- Email: [email protected]
A NEAT Way of Regulating Nuclear Export of mRNAs
Molecular Cell
Previews A NEAT Way of Regulating Nuclear Export of mRNAs Deirdre Scadden1,* 1Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK *Correspondence: [email protected] DOI 10.1016/j.molcel.2009.08.005
In this issue of Molecular Cell, Chen and Carmichael (2009) demonstrate that the noncoding RNA NEAT1 regulates gene expression by restricting nuclear export. Recent studies of the human transcriptome have demonstrated that, although a large proportion of the genome is transcribed, many transcripts lack protein coding capacity (Birney et al., 2007). Though it is possible that these noncoding RNAs (ncRNAs) may only represent transcriptional noise, it seems more likely that they are fulfilling important roles in eukaryotic cells (Mattick and Makunin, 2006). For example, Xist ncRNA is involved in silencing the inactive X chromosome, whereas NRON ncRNA regulates the nuclear trafficking of NFAT (nuclear factor of activated T cells) proteins. However, although the number of ncRNAs has increased exponentially, relatively few have been assigned functions. Several recent studies in both human and mouse have shed light on the function of the nuclear-restricted ncRNA NEAT1 (nuclear-enriched autosomal transcript; MEN3/b in mouse) (Clemson et al., 2009; Sasaki et al., 2009; Sunwoo et al., 2009). NEAT1 is an abundant 4 kb unspliced, polyadenylated ncRNA that is an integral component of nuclear paraspeckles. Paraspeckles are discrete structures that typically localize adjacent to nuclear speckles (Fox et al., 2005). Importantly, NEAT1 appeared to provide the crucial structural framework to nucleate paraspeckle formation. The precedent for a class of architectural nuclear ncRNAs was thus established. Although the function of paraspeckles is not wholly understood, the identity of associated proteins provides some clues. At least three nucleic-acid-binding proteins (p54nrb, PSF, and PSP1) are characteristically enriched in paraspeckles, and NEAT1 is required for their localization (Chen and Carmichael, 2009; Clemson et al., 2009). The presence of p54nrb in paraspeckles strongly suggests that they are involved in retention of mRNAs
that have undergone A-to-I editing by dsRNA-dependent adenosine deaminases (ADARs). Previous studies showed that mRNAs with structured or edited 30 UTRs specifically interacted with a p54nrb-containing complex to prevent nuclear export (Chen et al., 2008). mRNAs subject to this type of regulation include those with inverted repeated Alu (IRAlu) elements within their 30 UTR, which may be targets for extensive editing (Chen et al., 2008). Bioinformatic analyses have shown that as many as 333 human genes contain IRAlus within their 30 UTRs (Chen et al., 2008). Another example is the mouse nuclear transcript CTN-RNA, which is edited within its 30 UTR and is at least partially localized to paraspeckles (Prasanth et al., 2005). During stress, CTN-RNA is cleaved and released into the cytoplasm as mCat2 mRNA. Interestingly, although NEAT1 associates with paraspeckles and interacts with p54nrb, it does not appear to be edited (Clemson et al., 2009). Chen and Carmichael (2009) now describe an interesting study that effectively puts together various puzzle pieces and proposes a functional role for NEAT1 ncRNA. As mentioned above, previous studies showed that mRNAs containing IRAlus within their 30 UTR may undergo A-to-I editing and be retained in the nucleus via interaction with a p54nrb-containing complex. Nuclear retention was thought to prevent inappropriate translation of extensively edited mRNAs. The authors have now described experiments in human embryonic stem cells (hESCs) that at first glance are inconsistent with these previous data. Although mRNA encoding the LIN28 regulatory factor was substantially edited within the IRAlu elements in its 30 UTR, it was efficiently exported from the nucleus of hESCs. In
