Slide 1: Mechanisms of Transcription 生物学基地班 200431060023 魏昌勇 OUTLINE : OUTLINE How the series of bases in the DNA directs the production of the RNAs and proteins that perform cellular functions and define cellular identity. Objectives : Objectives Understand the structure of RNA polymerases
Understand the phases of the transcription cycle
Understand the differences between transcription and replication Slide 4: Gene expression is the process by which the information
in the DNA double helix is converted into the RNAs and
proteins whose activities bestow upon a cell its morphology
and functions. Transcription is the first step in the gene expression and involved copying DNA into RNA. Transcription is, chemically and enzymatically, very similar to DNA replication, but there are some important differences: : Transcription is, chemically and enzymatically, very similar to DNA replication, but there are some important differences: RNA is made of ribonucleotides (rather than deoxyribonuleotides)
RNA polymerase catalyzes the reaction (does not need a primer)
The synthesized RNA does not remain base-paired to the template DNA strand
Less accurate (one in 10000,compared to one in 10000000 for replication)
Transcription selectively copies only certain parts of the genome and makes one to several hundred, or even thousand, copies of any given section of the genome. (replication must copy the entire genome and do so once every cell division) Slide 6: Fig 12-1 Transcription of the DNA into RNA.(in the absence of the enzymes involved) Slide 7: Multiple RNA polymerases can transcribe the same gene at the same time.
A cell can synthesize a large number of RNA transcription in a short time. Topic 1: RNA Polymerase and The Transcription Cycle : Topic 1: RNA Polymerase and The Transcription Cycle Slide 9: RNA Polymerases Comes in Different Forms, but Share Many Features. 1.RNA polymerases performs essentially the same reaction in the cell,from
bacteria to humans.
2.The cellular RNA polymerases are made up of multiple subunits.
3.Bacteria have only a single RNA polymerases ,while in eukaryotic cells there
are three: RNA Pol Ⅰ，Ⅱ，Ⅲ.
4.Pol Ⅱ is the polymerases responsible for transcribing most genes——indeed,
essentially all protein-encoding genes.
5.Pol Ⅰand Pol Ⅲ are each involved in transcribing specialized, RNA-encoding
genes. Slide 10: Comparison of the crystal structures of prokaryotic
and eukaryotic RNA polymerases. Slide 11: The shape of each enzyme resembles a crab claw. Transcription by RNA polymerases Proceeds in a Series of steps : Transcription by RNA polymerases Proceeds in a Series of steps Initiation.
Termination. Initiation : Initiation A promoter is the DNA sequence that initially binds the RNA polymerase.
Promoter-polymerase complex undergoes structural changes required for initiation to proceed .
The base at the transcription site unwinds and producing a “bubble” of single-stranded DNA.
Transcription always occurs in a 5’ to 3’ direction. Transcription Initiation Involves three Defined Steps : Transcription Initiation Involves three Defined Steps The initial binding of polymerase to promoter to form what is called a closed complex.
The closed complex undergoes a transition to the open complex .
Promoter escape. Slide 16: Promoter escape Slide 17: Formation of a closed complex Slide 18: Transition to an open complex Elongation : Elongation Once the RNA polymerase has synthesized a short stretch of RNA(approximately ten bases) ,it shifts into the elongation phase.
This transcription requires further conformational change in polymerase that leads it to grip the template more firmly.
Function: synthesis RNA, unwinds the DNA in front, re-anneals it behind, dissociates the growing RNA chain from the template, performs proofreading. Termination : Termination Once the polymerase has transcribed the length of the gene (or genes), it must stop and released the RNA product. This step is called termination.
In some cells, termination occurs at the specific and well-defined DNA sequences called terminators. Some cells lack such termination sequences. Topic 2:The Transcription Cycle in Bacteria : Topic 2:The Transcription Cycle in Bacteria Bacteria Promoters Vary in Strength and Sequence, but Have Certain Defining Features : Bacteria Promoters Vary in Strength and Sequence, but Have Certain Defining Features The bacteria core RNA polymerases can, in principle, initiate transcription
at any point on a DNA molecule.
In cells, polymerases initiate transcription only at promoters.
An initiation factor called σ that converts core enzyme into the form that
initiates only at promoter. That form of the enzymes is called the RNA
In the case of E.coli, the predominant σ is called σ70.
Promoter recognized by σ70 contains two conserved sequences
(-35 and –10 regions/elements) separated by a non-specific stretch
of 17-19 nt.
Position +1 is the transcription start site Slide 25: Figure 12-5 Features of bacteria promoters. Various combination
of bacteria promoter elements are shown.
a. σ70 promoters contain recognizable –35 and –10 regions, but the
sequences are not identical.
b. UP-element is an additional DNA elements that increases polymerase
binding by providing the additional interaction site for RNA polymerase.
c. Another class of s70 promoter lacks a –35 region and has an
“extended –10 element” compensating for the absence of –35 region. The Factor Mediate Binding of Polymerase to the Promoter : The Factor Mediate Binding of Polymerase to the Promoter Fig 12-6 Regions of σ Those regions
σ factor that recognize specific
regions of the promoter are indicated
by arrows. Region 2.3 is responsible
for melting the DNA. Slide 27: Figure 12-7 σ and α subunits recruit RNA polymerases core
Enzyme to the promoter. The C-domain of the α subunit (α CTD)
Recognize the UP-element, while α region 2 and 4 recognize the -10 and -35
regions respectively. Transition to the Open Complex Involves Structural Changes in RNA Polymerase and in the Promoter DNA : Transition to the Open Complex Involves Structural Changes in RNA Polymerase and in the Promoter DNA Isomerization: essentially irreversible and, once complete, typically
guarantees that transcription will subsequently initiate (though
Regulation can still be imposed after this point in some cases. Slide 29: Figure 12-8 Channels into and out of the open complex. Slide 30: Transcription is Initiated by
RNA Polymerase without the
Need for a Primer Slide 31: RNA Polymerase Synthesizes
Several Short RNAs Before
Entering the Elongation Phase Slide 32: The Elongating Polymerase is a
Processive Machine that
Synthesizes and Proofreads
RNA Transcription is terminated by signals within the RNA sequence : Transcription is terminated by signals within the RNA sequence Terminators: the sequence that trigger the elongating polymerases to dissociate the DNA and release the RNA chain it has made.
