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Learning to Protect Your Genome on the Fly
Leading Edge
Previews Learning to Protect Your Genome on the Fly Mia T. Levine1 and Harmit S. Malik1,2,* 1Basic
Sciences Division Hughes Medical Institute Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA *Correspondence: [email protected] DOI 10.1016/j.cell.2011.12.001 2Howard
Piwi-interacting RNAs (piRNAs) help defend host genomes against germline transposons. In this issue of Cell, Khurana et al. show how alterations in the piRNA-encoding loci within a single generation allow a naive fly genome to overcome the initially insurmountable challenge imposed by a newly encountered mobile element. Host genomes defend against invading transposable elements via both genetically inherited piRNA clusters that encode de novo piRNAs as well as epigenetically inherited, maternal ‘‘trigger’’ piRNAs (Brennecke et al., 2007). Complexed with Piwi proteins, piRNAs target active transposons in the germline and silence their expression. These small RNAs also serve as seeds for more piRNA production, amplifying the defense response. A report in this issue of Cell shows that the piRNA defense repertoire can be dramatically remodeled within a single generation (Khurana et al., 2011). The authors demonstrate that even in the absence of maternally inherited trigger piRNAs, a naive fly genome can overcome the challenge imposed by a newly encountered mobile element and pass on this immunity to its offspring. P element transposons invaded the D. melanogaster species approximately 100 years ago (Daniels et al., 1990). All wild strains collected after the 1930s harbor this transposon family (‘‘P’’ strains), whereas a handful of those collected prior to this time are devoid of P elements (‘‘M’’ strains). The remarkably rapid spread of P elements is largely due to the phenomenon of P-M hybrid dysgenesis. When ‘‘M’’ females are crossed to ‘‘P’’ males, the germline cells of resulting female progeny are ravaged by active transposons, rendering these flies sterile. In contrast, female offspring resulting from the reciprocal cross (from ‘‘P’’ mothers) are fertile (Kidwell et al., 1977). This ‘‘parent-of-origin’’ effect is largely attribut-
able to the maternal deposition of trigger piRNAs (Brennecke et al., 2008). Khurana et al. revisit a 30-year-old intriguing finding that dysgenic daughters of a P-M cross recover fertility as they age (Bucheton, 1979). They first establish that young dysgenic daughters not only are less fertile than genetically identical, agematched nondysgenic daughters but also harbor elevated P element mRNA and a dearth of P element matching piRNAs. P element activity results in DNA damage, which induces the Chk2 DNA-damage-signaling checkpoint. Chk phosphorylation of the nuage protein Vasa directly or indirectly results in a breakdown of the nuage structures necessary for transposon silencing. P element activity therefore results in a dramatic overproliferation of a variety of unrelated ‘‘resident transposons’’ in the genome (Figure 1). In 3-week-old P-M dysgenic females, virtually all measurements of fertility and the genome defense system supporting fertility are restored to wild-type levels. Although the number of egg-producing chambers in dysgenic daughters is still severely compromised, the eggs produced become viable embryos and grow into fertile adults. Khurana et al. demonstrate that recovered dysgenic fertility is associated with production of P element cognate piRNAs, whose source is mysterious because dysgenic flies do not inherit maternally deposited trigger piRNAs. The authors first consider whether P element transposition into piRNA clusters over the several weeks of aging provides
