Biochemistry 201
Biological Regulatory Mechanisms
January 30, 2012
Transcription in Eukaryotes
REFERENCES
Books:
Chapter 17 of Molecular Biology of the Gene 6th Edition (2008) by Watson, JD, Baker, TA, Bell, SP, Gann, A, Levine, M,
Losick, R. 589-632.
Articles:
Chromosome conformation capture (CCC) technologies
de Wit, E. and de Laat, W. (2012) A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26: 11-24.
Elongation
BBA2013-- Issue 1874 devoted to reviews of transcription elongation
General Transcription Factors
Matsui, T., Segall, J., Weil, P.A., and Roeder, R.G. (1980) Multiple factors required for accurate initiation of transcription by purified RNA
polymerase II. J Biol Chem 255: 11992-11996.
Thomas, M.C., & Chiang, C.M. (2006). The general transcription machinery and general cofactors. Critical reviews in Biochemistry & Molecular
Biology, 41(3), 105-78.
Muller, F, Demeny, MA, & Tora, L. (2007). New problems in RNA polymerase II transcription initiation: matching the diversity of core promoters
with a variety of promoter recognition factors. The Journal of Biological Chemistry, 282(20), 14685-9.
Mediator and Other Components
*Kornberg, R.D. (2005) Mediator and the mechanism of transcriptional activation. Trends in Biochemical Sciences 30:235-239.
Fan, X, Chou, DM, & Struhl, K. (2006). Activator-specific recruitment of Mediator in vivo. Nature Structural & Molecular Biology, 13(2), 117-20.
Sikorski TW and Buratowski. (2009). The basal initiation machinery: Beyond the general transcription factors. Current Opinion in Cell Biology. 21
344-351.
What Do Activators Do?
Cosma, MP, Tanaka, T, & Nasmyth, K. (1999). Ordered recruitment of transcription and chromatin remodeling factors to a cell
cycle- and developmentally regulated promoter. Cell, 97(3), 299-311.
Bryant, GO, & Ptashne, M. (2003). Independent recruitment in vivo by Gal4 of two complexes required for transcription.
Molecular Cell, 11(5), 1301-9.
Bhaumik, S.R., Raha, T. Aiello, D.P., and Green, M.R. (2004) In vivo target of a transcriptional activator revealed by
fluorescence resonance energy transfer. Genes Dev 18: 333-343.
Vakoc, CR, Letting, DL, Gheldof, ... Blobel, GA (2005) Proximity among Distant Regulatory Elements at the B–Globin Locus
Requires GATA-1 and FOG-1. Molecular Cell 17:453-462
Fishburn, J., Mohibullah, N. and Hahn, S. (2005) Function of a eukaryotic transcription activator during the transcription cycle.
Molecular Cell 18:369-378.
Bulger M and Groudine M. Functional and Mechanistic Diversity of Distal Transcription Enhancers (2011). Cell 144:327-39
Role of the RNA Pol II CTD
*McCracken, S, Fong, N, Yankulov, K, et al. (1997). The C-terminal domain of RNA polymerase II couples mRNA processing
to transcription. Nature, 385(6614), 357-61.
Tietjen,J. ……Ansari, A. Chemical-genomic dissection of the CTD code (2010) NMSB: 17: 1154-1162
Mayer, A. ….Cramer, P. Uniform transitions of the general Pol II transcription apparatus (2010) NMSB 17:1272-79
Buratowski, S (2009) progression through the RNA polymerase II CTD cycle ( Review). Mol Cell 36: 541-546
Chapman, R… Eick, D. Molecular evolution of the RNA polymerase CTD. Trends in Genetics (2008): Jun;24(6):289-96.
