Molecular Cell
Previews Lighting Up pre-mRNA Recognition Cle´mentine Delan-Forino1 and David Tollervey1,* 1Wellcome Trust Center for Cell Biology, Michael Swann Building, King’s Buildings, Mayfield Road, Edinburgh, EH9 3JR *Correspondence:
[email protected] http://dx.doi.org/10.1016/j.molcel.2014.08.021
Systematic analyses, by UV crosslinking, of the precise binding sites for 23 different proteins across the yeast pre-mRNA population have given insights into the in vivo assembly of, and interactions between, pre-mRNA processing, packaging, and transport complexes. The picture of eukaryotic mRNA synthesis that has emerged over the past 30 years is one of daunting complexity. Every messenger RNA precursor (pre-mRNA) will interact with multiple processing, assembly, and transport complexes, each containing large numbers of different proteins. Moreover, it is clear that there is considerable heterogeneity in the precise details of the interactions between individual pre-mRNAs and both the core components and associated factors for each of these complexes. In consequence, it is not always clear to what extent results obtained for specific RNAs in vitro can be generalized to many or all pre-mRNAs in vivo. Moreover, there is ever-increasing evidence of crosstalk and interactions between different steps in mRNA maturation. These presumably enhance the overall efficiency and robustness of the pathway, but may be difficult to reproduce in a purified reductionist system. To address these important issues this issue, Baejen et al. (2014) have mapped the interaction of a large number of pre-mRNA binding proteins across all yeast pre-mRNAs and identify the conserved interactions that define key recognition steps during splicing, 30 -end formation, and transport. The development of RNA-immunoprecipitation techniques coupled with microarrays allowed the identification of large numbers of in vivo targets for RNA binding proteins (see, e.g., Hogan et al., 2008). This was very informative, but the lack of spatial information limited the insights obtained. The development of UV crosslinking and immunoprecipitation, combined with high-throughput sequencing (HITSCLIP), allowed precise protein binding sites to be identified across the transcriptome (Darnell, 2010). Two recent reports have used techniques related to CLIP to
systematically map the targets for multiple RNA-binding proteins—with the resulting large data sets allowing the discrimination between specific and general features in recognition. A previous analysis using CRAC mapped the targets for 13 RNA-binding proteins, concentrating on the distinctions between mRNA precursors and long noncoding RNAs (lncRNAs) (Tuck and Tollervey, 2013). The recent work used the photoactivated ribonucleoside 4-thiouracil (PARCLIP), which is incorporated into RNA transcripts in place of uracil and enhances the RNA-protein crosslinking efficiency (Hafner et al., 2010), in cells that had been harvested and resuspended in PBS. This was applied to map the targets of a remarkable 23 different factors involved in the nuclear maturation and transport of mRNA precursors (Baejen et al., 2014). Major conclusions drawn from the crosslinking analysis are outlined in Figure 1. Nascent transcripts, including the many lncRNAs that are transcribed from promoters that are divergent with mRNAs or located in the 30 regions of mRNAs, are rapidly capped and bound by Cbc1 and Cbc2 (Figure 1A). Analysis of factor co-occupancy on transcripts and colocalization around RNA binding sites, together with global comparison of binding profiles, led to the proposal that a checkpoint activity, formed by the combination of the surveillance and termination factors Nrd1 and Nab3 with the 30 end processing factor Rna15, induces early termination (Figure 1B). This activity may help determine which transcripts are terminated and targeted for degradation by the TRAMP and exosome RNA surveillance complexes or polyadenylated and packaged for nuclear export. These ideas are consistent with