contrast, the presence of the edited lin28 30 UTR within a reporter mRNA in differentiated cells largely resulted in nuclear retention (Chen et al., 2008). Even more baffling was the observation that both lin28 30 UTR-containing mRNAs specifically interacted with p54nrb in both cell types (Chen and Carmichael, 2009; Chen et al., 2008). However, the key to this apparent paradox came from the observation that paraspeckles were undetectable in hESCs. Moreover, Chen et al. went on to show that the absence of paraspeckles was attributable to the lack of NEAT1 expression in hESCs. This was consistent with recent studies that showed that NEAT1 was essential for paraspeckle formation (Clemson et al., 2009; Sasaki et al., 2009; Sunwoo et al., 2009). Interestingly, expression of NEAT1 was restored when hESCs differentiated, which suggested that paraspeckles might regulate gene expression during specific developmental stages. Further experiments conclusively demonstrated that nuclear retention of IRAlu-containing mRNAs depended not only on binding to p54nrb, but also on NEAT1 expression and paraspeckle formation. It is tempting to speculate that the p54nrb complex may mediate nuclear retention by interacting simultaneously with both NEAT1 and the target mRNA within paraspeckles, as shown schematically in Figure 1. NEAT1 ncRNA may thereby play an important role in regulating gene expression by governing nuclear export of mRNAs. Although it is exciting to assign a function for NEAT1, some questions remain. It will be intriguing to know whether nuclear retention of mRNAs is largely irreversible or whether other examples will be found in which mRNAs are stored only transiently, as seen for CTN-RNA (Prasanth et al., 2005). Transient storage
Molecular Cell 35, August 28, 2009 ª2009 Elsevier Inc. 395
Molecular Cell
Previews REFERENCES seems most likely, given that the cell is unlikely to expend Birney, E., Stamatoyannopoulos, energy to transcribe mRNAs J.A., Dutta, A., Guigo, R., Gingeras, that are not usefully emT.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., and ployed. It will also be imporThurman, R.E. (2007). Nature 447, tant to understand more 799–816. about how nuclear retention Chen, L.-L., and Carmichael, G.G. of mRNAs is regulated. For (2009). Mol. Cell 35, this issue, instance, whereas A-to-I edit467–478. ing of IRAlu-containing mRNA appears to be important Chen, L.-L., DeCerbo, J.N., and Carmichael, G.G. (2008). EMBO J. for interaction with p54nrb, 27, 1694–1705. NEAT1 also interacts specifinrb in the cally with p54 Clemson, C.M., Hutchinson, J.N., Sara, S.A., Ensminger, A.W., Fox, absence of editing. Moreover, Figure 1. The Fate of IRAlu-Containing mRNAs in Either A.H., Chess, A., and Lawrence, nuclear retention of edited Differentiated or Embryonic Stem Cells J.B. (2009). Mol. Cell 33, 717–726. (A) A schematic representation of how NEAT1 ncRNA may control the retenmRNAs is not absolute, as tion of structured or edited IRAlu-containing mRNAs within the nucleus of Fox, A.H., Bond, C.S., and Lamond, seen here and in another differentiated cells. NEAT1 has an essential role in the assembly and architecA.I. (2005). Mol. Biol. Cell 16, 5304– recent study (Hundley et al., ture of nuclear paraspeckles and localizes with the paraspeckle-associated 5315. proteins p54nrb, PSP1, and PSF. Heterodimeric protein complexes may 2008). Though A-to-I editing interact simultaneously with both NEAT1 ncRNA and IRAlu-containing mRNAs Hundley, H.A., Krauchuk, A.A., and may play some regulatory to mediate nuclear retention. Bass, B.L. (2008). RNA 14, 2050– role, it is possible that the (B) In the absence of NEAT1 ncRNA and paraspeckles, IRAlu-containing 2060. structured IRAlu elements mRNAs are exported from the nucleus of hESCs and translated. Mattick, J.S., and Makunin, I.V. within mRNAs are sufficient (2006). Hum. Mol. Genet. 15, R17– for nuclear retention. It would R29. be interesting to analyze the localization of IRAlu-containing mRNAs cells are also functionally important in Prasanth, K.V., Prasanth, S.G., Xuan, Z., Hearn, S., Freier, S.M., Bennett, C.F., Zhang, M.Q., and in ADAR-deficient mammalian cells. hESCs. Spector, D.L. (2005). Cell 123, 249–263. In identifying a function for NEAT1, Finally, although one can imagine why a mechanism exists in hESCs to ensure Chen et al. have made an important Sasaki, Y.T.F., Ideue, T., Sano, M., Mituyama, T., the expression of lin28 mRNA, it is impor- contribution to better understanding the and Hirose, T. (2009). Proc. Natl. Acad. Sci. USA tant to consider that all other IRAlu-con- many and varied roles of ncRNAs. It will 106, 2525–2530. taining mRNAs are also likely to be ex- now be exciting to see whether other Sunwoo, H., Dinger, M.E., Wilusz, J.E., Amaral, ported. Perhaps other mRNAs normally ncRNAs may similarly regulate gene P.P., Mattick, J.S., and Spector, D.L. (2009). Genome Res. 19, 347–359. retained in the nucleus of differentiating expression in eukaryotic cells.