Epub 2008 May 9. Review.PMID: 18472177
ChIP-exo technology
Rhee, HS and BF Pugh (2011) Comprehensive genome wide Protein-DNA Interactions at single nucleotide resolution. Cell 147:1408
Rhee, HS and BF Pugh (2012) Genome-wide structure and organization of eukaryotic pre-initiation complexes Nature 483: 295
Elongation Control
Rougvie A and Lis JT (1988) The RNA Polymerase II Molecule at the 5’ end of the uninduced hsp70 gene of D. melangaster is
transcriptionally engaged. Cell 54: 795-804
Zobeck, KL….Lis Jt (2010) Recruitment timing and dynamics of transcription factors at the Hsp70 Loci in Living Cells Mol Cell
40 965-75
Peterlin, BM and Price DH (2006) Controlling the Elongation Phase of transcription with P-TEFb Mol Cell 23: 297 – 305
Nechaev S…..Adelman K. (2010) Global Analysis of short RNAs reveals widespread Promoter Proximal Stalling and Arrest of Pol II
in Drosophila Science 327: 335-38
Gilchrist, DA,……Adelman, K. (2010) Pausing of RNA Polymerase II Disrupts DNA specified Nucleosome Organization to enable
precise gene regulation. Cell 143: 540-51
Chen, Y.,….Handa, H.(2009) DSIF, the Paf1 complex and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II
elongation. Genees Dev 23: 2765 -77
Liu, Y……Hahn, S. (2009) Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of
the PAF complex. MCB 29: 4852-63
Wu, C-H,….Gilmour, D. ( 2003)NELF and DSIF cause promoter proximal pausing on the Hsp70 promoter in drosophila. Genes Dev
17: 1402-14
Kim, J Guemah M and Roeder, RG.(2010) The human PAD1 Complex Acts in Chromatin Transcription elongation both
independently and cooperatively with SII (TFIIS) Cell 140: 491 -503
A link between Transcription and Translation
Harel-Sharvit, L., …..and Choder M. (2010). RNA polymerase II subunits Link transcription and mRNA decay to translation. Cell
143: 552-63
Important Points
1. Transcription initiation at Pol II promoters on naked DNA templates in vitro requires the general
transcription factors in addition to RNA polymerase II.
2. In vivo, transcription initiation also requires activators – proteins that bind directly to enhancers – as
well as Mediator and enzymes that modify chromatin structure.
3. At a typical eukaryotic promoter, activators guide the assembly of Mediator, the general transcription
factors, RNA polymerase and chromatin-modifying enzymes, often through weak, relatively non-specific
interactions. There appears to be no set order of assembly from one promoter to the next. Moreover,
different promoters have different requirements for these components.
4. The RNA polymerase CTD is a long series of 7-amino acid repeats. When transcription is initiated,
serine 5 of the repeat is phosphorylated by TFIIH. As elongation proceeds, serine 5 is gradually
dephosphorylated and serine 2 is gradually phosphorylated by enzymes carried along with the RNA
polymerase. This dynamic pattern of modification couples transcription to processing of the newlysynthesized RNA.
Eukaryotic Cells have three RNA polymerases
TYPE OF POLYMERASE
GENES TRANSCRIBED
RNA polymerase I
5.85, 18S, and 28S rRNA genes
RNA polymerase II
all protein-coding genes, plus snoRNA genes,
miRNA genes, siRNA genes, and some snRNA genes
RNA polymerase III
tRNA genes, 5S rRNA genes, some snRNA genes
and genes for other small RNAs
The rRNAs are named according to their “S” values, which refer to their rate of
sedimentation in an ultra-centrifuge. The larger the S value, the larger the rRNA.
Transcription Initiation by PolII requires many General
Transcription Factors
RNA Pol II
+ NTPs
+ DNA containing a real promoter
NO TRANSCRIPTION
promoter
RNA Pol II
+ NTPs
nuclear
extract
+ DNA with real promoter
TRANSCRIPTION INITIATION and ELONGATION
Purification scheme for partially purified general transcription
factors. Fractionation of HeLa nuclear extract (Panel A) and
nuclear pellet (Panel B) by column chromatography and the
molar concentrations of KCl used for elutions are indicated in
the flow chart, except for the Phenyl Superose column where
the molar concentrations of ammonium sulfate are shown. A
thick horizontal (Panel A) or vertical (Panel B) line indicates
that step elutions are used for protein fractionation, whereas a
slant line represents a linear gradient used for fractionation.