the recent proposal that 30 -end formation and the 30 -processing factors Hrp1 and Nab2 play key roles in distinguishing pre-mRNAs from lncRNAs (Tuck and Tollervey, 2013). Analyses of the binding of pre-mRNA splicing factors and proteins associated with the U1 and U2 small nuclear ribonucleoprotein complexes (U1 and U2 snRNPs) (Figure 1C) showed that the initial steps in spliceosome assembly in vivo closely resemble the pathway determined in vitro (Will and Lu¨hrmann, 2011). These analyses support a twostep model for initial recognition of introns in yeast. Initial intron recognition involves binding of Mud2 (the homolog of human U2AF65) to a polypyrimidine tract and Msl5 (the homolog of branch-point binding protein, BBP) to the intron branch point (IBP). This is followed by recruitment of the U2 snRNP to the IBP and independent binding of the U1 snRNP at the 50 splice site. Evidence also emerged for interactions between the splicing machinery and the pre-mRNA cleavage and polyadenylation system (Figure 1D). This was based on bioinformatics analyses that determined the relative timing of factor binding and release compared to pre-mRNA splicing and 30 -end formation, as a means to assess remodeling steps during premRNA maturation. These results were combined with protein colocalization data showing that the Mud2-Msl5 complex and Snp1 and Luc7 components of the snRNP U1 preferentially bind 30 -uncleaved RNAs and colocalize with Rna15, an early-binding component of the cleavage and polyadenylation factor 1A (CF1A) complex. The stimulation of splicing by pre-mRNA cleavage and polyadenylation has long been proposed in mammals (Will and Lu¨hrmann, 2011) but
Molecular Cell 55, September 4, 2014 ª2014 Elsevier Inc. 649
Molecular Cell
Previews
(pA) recognition (Figure 1D). Binding of the cleavage and polyadenylation factor (CPF) and CF1A complexes turned out to be strikingly similar to pA site recognition in human cells, with the curious exception of Mpe1, which binds 6 nt upstream of yeast pA sites suggesting an important function but is apparently absent in humans. Following 30 cleavage (Figure 1E), processing factors are released enabling recognition of cleaved mRNA by export factors and the poly(A) binding proteins Pub1 and Pab1 (Figure 1F). The proteins Nab2 and Yra1 and the serine/arginine (SR) proteins Npl3, Gbp2, and Hrb1 act as adaptors for the major transport factor Mex67 (see Hackmann et al., 2014), and showed clear differences in target mRNA preferences, whereas Mex67 itself was recruited to all pre-mRNAs without apparent sequence specificity (Figure 1F). Overall, the data support previous in vitro analyses, which is reassuring for the field, but bring new insights into system-level interactions. The results also show that several aspects of in vivo mRNA maturation in yeast more closely resemble human cells than anticipated. Pre-mRNA splicing, 30 cleavage, and polyadenylation each involve simple biochemical steps. It was therefore surprising when the spliceosome and mRNA 30 processing machinery were both found to comprise extremely large, multimegadalton complexes. The data reported by Baejen et al. (2014) are consistent with the idea that RNAbinding proteins show low-sequence specificity but high cooperativity in target site recognition. Many proteins each make a modest contribution to the overall specificity of binding and function of the entire complex, helping explain the evolution of massive processing machinery. ACKNOWLEDGMENTS
Figure 1. Model for the Successive Protein Interactions Made by Maturing pre-mRNAs Based on Data and Conclusions from (Baejen et al., 2014) See text for details.
was not previously observed in yeast. However, these conclusions do not obviously agree with genome-wide analyses indicating that splicing in yeast is frequently associated with transcriptional
pausing on terreich et 2010). Analyses tors gave
exon 2 regions (Carrillo Oesal., 2010; Alexander et al., 0
of further 3 -processing facinsight into polyadenylation
650 Molecular Cell 55, September 4, 2014 ª2014 Elsevier Inc.
This work was supported by a Wellcome Trust Fellowship to DT (77248). Work in the Wellcome Trust Centre for Cell Biology is supported by Wellcome Trust core funding (092076). REFERENCES Alexander, R.D., Innocente, S.A., Barrass, J.D., and Beggs, J.D. (2010). Mol. Cell 40, 582–593.
Molecular Cell
Previews Baejen, C., Torkler, P., Gressel, S., Essig, K., So¨ding, J., and Cramer, P. (2014). Mol. Cell 55, this issue, 745–757. Carrillo Oesterreich, F., Preibisch, S., and Neugebauer, K.M. (2010). Mol. Cell 40, 571–581. Darnell, R.B. (2010). Wiley Interdiscip Rev RNA 1, 266–286.
Hackmann, A., Wu, H., Schneider, U.-M., Meyer, K., Jung, K., and Krebber, H. (2014). Nat. Commun. 5, 3123. Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A.C., Munschauer, M., et al. (2010). J. Vis. Exp. 41, 2034.
