Post on 04-Jun-2018
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Gene Expression:
Transcription
Chapter 10
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• RNA is an intermediate between DNA and
protein
• types of RNAs
• the process of transcription
• posttranscriptional modifications of RNAs
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Central Dogma
red dashes :
post 1958
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Types of RNA• Messenger RNA (mRNA)
• Transfer RNA (tRNA)• Ribosomal RNA (rRNA)
• Small nuclear RNA (snRNA)
• microRNA (miRNA)
Evidence :
• need an intermediate between DNA (nucleus) and protein
synthesis (cytoplasm) in eukaryotes
• mRNAs direct protein synthesis
• nucleotide sequences of mRNAs are complementary to DNAs
RNA is intermediate between
DNA and protein :
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RNAs that are important for
translation
mRNA tRNA rRNA
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How was the role of RNA initially
determined?
Nucleotide Composition
• RNAs produced by organisms have
base ratios similar to organism’s DNA
DNA-RNA Hybridization
• Strands that are complementary can
base pair with each other
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DNA-RNA Hybridization
Double-stranded DNA
Denatured DNA
+ complementary
RNA
DNA-RNA
hybridization1. cytoplasmic RNA with nuclear
DNA
2. virus DNA and infected
bacterial RNA
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2 Differences between DNA and RNA
RNA:
RiboseDNA:
Deoxyribose
RNA:
Uracil
DNA:
Thymine
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RNA
• Does not usually form a double helix
• Usually transcribed from one strand of the DNA
Noncoding DNA strand (template) : complementary to mRNA
Coding DNA strand (nontemplate) : same sequence as mRNA (with U for T)
note : A ≠ U
G ≠ C
**
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RNA Transcription
• Using RNA polymerase, makes RNA using DNA as a template
• ** Transcription is regulated in each cell only certain genes are transcribed in 1 cell at 1 time
allows for regulation of protein synthesis in a cell
• RNA polymerase holoenzyme (E. coli )Five subunits: two subunits
one subunit
one ’ subunit
one subunit ( factor )
- recognizes transcription start sequence
Gene
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Requirements for RNA polymerase
1. Must identify beginnings and ends of genes
2. Must recognize correct DNA strand
3. Must accurately copy DNA into an RNA copy
Gene
RNA
pol
RNA
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Transcriptional Initiation
• Begins at a promoter sequence that RNA polymeraseassociates with before transcription
major site where gene transcription is controlled
• Consensus sequence (in E. coli )
-10 5’ TATAAT 3’ (Pribnow Box, -10 sequence)
-35 5’ TTGTCA 3’ (-35 sequence)
Describes binding site for RNA polymerase
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Promoters are ~60 bp long and
composed of consensus sequences
Conserved sequence : identical nucleotide sequences
Consensus sequence : some variation, but high frequency of
certain nucleotides in a group of sequences
(coding strand shown)
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DNA Footprinting Identifies
Consensus Sequences
T i ti l i iti ti l ti hi
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Transcriptional initiation : relationship
between DNA strands and RNA
-10 +1
consensus
Start of transcript
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Promoter of the rrnB gene in E. coli
-35 -10 +1consensus consensus
Start of
transcript
factor binds
- initiates transcriptionfactor binds
-increases transcription
-50consensus
other consensus sequences enhance or inhibit transcription by binding regulatory proteins
and factors can also recognize other regions of different genes (or proteins bound to them)
(not always present)
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Transcriptional Initiation in E. coli
1. Sigma ( ) subunit of RNA Polymerase recognizes -10 and-35
2. Holoenzyme (RNA polymerase, ’, subunits)
binds promoter
Closed Promoter Complex
Open Promoter Complex (DNA is unwound)
3. Transcriptional initiation occurs
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Closed promoter complex
Open promoter complex
Initiation
Elongation
(5’ 3’ for RNA)
(3’ to 5’ along the DNA)
(sigma factor dissociates)
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Transcriptional Termination in E. coli
1. Rho dependent : requires rho ( ) protein + specific
RNA stem-loop structure
