Chromatin structure and histone code Flashcards
what is chromatin?
chromosomes + associated proteins
what are the four levels of packaging?
1st : DNA + histones = nucleosomes
(beads on a string)
2nd : nucleosomes pack themselves into fibres of 30nm (solenoid)
3rd : 30nm fibres pack themselves into 80-1–nm fibres
4th : represented by the mitotic chromosomes
what do chromosomes consist of?
- DNA
- histone proteins
- non-histones proteins
- non-coding RNA
nucleosomes
- histones assemble to form an OCTAMER
- this is 2 molecules of each histones (H2A, H2B, H3 and H4) with the DNA molecule wrapped around the structure
- the N-terminal tails of the histone proteins are +ve charged and stick out of the octamer structure
compaction of nucleosomes
compaction of nucleosomes occurs to form higher order structures which involves:
- linker histones (H1) link together octamer cores (nucleosomes) to form a solenoid (30nm fibre)
- packaging proteins bind to histones tails to bring them together
what are histone remodelling factors?
- enzymes that remove and replace nucleosomes
euchromatin
- lightly staining areas of chromatin
- less DNA
- rich in genes
- made up of nucleosomes, but not dense higher order packaging (low order of packaging)
heterochromatin
- darkly stained areas
- more DNA
- few genes (most of the DNA is “useless” to the specific cell)
- dense higher order of packaging (has a lot of DNA to pack) of nucleosomes
facultative heterochromatin
- contains genes that are not expressed in that cell type
- DNA tightly packaged as heterochromatin
- BUT it may be packaged as euchromatin in other cell types as other cell types may need to express those certain genes
what determines whether nucleosomes are packed as HETEROCHROMATIN or EUCHROMATIN?
the type of cell
constitutive heterochromatin
- there is a section of heterochromatin that will NEVER become euchromatin as the cell will NEVER need those genes to be expressed
EXAMPLE: the production of a beard
- pre-puberty, skin cells on the face will not express the genes for hair follicles, this gene will be packaged under the category of “FACULTATIVE heterochromatin”
- post-puberty, chemicals (testosterone) will activate the genes for hair follicles and will therefore become euchromatin
- this will change the heterochromatin to allow the expression of the hair follicles for a beard to grow
- mashallah boys
what chemical modifications take place to convert heterochromatin to euchromatin and vice versa?
- methylation —-> coverts euchromatin to heterochromatin
- acetylation ——> converts heterochromatin to euchromatin
what are the enzymes that allow chemical modification of histone tails to take place?
- HAT –> histone acetyl transferase
- HMT –> histone methyl transferase
how does chemical modification occur?
-acetylation/methylation
- TF bind to DNA
- recruitment of histone modification enzymes (HAT/HMT) via N-CoA (nuclear coactivator)
- this leads to unpackaging of DNA
what is acetylation?
- the loss of +ve charge from the histone tails
what is methylation?
- addition of a methyl group to DNA
HATs
- histone acetyl transferase
- acetylate lysine residues (AA) on histones
- leads to unpacking of chromatin
HDACs
- histone deacetylases
- De-acetylate histones
- lead to compaction of chromatin
EXAMPLE : thyroid hormone receptors
- thyroid hormone receptor (TR) binds to the thyroid response element (TRE) on the DNA strand
- this recruits (HDAC/DM (de-methylase)) via the N-CoR (nuclear corepressor) which causes De-methylation
- Then we, recruit HAT and HMT via the N-CoA (nuclear coactivator), which then causes acetylation, so the DNA unwinds even more (making euchromatin).
- RNA Pol II binds and transcribes thyroid genes.
nuclear co-repressor (N-CoR)
-aids in the recruitment of HDAC and DM to remove chemical groups from DNA
nuclear co-activator (N-CoA)
- aids in the recruitment of HMT and HAT to add chemical groups to DNA
Histone modification via methylation
- histone tails are methylated by histone methyl transferase (HMTs)
- De-methylated by histone demethylase (HDMs)
- a lysine residue can be mono, di or tri methylated
Loops and chromatin domains
There is evidence that suggests
- Each loop may have a different degree of chromatin compaction
- The scaffold isolates the chromatin in one loop from the next loop
- So one loop may have open chromatin and active genes
The neighbouring loop could be tightly packed as heterochromatin
Methods to investigate chromatin structure- DNAse digestion
DNAse I cuts double stranded DNA - HYPERSENSITIVE SITES (HSS). They are:
- Sequences of DNA without histones
- May be naked DNA, or binding transcription factors
- Cut by very brief digestion with DNAse I
- Found in promoters and enhancers
-Histone binding protects DNA from DNase digestion
Marks for promoters and enhancers
- Promoters strongly enriched for H3K4me3
- Active enhancers enriched for H3K4me1
Histone code
- Histone “marks” are read by binding proteins
- Related domains are found in multiple code reading proteins e.g.
- Bromodomain proteins bind to acetylated lysines
- Tudor domain and chromodomain proteins read lysine methylation
Examples of how methylation has varying effects.
- Trimethylation of histone H3 lysine at position 9 (H3K9me3) associated with heterochromatin
- Monomethylation of histone H3 lysine at position 9 (H3K9me1) usually associated with active chromatin