The purification scheme for pol II, starting from sonication of
the nuclear pellet, followed by ammonium sulfate (AS)
precipitation is shown in Panel B. (Figures are adapted from
Flores et al., 1992 and from Ge et al., 1996)
NAME
# OF SUBUNITS
FUNCTION
TFIIA
3
Antirepressor; stabilizes TBP-TATA complex; coactivator
TFIIB
1
Recognizes BRE;Start site selection; stabilize TBP-TATA; pol II/TFIIF recruitment
1
~10
Binds TATA box; higher eukaryotes have multiple TBPs
Recognizes additional DNA sequences; Regulates TBP binding; Coactivator;
Ubiquitin-activating/conjugating activity; Histone acetyltransferase; multiple TAFs
TFIID
TBP
TAFs
TFIIF
2
Binds pol II; facilitates pol II promoter recruitment and escape; Recruits TFIIE and TFIIH;
enhances efficiency of pol II elongation
TFIIE
2
Recruits TFIIH; Facilitates forming initiation-competent pol II; promoter clearance
TFIIH
9
ATPase/kinase activity. Helicase: unwinds DNA at transcription startsite; kinase
phosphorylates ser5 of RNA polymerase CTD; helps release RNAP from promoter
Transcription Initiation by RNA Pol II
The stepwise assembly of the
Pol II preinitiation complex is
shown here. Once assembled
at the promoter, Pol II leaves
the preinitiation complex
upon addition of the
nucleotide precursors
required for RNA synthesis
and after phosphorylation of
serine resides within the
enzyme’s “tail”.
The Pol II promoter has many recognition regions
Positions of various DNA elements relative to the transcription start site (indicated by
the arrow above the DNA). These elements are:
BRE (TFIIB recognition element); there is also a second BRE site downstream of TATA
TATA (TATA Box);
Inr (initiator element);
DPE (downstream promoter element);
DCE (downstream core element).
MTE (motif ten element; not shown) is located just upstream of the DPE.
The GTFs are not sufficient to mediate activation:
Discovery and isolation of Mediator from Yeast
GTFs and RNA Pol II
Tx
1 unit
VP 16
GAL4
1 unit
crude lysate
10 units
4 years
mediator
50 units
Is Mediator Required for Transcription of all
Pol II -transcribed genes?
Control: ts subunit of Pol II
Rpb1
Rpb1ts
high T
Compare levels of all
mRNAs using microarrays
(37˚C for 45 min)
mRNAs decrease over time according to their half-lives.
A few mRNAs remain at some level (stable mRNAs).
Subunit of Mediator
Srb4ts
Same basic pattern
Subunit of TF II H
Kin28ts
Same basic pattern
Mediator is very large and has diverse roles
A)
PIC model from EM-study of polII (brown)-TFIIF
(light blue) and X-ray structure of TBP (white)
-IIB (yellow)--DNA; Arrow indicates direction of trx
B)
Model for PIC-mediator was produced by superimposing
an EM structure of Mediator-PolII on the PIC in A; head,
middle and tail regions shown
The Head region interacts with PolII-TFIIF complex; the mutants with general
effects on Trx are located in this region; the tail region interacts with
activators; mutants have more specific effects on transcription
SAGA is another important complex with multiple roles in
transcription, including being a coactivator
The core of SAGA, containing the Taf substructure (Yellow), is surrounded by three domains
responsible for distinct functions: activator binding (Tra-1), histone acetylation Gcn5), and TBP
regulation (Spt3). This structural organization illustrates an underlying principle of modularity
that may be extended to our understanding of other multifunctional transcription complexes.
The TAFs in TFIID also serve as coactivators
Assembly of PIC in presence of mediator, activators
and chromatin remodelers
Genomic Level Snapshots
ChIP-exo, a new technology for determining location at the genome scale
Comparison of ChIP-exo to ChIP-chip and ChIP-seq for Reb1 at
specific loci. The gray, green, and magenta filled plots,
respectively show the distribution of raw signals, measured by
ChIP-chip using Affymetrix microarrays having 5 bp probe
spacing (Venters and Pugh, 2009), ChIP-seq, and ChIP-exo.