Hogan, D.J., Riordan, D.P., Gerber, A.P., Herschlag, D., and Brown, P.O. (2008). PLoS Biol. 6, e255. Tuck, A.C., and Tollervey, D. (2013). Cell 154, 996– 1009. Will, C.L., and Lu¨hrmann, R. (2011). Cold Spring Harb. Perspect. Biol. 3, 3.
New pROSpects for PTP1B: micro-Managing Oncogene-Induced Senescence Robert S. Banh,1,2,3 Yang Xu,1,2,3 and Benjamin G. Neel1,2,* 1Princess
Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada 3Co-first Authors *Correspondence:
[email protected] http://dx.doi.org/10.1016/j.molcel.2014.08.015 2Department
Oncogene-induced senescence (OIS) provides an important, but incompletely understood, barrier to tumorigenesis. In this issue, Yang et al. (2014) surprisingly report that inactivation of PTP1B by reactive oxygen species is essential for OIS, via effects on AGO2 and microRNA maturation. Oncogene-induced senescence (OIS) prevents the progression of preneoplastic cells harboring oncogenic mutations. Senescence is characterized by altered morphology (increased cytoplasmic granularity and nuclear/cell size; presence of senescence-associated heterochromatin foci), activation of the p53/ p21CIP1 and/or p16INK4A/pRB pathways, and arrest of cell-cycle progression (Courtois-Cox et al., 2008). The precise mechanism(s) of OIS has been intensely studied and oft debated, with several studies reporting tissue-, species-, and oncogene-specific OIS pathways. Elevated levels of reactive oxygen species (ROS) are found in most senescent cells and are thought to play a causal role in OIS via as yet unclear pathways. In this issue of Molecular Cell, Yang et al. (2014) report that ROS promote senescence by inactivating the proteintyrosine phosphatase PTP1B, thereby enhancing tyrosyl phosphorylation of the miRNA-processing enzyme argonaute 2 (AGO2) and altering miRNA processing. These exciting findings advance the OIS field and also raise new questions for future research.
ROS have long been viewed as toxic metabolic byproducts but also are implicated in OIS. For example, oxidant stress or overexpression of ROS-generating enzymes (e.g., NADPH oxidases [NOXs]) induces premature senescence (Kodama et al., 2013). Before the work of Yang et al. (2014), there were two general, and nonexclusive, models for how ROS induce senescence (Figure 1). Excessive ROS can activate p38 MAPK (p38), which, via PRAK, triggers p53 activation and senescence. Alternatively, ROS cause DNA damage, and the DNA damage response evokes OIS. Increasing evidence also implicates ROS, particularly H2O2, as second messengers in cell signaling. Classical protein-tyrosine phosphatases (PTPs) contain a highly reactive cysteine, which not only is required for catalysis but also causes susceptibility to reversible oxidation/inhibition (Tonks, 2013). ROS-catalyzed PTP inactivation can confer switch-like positive feedback properties to growth-factor-, cytokine-, or integrin-evoked signaling, and specific PTPs are implicated as ROS targets. Yang et al. (2014) find that a substantial fraction of PTP1B is oxidized during
HRASV12-induced senescence of human lung (IMR-90) or mouse embryonic fibroblasts (MEFs). They identify Tyr-393 in AGO2, which is known to regulate miRNA loading (Shen et al., 2013), as a PTP1B target. ROS-evoked AGO2 phosphorylation causes decreased loading of miRNAs targeted against p21CIP1, leading to increased p21CIP1 levels and OIS (Figure 1). PTP1B (encoded by PTPN1) is perhaps the best understood classical PTP. PTP1B is a critical negative regulator of insulin and leptin signaling, as well as other receptor tyrosine kinases and cytokine receptors, and is known to undergo reversible oxidation (Feldhammer et al., 2013). However, a role for PTP1B in miRNA biogenesis or OIS was unanticipated. Yang et al. (2014) detect other proteins that undergo oxidation during OIS, but PTP1B inhibition alone accelerates HRASV12-induced senescence. Furthermore, OIS is blocked by the antioxidant N-acetyl cysteine (NAC), but PTP1B inhibition restores senescence. The authors interpret these data as evidence that PTP1B is the key, if not the only, ROS target in OIS.
Molecular Cell 55, September 4, 2014 ª2014 Elsevier Inc. 651