The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation
Post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks, but their roles in stem cell pluripotency remain poorly understood. Here, we use freshwater planarians as a model system to investigate this and uncover a role for CCR4-NOT mediated deadenylation of mRNAs in stem cell differentiation. Planarian adult stem cells, the so-called neoblasts, drive the almost unlimited regenerative capabilities of planarians and allow their ongoing homeostatic tissue turnover. While many genes have been demonstrated to be required for these processes, currently almost no mechanistic insight is available into their regulation. We show that knockdown of planarian Not1, the CCR4-NOT deadenylating complex scaffolding subunit, abrogates regeneration and normal homeostasis. This abrogation is primarily due to severe impairment of their differentiation potential. We describe a stem cell specific increase in the mRNA levels of key neoblast genes after Smed-not1 knock down, consistent with a role of the CCR4-NOT complex in degradation of neoblast mRNAs upon the onset of differentiation. We also observe a stem cell specific increase in the frequency of longer poly(A) tails in these same mRNAs, showing that stem cells after Smed-not1 knock down fail to differentiate as they accumulate populations of transcripts with longer poly(A) tails. As other transcripts are unaffected our data hint at a targeted regulation of these key stem cell mRNAs by post-transcriptional regulators such as RNA-binding proteins or microRNAs. Together, our results show that the CCR4-NOT complex is crucial for stem cell differentiation and controls stem cell-specific degradation of mRNAs, thus providing clear mechanistic insight into this aspect of neoblast biology.
Vyšlo v časopise:
The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation. PLoS Genet 9(12): e32767. doi:10.1371/journal.pgen.1004003
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004003
Souhrn
Post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks, but their roles in stem cell pluripotency remain poorly understood. Here, we use freshwater planarians as a model system to investigate this and uncover a role for CCR4-NOT mediated deadenylation of mRNAs in stem cell differentiation. Planarian adult stem cells, the so-called neoblasts, drive the almost unlimited regenerative capabilities of planarians and allow their ongoing homeostatic tissue turnover. While many genes have been demonstrated to be required for these processes, currently almost no mechanistic insight is available into their regulation. We show that knockdown of planarian Not1, the CCR4-NOT deadenylating complex scaffolding subunit, abrogates regeneration and normal homeostasis. This abrogation is primarily due to severe impairment of their differentiation potential. We describe a stem cell specific increase in the mRNA levels of key neoblast genes after Smed-not1 knock down, consistent with a role of the CCR4-NOT complex in degradation of neoblast mRNAs upon the onset of differentiation. We also observe a stem cell specific increase in the frequency of longer poly(A) tails in these same mRNAs, showing that stem cells after Smed-not1 knock down fail to differentiate as they accumulate populations of transcripts with longer poly(A) tails. As other transcripts are unaffected our data hint at a targeted regulation of these key stem cell mRNAs by post-transcriptional regulators such as RNA-binding proteins or microRNAs. Together, our results show that the CCR4-NOT complex is crucial for stem cell differentiation and controls stem cell-specific degradation of mRNAs, thus providing clear mechanistic insight into this aspect of neoblast biology.
Zdroje
1. SeydouxG, BraunRE (2006) Pathway to totipotency: lessons from germ cells. Cell 127: 891–904.
2. GarneauNL, WiluszJ, WiluszCJ (2007) The highways and byways of mRNA decay. Nat Rev Mol Cell Biol 8: 113–126.
3. BalagopalV, FluchL, NissanT (2012) Ways and means of eukaryotic mRNA decay. Biochim Biophys Acta 1819: 593–603.
4. WuX, BrewerG (2012) The regulation of mRNA stability in mammalian cells: 2.0. Gene 500: 10–21.
5. WangY, LiuCL, StoreyJD, TibshiraniRJ, HerschlagD, et al. (2002) Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A 99: 5860–5865.
6. MunchelSE, ShultzabergerRK, TakizawaN, WeisK (2011) Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay. Mol Biol Cell 22: 2787–2795.
7. GlisovicT, BachorikJL, YongJ, DreyfussG (2008) RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 582: 1977–1986.
8. WiederholdK, PassmoreLA (2010) Cytoplasmic deadenylation: regulation of mRNA fate. Biochem Soc Trans 38: 1531–1536.
9. ZhangX, VirtanenA, KleimanFE (2010) To polyadenylate or to deadenylate: that is the question. Cell Cycle 9: 4437–4449.
10. WeillL, BellocE, BavaFA, MendezR (2012) Translational control by changes in poly(A) tail length: recycling mRNAs. Nat Struct Mol Biol 19: 577–585.