Aggregated raw Reb1 signal distribution around all
791 instances of TTACCCG in the yeast genome
Many Paths to the PIC
Buratowski, 2009
The factors and assembly pathways used to form transcriptionally competent preinitiation complexes can be promoter
dependent. (1) TBP assembling onto promoter regions via TFIID leads to recruitment of the other basal initiation
factors, as outlined in the stepwise assembly pathway. In S. cerevisiae, this pathway is most often utilized at TATA-less
genes. At some mammalian promoters, histone H3K4 trimethylation helps to recruit the TFIID complex.
(2) Mediator bridges interactions between activators and the basal initiation machinery, and can stimulate basal
transcription as well. At some promoters Mediator can recruit TFIIH and TFIIE independently of RNApoII.
(3) TBP can also be brought to promoters by the SAGA complex. In S. cerevisiae, this pathway is most utilized at TATA
containing promoters. The Mot1 and NC2 complexes can repress this pathway by actively removing TBP from the TATA
element.
(4) Mot1 and NC2 can also have a positive role in transcription by removing non-productive TBP complexes from DNA,
thereby allowing functional PICs to form.
Regulatory sequences expand in number and complexity
with increased complexity of the organism
~ 30-100 bp
~ 100s bp
Could be 50kB
or more
Are distant enhancers in proximity to the promoter?
Chromosome conformation capture ( 3C)
3C is a variant of ChIP. Cells are treated with formaldehyde to create DNA-protein-DNA
cross-links. (Formaldehyde reacts with the amino groups on proteins and nucleic acids to
form protein-protein and DNA protein covalent linkages). The DNA is then treated with a
restriction nuclease that produces cohesive ends. Prior to the ligation step, the DNA is
diluted so that the DNA ligase will join two different DNA fragments only if they are
cross-linked. Finally, the cross-links are reversed and the DNA is purified, so that the
ligated DNA molecules can be quantified by PCR.
3C reveals proximity of enhancers and promoters eg. colocalization in the ligated DNA product; eliminating
transcription of a gene eliminates colocalization of enhancer and promoter sequences ( eg. b-globin locus)
Why are enhancer and promoter in close proximity during active
transcription?
= Nucleosomes
Looping via protein-protein
Interactions; intervening DNA
loops out; suggestive that the
direct interactions mediate
activation
RNA polymerase “transcription
factories”; in higher eukaryotes,
some evidence that transcription
occurs at a limited number of
positions; co-localization could be
result of activation
Enhancers can promote chromatin modification
over large distances
Groudine Cell 144: 327 ( 2011)
The RNA Polymerase II CTD (or tail)
Heptad repeat unit
YSPTSPS
P
P
P
proline can be cis or trans
Cis-proline is
well suited to
making hairpin
turns in
polypeptide
chains.
COOH
NH2
5 repeats in plasmodium
26 repeats in yeast
52 repeats in mammals
Regions upstream (R1) and
downstream (R3) of the heptad repeat
region are enriched in the submotifs
What is the role of the Pol II CTD?
Mouse RNA Pol II
wt
52
5
50 hrs.
HeLa
cells
Introduce
CTD construct
CTD
 - amaR
examine
RNAs
Splicing, processing of
3’ end, termination
were all affected
 - amanitin
Nature 385: 357 (1997)
How the Polymerase CTD Couples Transcription to other processes
Kinase/ phosphatase
TF II H,
mediator
YSPTSPS
P
Factors recruited
capping factors
elongation
pTEFb
(Cdk9)
In S. cerevisiae, shared by Cdk1 and Bur 1
YSPTSPS
P
P
Further
elongation
phosphatases (Rtr1(2?)