Kinky Binding and SECsy Insertions Simon J. Morley1,* and Mark Willett1 1Department of Biochemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK *Correspondence: [email protected] DOI 10.1016/j.molcel.2009.08.001
Here Budiman et al. (2009) demonstrate that the selective translation of selenocysteine-containing proteins can be regulated by the mutually exclusive binding of eIF4a3 and SECIS binding protein 2 (SBP2) to a cis-acting element in the 30 untranslated region (30 UTR) of the target mRNA. When dietary selenium is restricted, liver, kidney, and lung cells prioritize which selenocysteine (Sec)-containing proteins continue to be synthesized at the expense
of others. The selective mechanism has remained poorly understood, but the paper by Budiman et al. (2009) in this issue of Molecular Cell now sheds light
396 Molecular Cell 35, August 28, 2009 ª2009 Elsevier Inc.
on this process. Here the authors demonstrate that eukaryotic initiation factor 4a3 (eIF4a3) is both necessary and sufficient to mediate this selective translational
Previews A NEAT Way of Regulating Nuclear Export of mRNAs Deirdre Scadden1,* 1Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK *Correspondence: [email protected] DOI 10.1016/j.molcel.2009.08.005
In this issue of Molecular Cell, Chen and Carmichael (2009) demonstrate that the noncoding RNA NEAT1 regulates gene expression by restricting nuclear export. Recent studies of the human transcriptome have demonstrated that, although a large proportion of the genome is transcribed, many transcripts lack protein coding capacity (Birney et al., 2007). Though it is possible that these noncoding RNAs (ncRNAs) may only represent transcriptional noise, it seems more likely that they are fulfilling important roles in eukaryotic cells (Mattick and Makunin, 2006). For example, Xist ncRNA is involved in silencing the inactive X chromosome, whereas NRON ncRNA regulates the nuclear trafficking of NFAT (nuclear factor of activated T cells) proteins. However, although the number of ncRNAs has increased exponentially, relatively few have been assigned functions. Several recent studies in both human and mouse have shed light on the function of the nuclear-restricted ncRNA NEAT1 (nuclear-enriched autosomal transcript; MEN3/b in mouse) (Clemson et al., 2009; Sasaki et al., 2009; Sunwoo et al., 2009). NEAT1 is an abundant 4 kb unspliced, polyadenylated ncRNA that is an integral component of nuclear paraspeckles. Paraspeckles are discrete structures that typically localize adjacent to nuclear speckles (Fox et al., 2005). Importantly, NEAT1 appeared to provide the crucial structural framework to nucleate paraspeckle formation. The precedent for a class of architectural nuclear ncRNAs was thus established. Although the function of paraspeckles is not wholly understood, the identity of associated proteins provides some clues. At least three nucleic-acid-binding proteins (p54nrb, PSF, and PSP1) are characteristically enriched in paraspeckles, and NEAT1 is required for their localization (Chen and Carmichael, 2009; Clemson et al., 2009). The presence of p54nrb in paraspeckles strongly suggests that they are involved in retention of mRNAs
