Posttranscriptional Gene Regulation by Spatial Rearrangement of the 3′ Untranslated Region

Abstract

Translation termination at premature termination codons (PTCs) triggers degradation of the aberrant mRNA, but the mechanism by which a termination event is defined as premature is still unclear. Here we show that the physical distance between the termination codon and the poly(A)-binding protein PABPC1 is a crucial determinant for PTC recognition in human cells. “Normal” termination codons can trigger nonsense-mediated mRNA decay (NMD) when this distance is extended; and vice versa, NMD can be suppressed by folding the poly(A) tail into proximity of a PTC or by tethering of PABPC1 nearby a PTC, indicating an evolutionarily conserved function of PABPC1 in promoting correct translation termination and antagonizing activation of NMD. Most importantly, our results demonstrate that spatial rearrangements of the 3′ untranslated region can modulate the NMD pathway and thereby provide a novel mechanism for posttranscriptional gene regulation.

Autoregulation of the nonsense-mediated mRNA decay pathway in human cells

“…5A,B). An intermediate truncation of the 39 UTRs to z800 nt showed intermediate levels of reporter transcript, consistent with our previous findings of a gradual decline of NMD efficiency with decreasing distance between the TC and the poly(A) tail (Eberle et al 2008). To further test if the reason for the low reporter mRNA levels was, indeed, the 39-UTR length rather than the nucleotide sequence, we measured the transcript levels of a reporter construct that contained the reverted full-length 39-UTR sequence of UPF1 or SMG7.…”

“…It must be emphasized that according to the unified NMD model, a long 39 UTR will not necessarily trigger NMD, because the physical distance between the termination codon and the PABP rather than the number of nucleotides in between is the crucial parameter (Eberle et al 2008). Data from different laboratories indicate that a 39 UTR of >420 nt can trigger NMD (Eberle et al 2008;Singh et al 2008).…”

“…Data from different laboratories indicate that a 39 UTR of >420 nt can trigger NMD (Eberle et al 2008;Singh et al 2008). However, the majority of the z55% of human mRNAs with a 39 UTR of >500 nt (Supplemental Table III) are obviously not NMD substrates.…”

“…Many of these mRNAs probably have evolved means to avoid NMD. For example, spatial arrangements of the 39 UTR that bring the PABP in proximity to the termination codon can suppress NMD (Eberle et al 2008;Singh et al 2008). In addition, mRNAs might possess NMD-inhibitory sequences similar to the stability element in the Rous sarcoma virus (Weil and Beemon 2006).…”

“…The experimental evidence from several different model organisms suggests, for example, that long 39 UTRs can elicit NMD (Muhlrad and Parker 1999;Amrani et al 2004;Kertesz et al 2006;Behm-Ansmant et al 2007;Longman et al 2007;Eberle et al 2008;Kerenyi et al 2008;Singh et al 2008;Hansen et al 2009;Kebaara and Atkin 2009). A greater distance between the TC and PABP would impede transmission of the PABP-mediated termination-stimulating signal to the ribosome stalled at the TC, thus tilting the balance from efficient termination and ribosome release toward NMD.…”