In bacteria, terminators come in two type: Rho-independent and Rho-dependent (also called intrinsic terminators).
Rho-dependent terminator need Rho protein. Slide 34: Figure 12-9 Sequence of a Rho-dependent terminator. At the top is the sequence,
in the DNA, of the terminator. Below is shown the sequence of the RNA, and at
the bottom the structure of the terminator hairpin. Slide 35: Figure 12-10 Transcription
termination. Shown is a model
for how the Rho-independent
terminator might work. Slide 36: Figure 12-11 The ρ transcription
termination factor. The crystal
structure of the Rho termination
factor of shown in a top down
view. Topic 3 : Topic 3 Transcription in Eukaryotes RNA Polymerase II Core Promoters Are Made up of Combinations of Four Different Sequence Elements : RNA Polymerase II Core Promoters Are Made up of Combinations of Four Different Sequence Elements The eukaryotic are core promoter refers to the minimal set of sequence element required for accurate transcription initiation by the Pol II machinery in vitro.
Beyond——and typically upstream of ——the core promoter elements required for efficient transcription in vivo. Together these element constitute the regulatory sequences. Slide 39: Regulatory sequence: promoter proximal
elements, upstream Activator sequences
(UASs), enhancers, and a series of repressing
elements called silencers, boundary elements,
and insulators. RNA Pol II Forms a Pre-Initiation Complex with GTFs at the Promoter : RNA Pol II Forms a Pre-Initiation Complex with GTFs at the Promoter Pre-initiation complex, TBP, TAFs. TATA sequence
TF IID, TF IIA, TF IIB, TF IIF, TF IIE, TF IIH. Slide 41: Figure 12-13 Transcription initiation by
RNA polymerase II. The step-wide
assembly of the Pol II pre-initiation complex
is shown here. TBP Binds to and Distorts DNA Using a b Sheet Inserted into the Minor Groove : TBP Binds to and Distorts DNA Using a b Sheet Inserted into the Minor Groove Figure 12-14 TBP-DNA complex.
The TATA binding protein (TBP)
is shown here in purple complexed
with the DNA TATA sequence (shown
in gray) found at the start of many Pol II
genes. The Other General Transcription Factors also Have Specific Roles in Initiation : The Other General Transcription Factors also Have Specific Roles in Initiation TAFs. TBP is associated with about ten TAFs. Another TAF appears to regulate the binding of TBP to DNA.
TF IIB. This protein, a single polypeptide chain, enters the pre-initiation complex after TBF.
TF IIE and TF IIH. Slide 44: Figure 12-15 TFIIB-TBP-promoter Complex.
this structure shows the TBP protein bound
to the TATA sequence. In vivo, Transcription Initiation Requires Additional Proteins : In vivo, Transcription Initiation Requires Additional Proteins Figure 12-16 Assembly of the pre-
initiation complex in presence of
mediator, nucleosome modifiers
and remodelers, and transcriptional
activators. Mediator Consists of Many Subunits, Some Conserved From Yeast to Human : Mediator Consists of Many Subunits, Some Conserved From Yeast to Human Figure12-17 Comparison of the yeast
and human Mediators. The homologous
are shown in blue. A New Set of Factors Stimulate Pol II Elongation and RNA Proofreading : A New Set of Factors Stimulate Pol II Elongation and RNA Proofreading Figure 12-18 RNA processing enzymes are recruited by the tail polymerases. Elongation Polymerase is Associated with a New Set of Protein Factors Required for Various Types of RNA Processing : Elongation Polymerase is Associated with a New Set of Protein Factors Required for Various Types of RNA Processing Poly (A) tail.
3’ end polyadenylation Slide 49: Figure 12-19 The structural and
formation of the 5’RNA cap.
RNA processing a 5’ end capping. Slide 50: Figure 12-20 Polyadenylation and
Termination. RNA Pol I and III Recognize Distinct Promoters , Using Distinct Sets of Transcription Factors, but still Require TBP : RNA Pol I and III Recognize Distinct Promoters , Using Distinct Sets of Transcription Factors, but still Require TBP Pol I is required for the expression of only one gene, that encoding the rRNA precursor.
Pol III promoters come in various forms, and the vast majority have the unusual features of being located downstream of the transcription start site. Slide 52: Figure 12-21 Pol I promoter region.
Structure of the Pol I promoter.
Pol I txn factors. Slide 53: Figure 12-22 Pol III core promoter .
Shown here is the promoter for a yeast tRNA gene. Summary RNA polymerase : Summary RNA polymerase is the primary enzyme of the transcription
Resembles a crab claw
is generally composed of several subunits
Add nucleotides to the 3’ end of the growing RNA chain Transcription cycle : Transcription cycle Initiation (Formation of a closed complex, Transition to a open complex, promoter escape)
Elongation (Unwind the DNA in front of the enzyme, Synthesis of the RNA,RNA proofreading, Dissociation of RNA, Re-annealing of the DNA behind the enzyme)
Termination (Rho-independent terminators, Rho-dependent terminators)