Mayerhoff Flashcards
RNA polymerase II does what
mRNA transcription
how does euk RNA Pol II work
- DNA strand is separated (slightly bent to enable separation)
- RNA synth in active centre
- RNA transcript comes out of enzyme
what is the role of the clamp domain in RNA Pol II
- when RNA Pol II engages with DNA, the clamp domain sits MORE TIGHTLY on the enzyme thus BINDING IT
what is the role of the clamp domain in RNA Pol II
- when RNA Pol II engages with DNA, the clamp domain sits MORE TIGHTLY on the enzyme thus BINDING IT
what is the CARBOXY-TERMINAL DOMAIN (CTD) in RNA Pol ll
what is its role
- a seq of SEVEN aa that is repeated 25 TIMES in yeast and 52 TIMES in vertebrates
- PHOSPHORYLATION SITE (fo those aa) important for REGULATION of enzyme
to transcribe a gene, RNA Poll II has to do what
INITIATION 1) recognise a start point in dsDNA: PROMOTOR 2) BIND promotor 3) SEPARATE DNA strands 4) INITIATE transcription at start site ELONGATION 1) elongate until stop signal
what is a promotor
a DNA seq that determines the site of transcription INITIATION for a RNA Pol
what are the 3 main types of promotors in euk
1) TATA box
2) Initiator
3) CpG islands
describe TATA boxes
- strong
- sharp
- 10-15%
- inducible genes, prevalent in highly transcribed genes
describe Initiator complexes
- variable
- sharp
- 15-30%
- inducible genes, usually lacking TATA box
describe CpG islands
- weak
- broad
- 60-70%
- genes transcribed at a low rate (eg housekeeping genes)
the TSS (transcription start site) is what
+1
where is the TATA box
~30 bases BEFORE the TSS
give examples of genes that TATA boxes could act as a promotor for
mutations in the TATA box cause what
- highly transcribed genes O
- eg viral genes, cell cycle components, tissue specific genes
- mutations within the seq ABOLISHES function
- downstream/upstream movement of the TATA box causes shift the TSS
Initiator is what in comparison with the TATA box
an ALTERNATIVE
MUTUALLY EXCLUSIVE
where is the Initiator promotor found
- -2 to +4 (O encompasses TSS)
- if Initiator is moved up or downstream, the TSS moves too
- Initiator is less well defined
describe the precision of CpG islands
how common are they
whatare they rich in
- less precise TSS
- 70% of genes
- housekeeping genes
- GC rich (O less bendy)
what is req for transcription initiation (“Construction” of the polymerase complex on the promoter)
- RNA Pol
- General Transcription Factors (GTFs)
what is the function of GTFs
- position RNA Pol II on the promotor
- help separate DNA strands for transcription
- form the PREINITIATION COMPLEX: GTFs & RNA Pol II
what is the role of TFIID
- a GTF, it is the FIRST protein to bind DNA in formation of pre-initiation comple
- 14 different subunits (O big)
- cont TBP (TATA Box Binding Protein)
- TBP= interacts with minor groove of DNA, causing BEND of DNA
it is the first protein to bind DNA in formation of pre-initiation comple - TAFs (TBP Associaed Factors): recruit to TATA-less promotors (the promotors that don’t use TATA box), contacts to Initiator and DPE
size
what is the role of TFIIA
- 2 subunits
- binds DNA UPSTREAM of TATA box AFTER TFIID has bound
- binds to TBP
size
what is the role of TFIIB
- monomer
- binds DNA on EITHER side of the TATA box AFTER TFIIA
- binds to TBP
TFIID, TBP, TFIIA ANDTFIIB form what together
upstream promotor complex
after the upstream promotor complex is formed, what happens
what is formed
RNA Pol II joins
- it forms a Pol II/ TFIIF complex
- this complex then binds to the UPSTREAM promotor complex
- positions Pol II over the TSS
- forms the CLOSED PREINIIATION COMPLEX (PIC)
after the CLOSED PREINITIATION COMPLEX is formed, what happens next
- TFIIE (heterodimer) binds to Closed Preinitiation complex
- creates docking site for TFIIH
TFIIF is what size
heterodimer
after TFIIE has bound, what happens
TFIIH binds
- 10 subunits
- cont HELICASE (unwinds DNA)
- cont KINASE (phosphorylate RNA Pol II…?)
