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Introduction to Transcriptional Machinery. "DNA makes RNA, RNA makes protein, and proteins make us." Francis Crick. Central Dogma of Molecular Biology. RNA Polymerase of E. Coli. Transcribes all mRNA, rRNAs and tRNAs 7,000 molecules per cell

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Introduction to Transcriptional Machinery

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Introduction to transcriptional machinery

Introduction to Transcriptional Machinery

Dna makes rna rna makes protein and proteins make us francis crick

"DNA makes RNA, RNA makes protein, and proteins make us." Francis Crick

Central dogma of molecular biology

Central Dogma of Molecular Biology

Rna polymerase of e coli

RNA Polymerase of E. Coli

  • Transcribes all mRNA, rRNAs and tRNAs

  • 7,000 molecules per cell

  • 5,000 molecules are synthesizing RNA at any given time

  • M.W. of the holoenzyme is ~465 Kd

Rna polymerase of e coli1

RNA Polymerase of E. Coli

Factor controls specificity

 Factor Controls Specificity

Holoenzyme core enzyme

Holoenzyme & Core Enzyme

  • Holoenzyme binds promoters with half lives of hours - 1,000 time higher than core enzyme.

  • Holoenzyme has a drastically reduced ability to recognize “loose binding sites” - half life of <1sec – 104 time lower than core enzyme.

Transcription initiation

Transcription Initiation

Promoter elements in e coli

Promoter Elements in E. Coli

  • -35: recognition domain

  • -10: unwinding domain

  • Seperating distances

  • UP element

  • Start Point: purine in 90% of the genes


First level of regulation

First Level of Regulation

  • ~100 fold variationin the binding rate of RNA Pol to different promoters in vitro.

  • Binding rates correlate with the frequencies of transcription in vivo.


Introduction to transcriptional machinery

E. Coli has several  Factors

Introduction to transcriptional machinery

 Factors Recognize Promoters by Consensus Sequences



What was known in the 1960 s

What was known in the 1960’s

  • Jacob and Monod 1961 – genetic control mechanisms in prokaryotes

  • Anticipation for Eukarotes…

  • Eukaryotes – genomic complexity – reiterated DNA sequences

  • Lack of genetic approach

February 1969 strait of juan de fuca

February 1969, Strait of Juan de Fuca



Taken from: The eukaryotic tarnscriptional machinery, Robert G Roeder

3 rna polymerases

3 RNA Polymerases

  • Pol I localized within nucleoli – the sites of rRNA gene transcription

  • Pol II and Pol III

    restricted to the


Introduction to transcriptional machinery

3 RNA Polymerases

  • Roberto Weinmann - 1974

  • Differential sensitivities to the mushroom toxin  - amanitin

  • Pol I – rRNA synthesis

  • Pol II – adenovirus pre-mRNA

  • Pol III – cellular 5S and tRNA

Rna polymerases of eukaryotes

RNA Polymerases of Eukaryotes

  • Pol I - transcribes pre-ribosomal RNA (18S, 5.8S, 28S)

  • Pol II - mRNAs

  • Pol III - tRNAs, 5S RNAs and some specialized small RNAs.

Rna polymerase ii

RNA Polymerase II

  • 2002 – RNA Pol II structure

  • 2003 – transcription complex structure (RNA Pol II + TFIIS)

  • , ’, I, II,  - conserved in yeast and bacteria – evolutionary

    conserved mechanism

    of transcription

Significant homology between eukaryotic and bacterial rna polymerases in their structure

Significant homology between eukaryotic and bacterial RNA polymerases in their structure

Transcription mechanism

Transcription Mechanism

  • RNA Pol II can catalyze RNA synthesis

    but cannot initiate.

  • Assembly

  • Initiation

  • Elongation

  • Termination

Introduction to transcriptional machinery



Introduction to transcriptional machinery


  • Only GTF that creates sequence specific contact with DNA

  • Unusual Binding in minor groove

  • Causes

    DNA bending

Introduction to transcriptional machinery


  • 80% conserved between yeast and man

  • Large outer surface binds proteins

  • Deformation of DNA structure, but no strand separation

The transcriptional machinery

The transcriptional machinery

  • Initiation begins with the formation of the first phosphodiester bond and phosphorylation of Ser5 on the CTD by TFIIH.

  • mRNA passes through a positively charged exit channel, and once the RNA is approximately 18n long it becomes accessible to the RNA processing machinery.

  • Consistent with the coupling of transcript capping to early transcription events

Pre mrna processing

Pre-mRNA Processing

  • Addition of 5’ cap

  • Splicing – removal of intron sequences

  • Generation of 3’ poly-A tail.

  • 3’ cleavage

  • RNA serveillance by the exosome

  • Packaging of the mRNA for export

Occurs (most efficiently) co-transcriptionally

Transcription regulating elements

Transcription Regulating Elements

  • GTFs - required at any Pol II promoter

  • Enhancers – sequences, increase transcription

  • Transactivators - bind enhancers

  • Co-activators - act indirectly, not by binding to DNA, communication between transactivators and RNA PolII + GTS

  • Mediator - 20 proteins, Interacts with CTD

Major differences between pro eu

Major Differences between Pro & Eu

  • Prokaryotes RNA Pol has access to promoters and initiates transcription even in the absence of activators and repressors.