2. Rho independent-requires specific RNA stem-loop
structure only
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Both have stem loop structure
- causes RNA polymerase to pause
Termination : rho independent
and rho dependent
UUUUU present in rho independent terminator only
UUUUU present in rho independent terminator only
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Termination : rho independent
and rho dependent
rho independent
rho dependent
because of weak A-U base pairing, RNA
dissociates from DNA
Rho interaction with polymerase causesdissociation of RNA from DNA
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Overview of Bacterial Transcription
Initiation:
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Elongation:
Overview of Bacterial Transcription
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Termination:
Overview of Bacterial Transcription
Comparison of prokar otic messenger
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Comparison of prokaryotic messenger
RNA (mRNA) and its DNA
mRNA
DNA
• Open Reading Frame (ORF) : translatable segment, gene product
– AUG start codon
– UGA, UAA, UAG stop codons (nonsense codons)
– contains termination sequence but not promoter
• 5’ untranslated region (5’ UTR) : leader sequence that is not translated
• 3’ untranslated region (3’ UTR), sequence after stop codon that is not translated
- 5’ and 3’ UTRs regulate stability of mRNA and have roles in translation
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ribosomal RNA
(rRNA)
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Ribosomes : sites of protein synthesis
Composed of protein + rRNA :
50S subunit : 34 proteins+ 23S, 5S rRNA
30S subunit : 21 proteins, 16S rRNA
One transcript for all three rRNAs
23S rRNA + 16S rRNA + 5S rRNA
rRNAs : not translated ; no ORF, no start or stop codons, no UTRs
- catalyze peptide bonds during translation
S : Svedberg unit
- rate of sedimentation
in sucrose density gradient
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transfer RNA
(tRNA)
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Transfer RNA (tRNA)
*
*
aminoacyl tRNA synthetase :
attaches specific aa to tRNA
Similarities among tRNAs :
i. all ~80 nt long ; not translated, no ORF, no start or stop codons, no UTRs
ii. all have a cloverleaf shape : acceptor stem, T loop, D loop, anticodon loop
iii. modified bases : help to form loops (do not base pair)
ribothymidine
dihydrouridine
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Modified Bases in tRNAs
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Processing of tRNA Transcript
Removal of 3’ and 5’ ends
Add 3’ CCA
(eukaryotes),
remove introns
Modify specific
bases
P k ti d E k ti
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Prokaryotic and Eukaryotic
Transcription
Similarities :• both use promoters to indicate initiation of transcription
• ribonucleotides (inlcuding uracil) are used to make transcript
• transcription moves 5’ 3’
Differences :
• number of different RNA polymerases
• complexity of promoter sequences
• localization of transcription and translation
• modifications to mRNAs after transcription
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Eukaryotic Transcription
RNA polymerases:
RNA polymerase I: transcribes most rRNA genes
28S, 18S, 5.8S rRNAs
RNA polymerase II: transcribes mRNAs, most snRNAs,and miRNAs
RNA polymerase III: transcribes small genes such
as tRNAs, 5S rRNA, U6 snRNA
** all 3 enzymes cannot bind DNA themselves; recruited
prokaryotes :
only 1 RNA polymerase and primase ; both bind DNA directly
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1. UBF Binds the upstream promoter element,helps other proteins bind core promoter
Eukaryotic RNA Polymerase I Promoter
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2. TATA Binding Protein (TBP) Binds DNA, bends
DNA
Eukaryotic RNA Polymerase I Promoter
(**positions RNA polymerase)
(binds A-T region
nonspecifically)
e
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3. RNA Polymerase I Binds to TBP
Transcription preinitiation complex
Eukaryotic RNA Polymerase I Promoter
3 T f E k ti
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3 Types of Eukaryotic
RNA Polymerase III Promoters
55-80 bp downstream;
bind TFIIIA and/or TFIIIC
** binding of TFIIIC allows TFIIIB to bind near initiation site
binds TFIIIB
binding of other factors here
enhances TFIIIB binding toTATA
Two Types of Eukaryotic RNA
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Two Types of Eukaryotic RNA
Polymerase II Promoters
initiator region downstream
