Meccanismi di Regolazione dell’espressione genica
Fase Nucleare
•Scelta del gene che deve essere
espresso
•Maturazione dell’RNA
•Trasferimento Nucleo Citoplasma
Fase Citoplasmatica
•Sintesi delle catene polipeptidiche
•Modificazioni post-traduzionali
•Trasferimento delle proteine nelle
sedi di competenza
Unione di ribonucleotidi monofosfato per
formare una catena polinucleotidica
I precursori della sintesi sono i nucleotidi
trifosfato.
L’energia che occorre per la formazione del
legame fosfodiesterico è data
dall’eliminazione del pirofosfato per idrolisi
del legame.
ATP
ATP = Adenosin Trifosfato
ADP = Adenosin Difosfato
ADP
Classes of prokaryotic RNA
• ribosomal RNA (rRNA)
16S (small ribosomal subunit)
23S (large ribosomal subunit)
5S (large ribosomal subunit)
• transfer RNA (tRNA)
• messenger RNA (mRNA)
Structure of prokaryotic messenger RNA
5’
Shine-Dalgarno sequence
PuPuPuPuPuPuPuPu
initiation
AUG
translated region
3’
AAU
termination
The Shine-Dalgarno (SD) sequence base-pairs with a pyrimidine-rich
sequence in 16S rRNA to facilitate the initiation of protein synthesis
Classes of eukaryotic cellular RNAs
• ribosomal RNA (rRNA)
18S (small subunit)
28S (large subunit)
5.8S (large subunit)
5S (large subunit)
• transfer RNA (tRNA)
• messenger RNA (mRNA)
• heterogeneous nuclear RNA (hnRNA) (precursors of mRNA)
• small nuclear RNA (snRNA)
U1, U2, U3, U4, U5, U6, U7, U8, U9, U10...
• small cytoplasmic RNA (scRNA)
7SL RNA
What are the enzymes responsible for the synthesis of these RNAs?
The human RNA polymerases
Polymerase
Location
Product
RNA polymerase I
nucleolus
18S, 28S, 5.8S rRNA
RNA polymerase II
nucleoplasm
hnRNA/mRNA,
U1, U2, U4, U5 snRNA
RNA polymerase III
nucleoplasm
tRNA, 5S RNA,
U6 snRNA, 7SL RNA
mitochondrial
RNA polymerase
mitochondrion
all mitochondrial R
_____________________________________________________________________________________________
Sensitivity of the nuclear RNA polymerases to a-amanitin1
RNA pol I
RNA pol II
RNA pol III
1 cyclic
resistant
high sensitivity (binds with K = 10-8 M)
low sensitivity (binds with K = 10-6 M)
octapeptide from the poisonous mushroom Amanita phalloides
Structure of eukaryotic mRNA
Cap
5’
7mGppp
initiation
5’ untranslated region
AUG
translated region
UGA
termination
3’ untranslated region
polyadenylation signal
AAUAAA
(A)~200
3’
poly(A) tail
• all mRNAs have a 5’ cap and all mRNAs (with the exception
of the histone mRNAs) contain a poly(A) tail
• the 5’ cap and 3’ poly(A) tail prevent mRNA degradation
• loss of the cap and poly(A) tail results in mRNA degradation
b). Gene structure
promoter
region
exons (filled and unfilled boxed regions)
+1
introns (between exons)
transcribed region
mRNA structure
5’
3’
translated region
Legame al promotore della RNA polimerasi
Apertura della doppia elica
Inizio della sintesi
Allungamento
Terminazione
closed promoter complex
RNA polymerase
open promoter complex
initiation
elongation
termination
RNA product
Transcription
Direzione della sintesi
Filamento senso
Filamento antisenso
Sequence elements within a typical eukaryotic gene1
1
based on the thymidine kinase gene
octamer
transcription
element
+1
promoter
ATTTGCAT
GC
CAAT
GC
TATA
-130
-95
-80
-50
-25
TATA box (TATAAAA)
• located approximately 25-30 bp upstream of the +1 start site
• determines the exact start site (not in all promoters)
• binds the TATA binding protein (TBP) which is a subunit of TFIID
GC box (CCGCCC)
• binds Sp1 (Specificity factor 1)
CAAT box (GGCCAATCT)
• binds CTF (CAAT box transcription factor)
Octamer (ATTTGCAT)
• binds OTF (Octamer transcription factor)
Proteins regulating eukaryotic mRNA synthesis
General transcription factors
• TFIID (a multisubunit protein) binds to the TATA box
to begin the assembly of the transcription apparatus
• the TATA binding protein (TBP) directly binds the TATA box
• TBP associated factors (TAFs) bind to TBP
• TFIIA, TFIIB, TFIIE, TFIIF, TFIIH1, TFIIJ assemble with TFIID
RNA polymerase II binds the promoter region via the TFII’s
Transcription factors binding to other promoter elements and
transcription elements interact with proteins at the promoter
