eukaryotic transcription Flashcards
chromatin =
complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells that protect DNA
we know chromatin exists outside of metaphase as…
in experiments cell nuclei treated with deoxyribonuclease (cuts DNA randomly, eventually into single nucleotides) - when run on agarose gel it can be seen that increasing the time of digestion results in DNA becoming smaller as bands travelled further but was not fully cut = some DNA protected by nucleosomes
nucleosomes =
a structural unit of eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones
nucleosomes structure…
- consists of 8 protein histones which form a bundle =(H2A, H2B, H3, H4) x2
- around the outside, there are 1.65 turns of double-stranded DNA helix with roughly 10 base pairs per turn
- basic amino acids (lysine and arginine) positioned close to DNA as they are positive = attract to negative DNA - this holds the proteins and DNA together
- histones H2A and H2B are closely packed to form a dimer with positive N-terminal tails
DNA held to histone by…
strong electrostatic interactions between negative DNA + positive histone tails and positive N-terminal of helices
chromatin exists in two forms…
euchromatin and heterochromatin
euchromatin =
- less condensed
- activated chromatin
heterochromatin =
- highly condensed
- inactivated chromatin
DNA regions likely to be expressed are packaged in…
euchromatin - nucleosomes are less condensed to there is room for transcription activator proteins to bind
converting chromatin :
need to open up heterochromatin via modification to the histone proteins in order to activate genes (euchromatin):
lysine acetylation = addition of an acetyl group neutralises lysine, so the protein an DNA are no longer held together
lysine methylation = editing of a methyl group provides extra signal that another protein can recognise - allows binding to other proteins
linker histones:
= connects two strands of DNA between nucleosomes
e. g. Histone H1
- in heterochromatin (condensed) it connects two strands
- in euchromatin (nucleosomes are activated) it only binds to 1 of the strands, controlled by modification
in eukaryotes, most genes are…
repressed by chromatin by default and they need to be activated when needed (opposite in prokaryotes)
class 1 and class 3 promoters -
class 1 = ribosomal RNA
- relatively abundant as ribosomes are abundant and rRNA is very stable with high-efficiency transcription
class 3 = transfer RNA and other small RNAs
class 2 promoters -
messenger RNA and most small nuclear RNA
- snRNA involved in splicing
- have core promoter = comprises TATA element and specifices promoter start site
- have upstream promoter elements = contain motifs
- have enhancer elements = densely packed with motifs
motifs =
sequences located in the enhancer elements of promoters which act as binding sites for specific proteins
activation of class 2 promoters:
multiple proteins bind in various combinations to allow activation
upstream promoter elements and enhancer elements comprise of motifs of about 6-12 base pairs, each bound by a specific activator protein
activator proteins -
have 2 domains connected by linkers:
DNA binding domain = interacts with specific DNA nucleotide sequences
Activation domain = binds to other proteins
how to show test if a specific activator protein binds to a specific motif to activate the promotor:
- plasmid 1 is set up to replicate and propagate E.coli but also has elements enabling it to be recognised in eukaryotic cells as well
- plasmid 2 is set up that has a reporter gene and a promoter which will only be activated by the specific protein we are testing
- these plasmids are placed within nucleus of mammalian cells - plasmid 1 will produce the specific protein which will be translated in the cytoplasm and as this is a nuclear protein it will be transported back into the nucleus = it will bind to its sepcific binding site on plasmid 2 to drive expression of the reporter gene to produce a protein
- without plasmid 1 or if there is a mutation in the protein binding site, the reporter gene will not be expressed = proves protein is needed for expressing the reporter gene
the DNA binding domain of activator proteins -
= recognises specific DNA sequences
- DNA binding occurs in the major groove od the double helix of DNA
the activation domain of activator proteins -
= binds to other proteins (recruiting them)
- recruitment of histone acetyltransferases
- recruitment of chromatin remodelling factors
- recruitment of coactivators
recruitment of histone acetyltransferases by activator proteins -
activation domain binds to histone acetyltransferases and brings them close to where the activator protein is bound in order to acetylate glycine (removes positive charge) = weakness the contact between the nucleosome and DNA
recruitment of chromatin remodelling factors by activator proteins -
activation domain binds to proteins that act as chromatin remodelling factors and bring them into the activator protein
- DNA binding domain binds to a free bit of DNA next to a nucleosome
- there is a hinge in the middle of the nucleosome
- a translocation domain binds another part of the DNA running around the nucleosome
ATP hydrolysis deforms the DNA and pulls it around the nucleosome, the translocation domain allows it to run through = the DNA ends up moving relative to the nucleosome
nucleosome is moved up and down the DNA = nucleosomes can be cleared away from the binding site on the promoter to create space for RNA pol
recruitment of coactivators by activator proteins -
coactivators do not bind to DNA directly - they bind to activator proteins that bind to DNA
coactivators bind RNA pol 2 and stabilise its binding to the promoter
.general transcription factors -
required for specific initiation and efficient elongation
there are 5 for RNA pol II:
- TBP (TATA-binding protein) = binds in the minor groove
- TFIIH = phosphorylates ser 5 repeats on RPB1 - enabling promoter clearance and interacts with RNA processing factors
- TFIIE
- TFIIF