Gene

Gene expression
Process and regulation
The Central Dogma
Gene expression = Transcription + Translation
Transcription

Generation of single stranded RNA from a DNA template (gene)
Catalysed by RNA Polymerases
Generates:
mRNA - messenger RNA
tRNA - transfer RNA
rRNA - ribosomal RNA
Occurs in prokaryotes and eukaryotes by essentially identical processes
Transcription

The steps in transcription
DNA unzips and RNA polymerase enzyme binds to one strand of DNA – transcription initiation.
RNA polymerase makes an elongating chain of RNA nucleotides, each new RNA nucleotide complementary to the DNA nucleotide – strand elongation.
The completed mRNA molecule is released from RNA polymerase - DNA complex and can begin translation – transcription termination.
In eukaryotic cells this means first moving from the nucleus into the cytoplasm.
In prokaryotic cells (bacteria), ribosomes can bind and begin translation before polymerase has completed of the new mRNA strand.
Sample questions
Which of the following are involved in transcription
DNA
mRNA
Ribosome
tRNA
RNA polymerase
How the transcription start?
How the transcription stop?
Prokaryotes : Relatively Simple….
Eukaryotes : Not so Simple….
Why the transcription process in prokaryotes is different from eukaryotes?
Eukaryote gene structure
Where the transcription start?
Transcription start site (TSS)

How the transcription initiate?
The control region
Transcription factors
Transcription-control region
Promoters: TATA box, Initiators, CpG islands
Other types of control elements located near transcription start sites: Promoter-proximal elements
Sequences located far from genes they regulate: distant enhancers
Promoters
Direct binding of RNA polymerase II to DNA. Determine the site of transcription initiation.
Three principal types of promoter sequences:
TATA box: the most common, is prevalent in rapidly transcribed genes. Located about 30 bases upstream (-30) from the transcription start site. required for any significant transcription to occur.
Initiator promoter are found in some genes
CpG islands are characteristic of gene transcribed at a low rate
Promoter-proximal elements
Occurs within 200 base pairs upstream of a start site.
Several such elements
Containing 10 - 20 base pairs
Help regulate a particular gene
How Does One Identify
Transcription-Control
Sequences for a Gene?
Promoter-Proximal Elements are Critical for Transcriptional Control
Enhancers
Contain multiple short control elements
Located from 200 – 10kb upstream or downstream from promoter.
Within an intron.
Still More Transcription-
Control Sequences:
Identification of Enhancers
Transcription Initiation by RNA Polymerase II

How the RNA polymerase activate?
Is RNA polymerase working alone?

How mRNA generate?

RNA polymerase II cannot bind to a promoter by itself.

It requires other protein factors – transcription factors- that are added in a specific order to the promoter and interact with RNA polymerase II to efficiently transcribe the mRNA.
Basal Transcription Factors

The basal transcription factors are typically defined as the minimal complement of proteins necessary to reconstitute accurate transcription from a minimal promoter (such as a TATA element or initiator sequence).
Regulatory Transcription Factors

bind to sequences farther away from the initiation site and serve to modulate levels of transcription
Basal Transcription factors

Biochemical Reconstitution
Revealed an Ordered Assembly
of Factors for Initiation
Model of RNA PolII Preinitiation Complex
How transcription factors bind to the DNA?
How they activate or repress the transcription process?
A Modular Structure is Common to many Transcription Factors
Numerous Structural Types of DNA-binding Domains
Helix-turn-helix

Homeodomain – 60 amino acid helix-turn-helix first found in homeodomain proteins

Zinc-finger – C2H2 or C4 amino acid signature

Leucine zipper and basic zipper (bZip)

Basic helix-loop-helix (bHLH) – like bZip but two α-helices separated by nonhelical loop
DNA-binding proteins often fit into the major groove of the double helix
Helix-turn-helix
Homeodomain
Zinc-finger
bZip
helix-loop-helix
Demonstration that Activator Proteins have Distinct Functional Domains
GAL is a transcription factor
GAL4 bind to UAS-GAL, activate the expression of the lacZ gene, release B-galactosidase
Some Transcription Factors in the Nuclear Receptor Superfamily
Model of Hormone-dependent Gene Activation by Homodimeric Receptors