promoterelement- these genes are usually transcribed by pol II in all cells throughout development
TATA Bi di P t i b d th DNA
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TATA Binding Protein bends the DNA
when it binds
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Eukaryotic RNA Polymerase II
• Does not bind to DNA directly (similar to pol Iand III)
• Requires general transcription factors to
associate with the DNA :1. TBP binds to TATA box
2. TBP associated factors (TAFs) bind to
generate preinitiation complex3. RNA polymerase binds to promoter
4. RNA polymerase is phosphorylated
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Initiation of
Transcription:
Preinitiation
Complex(subunit of TFIID)
Initiation of Transcription Acti ator
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Initiation of Transcription: Activator
Proteins Bind Enhancers
enhancers can be upstream
or downstream of promoter
- activators bind, ↑ transcription
silencers are often upstream
of promoters
- repressors bind, ↓ transcription
**Tissue specific gene expression :
due to binding of transcription factors
to specific promoters
DNA bends
to bind
activator/enhancer
to polymerase
Regulation of Transcriptional
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Regulation of Transcriptional
Initiation
Combinatorial Control
• RNA polymerase II complex contains proteinsthat link activators/repressors to core enzyme
• modular assembly of different factors on a
basal transcription machinery
- allows for controlled transcription of specific
genes in certain cells at a particular time
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Initiation of Transcription:
1. Preinitiation complex
2. Phosphorylation of RNA polymerase
3. DNA strands are separated4. RNA polymerase begins to transcribe
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Initiation of Transcription
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Initiation of Transcription
(primer : 10-12 bp)
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Transcriptional Elongation
• 5’ to 3’• * Disruption of histones (HATs) in chromatin
• Proofreading
rate : ~60 nucleotides/second !
Proofreading by RNA Polymerase II
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Proofreading by RNA Polymerase II
stimulated by TFIIS
extrusion of short region
of RNA
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Eukaryotic DNA Transcription
Prokaryotic and Eukaryotic
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Prokaryotic and Eukaryotic
Transcription
Differences :
• eukaryotes : transcription occurs in nucleus,translation in cytoplasm
- prokaryotes : transcription and translation is“coupled”, both occur in the cytoplasm
• eukaryotes : promoters more complex (transcriptionfactors)
• eukaryotes: posttranscriptional modification of mRNA
• # of different RNA polymerases (eukaryotes: 3,
prokaryotes: 1)
Coupled Transcription and
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Coupled Transcription and
Translation in Prokaryotes
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PostranscriptionalModifications :
1. modify 5’ end
2. modify 3’ end
3. remove intervening sequences
Post Transcriptional Modifications in
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Eukaryotic ribosomes : RNA and protein
Post Transcriptional Modifications inEukaryotes – ribosomal RNAs
http://biosiva.50webs.org/translation.htm
Post Transcriptional Modifications in
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1. Processing of ribosomal transcript
2. Base modification by small nucleolar ribonucleoprotein particles
(snoRNPs) : small RNAs and proteins
- uridines pseudouridines
- methylated riboses
Post Transcriptional Modifications inEukaryotes – ribosomal RNAs
Post Transcriptional Modifications in
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rRNA is transcribed by RNA polymerase I in multiple copies
Post Transcriptional Modifications inEukaryotes – RNA polymerase I
Post Transcriptional Modifications in
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Post Transcriptional Modifications in
Eukaryotes – RNA polymerase II
RNA polymerase II transcripts:
5’ CAP
3’ poly A tail
Intron removal
important for :
1. export from nucleus
2. mRNA stability
3. translation initiation
5’ CAP
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5’ CAP
functions of cap :
1. protects mRNA from 5’3’ degradation
2. needed for removing 1st intron
3. needed for mRNA export from nucleus
4. ribosome recognizes and binds – needed for translation
3’ polyA Tail