11. CollartMA, PanasenkoOO (2011) The Ccr4-Not complex. Gene
12. MillerJE, ReeseJC (2012) Ccr4-Not complex: the control freak of eukaryotic cells. Crit Rev Biochem Mol Biol 47: 315–333.
13. WahleE, WinklerGS (2013) RNA decay machines: deadenylation by the Ccr4-not and Pan2-Pan3 complexes. Biochim Biophys Acta 1829: 561–570.
14. KerrSC, AzzouzN, FuchsSM, CollartMA, StrahlBD, et al. (2011) The Ccr4-Not complex interacts with the mRNA export machinery. PLoS One 6: e18302.
15. PanasenkoO, LandrieuxE, FeuermannM, FinkaA, PaquetN, et al. (2006) The yeast Ccr4-Not complex controls ubiquitination of the nascent-associated polypeptide (NAC-EGD) complex. J Biol Chem 281: 31389–31398.
16. KrukJA, DuttaA, FuJ, GilmourDS, ReeseJC (2011) The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes Dev 25: 581–593.
17. ReeseJC (2013) The control of elongation by the yeast Ccr4-not complex. Biochim Biophys Acta 1829: 127–133.
18. CollartMA, PanasenkoOO, NikolaevSI (2013) The Not3/5 subunit of the Ccr4-Not complex: a central regulator of gene expression that integrates signals between the cytoplasm and the nucleus in eukaryotic cells. Cell Signal 25: 743–751.
19. MailletL, TuC, HongYK, ShusterEO, CollartMA (2000) The essential function of Not1 lies within the Ccr4-Not complex. J Mol Biol 303: 131–143.
20. AlbertTK, LemaireM, van BerkumNL, GentzR, CollartMA, et al. (2000) Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits. Nucleic Acids Res 28: 809–817.
21. TemmeC, ZaessingerS, MeyerS, SimoneligM, WahleE (2004) A complex containing the CCR4 and CAF1 proteins is involved in mRNA deadenylation in Drosophila. EMBO J 23: 2862–2871.
22. NouschM, TechritzN, HampelD, MilloniggS, EckmannCR (2013) The Ccr4-Not deadenylase complex constitutes the major poly(A) removal activity in C. elegans. J Cell Sci 126 (Pt 18) 4274–85.
23. LauNC, KolkmanA, van SchaikFM, MulderKW, PijnappelWW, et al. (2009) Human Ccr4-Not complexes contain variable deadenylase subunits. Biochem J 422: 443–453.
24. AslamA, MittalS, KochF, AndrauJC, WinklerGS (2009) The Ccr4-NOT deadenylase subunits CNOT7 and CNOT8 have overlapping roles and modulate cell proliferation. Mol Biol Cell 20: 3840–3850.
25. MittalS, AslamA, DoidgeR, MedicaR, WinklerGS (2011) The Ccr4a (CNOT6) and Ccr4b (CNOT6L) deadenylase subunits of the human Ccr4-Not complex contribute to the prevention of cell death and senescence. Mol Biol Cell 22: 748–758.
26. KadyrovaLY, HabaraY, LeeTH, WhartonRP (2007) Translational control of maternal Cyclin B mRNA by Nanos in the Drosophila germline. Development 134: 1519–1527.
27. SuzukiA, IgarashiK, AisakiK, KannoJ, SagaY (2010) NANOS2 interacts with the CCR4-NOT deadenylation complex and leads to suppression of specific RNAs. Proc Natl Acad Sci U S A 107: 3594–3599.
28. Van EttenJ, SchagatTL, HritJ, WeidmannCA, BrumbaughJ, et al. (2012) Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J Biol Chem 287: 36370–36383.
29. GoldstrohmAC, WickensM (2008) Multifunctional deadenylase complexes diversify mRNA control. Nat Rev Mol Cell Biol 9: 337–344.
30. ZaessingerS, BusseauI, SimoneligM (2006) Oskar allows nanos mRNA translation in Drosophila embryos by preventing its deadenylation by Smaug/CCR4. Development 133: 4573–4583.
31. ChicoineJ, BenoitP, GamberiC, PaliourasM, SimoneligM, et al. (2007) Bicaudal-C recruits CCR4-NOT deadenylase to target mRNAs and regulates oogenesis, cytoskeletal organization, and its own expression. Dev Cell 13: 691–704.
32. Behm-AnsmantI, RehwinkelJ, DoerksT, StarkA, BorkP, et al. (2006) mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev 20: 1885–1898.