that have undergone A-to-I editing by dsRNA-dependent adenosine deaminases (ADARs). Previous studies showed that mRNAs with structured or edited 30 UTRs specifically interacted with a p54nrb-containing complex to prevent nuclear export (Chen et al., 2008). mRNAs subject to this type of regulation include those with inverted repeated Alu (IRAlu) elements within their 30 UTR, which may be targets for extensive editing (Chen et al., 2008). Bioinformatic analyses have shown that as many as 333 human genes contain IRAlus within their 30 UTRs (Chen et al., 2008). Another example is the mouse nuclear transcript CTN-RNA, which is edited within its 30 UTR and is at least partially localized to paraspeckles (Prasanth et al., 2005). During stress, CTN-RNA is cleaved and released into the cytoplasm as mCat2 mRNA. Interestingly, although NEAT1 associates with paraspeckles and interacts with p54nrb, it does not appear to be edited (Clemson et al., 2009). Chen and Carmichael (2009) now describe an interesting study that effectively puts together various puzzle pieces and proposes a functional role for NEAT1 ncRNA. As mentioned above, previous studies showed that mRNAs containing IRAlus within their 30 UTR may undergo A-to-I editing and be retained in the nucleus via interaction with a p54nrb-containing complex. Nuclear retention was thought to prevent inappropriate translation of extensively edited mRNAs. The authors have now described experiments in human embryonic stem cells (hESCs) that at first glance are inconsistent with these previous data. Although mRNA encoding the LIN28 regulatory factor was substantially edited within the IRAlu elements in its 30 UTR, it was efficiently exported from the nucleus of hESCs. In
contrast, the presence of the edited lin28 30 UTR within a reporter mRNA in differentiated cells largely resulted in nuclear retention (Chen et al., 2008). Even more baffling was the observation that both lin28 30 UTR-containing mRNAs specifically interacted with p54nrb in both cell types (Chen and Carmichael, 2009; Chen et al., 2008). However, the key to this apparent paradox came from the observation that paraspeckles were undetectable in hESCs. Moreover, Chen et al. went on to show that the absence of paraspeckles was attributable to the lack of NEAT1 expression in hESCs. This was consistent with recent studies that showed that NEAT1 was essential for paraspeckle formation (Clemson et al., 2009; Sasaki et al., 2009; Sunwoo et al., 2009). Interestingly, expression of NEAT1 was restored when hESCs differentiated, which suggested that paraspeckles might regulate gene expression during specific developmental stages. Further experiments conclusively demonstrated that nuclear retention of IRAlu-containing mRNAs depended not only on binding to p54nrb, but also on NEAT1 expression and paraspeckle formation. It is tempting to speculate that the p54nrb complex may mediate nuclear retention by interacting simultaneously with both NEAT1 and the target mRNA within paraspeckles, as shown schematically in Figure 1. NEAT1 ncRNA may thereby play an important role in regulating gene expression by governing nuclear export of mRNAs. Although it is exciting to assign a function for NEAT1, some questions remain. It will be intriguing to know whether nuclear retention of mRNAs is largely irreversible or whether other examples will be found in which mRNAs are stored only transiently, as seen for CTN-RNA (Prasanth et al., 2005). Transient storage
Molecular Cell 35, August 28, 2009 ª2009 Elsevier Inc. 395
Molecular Cell
Previews REFERENCES seems most likely, given that the cell is unlikely to expend Birney, E., Stamatoyannopoulos, energy to transcribe mRNAs J.A., Dutta, A., Guigo, R., Gingeras, that are not usefully emT.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., and ployed. It will also be imporThurman, R.E. (2007). Nature 447, tant to understand more 799–816. about how nuclear retention Chen, L.-L., and Carmichael, G.G. of mRNAs is regulated. For (2009). Mol. Cell 35, this issue, instance, whereas A-to-I edit467–478. ing of IRAlu-containing mRNA appears to be important Chen, L.