why is it called a closed preinitiation complex
because DNA is still mostly in a DOUBLE HELIX
at every promotor how many peptides are present
33 peptides
combined mass of 1.5MDa
what is the order of TFII binding
D A B F E H
how do we transition from transition to transcription
by going from CLOSED PREINITIATION COMPLEX to OPEN PREINITIATION COMPLEX (PIC)
what happens to form the Open Preinitiation complex
- TFIIH HELICASE subunit unwinds DNA (req ATP)
- this pushes back on the promotor bound GTFs, forming transcription bubble
how is the INITIALLY TRANSCRIBING COMPLEX formed
- TFIIB releases RNA exit channel
- TFIIH KINASE activity phosphorylates CARBOXY-TERMINAL DOMAIN (CDT) of Pol II
- recuits capping factors
- TBP/TFIID are left at promotor
- other GTFs dissociate
the DNA template is read from which direction
3’->5’
for PAUSING of transcription which factors are req
1) NELF (negative elongation factor)
2) DSIF (DRB Sensitivity Inducing Factor)
which factor makes transcription continue
P-TEFb= cyclin-CDK
- phosphorylates NELF and DSIF
- phosphorylates Poll II CTD
- causes Pol II to switch to ELONGATION mode, enzymes become processive, splicing factors also recruited
give an example of a viral example of the use of RNA Pol II
what is the significance for treatment
HIV uses RNA Pol ll
- maximises elongation efficiency
- TAR hairpin formed (RNA base pairs with itself)
- binds Tat protein
- recruits P-TEFb (positive factor to help overcome neg factors)
- switches to elongation
DRUGGABLE TARGET?
what are proximal promotor elements
- seq close to TSS, position may affect activity
- short ~6-10bp
- often direction INDEPENDENT
- often TISSUE SPECIFIC
what are distal “enhancer” elements
- far from promotor(up to 50,000bp up/downstream or intronic)
- typically ~50-200bp, but composed of several functional elements
- direction independent
- usuallu tissue specific
whta is a transcription factor
transcription factor: protein (other than RNA Pol) that initiates or regulates transcription in eukaryotic cells
specific transcription factors are what
- Transcription Activators or Transcription Repressors
- Stimulate or inhibit transcription of particular genes by binding to their regulatory sequences
- Many: ~1,400 in human genome
- Modular domain structure
GTFs are for what
combining with RNA Pol ll to make the preinitiation complex
what is the structure of a specific transcription factor
how are domains linked
2 main domains
- DNA binding domain: recognises specific seq
- an ACTIVATION or REPRESSION domain: alters transcription rates
linked by: flexible, disorded protein domain
describe DNA binding domains in specific transcription factors
give an example of a DNA binding domain, where is it found
- often DIMERS: homo/hetero
- NON-COVALENT INTERACTIONS are SEQ SPECIFIC: H bonds, ionic interactions
- a helix inserts into MAJOR GROOVE of DNA
eg helix-turn-helix in Bacteriophage 434 repressor
describe Zinc-finger proteins
what are they
- a DNA BINDING DOMAIN
- short seq folds around co-ordinated Zn2+
- cysteine and histidine side chains
what are the 2 types of Zinc-finger proteins
C2H2 zinc finger
- most common on humans
- monomer
C4
- in ~50 transcription factors
- steroid receptor superfamily or nuclear rceptors
- homo/heterodimer
whata re Leucine-zipper proteins
describe them
DNA BINDING DOMAIN
- extended alpha helices
- basic residues interact with DNA backbone in major groove
- coiled coil dimerization (stabilises by HYDROPHOBIC interactions between monomers)
- can form heterodimers
- dimers ‘grip’ DNA
what are basic helix-loop-helix (bHLH) proteins
describe them
DNA BINDING DOMAIN
- bind at N-termini
- non-helical loops from leucine zipper-like coiled coil dimerization domains
- can form heterodimers
describe DNA binding activation domains
- structurally diverse
- often rich in one type of aa
- may have intrinsically disordered conformation, but become more ordered with a co-activator
what do many transcription factors bind as?
