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Transcription Biology Review
Bios 691 – Systems Biology
January 2008
Outline
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Gene structure
Chromatin structure & modifications
Transcription apparatus
Transcription factors and cofactors
Elongation and termination
RNA capping, splicing, and adenylation
RNA processing and miRNA’s
Chromosome Organization
• Mammalian chromosomes
tend to fill discrete regions
within the nucleus
• An elaborate network of fibrils
maintains these arrangements
• RNA ‘factories’ at distinct
locations do most of the
transcription work
• Nucleoli are factories for
rRNA
Chromatin Structure
• Protein scaffolds
anchor the DNA
• Within the scaffold
there are loops
• Most transcription
happens on the loops
• Much chromatin is
wrapped in 30nm
‘heterochromatin’
Fine Structure of Chromatin
• Heterochromatin – inaccessible
– Bound with many proteins
– Centromeres; telomeres; some other areas
• Euchromatin – accessible
– Still needs to be opened
Telomeric Heterochromatin and Sirtuins
Euchromatin: 30 nm & open
DNA Packaging & Nucleosomes
Gene Structure – Exons & Introns
Exon Size
distribution
Gene Structure – Initiation Sites
• Most (~2/3) genes have
multiple promoters
• Most promoters are either
‘sharp’:
– Very narrow range
– Usually TATA + Inr
– Often tissue specific
• or ‘broad’:
– Typically 70 bp range
– Rarely TATA / Inr
– Often widespread
Histones and Modifications
DNA contacts histones on their tails
Histone tails can be modified
Histones can stay loose or assemble tightly
Proteins Modify Histones
DNA Methylation
Adding a Methyl to Cytosine
Cytosine methylation is passed on to daughter cells
Controlling Transcription
DNA-Binding Proteins
• All proteins interact weakly
with DNA
• Proteins with projecting
amino acids interact with
the DNA major groove
• Hydrogen bonds stabilize
position of proteins on DNA
• Proteins that line up several
amino acid contacts bind
strongly to specific DNA
sequences
Transcription Factor Families
• Several structures line
up amino acids
– Helix-turn-Helix
(Homeodomain)
– Helix-loop-helix
– Zinc Finger
• Mostly dimers
• These families have
proliferated because of
their role in attracting
transcription apparatus
Cofactors
• Frequently the effect of
DNA-binding proteins
depends on co-factors
• E.g. ER sits on the DNA
but requires estrogen as a
co-factor to function
• Myc requires Max as a cofactor to stimulate
transcription
• If Max is coupled with Mad
instead, the genes are
repressed
Kick-starting Pol II & Elongation
• Mediator protein
bridges TF proteins
and RNA Pol II
• Contains kinase
domains – may
phosphorylate CTD
of RNA Pol II
Initiating Transcription
TBP on a
TATA Box
RNA Polymerase II
RNA Polymerase II Structure
RNA (red) copied from DNA (blue)
by RNA Polymerase II
The cycle of adding nucleotides
Terminating Transcription
RNA Processing
RNA Processing Steps
• Nucleus
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capped,
spliced,
cleaved,
polyadenylated
• Exported
• Cytoplasm
– stored
– translated
– degraded
Capping mRNA
The RNA factory
RNA Splicing
Poly-adenylating RNA
•Poly-A Polymerase adds ~100150 Adenines to 3’ end
•After export to cytoplasm,
nucleases chop off ~10-20 A’s at
a bite
•Nucleases compete with
ribosomes for mRNA’s
•When ~30 A’s left degradation
speeds up
RNA Export
• RNA has to be passed through nuclear
pores to show up in the cytoplasm (where
we measure it)
Micro RNA’s
P-Bodies
• Loci where RNA
accumulates and
is degraded
• Have their own
structural proteins
Implications for Systems Biology
• Levels of TF’s on a promoter may not
predict levels of transcripts
• Rate of transcription may not predict level
of mRNA in the cytoplasm
• Levels of mRNA in cytoplasm may not
predict levels of protein