1440 Cell 147, December 23, 2011 ª2011 Elsevier Inc.
genetically encoded, de novo P element cognate piRNAs. If that were the case, all resulting progeny from aged dysgenic females should inherit at least one characteristic ‘‘seed’’ event of a novel insertion of a P element into an existing piRNA cluster in their genome. Contrary to this expectation, germline transposition events of P elements into piRNA clusters are not detected. Instead, the authors demonstrate that the P element cognate piRNAs arose from pre-existing P element insertions in paternally inherited piRNA clusters. Intriguingly, the primary piRNA transcript containing these P elements is also present in young dysgenic daughters, but processing of this primary piRNA transcript is impaired. In contrast, the piRNA primary transcript processing is efficient in nondysgenic daughters that inherited maternal trigger piRNAs and is mysteriously restored in aged dysgenic females. In contrast to P elements, the authors find that other resident transposons do jump into piRNA clusters approximately three times more frequently than expected by chance, supporting the previously proposed notion that piRNA clusters might actively attract mobile elements by virtue of their unique chromatin-binding proteins (Klattenhoff et al., 2009). These insertions into piRNA clusters are inherited and lead to improved silencing of the cognate transposons in later generations, likely by virtue of de novo trigger piRNAs. Thus, there is ample rewriting of the genomic piRNA clusters even in the short course of a single generation, which replenishes the epigenetically inherited
lead to the production of suitable piRNAs. This is consistent with the authors’ observations that in aged females, only a minor fraction of ovarioles are able to resume egg production. Even if P element cognate piRNAs are produced, the germline genome needs to recover from the DNA-damage checkpoint. The authors propose that the persistence of DNA damage may lead to adaptation of the Chk2 checkpoint, allowing Vasa accumulation, nuage assembly, and thereby transposon silencing to proceed. Intriguingly, other checkpoint functions decline in aging oocytes (Nagaoka et al., 2011). Compromised Chk2 function associated with aging may contribute to fertility restoration in dysgenic daughters. Thus, increased age might allow for better P element cognate piRNA production as well as an impairment of checkpoints, both of which might be necessary for the dramatic recovery of fertility (Figure 1). Figure 1. Restoration of piRNA-Mediated Transposon Control during Hybrid Dysgenesis in Drosophila
In nondysgenic females, maternally inherited piRNAs from P strain mothers lead to P element silencing, piRNA machinery assembly at nuage, piRNA precursor transcript processing, and no impairment in repression of resident transposons. In contrast, young dysgenic females inherit active P elements from father without maternal ‘‘trigger’’ piRNAs, leading to unregulated P element activity, DNA damage, and Chk2 signaling. Consequent breakdown of the piRNA processing center, nuage, results in resident transposon activation and new insertion events, genomic instability, and sterility. With age, an increasing fraction of ovarioles might experience either or both of the following two stochastic events: (1) new insertions that lead to de novo piRNA production from paternal P element-bearing piRNA clusters and (2) a Chk2 signaling override (or impairment) that results in nuage assembly despite persistent DNA breaks.
trigger piRNAs and reinforces the silencing of other germline transposons. Can this increased piRNA repertoire of unrelated elements also explain the de novo production of P element cognate piRNAs? The P element matching primary piRNA transcript is a long mosaic of segments from a variety of mobile elements including the P element. Even though the P element section of the primary transcript is not processed in young dysgenic daughters, the flanking elements are likely processed. Maternally inherited, cognate trigger piRNAs must promote this processing in nondysgenic daughters of ‘‘P’’ mothers. In aging dysgenic females, the piRNA cluster diversification (by virtue of increasing insertions of unrelated transposons) may increase the likelihood that the P element segment of the primary piRNA transcript from the paternal piRNA cluster is appropriately processed (Figure 1). This could happen by virtue of higher
