Regolazione dell’espressione genica

CAP

Cytoplasm

Nucleus

DNA

RNA

Processing

Export

Degradation

Rat1pExos.

Nuclear pore

AAAAAA

Rrp6p

?

cap orf AAAAAAAAAAAAA5’ UTR 3’ UTR

Struttura di un mRNA

Regolazione della stabilità degli mRNA:

- deadenilazione, decapping e degradazione esonucleolitica (Pab1 polyA binding protein, Dcp1 decaping enzyme, Xrn1 esonuclaesi 5’-3’, esosoma esonucleasi 3’-5’)

- taglio endonucleolitico e degradazione esonucleolitica (sequenze ARE, mRNA per recettore transferrina, siRNA)

Regolazione della traduzione degli mRNA:

- sequenze regolative al 5’ UTR (mRNA per ferritina)

- sequenze regolative al 3’ UTR (interazione tra miRNA e mRNA - lin4/lin14, let7/lin-41)

mRNA Decay in Eukaryotes

I Major pathways

B. Deadenylation-dependent decaya. Steps and machinery in yeast

a) Deadenylationb) Decappingc) 5’ to 3’ exonucleolytic decayd) 3’ to 5’ decay by the exosome

b. Related mechanisms and components in mammals and plants

C. Deadenylation-independent decay: Nonsense-mediated decay

II Regulation

I. Decay mediated by endonucleases in animal systems: Transferrinreceptor mRNA decay

II. Modulation of mRNA decay in vivo by RNA-binding proteins:AUUUA-binding proteins in mammals

Common methods to monitor mRNA Decay Rates in Eukaryotic Systems

A. Inhibition of transcription with chemicals or a temperature-sensitive RNP

B. Regulated promotersC. In vivo systems

NORTHERN BLOT di RNA trattati con oligo + Rnasi H

AAAAA

TTTTT Rnasi H

AAAAA

TTTTT+cap cap

La degradazione inizia con l’accorciamento della coda di polyAe successiva veloce degradazione del corpo dell’mRNA

La degradazione successiva alla deadenilazione procede in direzione 5’-3’

A 15 minuti dalla repressione trascrizionale i trascritti deadenilati che si accumulano in xrn1 rimangono nel sopranatante (hanno perso il cap) e hanno dimensioni uguali a quelle del corpo dell’mRNA.

Questo dimostra che la degradazione parte dal 5’ dell’mRNA dopo che è avvenuto il decapping

Immunoprecipitazione con anticorpi diretti contro il cap

in ceppi selvatici e mutanti pre l’esonucleasi 5’-3’ Xrn1p

Degradazione dell’mRNA

Inizio della Traduzione

Pab reprime l’enzima di decapping

Modulation of mRNA stability by ARE-binding proteins

AU-rich elements (AREs) are known to target many labile proto-oncogene,lymphokine and cytokine mRNAs for rapid decay in mammalian cells

c-fos 5’ - AAAACGUUUUAUUGUGUUUUUAAUUUAUUUAUUAAGAUGG AUUCUCAGAUAUUUAUAUUUUUAUUUUAUUUUUUU - 3’

These elements usually contain multiple copies of the sequence AUUUA¸ Deletion of AUUUAs stabilize¸ Insertion of AUUUAs into stable mRNAs destabilize (also in plants)

Many RNA-binding proteins have been reported to interact with AREs

HuR

¸ Ubiquitously expressed member of the ELAV family of RNA binding proteins¸ Binding requirements in vitro indicative of role in ARE-mediated decay¸ Overexpression increases the in vivo stability of ARE-containing transcripts¸ HuR shuttles between the nucleus and cytoplasm¸ Suggested to bind ARE-containg mRNAs in the nucleus and escort them to the

cytoplasm, protecting the transcripts from decay

A protein that destabilizes an ARE-containing RNA is TTP (Tristetrapolin; zincfinger protein)

