new skeleton

topic 1

Hierarchical Organisation and the 3D Toolbox

Hierarchical Organisation and the 3D Toolbox topics 1

1.      The mammalian genome is organised into a complex hierarchy:

Hierarchical Organisation and the 3D Toolbox 1.      The mammalian genome is organised into a complex hierarchy: topics

Hierarchy includes 1,2,3      Examples

Hierarchical Organisation and the 3D Toolbox 2

2.      To study this architecture researchers use a specialised toolbox

Hierarchical Organisation and the 3D Toolbox 3

3.      Dna accessibility

Hierarchical Organisation and the 3D Toolbox 3.      Dna accessibility topics

Name of tool 1 – dhss      mechanism      Function      Name of tool 2 – atac seq      Mechanism      Function

Hierarchical Organisation and the 3D Toolbox 4

4.      3d mapping:

Hierarchical Organisation and the 3D Toolbox 4.      3d mapping: topics

Tool 1 – 3c      Function      Tool 2 – 4c      Function      Tool 3 – hic      Function      Tool 4 – capture c      Function

topic 2

CTCF and Cohesin

CTCF and Cohesin topics 1

1.      TADS

CTCF and Cohesin 1.      TADS topics

Definition      Function

CTCF and Cohesin topics 2

2.      These domains are established and maintained by two key architectural regulators: CTCF and the Cohesin complex.

CTCF and Cohesin topics 3

3.      Ctcf

CTCF and Cohesin 3.      Ctcf topics

Known as      Definition      Mechanism      Location

CTCF and Cohesin topics 4

4.      Cohesion

CTCF and Cohesin 4.      Cohesion topics

Known as      Definition      Contains

CTCF and Cohesin topics 5

5.      Loop extrusion model

CTCF and Cohesin 5.      Loop extrusion model topics

Mechanism      Function      Experiment      Experiment outcome

topic 3

Histone modifications and the code

Histone modifications and the code topics 1

1.      Histone code

Histone modifications and the code 1.      Histone code topics

Function

Histone modifications and the code topics 2

2.      The code contains writers readers and erasers

Histone modifications and the code 2.      The code contains writers readers and erasers topics

Writers example and what for      Erasers example      Readers example

Histone modifications and the code topics 3

3.      Enhancer classification

Histone modifications and the code 3.      Enhancer classification topics

Type 1 – primed      Marked by      Deposited by      Type 2 – active      Marked by      deposited by      type 3 – poised      characterised by

Histone modifications and the code topics 4

4.      Super enhancers

Histone modifications and the code 4.      Super enhancers topics

Definition      Function      Essential for      Example      Cancer

topic 4

Structural histone variants

Structural histone variants topics 1

1.      Beyond post-translational modifications, histone variants impact 3D structure:

Structural histone variants topics 2

2.      Linker histone h1

Structural histone variants 2.      Linker histone h1 topics

Mechanism      Function      Loss leads to

Structural histone variants topics 3

3.      Cenp-a

Structural histone variants 3.      Cenp-a topics

Definition      Function

Structural histone variants topics 4

4.      H3.3 and h2a.x

Structural histone variants 4.      H3.3 and h2a.x topics

Function

topic 5

Clinical Consequences of 3D Rearrangement

Clinical Consequences of 3D Rearrangement topics 1

1.      Structural variants

Clinical Consequences of 3D Rearrangement 1.      Structural variants topics

Function      Result

Clinical Consequences of 3D Rearrangement topics 2

2.      TAD fusion

Clinical Consequences of 3D Rearrangement 2.      TAD fusion topics

KNOWN AS      Mechanism      Function      Example

Clinical Consequences of 3D Rearrangement topics 3

3.      Neo tads

Clinical Consequences of 3D Rearrangement 3.      Neo tads topics

Known as      Mechanism      Function      Example

Clinical Consequences of 3D Rearrangement topics 4

4.      Tad shuffling

Clinical Consequences of 3D Rearrangement 4.      Tad shuffling topics

Known as      Mechanism      Function      Example

topic 5

Chromatinopathies

Chromatinopathies topics 1

1.      Many developmental syndromes arise from mutations in architectural or epigenetic regulators:

Chromatinopathies topics 2

2.      Cornelia de lange syndrome

Chromatinopathies 2.      Cornelia de lange syndrome topics

Cause      Examples

Chromatinopathies topics 3

3.      Rubinstein taybi syndrome

Chromatinopathies 3.      Rubinstein taybi syndrome topics

Cause      Examples

Chromatinopathies topics 4

4.      Kabuki syndrome

Chromatinopathies 4.      Kabuki syndrome topics

Cause

Chromatinopathies topics 5

5.      B cell lymphone

Chromatinopathies 5.      B cell lymphone topics

Cause      resu