quantity or greater diversity of piRNAs that facilitate processing of junctional sequences close to P element segments in the primary transcript. Further work will be necessary to investigate these alternatives and shed light on this poorly understood step of primary piRNA transcript processing (Siomi et al., 2011). Under either scenario, once P element cognate piRNAs are initially made, they can more robustly mount piRNA defense via the canonical ping-pong amplification cycle (Brennecke et al., 2007; Gunawardane et al., 2007) that appears to be fully restored in aged dysgenic females. Thus, the ‘‘bystander effect’’ that leads to the initial hypermobilization of unrelated mobile elements by P-M dysgenesis might also contribute to P element silencing. Under this scenario, the primary difference between the young and aged dysgenic females is the additional sampling of rare stochastic events that
ACKNOWLEDGMENTS We are supported by NIH grants F32GM097897 (M.T.L.) and R01GM074108 (H.S.M.) and HHMI. We thank Nitin Phadnis and Maulik Patel for discussion and comments. REFERENCES Brennecke, J., Aravin, A.A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., and Hannon, G.J. (2007). Cell 128, 1089–1103. Brennecke, J., Malone, C.D., Aravin, A.A., Sachidanandam, R., Stark, A., and Hannon, G.J. (2008). Science 322, 1387–1392. Bucheton, A. (1979). Genetics 93, 131–142. Daniels, S.B., Peterson, K.R., Strausbaugh, L.D., Kidwell, M.G., and Chovnick, A. (1990). Genetics 124, 339–355. Gunawardane, L.S., Saito, K., Nishida, K.M., Miyoshi, K., Kawamura, Y., Nagami, T., Siomi, H., and Siomi, M.C. (2007). Science 315, 1587–1590. Khurana, J.S., Wang, J., Xu, J., Koppetsch, B.S., Thomson, T.C., Nowosielska, A., Li, C., Zamore, P.D., Weng, Z., and Theurkauf, W.E. (2011). Cell 147, this issue, 1551–1563. Kidwell, M.G., Kidwell, J.F., and Sved, J.A. (1977). Genetics 86, 813–833. Klattenhoff, C., Xi, H., Li, C., Lee, S., Xu, J., Khurana, J.S., Zhang, F., Schultz, N., Koppetsch, B.S., Nowosielska, A., et al. (2009). Cell 138, 1137–1149. Nagaoka, S.I., Hodges, C.A., Albertini, D.F., and Hunt, P.A. (2011). Curr. Biol. 21, 651–657. Siomi, M.C., Sato, K., Pezic, D., and Aravin, A.A. (2011). Nat. Rev. Mol. Cell Biol. 12, 246–258.
Cell 147, December 23, 2011 ª2011 Elsevier Inc. 1441
Previews Learning to Protect Your Genome on the Fly Mia T. Levine1 and Harmit S. Malik1,2,* 1Basic
Sciences Division Hughes Medical Institute Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA *Correspondence: [email protected] DOI 10.1016/j.cell.2011.12.001 2Howard
Piwi-interacting RNAs (piRNAs) help defend host genomes against germline transposons. In this issue of Cell, Khurana et al. show how alterations in the piRNA-encoding loci within a single generation allow a naive fly genome to overcome the initially insurmountable challenge imposed by a newly encountered mobile element. Host genomes defend against invading transposable elements via both genetically inherited piRNA clusters that encode de novo piRNAs as well as epigenetically inherited, maternal ‘‘trigger’’ piRNAs (Brennecke et al., 2007). Complexed with Piwi proteins, piRNAs target active transposons in the germline and silence their expression. These small RNAs also serve as seeds for more piRNA production, amplifying the defense response. A report in this issue of Cell shows that the piRNA defense repertoire can be dramatically remodeled within a single generation (Khurana et al., 2011). The authors demonstrate that even in the absence of maternally inherited trigger piRNAs, a naive fly genome can overcome the challenge imposed by a newly encountered mobile element and pass on this immunity to its offspring. P element transposons invaded the D. melanogaster species approximately 100 years ago (Daniels et al., 1990). All wild strains collected after the 1930s harbor this transposon family (‘‘P’’ strains), whereas a handful of those collected prior to this time are devoid of P elements (‘‘M’’ strains). The remarkably rapid spread of P elements is largely due to the phenomenon of P-M hybrid dysgenesis. When ‘‘M’’ females are crossed to ‘‘P’’ males, the germline cells of resulting female progeny are ravaged by active transposons, rendering these flies sterile. In contrast, female offspring resulting from the reciprocal cross (from ‘‘P’’ mothers) are fertile (Kidwell et al., 1977). This ‘‘parent-of-origin’’ effect is largely attribut-
