RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD

Abstract

Nonsense-mediated mRNA decay (NMD) is a conserved RNA decay pathway that degrades aberrant mRNAs and directly regulates many normal mRNAs. This dual role for NMD raises the possibility that its magnitude is buffered to prevent the potentially catastrophic alterations in gene expression that would otherwise occur if NMD were perturbed by environmental or genetic insults. In support of this, here we report the existence of a negative feedback regulatory network that directly acts on seven NMD factors. Feedback regulation is conferred by different branches of the NMD pathway in a cell type-specific and developmentally regulated manner. We identify feedback-regulated NMD factors that are rate limiting for NMD and demonstrate that reversal of feedback regulation in response to NMD perturbation is crucial for maintaining NMD. Together, our results suggest the existence of an intricate feedback network that maintains both RNA surveillance and the homeostasis of normal gene expression in mammalian cells.

Figure 1. NMD Factor mRNAs Are Negatively Regulated by NMD

(A and B) Quantitative polymerase-chain reaction (qPCR) analysis of total cellular RNA from HeLa cells depleted of UPF1 (A) or UPF3B (B) using RNAi. The values shown are the average fold change (mean ± SEM) from three independent experiments relative to cells transfected with a negative-control siRNA (against luciferase [LUC]; a value of 1 indicates no change). Values were normalized against the housekeeping GAPDH and β-ACTIN transcripts. Statistical analysis was performed using the Student’s t test. *p < 0.05; **p < 0.01; ***p < 0.001. (C and D)) qPCR analysis of pre-mRNA and mature mRNA levels in HeLa cells depleted of UPF1 (C) or UPF3B (D). The results are from three independent experiments performed separately from those in (A) and (B). Data were quantified and statistically analyzed as in (A).

Figure 2. NMD Factor mRNAs Are Targeted for Decay by NMD

(A) qPCR analysis of total cellular RNA from HeLa cells incubated with actinomycin D (5 µg/ml) for the times shown. Cells were transfected with siRNAs and cultured for 40 hr prior to actinomycin D treatment. (Dashed line) Luciferase siRNA-treated cells. (Solid line) UPF1 siRNA and SMG1 siRNA-treated cells (the latter only for analysis of UPF1 mRNA half-life). Data were quantified and statistically analyzed as in Figure 1A, and mRNA half-life was calculated by linear regression analysis. (B) Northern blot analysis of total cellular RNA from HeLa Tet-off cells transiently transfected with Tet-regulated β-globin (βwt) (Singh et al., 2008a) and βUPF1 reporter constructs, the latter of which was made by replacing the β-globin 3′UTR in βwt with the full-length human UPF1 3′UTR (1.7 kb; generated by RT-PCR from HeLa cell total RNA). The internal control is β-globin mRNA from a constitutively expressed construct (Singh et al., 2008a). mRNA half-life was calculated by linear regression analysis from two experiments. Data were quantified and statistically analyzed as in Figure 1A.

Figure 3. Different Branches of the NMD Pathway Participate in Feedback Regulation

(A–C) Level of NMD factor and NMD substrate transcripts in HeLa cells transfected with siRNAs against the indicated molecules versus luciferase (a value of 1 indicates no difference), as assayed by qPCR analysis. Data were quantified and statistically analyzed as in Figure 1A. (D) Level of NMD factor transcripts in LCLs from individuals carrying UPF3B mutations (e.g., Fam1, III-1 is family 1, 3rd generation, patient 1) versus control individuals (a value of 1 indicates no difference). Data were quantified in triplicate by qPCR and statistically analyzed as in Figure 1A.

Figure 4. The UPF3B-dependent Feedback Pathway Is Cell Type Specific and Developmentally Regulated

All panels show the level of NMD factor and NMD substrate transcripts in the experimental sample versus the control (a value of 1 indicates no difference), as assayed by qPCR analysis, and are quantified and statistically analyzed as in Figure 1A using the housekeeping transcripts Rpl19 and β-Actin for normalization. (A) MEFs from Upf3b^−/y (mutant) and Upf3b^+/y (control) embryos (n = 3). (B) Upf3b^+/y MEFs transfected with Upf1 siRNA versus luciferase siRNA (control); average values from three independent experiments. (C) Upf3b^−/y versus control Upf3b^+/y ES cells, differentiated into EBs for the days shown; average values from two independent experiments.

Figure 5. The UPF3B-dependent Feedback Pathway Is Tissue and Cell Type Specific In Vivo

All panels show the level of NMD factor and NMD substrate transcripts in the experimental sample versus the control (a value of 1 indicates no difference), as assayed by qPCR analysis, and are quantified and statistically analyzed as in Figure 1A using the housekeeping transcripts Rpl19 and β-Actin for normalization. (A) Adult Upf3b^−/y versus control littermate Upf3b^+/y mice tissues (n = 3). (B) Mature hematopoietic cells purified from adult Upf3b^−/y versus control littermate Upf3b^+/y mice (n = 3).

Figure 6. Physiological Role of the NMD Feedback Regulatory Pathway

(A) The magnitude of NMD as measured by luciferase activity (assayed as described previously [Bhardwaj et al., 2008]) in HeLa cells cotransfected with (1) PTC+ and PTC− versions of a Renilla-luciferase NMD reporter (50 ng) (Boelz et al., 2006), (2) the indicated expression vectors (EV is empty vector), and (3) a firefly luciferase construct as an internal control (50 ng). The ratio of luciferase activity from the PTC− and PTC+ reporters in EV-transfected cells is set as 1. To achieve modest (~2- to 3-fold) overexpression of the NMD factors, the following concentrations of NMD factor expression plasmids were transfected: UPF1 (2 ng), UPF2 (5 ng), UPF3A (5 ng), UPF3B (2 ng), SMG1 (100 ng), SMG5 (25 ng), SMG6 (25 ng), and SMG7 (25 ng) (this is based on the dose-response experiments shown in Figures S6A and S6B [the amount of EV control transfected for each factor was adjusted accordingly]). Data were quantified and statistically analyzed as in Figure 1A. (B) qPCR analysis of total cellular RNA from HeLa cells transfected as in (A), quantified and statistically analyzed as in Figure 1A. (C) qPCR analysis of total cellular RNA from HeLa cells transfected with UPF1 or luciferase (Luc) siRNAs, incubated for 24 hr, transfected with a dose of SMG1 or UPF2 siRNA sufficient to downregulate SMG1 or UPF2, respectively, to the endogenous level before treatment, followed by culture for 24 hr (see Figure S3E). UPF2, which is not rate limiting for NMD in HeLa cells (see A), serves as a negative control. Data were quantified and statistically analyzed as described in Figure 1 A. (D) Cell counts of HeLa cells transfected with SMG1 expression vector (solid line) or EV (dashed line) (100 ng of vector was chosen to achieve ~3-fold SMG1 over-expression; see A and Figure S6B), calculated from three independent experiments. Cell doubling time was calculated by linear regression analysis. Data were quantified and statistically analyzed as described in Figure 1A.

Figure 7. Model

Negative feedback regulatory loops buffer NMD from genetic and environmental perturbations, allowing NMD to maintain its functions in regulating gene expression and RNA surveillance.