  • Eukaryotes - promoters are generally inactive in vivo

  • Transcription in eukaryotes is seperated in both space and time from translation

Introduction to transcriptional machinery

The CTD is Phosphorylated at Initiation

Introduction to transcriptional machinery


  • Highly conserved tandemly repeated heptapeptide motif (YSPTSPS)

  • Platform for ordered assembly of the different families of pre-mRNA processing machinery

  • Undergoes phosphorylation and dephosphorylation during the transcription cycle

Introduction to transcriptional machinery


  • P-TEFb contains CDK9 and cyclin T

  • It couples RNA processing to transcription by phosphorylating Ser2 of CTD

  • RNA Pol II is recycled through dephosphorylation of Ser2 by the phosphatase activity of Fcp1

Ctd phosphorylation during transcription

CTD Phosphorylation During Transcription

Splicing alternative splicing

Splicing (& Alternative Splicing)

Expansive role of transcription

Expansive role of Transcription

  • RNA surveillance – Exosome associates with Spt6 EF

  • Coupling of transcription to mRNA export

  • 19S particle of the Proteosome recruited to active promoters – important for efficient RNA Pol II elongation

Translation and post translation

Translation and Post-Translation

  • Bacteria – translation occurs as the nascent transcript emerges from the RNA polymerase

  • It is assumed that in eukaryotes transcription and translation are spatially separated events

  • Protein synthesis – solely a cytoplasmic event? (1977 – Gozes et al, 2001 lborra et al)

Traditional view of gene expression

Traditional View of Gene Expression

Contemporary view of gene expression

Contemporary View of Gene Expression

Introduction to transcriptional machinery

The Sister


of a Mitotic Pair

Introduction to transcriptional machinery

Chromatin Packing

2 nm


Double helix




30 nm fiber of

Packed nucleosomes


30 nm

Chromosomal loops

Attached to nuclear


300 nm

Condensed section

of metaphase


700 nm


Entire metaphase


1400 nm

5-10 mm

Chromatin structure

GC Pairs Are Preferred


Histone Core

AT Pairs Are Preferred

Chromatin Structure

  • DNA accessibility – a major challenge in a chromatin environment

  • Nucleosomes –


    blocks of


Introduction to transcriptional machinery

Structure of the Nucleosome

  • 146 bp are wrapped around the histone core

  • 1.75 times

  • ~0-80 bp in the linker sequences between nucleosomes

  • Human genome (~6x109 bp) contains ~3x107

  • nucleosomes

  • The histone core (octamer) consists of two copies of:

    • Histones H2A, H2B, H3 and H4

    • Histone H1 binds in the spacing linker sequence

Introduction to transcriptional machinery

The Nucleosome











Introduction to transcriptional machinery


  • Highly conserved throughout eukaryotic evolution

  • Mutations in histones encoding genes are often lethal

  • Highly abundant (~60 million copies/cell)

  • Additional non-histone proteins play a role in the chromatin structure and function

Introduction to transcriptional machinery

Types and Properties of Histones

Introduction to transcriptional machinery

Interaction of DNA with Positively Charged Residues in the Nucleosome Core


Red: The positively charged lysines & arginines

The DNA is wrapped along these residues

Introduction to transcriptional machinery

H1 Histone

  • In the presence of H1, 166 bp

  • are protected from nucleolytic cleavage ->

  • full two tight loops (83 x 2 bp).

  • When histone H1 is extracted, the resulting structure is the 11 nm “beads-on-a-string”

Introduction to transcriptional machinery

View Along the Axis of One Turn of the 30nm Fiber



H1 Histone


Introduction to transcriptional machinery

Side View of the 30nm Fiber

Histone core

11 nm fiber

30 nm fiber


Histone H1


Histone H1

Chicken and egg scenario

“Chicken and Egg” Scenario

  • heterochromatin and euchromatin

  • How do TFs access the DNA in the first place?

  • Example: GR, NF1 and MMTV gene (Di Groce et al., 1999)

Histone code hypothesis

Histone Code Hypothesis

  • language of covalent post-translational histone modifications

  • acetylation

  • phosphorylation

  • methylation

  • ubiquitylation

  • ADP-ribosylation and

  • glycosylation

Regulation of nucleosome stability

Regulation of Nucleosome Stability

  • Sequence elements

  • Post-translational modifications

  • Nucleosome remodeling complexes

  • Transcriptional Elongation

Nucleosome depletion at promoters

Nucleosome Depletion at Promoters

Taken from: The transcriptional regulatory code of eukaryotic cells, Barrera & Ren

Dynamic histone methylation

Dynamic Histone Methylation

  • Histone methylation is irreversible!

  • Methylation is dynamic - alterations in H3-K4 and H3-K9 methylation – (Martinowich et al. 2003)

  • Required: a mechanism for removal of long- term histone modifications!

Histone variants

Histone Variants

  • H2AZ prevents spread of heterochromatin and gene silencing in transcriptionally active regions

  • H3.3 enriched in histone modifications that correspond to transcriptional activation

Histone exchane

Histone Exchane

  • SWI/SNF and the RSC exchange H2A-H2B dimers

  • FACT - EF that removes one H2A-H2B dimer from the nucleosome

  • SWR1 (ATPase) selectively exchanges H2A histone variants

Histone exchange

Histone Exchange

Taken from: Recenthighlights of RNA-poly-II-mediated transcription Sims, Mandal & Reinberg

Introduction to transcriptional machinery

Histone Octamer




How this helps transcription

How this Helps Transcription?

Taken from: Recenthighlights of RNA-poly-II-mediated transcription Sims, Mandal & Reinberg

Take home message

Take Home Message

  • Complexity of the transcription is the rule, not the exception.

  • Transcription is coupled to mRNA processing, RNA surveillance and export, among other cellular processes.

  • Chromatin structure – transcription regulatory code.

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