able to the maternal deposition of trigger piRNAs (Brennecke et al., 2008). Khurana et al. revisit a 30-year-old intriguing finding that dysgenic daughters of a P-M cross recover fertility as they age (Bucheton, 1979). They first establish that young dysgenic daughters not only are less fertile than genetically identical, agematched nondysgenic daughters but also harbor elevated P element mRNA and a dearth of P element matching piRNAs. P element activity results in DNA damage, which induces the Chk2 DNA-damage-signaling checkpoint. Chk phosphorylation of the nuage protein Vasa directly or indirectly results in a breakdown of the nuage structures necessary for transposon silencing. P element activity therefore results in a dramatic overproliferation of a variety of unrelated ‘‘resident transposons’’ in the genome (Figure 1). In 3-week-old P-M dysgenic females, virtually all measurements of fertility and the genome defense system supporting fertility are restored to wild-type levels. Although the number of egg-producing chambers in dysgenic daughters is still severely compromised, the eggs produced become viable embryos and grow into fertile adults. Khurana et al. demonstrate that recovered dysgenic fertility is associated with production of P element cognate piRNAs, whose source is mysterious because dysgenic flies do not inherit maternally deposited trigger piRNAs. The authors first consider whether P element transposition into piRNA clusters over the several weeks of aging provides
1440 Cell 147, December 23, 2011 ª2011 Elsevier Inc.
genetically encoded, de novo P element cognate piRNAs. If that were the case, all resulting progeny from aged dysgenic females should inherit at least one characteristic ‘‘seed’’ event of a novel insertion of a P element into an existing piRNA cluster in their genome. Contrary to this expectation, germline transposition events of P elements into piRNA clusters are not detected. Instead, the authors demonstrate that the P element cognate piRNAs arose from pre-existing P element insertions in paternally inherited piRNA clusters. Intriguingly, the primary piRNA transcript containing these P elements is also present in young dysgenic daughters, but processing of this primary piRNA transcript is impaired. In contrast, the piRNA primary transcript processing is efficient in nondysgenic daughters that inherited maternal trigger piRNAs and is mysteriously restored in aged dysgenic females. In contrast to P elements, the authors find that other resident transposons do jump into piRNA clusters approximately three times more frequently than expected by chance, supporting the previously proposed notion that piRNA clusters might actively attract mobile elements by virtue of their unique chromatin-binding proteins (Klattenhoff et al., 2009). These insertions into piRNA clusters are inherited and lead to improved silencing of the cognate transposons in later generations, likely by virtue of de novo trigger piRNAs. Thus, there is ample rewriting of the genomic piRNA clusters even in the short course of a single generation, which replenishes the epigenetically inherited
lead to the production of suitable piRNAs. This is consistent with the authors’ observations that in aged females, only a minor fraction of ovarioles are able to resume egg production. Even if P element cognate piRNAs are produced, the germline genome needs to recover from the DNA-damage checkpoint. The authors propose that the persistence of DNA damage may lead to adaptation of the Chk2 checkpoint, allowing Vasa accumulation, nuage assembly, and thereby transposon silencing to proceed. Intriguingly, other checkpoint functions decline in aging oocytes (Nagaoka et al., 2011). Compromised Chk2 function associated with aging may contribute to fertility restoration in dysgenic daughters. Thus, increased age might allow for better P element cognate piRNA production as well as an impairment of checkpoints, both of which might be necessary for the dramatic recovery of fertility (Figure 1). Figure 1. Restoration of piRNA-Mediated Transposon Control during Hybrid Dysgenesis in Drosophila
In nondysgenic females, maternally inherited piRNAs from P strain mothers lead to P element silencing, piRNA machinery assembly at nuage, piRNA precursor transcript processing, and no impairment in repression of resident transposons. In contrast, young dysgenic females inherit active P elements from father without maternal ‘‘trigger’’ piRNAs, leading to unregulated P element activity, DNA damage, and Chk2 signaling. Consequent breakdown of the piRNA processing center, nuage, results in resident transposon activation and new insertion events, genomic instability, and sterility. With age, an increasing fraction of ovarioles might experience either or both of the following two stochastic events: (1) new insertions that lead to de novo piRNA production from paternal P element-bearing piRNA clusters and (2) a Chk2 signaling override (or impairment) that results in nuage assembly despite persistent DNA breaks.