¸ Binds the ARE of TNFα¸ TNFα mRNA is stabilize d in TTP deficient mice

TTP knock out

ARE-containing mRNAs are stabilized

actinomycin

Stabilita’ dell’mRNA

Degradazione dell’mRNA

Cell, Vol 120, 623-634, 11 March 2005

Involvement of MicroRNA in AU-Rich Element-Mediated mRNA Instability

AU-rich elements (AREs) in the 3’untranslated region (UTR) of unstable mRNAs dictate their degradation. An RNAi-based screen performed in Drosophila S2 cells has revealed that Dicer1, Argonaute1 (Ago1) and Ago2, components involved in microRNA (miRNA) processing and function, are required for the rapid decay of mRNA containing AREs of tumor necrosis factor-Éø. The requirement for Dicer in the instability of ARE-containing mRNA (ARE-RNA) was confirmed in HeLa cells. We further observed that miR16, a human miRNA containing an UAAAUAUU sequence that is complementary to the ARE sequence, is required for ARE-RNA turnover. The role of miR16 in ARE-RNA decay is sequence-specific and requires the ARE binding protein tristetraprolin (TTP). TTP does not directly bind to miR16 but interacts through association with Ago/eiF2C family members to complex with miR16 and assists in the targeting of ARE. miRNA targeting of ARE, therefore, appears to be an essential step in ARE-mediated mRNA degradation.

ARE-Mediated mRNA Instability in Drosophila S2 Cells(A) S2 cells were stably transfected with a Cu2+-inducible expression vector containing globin gene or -globin gene fused with the 3’UTR of either TNF-α, IL-6, or IL-8. These cells were labeled as control, ARETNF, AREIL-6, and AREIL-8, respectively. Gene expression was induced by CuSO4 (0.5 mM). ActD (10É g/ml) was added 10 hr after Cu2+ treatment, and total RNA was isolated at different time periods after ActD addition. The stability of these ARE-containing mRNAs was determined by measuring -globin mRNA levels with real-time PCR.(B) The same experiments were performed as in (A) except that the É¿-globin gene was fused with inverted 3ÅåUTR of TNF-Éø (inv-ARETNF) or a TNF-α 3’UTR, in which ARE was deleted.(C) The stability of -globin mRNA containing ARETNF, inv-ARETNF, or 3’ARE was determined as in (A) at different times after Cu2+ removal.(D) S2 cells stably expressing RNA containing the ARE of TNF-Éø (ARETNF-RNA) were treated with two rounds of RNAi for dTTP or dHuR. The mRNA level of dTTP and dHuR in the RNAi-treated or -untreated cells were examined by RT-PCR.(E) Stability of the ARETNF-RNA in the cells described in (D) was measured by real-time PCR. dTTP RNAi- and dHuR RNAi-treated cells are indicated as dTTPd and dHuRd, respectively.

 Core Elements of the miRNA System Are Required for ARE-Mediated mRNA Instability(A) ARETNF-RNA-expressing S2 cells were treated with RNAi of dDicer1 or an unrelated gene dPgrp. The levels of dDicer1 and dPgrp mRNA were determined by RT-PCR.(B) Stability of ARETNF-RNA in dDicer1 RNAi-treated (dDicer1d), dPgrp RNAi-treated (dPgrpd), or untreated (control) cells was measured by real-time PCR.(C) ARETNF-RNA expressing S2 cells were treated with RNAi of dAgo1, or dAgo2, or dPgrp. The mRNA level of dAgo1, dAgo2, and dPgrp were determined by RT-PCR.(D) Stability of ARETNF-RNA in the cells treated with different RNAi in (C) was measured by real-time PCR. The cells in which the expression of dAgo1 or dAgo2 was suppressed by RNAi are indicated as dAgo1d and dAgo2d.(E) Dicer protein levels in HeLa cells stably transfected with pSuper empty vector (HeLa) or Dicer siRNA expression vector (Dicerd) were measured by Western blotting with anti-human Dicer antibody.(F) Primer extensions using 32P-labeled primer of Let7a or miR16 were performed with no RNA (-RNA) or total RNA from HeLa or Dicerd HeLa cells. Arrows indicate the extension products. Star (*) points to an unrelated product generated from Let7a primer alone. Diamonds indicate possible precursors.

