Biochemistry 201Biological Regulatory MechanismsJanuary 30, 2012

Transcription in Eukaryotes

REFERENCESBooks: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.

ElongationBBA2013-- 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

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 TranslationHarel-Sharvit, L., …..and Choder M. (2010). RNA polymerase II subunits Link transcription and mRNA decay to translation. Cell 143: 552-63

ChIP-exo technologyRhee, HS and BF Pugh (2011) Comprehensive genome wide Protein-DNA Interactions at single nucleotide resolution. Cell 147:1408Rhee, HS and BF Pugh (2012) Genome-wide structure and organization of eukaryotic pre-initiation complexes Nature 483: 295

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 newly-synthesized 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

+ DNA with real promoter

TRANSCRIPTION INITIATION and ELONGATION

nuclear extract

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

TFIID TBP 1 Binds TATA box; higher eukaryotes have multiple TBPs TAFs ~10 Recognizes additional DNA sequences; Regulates TBP binding; Coactivator;

Ubiquitin-activating/conjugating activity; Histone acetyltransferase; multiple 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

1 unit

10 units

crude lysate

4 years

50 units

mediator

VP 16

GAL4

Is Mediator Required for Transcription of all Pol II -transcribed genes?

mRNAs decrease over time according to their half-lives.

A few mRNAs remain at some level (stable mRNAs).

Control: ts subunit of Pol II

Compare levels of all mRNAs using microarrays

Rpb1

Rpb1ts (37˚C for 45 min)

high T

Subunit of Mediator

Same basic pattern

Same basic pattern

Subunit of TF II H

Srb4ts

Kin28ts

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

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

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

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

ChIP-exo, a new technology for determining location at the genome scale

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.

Many Paths to the PIC

Buratowski, 2009

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?

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.

Chromosome conformation capture ( 3C)

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. -globin locus)

Why are enhancer and promoter in close proximity during active transcription?

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)

= Nucleosomes

The RNA Polymerase II CTD (or tail)

Cis-proline is well suited to making hairpin turns in polypeptide chains. COOH

NH2

Regions upstream (R1) and downstream (R3) of the heptad repeat region are enriched in the submotifs

YSPTSPSP P P

proline can be cis or trans

5 repeats in plasmodium 26 repeats in yeast52 repeats in mammals

Heptad repeat unit

5 - amaR CTD

Mouse RNA Pol II

wt

52

What is the role of the Pol II CTD?

examine RNAs

50 hrs.

HeLacells Introduce

CTD construct - amanitin

Splicing, processing of 3’ end, termination were all affected

Nature 385: 357 (1997)

How the Polymerase CTD Couples Transcription to other processes

YSPTSPS

Pcapping factorsTF II H,

mediator

elongation

YSPTSPS

P P

YSPTSPS

P

3’ end processing factors

splicing components histone methylase DNA repair enzymes

Further elongation

phosphatases (Rtr1(2?)

pTEFb

(Cdk9)

Kinase/ phosphataseFactors recruited

In S. cerevisiae, shared by Cdk1 and Bur 1

YSPTSPS Mediator, activators, GTFs

Phosphatases (Fcp1, ssu72)Termination

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 metabolism1.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 etcb. Allosteary: guanosyl transferase of capping enzyme activated by interaction with phosphorylated CTDc. 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 non-coding 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

See Tietjen…..Ansari NMSB(2010) 17: 1154Mayer….Cramer NMSB (2010): 1272

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?

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

Paused polymerase

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 )

What triggers release to productive elongation?1)pTEFb phosphorylates polymerase CTD, Spt5, NELF2) 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

NRG ( 2012) 13: 720

Potential roles of Paused Polymerase

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)

Spt4/5PAF

Tat-SF1Physical interaction

Phosphorylation of Spt5 CTD by Bur-1 required for PAFentry into elongation complex

Using chromatin template and completely reconstituted factors, PAF stimulates elongation synergistically with TFIIS (independent of other activities of the PAF complex)

PAF

PAF TFIIS Physical interaction

∆PAF ∆TFIIS Synthetic lethal

Each elongation factor also interacts with RNAP

Coupling between Transcription and Translation through Rpb 4/7

Bacterial RNAP Eukaryotic RNAP

Stalk

Stalk

1.Rpb4/7: eukaryotes and archae2.Loosely associated with RNAP3.Not essential4.In molar excess over RNAP subunits

Nuclear export

Assembly into polysomes

Evidence

1.Physical/genetic interaction between Rpb4/ EIF32. Rpb4 physically associated with polysomes3. ∆ Rpb4/7 cells have abnormal polysomes and are sensitive to translation inhibitors4. Rpb4 association with polysomes contingent on its association with RNA polymerase