chapter 13 part 2 Flashcards
what does positron effect variegation (PEV) is drosophila illustrate?
the effect of chromatin compaction on gene expression
what on the flies with variegated eye color had happened?
the X chromosomes had undergone chromosomal inversion
-the white gene had been moved from its normal position near the telomere to a region near the centromeric heterochromatin
what does the occurrence of PEV show?
gene expression can be silenced by the gene’s chromosomal position
-silencing is a feature of chromatin structure that can be transmitted from one cell generation to the next
what do E(var) mutations do
these enhance mutant phenotypes by encouraging spread of heterochromatin = more white & less red
what do Sur(var) mutations do?
restrict heterochromatin spread or interfere with its formation; this suppresses mutant phenotypes so more wild-type cells are seen = more red & less white
what are some Sur(var) mutations caused by?
defective expression of heterochromatin protein-1 (HP-1)
what is HP-1
it is a nucleosome binding protein that targets lysine in position 9 of histone H3 (H3K9me) if they carry a methyl group
what happens in the absence of HP-1
interferes with heterochromatin formation & suppresses variegation (more euchromatin = more red eye cells)
what does a second group of su(var) genes encode?
enzymes that add methyl groups to histone proteins
-called histone methyltransferases (HMTs)
-target lysine & arginine residues like (H3K9me)
what are the five features of epigenetic modifications
- epigenetic modification patterns alter chromatin structure
- they are transmissible during cell division
- they are reversible
- they are directly associated with gene transcription
- they do not alter DNA sequence
what is the defining feature of eukaryotic DNA
is its packing into chromatin
what are chromatin remodeling and modifying enzymes recruited to specific sites by?
trans-acting factors that bind target DNA sequences
what do chromatin remodelers & chromatin modifiers mediate?
the reversible transition from inactive, heterochromatin DNA to active, euchromatic DNA
what are epigenetic marks (like PEV) maintaned?
through cell division cycles
how are is the original epigenetic state quickly reestablished after replication?
based on the epigenetic marks present on the old histones to modify the newly deposited histones
what are open promoters?
they are constitutively expressed genes
about open promoters…!
they have a nucleosome-depleted region (NDR) of 100-150 bp immediately upstream of the start site
-do not have a TATA box
-have an A/T tract
what do open promoters have instead of a TATA box?
a poly A/T tract
what does the poly A/T tract of open promoters contain?
binding sequences (BS) that attract transcriptional activators (ACT)
what is the binding region of open promoters flanked by? ??? binding region of transcriptional activators?
flanked by sequences that help position one nucleosome upstream (-1) & one downstream (+1) of the NDR (nucleosome depleted region)
what does the downstream nucleosome from the ACT contain?
variant histone H2A called H2AZ
-that is more easily modified for removal from the transcription start site
about H2AZ
it is a variant histone in a nucleosome downstream the NDR
-it is easier to modify for removal from the transcription start site
what are covered promoters?
characterize genes whose transcription is regulated
-transcription is blocked until nucleosomes are displaced or removed from the promoter
transcription is blocked until what?
nucleosomes are displaced or removed from the promoter
-these promoters contain TATA boxes & other transcription-factor binding sequences
what is there an active competition between for binding?
nucleosomes & transcription factors
what is chromatin remodeling
refers to modifications that reposition nucleosomes to open or close promoters & other regulatory sequences
what is closed chromatin produced by?
modifications that cause regulatory sites to be covered by nucleosomes, restricting access by regulatory proteins
-these modifications increase interaction between DNA & nucleosomes
what is the association between DNA & nucleosomes with open chromatin?
a relaxed association
-this allows regulatory proteins to access the DNA sequences
what are the regions of chromatin that are sensitive to DNase 1 digestion?
DNase 1 hypersensitive sites
what type of chromatin do DNase 1 hypersensitive sites contain?
