chromatin structure and histone code Flashcards
(21 cards)
what are histones?
proteins responsible for the first level of packaging
what are nucleosomes?
→DNA wrapped around 8 core histones is called a nucleosome.
→octamer core is made up of a pair of H2A, H2B, H3 and H4 histones.
→the positively-charged N-terminal tails are outside the octamer core.
what are the 4 levels of chromatin folding?
→Histones are proteins responsible for the first level of packaging, creating nucleosomes.
→7-fold packaging
→Nucleosomes fold further into 30nm fibers called solenoids (beads on a string)
→6-fold packaging
→ The solenoid fibres fold into 80-100 nm fibres,
→ 3-fold packaging
→the solenoid fibers coil to form the mitotic chromosome.
→ 10,000-fold packaging.
how much DNA is inside a cell?
6ft
what are the 4 components of DNA?
→DNA
→histone proteins
→non-coding RNA
→non-histone proteins
what does compaction of nucleosomes involve?
→ linker histones (eg. H1)
→interactions of histones tails with adjacent nucleosomes
→ binding of packing proteins to histone tails (this plays a vital role in gene access)
what happens to the histones during transcription?
→nucleosomes must be removed from the DNA in front of the polymerase, and replaced behind the polymerase.
→Histone remodelling factors are enzymes that remove and replace nucleosomes.
what is the difference between heterochromatin and euchromatin?
EUCHROMATIN:
→lightly staining areas of chromatin
→ rich in genes
→made up of nucleosomes, but not dense, higher order packaging
HETEROCHROMATIN
→darkly staining areas of chromatin
→few genes
→dense, higher order of packaging of nucleosomes
what is constitutive heterochromatin?
→ remains condensed throughout the cell cycle and development.
→contains highly repetitive sequences that are not transcribed and play a role in chromosome structure.
what is facultative heterochromatin?
→contains genes that are not expressed in that cell type.
→ DNA is as tightly packaged as constitutive heterochromatin, but it may be packaged as heterochromatin in other cell types.
what determines whether nucleosomes are euchromatin or heterochromatin?
→chemical modification of lysine residues on histone tails:
→ acetylation
→methylation
how do chromosomes appear when histones are extracted?
→They don’t completely fall apart.
→ they appear as long DNA loops attached to a scaffold of tightly bound proteins.
→each loop may have a different degree of chromatin compaction.
→The scaffold isolates the chromatin in one loop from the next loop.
→one loop may have open chromatin and active genes, while the neighbouring loop may be tightly packed as heterochromatin.
how is chromatin structure studied?
→DNAse digestion.
→DNAse I cuts double-stranded DNA.
→Histone binding protects the DNA from DNAse digestion.
→there are DNAse I sensitive sites (HSS):
→sequences of DNA without histones
→it may be naked DNA or binding transcription factors
→ cut by very brief digestion with DNAse I
→found in promoters and enhancers
how do proteins fit in DNA if it is so tightly packed?
→transcription factors open up the chromatin structure. → they recruit basal transcription factors.
how do the transcription factors open up the chromatin structure?
→The transcription factors recruit chromatin modifying enzymes via a nuclear coactivator (NCoA) or corepressor (NCoR).
what are the four different chromatin modifying enzymes and what are their functions?
HISTONE ACETYL TRANSFERASES (HATs):
→acetylate lysine residues on histones, which leads to unpacking of chromatin
HISTONE METHYL TRANSFERASES (HMTs):
→methylate lysine residues on histones, which leads to compaction of chromatin
HISTONE DEACETYLASES (HDACs): → de-acetylate histones
DEMETHYLASES (DMs):
→de-methylate histones
how does the thyroid hormone receptor work?
→ (TR) thyroid hormone receptor binds to the thyroid response element (TRE) on the DNA.
→triggers the recruitment of the histone modification enzymes HDAC and DM via the N-CoR (which causes demethylation).
→A T3 (thyroid hormone) bonds to the TR.
→the histone modification enzymes HAT and HMT are recruited via the N-CoA (which causes acetylation, ie. the unpacking of DNA)
what is the histone code?
→a set of histone modifications that determine whether the chromatin is open or closed
how are histone marks read?
→Histone ‘marks’ (modifications) are read by binding proteins.
→Related domains are found in multiple code reading proteins.
Histone ‘marks’ aren’t read in isolation:
→there are multiple lysine residues on each histone
→there are multiple modifications
→ac, me1, me2, me3, etc.
→there are other histone modifications, eg. phosphorylation of serine ‘Code readers’ are protein complexes that read the combination of marks.
are methylation and acetylation the same?
→The methylation seems more complex than the acetylation.
→ While the methylation of some lysine residues causes chromatin condensation, the methylation of other lysine residues causes chromatin decondensation.
→The effect may also vary if the residue is mono-, di- or tri-methylated.
what are two examples of marks for promoters and enhancers?
→ promoters are strongly enriched in H3K4me3
→ active enhancers are enriched for H3K4me1
