Lecture 11 - Epigenome: Chromatin Marks

How is a necklace an analogy for DNA?

string - DNA

Beads - Histone octomers

areas with more beads = heterochromatin

areas with less beads = euchromatin

Describe what a nucleosome is

Nucleosome

• involves hisones, thier tails, and DNA

Assembly

• DNA strands can have histone octomers around folded regions

  • contain 2x each of H2A, H2B, H3, H4

• Histone tails are AA strings not assmebled

Describe how we decode histone marks like H3K27me3

• H3 = Histone 3

• K27 = Lysine 27

• me3 = 3 methyl groups

All added post-translationally , after translation and assembly of histone protein

What are different ways the post-translational modification (PTMs) can interact with DNA throughout he histone protein?

Case 1: Loose

• Loosen interaction between DNA + protein (histone)

• DNA less associated (connected) with nucleosome → opening chromatin

• facilitate interaction with transcription machinery → euchromatin

Case 2: Strengthen

• Strengthen interaction between DNA + protein

• DNA will become strongly associated with nucleosome → closing chromatin

• Less interaction with transcription machinery → heterochromatin’

PTMs can change accessibility of the promoter region of genes

What facilitates moving of nucleosomes?

• DNA methylation → transposons inhibits

• Histone PTMs (histone tails) → can either inhibit or promote

• Other protein → use energy

What are differnet types fo epigenetic variation?

• Cytosine DNA methylation

• Histone modifications and variants

• Nucleosome position and 3D structure

What are features of Histone PTMs?

• Many flavors

  • ex: phosphorylation, methylation, acetylation

• Function often unknown

• Combinations matter

• Histone “Code”

• different PTMs are identified at specific histone proteins each with different functions

• PTMs work in combinations, not isolated

Describe the process of immunopurification with histone PTMs

1) Crosslink DNA to protein

2) fragment chromatin with sonicator or fragmentase

3) Immunopurify

4) Reverse crosslink chromatin → DNA no longer attached to protein

5) Elute DNA

6) Add Illumina adapters and seq the DNA

7) Align + count reads → tells you how much DNA associates with a given Histone PTM

Takeaways fr9om H3K27me3 in Arabidopsis

Top Graph

• larger green rectangles - exons

• black lines - introns

• smaller green rectangles - UTR

Top Graph Takeaways

• Genes with HeK27me3 tend to have lower expression than without

• Genes with H3K27me# tend to be in highly specific tissues

Bottom Graph

• highest proportion of H3K27me3 have low expression

• H3K27 have higher tissue specificity

Conclusions on H3K27Ac experiments

• H3K27Ac associated with higher gene expression and is not dependent on H3K4me

• H3K27Ac in liver associated with increase in expression

What can chromatin marks define

• functional states

• different combinations of histone PTMs define a functional state

• predict functional states depending in data sets

H3.3

• RNAPII colocalize with regions on the chromosome with H3.3 and activating HPTMs

  • likely associated with high expression

The presence of a single histone post-translational modification can determine expression of a gene.  True or false?

False; work of combination of different PTMs

Immunopurification was used to identify piwiRNas, to determine sites of DNA methylation and to identify regions of DNA associated with histone post-translational modifications.  True or false?

True

There are multiple ways in which lysine 27 of the Histone 3 protein can be post-translationally modified.  True or false?

True; ex: me3 or Ac

H3K27me3 is associated with gene repression in both plants and animals.  True or false?

true

Determining if a histone protein co-localizes with RNA Polymerase II can provide a clue that a histone protein may be associated with transcription.  True or false?

True