Chromatin Structure and Histone Code Flashcards
What are chromatin made from?
They are made from histones and nucleosomes or in other words they are made of chromosomes and associated proteins.
What are histones?
They are proteins responsible for the 1st level of packaging. With DNA, they form nucleosomes.
What are nucleosomes?
They are ‘beads on a string’ and is basically made up of histones and DNA.
Nucleosomes structure increases DNA packaging by 7-fold.
Histones assemble to form an octamer core
2 molecules each of histones H2A, H2B, H3 and H4
Note: N-terminal tails outside the octamer core
How are chromatin structured in high order?
-When chromatin is extracted at physiological salt concentration, much of it appears as a 30nm thick fibre
-The fibre is actually made up of nucleosomes tightly packed together
-The 30nm fibre can be further compacted to form 80-100nm fibres
-Compaction of nucleosomes to form higher order structures involves
o Linker histones (e.g. H1)
o Interaction of histone tails with adjacent
nucleosomes
o Binding of packing proteins to histone tails
What is the overview of the levels of structure of chromosomes?
-HISTONES: proteins responsible for the 1ST LEVEL OF PACKAGING
o DNA + HISTONES = NUCLEOSOMES
o NUCLEOSOME structure increases DNA packaging
7-fold
-Nucleosomes pack themselves in fibres of 30nm constituting the 2nd LEVEL OF PACKAGING
o Increases packaging 6-fold
- 30nm fibres pack themselves into 80-100nm fibres constituting the 3rd LEVEL OF PACKAGING
o Increases packaging 3-fold
-The 4th LEVEL OF PACKAGING is represented by the mitotic chromosome.
o Represents 10000-fold packaging
What are chromosomes mainly made out of and when is it packaged?
Chromosomes consist predominantly of DNA, Histone proteins, non-histone proteins and non-coding RNA.
In the interphase chromosome almost all is DNA packaged at 1st level forming nucleosomes and much DNA is tightly packed in higher order structures.
Why is the structure of the DNA not static (not permanent)?
During transcription, or DNA replication, nucleosomes must be removed from the DNA in front of the polymerase, and replaced behind the polymerase
Histone remodelling factors: Enzymes that remove and replace nucleosomes
o Euchromatin and heterochromatin
What is Euchromatin?
Lightly staining areas of chromatin
Rich in genes
Made up of nucleosomes, but not dense higher order packaging
What is Heterochromatin?
-Darkly staining areas of chromatin
-Few genes
-Dense higher order packaging of nucleosomes
-Facultative heterochromatin
o Contains genes not expressed in that cell type
o DNA tightly packaged as heterochromatin
o But may be packaged as euchromatin in other cell types
What determines whether nucleosomes are packed as euchromatin or heterochromatin?
- Chemical modification of lysine residues in histone tails
-Acetylation
-Methylation
-Chromatin and gene expression
o Transcription factors , co-activators and
repressors, histone acetylation
What are loops of DNA and scaffolding?
-Chromosomes treated to extract histones and most non-histone proteins
- They don’t completely fall apart
-Appear as long DNA loops attached to a scaffold of tightly bound proteins
-There is evidence that suggests
o Each loop may have a different degree of
chromatin compaction
o The scaffold isolates the chromatin in one loop
from the next loop
o So one loop may have open chromatin and active
genes
o The neighbouring loop could be tightly packed as
heterochromatin
What is a method to investigate chromatin structure?
DNAse digestion.
How does DNAse digestion work?
DNAse I cutes double stranded DNA.
However histones binding protects DNA from DNAse digestion.
Areas that are not protected by histones such as naked DNA or transcription factors are considered to be DNAse I sensitive sites (HSS).
These areas are cut very briefly via digestion using the enzyme which are found within promoters and enhancers.
What are regulatory transcription factors?
They bind to promoters and enhancers and recruit general transcription factors which assemble an initiation complex which recruits RNA polymerase.
If DNA is tightly packaged in higher order chromatin structures, how can all these proteins get at the DNA?
First TF opens up chromatin structure. Then recruits basal transcription factors. TFs recruit chromatin modifying enzymes via a nuclear coactivator (NCoA) or corepressor (NCoR). Then transcription occurs