trigger piRNAs and reinforces the silencing of other germline transposons. Can this increased piRNA repertoire of unrelated elements also explain the de novo production of P element cognate piRNAs? The P element matching primary piRNA transcript is a long mosaic of segments from a variety of mobile elements including the P element. Even though the P element section of the primary transcript is not processed in young dysgenic daughters, the flanking elements are likely processed. Maternally inherited, cognate trigger piRNAs must promote this processing in nondysgenic daughters of ‘‘P’’ mothers. In aging dysgenic females, the piRNA cluster diversification (by virtue of increasing insertions of unrelated transposons) may increase the likelihood that the P element segment of the primary piRNA transcript from the paternal piRNA cluster is appropriately processed (Figure 1). This could happen by virtue of higher
quantity or greater diversity of piRNAs that facilitate processing of junctional sequences close to P element segments in the primary transcript. Further work will be necessary to investigate these alternatives and shed light on this poorly understood step of primary piRNA transcript processing (Siomi et al., 2011). Under either scenario, once P element cognate piRNAs are initially made, they can more robustly mount piRNA defense via the canonical ping-pong amplification cycle (Brennecke et al., 2007; Gunawardane et al., 2007) that appears to be fully restored in aged dysgenic females. Thus, the ‘‘bystander effect’’ that leads to the initial hypermobilization of unrelated mobile elements by P-M dysgenesis might also contribute to P element silencing. Under this scenario, the primary difference between the young and aged dysgenic females is the additional sampling of rare stochastic events that
ACKNOWLEDGMENTS We are supported by NIH grants F32GM097897 (M.T.L.) and R01GM074108 (H.S.M.) and HHMI. We thank Nitin Phadnis and Maulik Patel for discussion and comments. REFERENCES Brennecke, J., Aravin, A.A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., and Hannon, G.J. (2007). Cell 128, 1089–1103. Brennecke, J., Malone, C.D., Aravin, A.A., Sachidanandam, R., Stark, A., and Hannon, G.J. (2008). Science 322, 1387–1392. Bucheton, A. (1979). Genetics 93, 131–142. Daniels, S.B., Peterson, K.R., Strausbaugh, L.D., Kidwell, M.G., and Chovnick, A. (1990). Genetics 124, 339–355. Gunawardane, L.S., Saito, K., Nishida, K.M., Miyoshi, K., Kawamura, Y., Nagami, T., Siomi, H., and Siomi, M.C. (2007). Science 315, 1587–1590. Khurana, J.S., Wang, J., Xu, J., Koppetsch, B.S., Thomson, T.C., Nowosielska, A., Li, C., Zamore, P.D., Weng, Z., and Theurkauf, W.E. (2011). Cell 147, this issue, 1551–1563. Kidwell, M.G., Kidwell, J.F., and Sved, J.A. (1977). Genetics 86, 813–833. Klattenhoff, C., Xi, H., Li, C., Lee, S., Xu, J., Khurana, J.S., Zhang, F., Schultz, N., Koppetsch, B.S., Nowosielska, A., et al. (2009). Cell 138, 1137–1149. Nagaoka, S.I., Hodges, C.A., Albertini, D.F., and Hunt, P.A. (2011). Curr. Biol. 21, 651–657. Siomi, M.C., Sato, K., Pezic, D., and Aravin, A.A. (2011). Nat. Rev. Mol. Cell Biol. 12, 246–258.
Cell 147, December 23, 2011 ª2011 Elsevier Inc. 1441