YSPTSPS
Phosphatases (Fcp1, ssu72)
splicing components
histone methylase
DNA repair enzymes
P
3’ end processing factors
Termination
YSPTSPS
Mediator, activators, GTFs
TECs are community organizers
The major steps in mRNA processing (trx, 5’ capping, polyA addition, splicing) all occur together on a transcript extruded
from the exit channel of RNAP although they can be reconstituted independently in vivo
Principles of “cotranscriptionality” to integrate nuclear metabolism
1.Permits coupling between different biogenesis steps; eg crosstalk; suspected when decreasing one step has effects on 2nd;
could always be indirect
a. Landing pad—increase concentration of reactants—proteins involved in capping etc
b. Allosteary: guanosyl transferase of capping enzyme activated by interaction with phosphorylated CTD
c. Kinetic coupling—optimize timing
2. Impose order or control
a. Juxtaposition of proteins permits assembly, competitive interactions handoffs; often mutually exclusive PPis
b. directions emanating from phopshorylation state of CTD
3. A locator for nuclear machines –DNA repair, modification etc
Bentley: Cotranscriptionality Mol cell rev 2009
Fast elongation favors exon skipping whereas slow elongation
favors exon inclusion
De la mata
What don’t we know about the CTD?
1.
What is the role of Ser-7 phosphorylation?
Ser-7 shows high phosphorylation across highly transcribed protein
coding genes in S. cerevisae, but no role yet ascribed to this modification
2.
What is the significance of different markings when comparing noncoding and protein coding genes and how is this difference set up?
3.
To what extent do interdependent and co-occurrence of marks set-up
bivalent/multivalent recognition patterns
4.
Genome wide ChIP analysis indicates some factors thought to be recruited by
Ser-2 phosphorylation appear either signficantly prior to or after that event.
Explanation?
See Tietjen…..Ansari NMSB(2010) 17: 1154
Mayer….Cramer NMSB (2010): 1272
What is known about the role of Spt4/5 in elongation control?
Spt5: essential in yeast
A promoter proximal pause is characteristic of transcription of many genes in
higher eukaryotes
Characteristics of paused polymerase ( pioneering work by
John Lis Hsp70 locus in Drosophila)
1.In open complex ( KMnO4 footprinting)
2.Some fraction can elongate (nuclear run-on experiments)
Later work:
3. Ser-5 phosphorylated on CTD
4. Spt4/5 (DSIF) and NELF associated with paused polymerase ( ChIP; + required
to recapitulate pause in vitro )
Paused
polymerase
What triggers release to productive elongation?
1)pTEFb phosphorylates polymerase CTD, Spt5, NELF
2) Backtracking relieved ( SII)
3) NELF dissociation
Genome wide studies sequencing 5’ capped short mRNAs found them associated with
~30% of all genes in Drosophila; positions of their 3’ ends correspond to positions of
stalled polymerase, and were also regions of high GC content; length of short mRNAs
increases when SII is depleted suggesting that paused polymerases had backtracked and
their mRNAs had been cleaved by SII
Adelman, Science, Cell 2010
Potential roles of Paused Polymerase
NRG ( 2012) 13: 720
Spt4/5 is also connected to other elongation complexes
Using activity based assay, Spt4/5, PAF and Tat-SF1 required for efficient elongation (DNA template)
Spt4/5
PAF
Phosphorylation of Spt5 CTD by Bur-1 required for PAF
entry into elongation complex
Tat-SF1
Physical interaction
PAF
Using chromatin template and completely
reconstituted factors, PAF stimulates elongation
synergistically with TFIIS (independent of other
activities of the PAF complex)
PAF
TFIIS
∆PAF ∆TFIIS
Physical interaction
Synthetic lethal
Each elongation factor also interacts with RNAP
Coupling between Transcription and Translation through Rpb 4/7
Stalk
Stalk
1.Rpb4/7: eukaryotes and archae
2.Loosely associated with RNAP
3.Not essential
4.In molar excess over RNAP subunits
Bacterial RNAP
Eukaryotic RNAP
Evidence
1.Physical/genetic interaction between Rpb4/ EIF3
2. Rpb4 physically associated with polysomes
3. ∆ Rpb4/7 cells have abnormal polysomes and are
sensitive to translation inhibitors
4. Rpb4 association with polysomes contingent on
its association with RNA polymerase