33. EulalioA, HuntzingerE, NishiharaT, RehwinkelJ, FauserM, et al. (2009) Deadenylation is a widespread effect of miRNA regulation. RNA 15: 21–32.
34. FabianMR, MathonnetG, SundermeierT, MathysH, ZipprichJT, et al. (2009) Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell 35: 868–880.
35. RougetC, PapinC, BoureuxA, MeunierAC, FrancoB, et al. (2010) Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467: 1128–1132.
36. FabianMR, CieplakMK, FrankF, MoritaM, GreenJ, et al. (2011) miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4-NOT. Nat Struct Mol Biol 18: 1211–1217.
37. ChekulaevaM, MathysH, ZipprichJT, AttigJ, ColicM, et al. (2011) miRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifs. Nat Struct Mol Biol 18: 1218–1226.
38. ZhengX, DumitruR, LackfordBL, FreudenbergJM, SinghAP, et al. (2012) Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation. Stem Cells 30: 910–922.
39. AboobakerAA (2011) Planarian stem cells: a simple paradigm for regeneration. Trends Cell Biol 21: 304–311.
40. GentileL, CebriaF, BartschererK (2011) The planarian flatworm: an in vivo model for stem cell biology and nervous system regeneration. Dis Model Mech 4: 12–19.
41. RinkJC (2013) Stem cell systems and regeneration in planaria. Dev Genes Evol 223: 67–84.
42. WagnerDE, WangIE, ReddienPW (2011) Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science 332: 811–816.
43. GuoT, PetersAH, NewmarkPA (2006) A Bruno-like gene is required for stem cell maintenance in planarians. Dev Cell 11: 159–169.
44. ReddienPW, OviedoNJ, JenningsJR, JenkinJC, Sanchez AlvaradoA (2005) SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells. Science 310: 1327–1330.
45. RouhanaL, ShibataN, NishimuraO, AgataK (2010) Different requirements for conserved post-transcriptional regulators in planarian regeneration and stem cell maintenance. Dev Biol 341: 429–443.
46. SalvettiA, RossiL, LenaA, BatistoniR, DeriP, et al. (2005) DjPum, a homologue of Drosophila Pumilio, is essential to planarian stem cell maintenance. Development 132: 1863–1874.
47. ShibataN, RouhanaL, AgataK (2010) Cellular and molecular dissection of pluripotent adult somatic stem cells in planarians. Dev Growth Differ 52: 27–41.
48. SolanaJ, LaskoP, RomeroR (2009) Spoltud-1 is a chromatoid body component required for planarian long-term stem cell self-renewal. Dev Biol 328: 410–421.
49. RouhanaL, VieiraAP, Roberts-GalbraithRH, NewmarkPA (2012) PRMT5 and the role of symmetrical dimethylarginine in chromatoid bodies of planarian stem cells. Development 139: 1083–1094.
50. SolanaJ, KaoD, MihaylovaY, Jaber-HijaziF, MallaS, et al. (2012) Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biol 13: R19.
51. OnalP, GrunD, AdamidiC, RybakA, SolanaJ, et al. (2012) Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells. EMBO J 31: 2755–2769.
52. LabbeRM, IrimiaM, CurrieKW, LinA, ZhuSJ, et al. (2012) A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells 30: 1734–1745.
53. BlytheMJ, KaoD, MallaS, RowsellJ, WilsonR, et al. (2010) A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PLoS One 5: e15617.
54. WagnerDE, HoJJ, ReddienPW (2012) Genetic regulators of a pluripotent adult stem cell system in planarians identified by RNAi and clonal analysis. Cell Stem Cell 10: 299–311.
55. SolanaJ (2013) Closing the circle of germline and stem cells: the Primordial Stem Cell hypothesis. Evodevo 4: 2.
56. AboobakerAA, KaoD (2012) A lack of commitment for over 500 million years: conserved animal stem cell pluripotency. EMBO J 31: 2747–2749.
57. Jaber-HijaziF, LoPJ, MihaylovaY, FosterJM, BennerJS, et al. (2013) Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation. Developmental biology 384: 141–153.
58. AbrilJF, CebriaF, Rodriguez-EstebanG, HornT, FraguasS, et al. (2010) Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea. BMC Genomics 11: 731.
59. AdamidiC, WangY, GruenD, MastrobuoniG, YouX, et al. (2011) De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res 21: 1193–1200.
60. RobbSM, RossE, Sanchez AlvaradoA (2008) SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res 36: D599–606.
61. MochizukiK, Nishimiya-FujisawaC, FujisawaT (2001) Universal occurrence of the vasa-related genes among metazoans and their germline expression in Hydra. Dev Genes Evol 211: 299–308.