why are transcription factor interactions important
DIMERS
- transcription factor interaction increasse gene control options
what effect does co-operation of monomeric transcription factors have
- inc affinity
- stabilises binding to composite site
what is the enhancosome
Multiple transcription factors co-operate at distant regulatory sites
what regulates regulators
- the transcription of TRANSCRIPTION FACTORS themselves is regulated
- LIGAND BINDING: interaction w/ ligands eg drugs
explain the role of nuclear receptors and ligand binding in
- interact with steroid hormones
- have a DNA binding domain and activation domain and ligand binding domain which make TF
- bind w/ LIPID SOL HORMONES
- family of ~50 transcrtiption factors
- bind as HOMO or HETEROdimers
C4 zinc finger proteins
what does ligand binding do to nuclear receptors
changes subcellular localisation
because TFs can only bind DNA if they are in the NUCLEUS
how is subcellular localisation of TFs changed
in cytosol (O cannot bind DNA)
- before hormone binds to TF, the TF interacts with CHAPERONES, which prevent TF from moving to nucleus
- hormone diffuses into cell, and binds to LIGAND BINDING DOMAIN of TF
- causes CHANGE IN SHAPE, conformational change of LF domain
- O free from chaperones
- O can move to nucleus
- DNA binding domain can now bind
- Activation domain can activate gene
what are the 3 basic mechanisms that underoin transcriptional activation
1) Modulation of chromatin structure
- impacts the ability of general transcription factors to bind
2) Recruitment of RNA polymerase
- Via mediator complex or recruitment of general transcription factors (TFIID)
3) Stimulation of elongation
- Via recruitment of P-TEFb or other elongation factors
how is chromatin structure modulated
more tightly packed means less access for TF and RNA Pol II
heterochromatin describe
- inactive genes
- more condensed
- dark staining
- histone deacylation
- centromeres, telomeres
histones being more acetylated means what
- LESS densely packed
- O more accessible
histone acetlyl transferases make DNA more/less accessible
MORE
which TF is used to repress transcription
HISTONE DEACETYLASE CO-REPRESSOR (HDAC) - recruited to promotor via binding to transcription REPRESSOR DOMAIN - causes HYPOACETYATION - inc DNA-HISTONE interaction - inc packaging to 30nm fibre thus preventing GTFs binding
which TF is used to activate transcription
HISTONE ACETYL TRANSFERASE (HAT) - co-activator receruited to promotor via binding to TRANSCRIPTION FACTOR ACTIVATOR DOMAIN - causes HYPERACETYLATION - dec DNA-HISTONE interaction - dec packaging to 30nm fibre thus allowing GTFs to bind
if DNA is too tightly packed for even TFs to reach, how is it accessed
PIONEER TFs
- bind one side of DNA helix even if DNA is wrapped around histone octamer
- recruit histone acetlyl transferase
- recruits more TFs once DNA= partially accessible
how is RNA Pol ll recruited
- via activation domains that recruit TFII
- use MEDIATOR (connects RNA Poll ll and TFs)
- mediator of transcription
- molecular BRIDGE to RNA POL II
- multiple subunits : some essential to all genes, some specific to 3-10% of genes
how is the mediator recruited
- activation domain interacts with MEDIATOR
- mediator can simulatneously contact multiple activators (cooperativity)
- DNA looping: enhancers
incorrect transcription or transcription of mRNA that should not have been transcribed can cause what
- multiple toes (dominant HOXD13 mutation)
- multiple wings on fly