-L., DeCerbo, J.N., and Carmichael, G.G. (2008). EMBO J. for interaction with p54nrb, 27, 1694–1705. NEAT1 also interacts specifinrb in the cally with p54 Clemson, C.M., Hutchinson, J.N., Sara, S.A., Ensminger, A.W., Fox, absence of editing. Moreover, Figure 1. The Fate of IRAlu-Containing mRNAs in Either A.H., Chess, A., and Lawrence, nuclear retention of edited Differentiated or Embryonic Stem Cells J.B. (2009). Mol. Cell 33, 717–726. (A) A schematic representation of how NEAT1 ncRNA may control the retenmRNAs is not absolute, as tion of structured or edited IRAlu-containing mRNAs within the nucleus of Fox, A.H., Bond, C.S., and Lamond, seen here and in another differentiated cells. NEAT1 has an essential role in the assembly and architecA.I. (2005). Mol. Biol. Cell 16, 5304– recent study (Hundley et al., ture of nuclear paraspeckles and localizes with the paraspeckle-associated 5315. proteins p54nrb, PSP1, and PSF. Heterodimeric protein complexes may 2008). Though A-to-I editing interact simultaneously with both NEAT1 ncRNA and IRAlu-containing mRNAs Hundley, H.A., Krauchuk, A.A., and may play some regulatory to mediate nuclear retention. Bass, B.L. (2008). RNA 14, 2050– role, it is possible that the (B) In the absence of NEAT1 ncRNA and paraspeckles, IRAlu-containing 2060. structured IRAlu elements mRNAs are exported from the nucleus of hESCs and translated. Mattick, J.S., and Makunin, I.V. within mRNAs are sufficient (2006). Hum. Mol. Genet. 15, R17– for nuclear retention. It would R29. be interesting to analyze the localization of IRAlu-containing mRNAs cells are also functionally important in Prasanth, K.V., Prasanth, S.G., Xuan, Z., Hearn, S., Freier, S.M., Bennett, C.F., Zhang, M.Q., and in ADAR-deficient mammalian cells. hESCs. Spector, D.L. (2005). Cell 123, 249–263. In identifying a function for NEAT1, Finally, although one can imagine why a mechanism exists in hESCs to ensure Chen et al. have made an important Sasaki, Y.T.F., Ideue, T., Sano, M., Mituyama, T., the expression of lin28 mRNA, it is impor- contribution to better understanding the and Hirose, T. (2009). Proc. Natl. Acad. Sci. USA tant to consider that all other IRAlu-con- many and varied roles of ncRNAs. It will 106, 2525–2530. taining mRNAs are also likely to be ex- now be exciting to see whether other Sunwoo, H., Dinger, M.E., Wilusz, J.E., Amaral, ported. Perhaps other mRNAs normally ncRNAs may similarly regulate gene P.P., Mattick, J.S., and Spector, D.L. (2009). Genome Res. 19, 347–359. retained in the nucleus of differentiating expression in eukaryotic cells.
Kinky Binding and SECsy Insertions Simon J. Morley1,* and Mark Willett1 1Department of Biochemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK *Correspondence: [email protected] DOI 10.1016/j.molcel.2009.08.001
Here Budiman et al. (2009) demonstrate that the selective translation of selenocysteine-containing proteins can be regulated by the mutually exclusive binding of eIF4a3 and SECIS binding protein 2 (SBP2) to a cis-acting element in the 30 untranslated region (30 UTR) of the target mRNA. When dietary selenium is restricted, liver, kidney, and lung cells prioritize which selenocysteine (Sec)-containing proteins continue to be synthesized at the expense
of others. The selective mechanism has remained poorly understood, but the paper by Budiman et al. (2009) in this issue of Molecular Cell now sheds light
396 Molecular Cell 35, August 28, 2009 ª2009 Elsevier Inc.
on this process. Here the authors demonstrate that eukaryotic initiation factor 4a3 (eIF4a3) is both necessary and sufficient to mediate this selective translational