 miR16 Is Required for ARETNF-RNA Turnover(A) The sequence of miR16. The sequence in miR16 that complements ARETNF is shown in bold.(B) The predicted precursors of miR16 encoded by two different genes. The double-strand intermediates of miR16 are shown in bold. The sequences that are targeted by siRNA in our experiments are underlined.(C) The sequence of siRNA used to selectively target pre-miR16-1 and pre-miR16-2.(D) HeLa cells were treated with two rounds of siRNA of pre-miR16-1 (si-miR16-1) or pre-miR16-2 (si-miR16-2). The levels of miR16 were measured by primer extension.(E) Northern blot analysis of the samples described in (D) using probes for miR16 or Let7a.(F) The expression vector of ARETNF-RNA was cotransfected at the second round of siRNA transfection. The stability of ARETNF-RNA was measured by real-time PCR 48 hr after transfection.(G) The expression vector of ARETNF-RNA was cotransfected with anti-miR16 or anti-miR21 2Åå-O-methyl oligonucleotide (5 nM final concentration in medium). The stability of ARETNF-RNA was measured by real-time PCR 24 hr after transfection.(H) The expression vector of ARECox2-RNA or (I) AREuPAR-ARE was cotransfected at the second round of si-miR16-1 transfection. The stability of ARECox2-RNA and AREuPar-RNA were measured by real-time PCR 48 hr after transfection.

Inizio della Traduzione

Pab reprime l’enzima di decapping

Degradazione dell’mRNA

Metabolismo del Ferro

Feextracellulare

Feintracellulare

Fe inferritinaTransferrina

Recettore Transferrina

+ ferro- ferro

1) Default:

- deadenilazione, decapping e degradazione esonucleolitica (Pab1 polyA binding protein, Dcp1 decaping enzyme, Xrn1 esonuclaesi 5’-3’)

2) Regolati:

- taglio endonucleolitico e degradazione esonucleolitica (mRNA per recettore transferrina, sequenze ARE)

3) Controllo di qualità -

- NMD

Regolazione della stabilità degli mRNA:

spliceosome

UAPAlyUAP

Alyspliced mRNP

UAP UAP

Aly

TapAly

UAP56 is a splicing factor; it recruits Aly to the mRNA

nuclear pore complex

Splicing is required for efficient mRNA export and for the Nonsense Mediated Decay

pre-mRNA splicing and gene expression

Nucleus

Cytoplasm

AAAA

AAAA

TRANSLATIONLOCALIZATION

TRANSCRIPTION

AAAA

Nonsense-mediated mRNA decay (NMD)

PTC AAAA

AAAA

Exon Junction Complex (EJC)

AAAA

20-24 nts

EJC

The Exon Junction Complex is an assemblage of proteins deposited on mRNA 20-24 nts upstream of the exon-exon junction as a consequence of splicing

SPLICING

exon 1

20-24 nts

EJC

exon 1exon2

splicing

intron

mRNA export

nonsense-mediated mRNA decay

mRNA

localization

REF/Aly

Upf2

Upf3

RNPS1

Upf1

TAPp15

SRm160

UAP56

pinin

exon2

Magoh

Y14

splicing

eIF4AIII

?

?

?

MLN51

eIF4E

poly A

bindi

ng pro

tein

eIF4G

UAG

Normal termination

upf1

upf1

eIF4E

poly A

bindi

ng pro

tein

eIF4G

UAG

UAG

nonsense mediated mRNA decay

upf2/3

degradation

upf1

rf3