lecture 4 Flashcards
post translational modifications of histones
acetylation and methylation
the histone code
types and arrangement of modifications on the N terminal tail are a code that tells you what the transcriptional state of the underlying DNA is
enzymes such as HATs _____ the code
write
enzymes such as histone deacetylases _____ the code
erase
proteins such as bromodomain proteins ____ the code
read and bind to acetyl lysines
chromodomains proteins and PWWP proteins bind to
methyl lysines
ATP dependent chromatin remodelers, they
use ATP from ATP hydrolysis to change the structure of chromatin
there are 4 different families of the chromatin remodelers
SWI2/SNF2, ISWI, CHD/Mi2 and Ino80
the families are characterised by
additional domains and structure of the ATPase domain
they can use the energy from ATP hydrolysis to one or more of these reactions
slide nucleosomes along DNA, unwrapping of DNA from the nucleosome, remove nucleosome, spacing of nucleosomes and exchange histones for histone variants
the catalytic subunit SWI/SNF is called Snf2 ir Swi2
it hydrolysis 1000 ATP molecules per min in the presence of DNA or nucleosomes
Snf2 is related to
DNA helicases
Snf2 is though to be a molecular motor that uses the energy from
ATP hydrolysis to track along side DNA and induce torsion which introduces loops and change in structure, results in disruption of histone DNA interactions and movement o the nucleosome
they change the position of DNA around the nucleosome
makes potential binding sites accessible
bromodomains in Snf2 help tether it to acetylated nucleosomes
human SWI?SNF (hBRM and BRG1) are very similar to the
yeast SWI/SNF
SWI/SNF mutations can causes
cancer as they are tumor suppressors
transcription repression by recruiting chromatin modifying factors eg
histone deacetylases (HDACs), ATP-dependent remodelers and histone methylases
histone deacetylases
repressed regions are hypoacetylated (low)
mediated by HDACs
4 major groups of HDACs: class I, II and IV (classical HDACs dependent of zinc in their active site). class III is SIr2 family (use NAD as a co factor)
HDACs commonly function in
large multi subunit complexes eg SIN3 co repressor
URS (upstream repressing sequence) is bound to by
DNA binding domain, then Ume6 brings the HDAC complex to chromatin. Rpd3 (the catalytic subunit) then deacetylates the lysines from the histone tails
co repressor as it doesn’t bind to DNA directly
some ATP dependent remodelers mediate transcriptional repression
eg the NuRD complex which belongs to the Mi2/CHD family
the NuRD complex plays roles in
normal differentiation and tumourogenesis (supressed the transcription of tumour supressor genes)
NuRD cause the chromatin to be more
tight and very regularly, causes a closed chromatin structure turning transcription off
not all ATP dependent remodeling complexes are used for
increasing transcription
heterochromatin
there are 2 types of chromatin: euchromatin and heterochromatin
euchromatin is gene rich and has the potential to be transcribed
heterochromatin is gene poor, contains repetitive regions and associated with transcriptional silencing
heterochromatin is found at
centromeres and telomeres
features of heterochromatin
hypoacetylation, specific histone H3 methylation (eg Lys9 + Lys27) and association of specific silencing factors
assembly of H3Lys9me):
in order for a lysine to be methylated it must be
deacetylated
HDACs remove the
acetyl group
methylation of Lys9 on histone H3 is mediated by
suvar39
methyl is recognised by
HP1 (heterochromatin protein 1)
methyl is recognised by
HP1 (heterochromatin protein 1)
heterochromatin protein 1is a
chromodomain protein
chromodomains often recognise and bind to
methylated lysine residues
the chromodomains of HP1 is specific for
H3 Lys9me2/3 (di(2) or tri(3) methylated)
HP1 interacts with itself to bring adjecent nucleosomes close together to form
compact nucleosomal arrays
acts as an interaction platform for the recruitment of further activities that prevent recruitment/activity of
RNA pol II
reporter silencing assays
ade6 gene is in euchromatin and being expressed
when ade6 gene is expressed cells can make their own adenine and colonies are white
ade6 gene was deleted at normal location and was put in the middle of heterochromatin. HP1 will assemble over the ade6 gene so it can no longer be expressed. the cells is the colonies now are red
mutate a gene in heterochromatin then the colonies are white/pink