and further stabilize (or inhibit) formation of a functional
preinitiation complex
1TFIIH
is also involved in phosphorylation of RNA polymerase II, DNA repair
(Cockayne syndrome mutations), and cell cycle regulation
Nome
TF2D
TBP + TAF
Alias
Chromosoma
TAF1
250
Xq13.1
TAF1L
250like
9p21.1
TAF2
150
8q24.12
TAF3
140
10p15.1
TAF4
135
20q13.33
TAF4B
105
18q11.2
TAF5
100
10q24-10q25.2
TAF6
80
7q22.1
TAF6L
11q12.3
TAF7
55
5q31
TAF7L
50
Xq22.1
TAF8
43
6p21.1
TAF9
32
5q11.2-5q13.1
TAF10
30
11p15.3
TAF11
28
6p21.31
TAF12
20-15
1p35.3
TAF13
18
1p13.3
TAF15
68
17q11.1-q11.2
GTF 2
Binding of the general transcription factors
E
F
TAFs
TFIID
B
H
TBP
A
J
-25
+1
• TFIID (a multisubunit protein) binds to the TATA box
to begin the assembly of the transcription apparatus
• the TATA binding protein (TBP) directly binds the TATA box
• TBP associated factors (TAFs) bind to TBP
• TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, TFIIJ assemble with TFIID
Binding of RNA polymerase II
E
F
TFIID
B
H
TBP
A
J
RNA pol II
• RNA polymerase II (a multisubunit protein) binds to
the promoter region by interacting with the TFII’s
• TFs recruit histone acetylase to the promoter
Steps in mRNA processing (hnRNA is the precursor of mRNA)
• capping (occurs co-transcriptionally)
• cleavage and polyadenylation (forms the 3’ end)
• splicing (occurs in the nucleus prior to transport)
exon 1
intron 1
exon 2
Transcription of pre-mRNA and capping at the 5’ end
cap
Cleavage of the 3’ end and polyadenylation
cap
cap
poly(A)
Splicing to remove intron sequences
cap
poly(A)
Transport of mature mRNA to the cytoplasm
Polyadenylation
• cleavage of the primary transcript occurs approximately
10-30 nucleotides 3’-ward of the AAUAAA consensus site
• polyadenylation catalyzed by poly(A) polymerase
• approximately 200 adenylate residues are added
cleavage
AAUAAA
mGpppNmpNm
AAUAAA
mGpppNmpNm
A A
A
polyadenylation
A
A
A
3’
• poly(A) is associated with poly(A) binding protein (PBP)
• function of poly(A) tail is to stabilize mRNA
Splicing
Rimozione di un introne attraverso due
reazioni sequenziali di trasferimento di
fosfato, note come transesterificazioni.
Queste uniscono due esoni rimuovendo
l’introne come un “cappio”
GENE PREDICTION
GeneScan
GrailEXP
Promoter 2.0
Omiga 2.0
GeneMark
F GENE SH
Recognition of splice sites
• invariant GU and AG dinucleotides at intron ends
• donor (upstream) and acceptor (downstream) splice sites
are within conserved consensus sequences
donor (5’) splice site
branch site
acceptor (3’) splice site
G/GUAAGU..................…A.......…YYYYYNYAG/G
U1
U2
•small nuclear RNA (snRNA) U1 recognizes the
donor splice site sequence (base-pairing interaction)
• U2 snRNA binds to the branch site (base-pairing interaction)
Y= U or C for pyrimidine; N= any nucleotide
Chemistry of mRNA splicing
• two cleavage-ligation reactions
• transesterification reactions - exchange of one
phosphodiester bond for another - not catalyzed by
traditional enzymes
• branch site adenosine forms 2’, 5’ phosphodiester bond
with guanosine at 5’ end of intron
intron 1
Pre-mRNA
2’OH-A
5’
exon 1
G-p-G-U
-
A-G-p-G
branch site adenosine
exon 2
First clevage-ligation (transesterification) reaction
3’
intron 1
Step 2: binding of U4, U5, U6
U2
U4 U6
2’OH-A
exon 1
5’
U5
G-p-G-U
-
exon 2
A-G-p-G
3’
U1
Step 3: U1 is released,
then U4 is released
intron 1
2’OH-A
U6
exon 1
5’
G-p-G-U
-
U5
U2
exon 2
A-G-p-G
3’
Step 4: U6 binds the 5’ splice site and
the two splicing reactions occur,
catalyzed by U2 and U6 snRNPs
intron 1
2’OH-A
U2
U6
U-G-5’-p-2’-A
A
mRNA
5’
3’ G-A
G-p-G
U5
3’
• ligation of exons releases lariat RNA (intron)
intron 1
Splicing
intermediate
U-G-5’-p-2’-A
A
5’
exon 1
exon 2
G-OH
O 3’
A-G-p-G
A -
3’
Second clevage-ligation reaction
intron 1
Lariat
U-G-5’-p-2’-A
A
Spliced mRNA
exon 1
5’
3’ G-A
exon 2
G-p-G
3’
Trans-splicing
Nei protozoi e in un nematode
Differenti molecole di mRNA dallo stesso gene
Splicing alternativo
Uso di promotori alternativi
Uso di segnali di poliadenilazione alternativi
“Enhancers”
Nei geni degli eucarioti gli enhancers possono distare dalla regione
codificante anche più di 50 Kb.