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3 polyA Tail
• RNA is cut by endonuclease
downstream from AAUAAA
• polyA tail (15-250 adenosines)
added by polyA polymerase
Importance :
1. required for removal of last intron
2. helps mRNA to be translated
3. improves mRNA stability (protects from nucleases)
Intron
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Removal
introns : interveningDNA sequences that
do not code for protein
• transcribed into preRNA,
but are removed before
RNA is translated
• present in mRNA, rRNA,
and tRNA(prokaryotes: tRNA, rRNA only)
exons : sequences
present in mature RNA
E1 I1 E2 I2 E3
E id f P f I t i DNA
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Evidence for Presence of Introns in DNA
DNA-mRNA
hybridization
Intron Removal (in vitro): Self splicing
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Intron Removal (in vitro): Self splicing
Group I Intron
Intron acts as an enzyme : ribozyme
Intron Removal (in vitro): Self splicing
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Intron Removal (in vitro): Self splicing
Group II Intron
Intron acts as an enzyme : ribozyme
Intron Removal: Self splicing
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Intron Removal: Self splicing
Group II Intron
Lariat structure
in intron
Intron Removal in Eukaryotes (in vivo):
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Intron Removal in Eukaryotes (in vivo):
Protein Mediated
Spliceosome : protein-RNA complex required for removal of intron- composed of snRNPs (U1,U2,U4,U5,U6)
(small nuclear ribonucleoproteins)
Consensus sequences required:
• 5’ end of the intron
• 3’ end of the intron
• within intron: lariat branch point
Intron Removal: Sequence of
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q
Steps
1. U2AF binds 3’ end and Py-rich tract
2. U1 binds 5’ end ; U2 base pairs with branch point
3. U4, U5, U6 cause release of U1 and bring two exons
together
4. U4 is released, intron lariat generated
5. U5 facilitates release of lariat and ligation of the two
exons
Intron Removal: Sequence of Steps
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Intron Removal: Sequence of Steps
1.
2.
3.
4.
5.
• over 98% of introns undergo this splicing reaction
Advantages of Introns
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Advantages of Introns• Exon shuffling over time to produce novel
gene products : variation• needed for mature mRNA export : reduce
production of nonfunctional protein
• ** alternative splicing: produce more thanone gene product from one gene
rat -tropomyosin
Splicing Repressors
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Splicing Repressors
Prevent recognition of 3’ splice junction, forces next 3’
junction to be used
Splicing Enhancers
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Splicing Enhancers
Promotes recognition and use of poorly recognizedintron-exon junctions
Alternate Splicing for Gene with
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Alternate Splicing for Gene with
Two Promoters
Trans-Splicing
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p g Attaches 5’ end of one mRNA to different mRNA
(seen mostly in worms, some human genes)
RNA Editing
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RNA Editing
• Guide RNA Editing- guide RNA provides complementary
sequence for mRNA RNAs base pair
- RNA is cleaved by endonuclease
- nucleotide is inserted
- RNA ligase closes the break
• Nucleotide Substitution
- deamination of specific bases
(possible if sequence of DNA is slightly different than sequence of encoded protein)
RNA Editing
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RNA Editing
Guide RNA
editing
RNA Editing through
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Deamination of Specific Bases
(changes mRNA codon)- used by enzyme AID
(on DNA) in somatic
hypermutation of Ig gene
- can introduce a STOPcodon (UAA)
- can alter the function of a
glutamate receptor
microRNA
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microRNA
Result : Gene silencing
1. Translation of target mRNA blocked and/orendonuclease degradation of RNA
2. Transcript can be blocked in nucleus byfostering a repressive chromatin structure
microRNA (miRNA)
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microRNA (miRNA)
microRNA (miRNA)
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microRNA (miRNA)
(RNA Induced Silencing Complex)
delete loop, incorporate 1 strand into RISC
Revised Central Dogma
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Revised Central Dogma
RNA tumor viruses,HIV