelly acts on a key gene - ‘Dnmt3’ - which codes for a DNA methyltransferase that influences “queen
    genes”.
  3. ➢ When Dnmt3 is “on”, the queen genes are silenced
    - larvae ➔ default “worker” bees.
  4. ➢ Royal jelly turns Dnmt3 “off”, the queen genes are activated
    - larvae ➔ queen bees
42
Q

Environmental factors can control epigenetically controlled development:
Queen versus worker bee

A

diagram slide 21

royal jelly - 13 days faster development

worker jelly - 18 days slower development

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