62. OriiH, SakuraiT, WatanabeK (2005) Distribution of the stem cells (neoblasts) in the planarian Dugesia japonica. Dev Genes Evol 215: 143–157.
63. InoueT, KumamotoH, OkamotoK, UmesonoY, SakaiM, et al. (2004) Morphological and functional recovery of the planarian photosensing system during head regeneration. Zoolog Sci 21: 275–283.
64. ReddienPW, BermangeAL, MurfittKJ, JenningsJR, Sanchez AlvaradoA (2005) Identification of genes needed for regeneration, stem cell function, and tissue homeostasis by systematic gene perturbation in planaria. Dev Cell 8: 635–649.
65. ScimoneML, MeiselJ, ReddienPW (2010) The Mi-2-like Smed-CHD4 gene is required for stem cell differentiation in the planarian Schmidtea mediterranea. Development 137: 1231–1241.
66. EisenhofferGT, KangH, Sanchez AlvaradoA (2008) Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell 3: 327–339.
67. PearsonBJ, Sanchez AlvaradoA (2010) A planarian p53 homolog regulates proliferation and self-renewal in adult stem cell lineages. Development 137: 213–221.
68. GamberiC, GottliebE (2002) Internally controlled poly(A) tail assay to study gene regulation. Biotechniques 33: 476–480, 476, 478, 480.
69. GamberiC, PetersonDS, HeL, GottliebE (2002) An anterior function for the Drosophila posterior determinant Pumilio. Development 129: 2699–2710.
70. SallesFJ, LieberfarbME, WredenC, GergenJP, StricklandS (1994) Coordinate initiation of Drosophila development by regulated polyadenylation of maternal messenger RNAs. Science 266: 1996–1999.
71. SallesFJ, StricklandS (1995) Rapid and sensitive analysis of mRNA polyadenylation states by PCR. PCR Methods Appl 4: 317–321.
72. HayashiT, AsamiM, HiguchiS, ShibataN, AgataK (2006) Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting. Dev Growth Differ 48: 371–380.
73. RouhanaL, WeissJA, ForsthoefelDJ, LeeH, KingRS, et al. (2013) RNA interference by feeding in vitro-synthesized double-stranded RNA to planarians: methodology and dynamics. Dev Dyn 242: 718–730.
74. AzzouzN, PanasenkoOO, DeluenC, HsiehJ, TheilerG, et al. (2009) Specific roles for the Ccr4-Not complex subunits in expression of the genome. RNA 15: 377–383.
75. ReschAM, PalakodetiD, LuYC, HorowitzM, GraveleyBR (2012) Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One 7: e34447.
76. GoldstrohmAC, SeayDJ, HookBA, WickensM (2007) PUF protein-mediated deadenylation is catalyzed by Ccr4p. J Biol Chem 282: 109–114.
77. MarsonA, LevineSS, ColeMF, FramptonGM, BrambrinkT, et al. (2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134: 521–533.
78. FriedlanderMR, AdamidiC, HanT, LebedevaS, IsenbargerTA, et al. (2009) High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci U S A 106: 11546–11551.
79. Gonzalez-EstevezC, ArseniV, ThambyrajahRS, FelixDA, AboobakerAA (2009) Diverse miRNA spatial expression patterns suggest important roles in homeostasis and regeneration in planarians. Int J Dev Biol 53: 493–505.
80. PalakodetiD, SmielewskaM, LuYC, YeoGW, GraveleyBR (2008) The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA 14: 1174–1186.
81. LuYC, SmielewskaM, PalakodetiD, LovciMT, AignerS, et al. (2009) Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea. RNA 15: 1483–1491.
82. FelixDA, AboobakerAA (2010) The TALE class homeobox gene Smed-prep defines the anterior compartment for head regeneration. PLoS Genet 6: e1000915.
83. CebriaF, NewmarkPA (2005) Planarian homologs of netrin and netrin receptor are required for proper regeneration of the central nervous system and the maintenance of nervous system architecture. Development 132: 3691–3703.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2013 Číslo 12
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- The NuRD Chromatin-Remodeling Enzyme CHD4 Promotes Embryonic Vascular Integrity by Transcriptionally Regulating Extracellular Matrix Proteolysis
- Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
- Quantifying Missing Heritability at Known GWAS Loci
- Smc5/6-Mms21 Prevents and Eliminates Inappropriate Recombination Intermediates in Meiosis