lecture 9 Flashcards
what do histone acetyl transferases do
they transfer acetyl moiety from acetyl-CoA to the epsilon-amino group of a lysine residue on a substrate protein
they can also acetylate non-histone proteins, these are sometimes termed lysine acetyl transferases or acetylases
histone post-translational modifications
sense and use cellular metabolites
they are small metabolites in their own right
many epigenetic modifiers depend on metabolites as cofactor substrates
3 major classes of histone acetyl transferases
writers, readers, erasers
what determines which lysines are acetylated by any given histone acetylase
- docking domains on the histone acetyl transferase
2. most hats exist within multi-subunit complexes in vivo, many of which are transcriptional co-activator complexes
docking domains in the HAT
hats containing bromodomains dock onto specific acetyl lysine residues
hats containing chromodomains dock onto specific methylated lysines
HAT can acetylate another nearby lysine residue in cis or trans
what does cis mean
in same protein as docking acetyl-lysine
what does trans mean
lysine in another associated protein becomes acetlyated
most hats exist within multi-subunit complexes in vivo, many of which are transcriptional co-activator complexes. how does this affect hats?
- by targeting localisation - brings the hats into the vicinity of its specific substrate
- after subunit specificity and the activity of the hat catalytic subunit within a complex the hat may have greater activity toward a specific lysine compared to the activity of the catalytic subunit alone
- mediate regulation of the hat activity in response to signalling pathways
class 3 histone deacetylases (HDACs)
Sirtuin
originally identified as Sir2
their HDAC activity couples histone deacetlyation to cleavage of high energy bond in nicotinamide adenine dinucleotide to generate O-acetyl-ADP ribose and nicotinamide
nicotinimide inhibits SIRTs linking the NAD+ salvage pathway to regulation of SIRT activity
MEF2 transcription factor is inhibited by certain class 2 hdacs which are shuttled into cytoplasm in response to calcium and other signals several HDACs are components of transcriptional corepressor complexes class 2 HDACs are highly regulated
how does histone acetylation make dna accessible?
- decreases interactions of histones with dna
- positive charge of k neutralised by acetylation and prevents binding of histones to dna and chromatin compaction - recruits chromatin domain proteins with bromodomains
- bromodomain structure is an unusual left handed up and down bundle of 4 helices with a left handed twist
- a deep hydophobic pocket in the bromodomain creates a binding site for acetylated moiety - prevents methylation of the same lysine residue
- lysines can be methylated 1,2 or 3 times by methyltransferases that use adenosyl methionine as a substrate
- depending on the residue and no of methyl groups, methylation can be associated with repression or activation of transcription
HATs and HDACs in activation and repression
many transcriptional co-activator complexes are recruited by dna binding transcriptional activators - including hats
transcriptional corepressor complexes are recruited by dna binding transcriptional repressors - including HDACs
HATs are transcriptional co-activators
in response to signalling pathways, certain dna binding transcription factors can bind to co-activator complexes containing acetyltransferases and recruit them to specific recognition sequences in DNA
the co-activator is unable to bind dna itself
the hat with coactivator complex acetylates specific lysine residues in core histones
DNA is made accessible by RNAP2 and other proteins that promote gene transcription
where do n terminal tails of histones stick out from the nucleosome core
and what does is the modification of these tails likely to affect
n terminal tails stick out from the nucleosome core between gyres of dna and contact adjacent nucleosomes
modification of the tails is likely to affect inter-nucleosomal interaction and affect overall structure and function of the chromatin
histone modification implications
chromatin structure is a source of epigenetic information
post-translational modifications and histone variants contribute to structural and functional characteristics of chromatin
the combination of histone modification constitutes the histone code
histone code influences chromatin modelling/ condensation and defines actual or potential transcription states
a multitude of histone modifying enzymes is involved in chromatin remodelling
the histone code
different combinations of histone modifications affect chromatin structure in different ways
histone modifications are independent - they influence one another by steric hindrance or creating PTMs such as Ac-lys and MeLys that act as docking sites for bromodomain and chromodomains respectively
histones can be combinatorially modified to elicit a specific nuclear response
H3K4 methylation and H3K9 acetylation are hallmarks of active chromatin
H3K27 and H3K9 methylation are hallmarks of silent chromatin