OPEN chromatin
what is DNase 1?
it is a DNA digesting enzyme that randomly cuts DNA not protected by histones
where does hypersensitivity occur
in the immediate vicinity of transcribed genes & surrounding promoters, enhancers, & other transcription-regulating sequences
-any region lacking nucleosomes
chromatin immunoprecipitation
(ChIP)
- is a more direct lab approach
-identifies where proteins are bound to DNA
-TFs are chemically cross-linked to the chromatin to which they are bound
-an antibody specific to the TF of interest is used to precipitate the chromatin bound to the TF
-DNA is released & analyzed to determine the sequence to which the transcription factor was bound
what are chromatin remodelers?
protein complexes that move nucleosomes in three principle ways
what are the three principle ways that chromatin remodelers move nucleosomes?
-slide nucleosomes along the same piece of DNA until promoter or enhancer sequences are accessible
-reposition nucleosomes from on piece of DNA to another
-change the composition of Histone Octomers, activating genes
what are the chromatin remodelers?
-SWI/SNF
-ISWI complex
-SWRI complex
is SWI/SNF in all eukaryotes?
yes, but it was first described in yeast
what does SWI/SNF do?
it opens chromatin by ejecting or displacing nucleosomes
-this usually uncovers promoter &/or enhancers which facilitates transcription
what does ISWI complex do?
contains remodelers that mainly control placement of nucleosomes into a position that silences transcription
-these proteins can measure the length of linker DNA between nucleosomes & place the nucleosomes at regular intervals where they will cover promoters
can some nucleosomes block ISWI activity?
yes
what is the SWR1 complex responsible for?
replacing common histone H2A protein with a variant called H2AZ
how does H2AZ differ from the common form?
by amino acids internal to the protein & the amino acid protein tail
-these differences alter its pairing with other H2A proteins & interactions with H3/H4 tetramers in the nucleosome
what do chromatin modifier proteins do & how?
chemically alter histone proteins in the nucleosome by adding or removing chemical groups
-these modifications alter the strength of the nucleosome-DNA associations
-can cause chromosome structure to relax, forming open promoter
- or to condense, leading to closed promoter structure
what are the major chemical modifications?
addition or removal of
-acetyl (COCH3)
-methyl (CH3) groups
what are readers
proteins that recognize modified histones
what are writers
enzymes add chemical groups to chromatin
what are erasers
enzymes remove groups from chromatin
what do writers, erasers, & readers ultimately do?
modify histone tails, producing an opened or closed chromatin state
what is the most frequently targeted acetylation target?
lysine (K)
what is the most frequently targeted methylation targets?
lysine (K) & arginine (R)
what are the targets for phosphorylation?
Serine (S) & threonine (T)
what do recent experiments suggest about histone code
their is a histone code
chromatin exists in a limited number of distinct states
what are histone acetyltransferases recruited by?
(HATs) - act as writers
recruited by activators & ADD acetyl groups
what are acetyl groups removed by?
histone deacetylases (HDACs)
which are recruited by repressors
act as erasers!!!!
what do histone deacetylases do?
remove acetyl groups
erasers!!
what does acetylation do?
neutralizes the positive charge & relaxes histone/DNA interaction
what are methyl groups added to & by what?
the N-terminal histone tails
-by histone methyltransferases (act as writers)
what does methylation play a role in?
converting open to closed chromatin
does methylation relax or condense chromatin?
depending on the residue target, it can either relax or condense it
what is demethylation carried out by?
histone demethylases (HDMTs)
-erasers!
what do pioneer factors do>
bind to DNA & open heterochromatin by recruiting chromatin modifier & remodeling complexes
-alternatively, they may bind DNA to prep chromatin for when other transcription factors become available
can pioneer factors be a single protein?
yes!
can proteins that are not pioneer factors, by themselves, associate together to form a pioneer complex?
yes!
what can pioneer factors initiate?
transition from heterochromatin to euchromatin
