Pattern formation in developing tissues is driven by the interaction of extrinsic signals with intrinsic transcriptional networks that together establish spatially and temporally restricted profiles of gene expression. How this process is orchestrated at the molecular level by genomic cis-regulatory modules is one of the central questions in developmental biology. Here we have addressed this by analysing the regulation of Pax3 expression in the context of the developing spinal cord. Pax3 is induced early during neural development in progenitors of the dorsal spinal cord and is maintained as pattern is subsequently elaborated, resulting in the segregation of the tissue into dorsal and ventral subdivisions. We used a combination of comparative genomics and transgenic assays to define and dissect several functional cis-regulatory modules associated with the Pax3 locus. We provide evidence that the coordinated activity of two modules establishes and refines Pax3 expression during neural tube development. Mutational analyses of the initiating element revealed that in addition to Wnt signaling, Nkx family homeodomain repressors restrict Pax3 transcription to the presumptive dorsal neural tube. Subsequently, a second module mediates direct positive autoregulation and feedback to maintain Pax3 expression. Together, these data indicate a mechanism by which transient external signals are converted into a sustained expression domain by the activities of distinct regulatory elements. This transcriptional logic differs from the cross-repression that is responsible for the spatiotemporal patterns of gene expression in the ventral neural tube, suggesting that a variety of circuits are deployed within the neural tube regulatory network to establish and elaborate pattern formation.
Vyšlo v časopise: Distinct Regulatory Mechanisms Act to Establish and Maintain Pax3 Expression in the Developing Neural Tube. PLoS Genet 9(10): e32767. doi:10.1371/journal.pgen.1003811 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003811
1. DavidsonEH (2010) Emerging properties of animal gene regulatory networks. Nature 468 : 911–920.
2. LevineM (2010) Transcriptional enhancers in animal development and evolution. Curr Biol 20: R754–763.
3. AlonU (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8 : 450–461.
4. JessellTM (2000) Neuronal specification in the spinal cord: inductive signals and transcriptional codes. Nat Rev Genet 1 : 20–29.
5. BalaskasN, RibeiroA, PanovskaJ, DessaudE, SasaiN, et al. (2012) Gene regulatory logic for reading the Sonic Hedgehog signaling gradient in the vertebrate neural tube. Cell 148 : 273–284.
6. BriscoeJ, PieraniA, JessellTM, EricsonJ (2000) A homeodomain protein code specifies progenitor cell identity and neuronal fate in the ventral neural tube. Cell 101 : 435–445.
7. ChamberlainCE, JeongJ, GuoC, AllenBL, McMahonAP (2008) Notochord-derived Shh concentrates in close association with the apically positioned basal body in neural target cells and forms a dynamic gradient during neural patterning. Development 135 : 1097–1106.
8. EricsonJ, MortonS, KawakamiA, RoelinkH, JessellTM (1996) Two critical periods of Sonic Hedgehog signaling required for the specification of motor neuron identity. Cell 87 : 661–673.
9. OosterveenT, KurdijaS, AlekseenkoZ, UhdeCW, BergslandM, et al. (2012) Mechanistic differences in the transcriptional interpretation of local and long-range Shh morphogen signaling. Dev Cell 23 : 1006–1019.
10. PetersonKA, NishiY, MaW, VedenkoA, ShokriL, et al. (2012) Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev 26 : 2802–2816.
11. EricsonJ, RashbassP, SchedlA, Brenner-MortonS, KawakamiA, et al. (1997) Pax6 controls progenitor cell identity and neuronal fate in response to graded Shh signaling. Cell 90 : 169–180.
12. NovitchBG, ChenAI, JessellTM (2001) Coordinate regulation of motor neuron subtype identity and pan-neuronal properties by the bHLH repressor Olig2. Neuron 31 : 773–789.
13. SanderM, PaydarS, EricsonJ, BriscoeJ, BerberE, et al. (2000) Ventral neural patterning by Nkx homeobox genes: Nkx6.1 controls somatic motor neuron and ventral interneuron fates. Genes Dev 14 : 2134–2139.
14. VallstedtA, MuhrJ, PattynA, PieraniA, MendelsohnM, et al. (2001) Different levels of repressor activity assign redundant and specific roles to Nkx6 genes in motor neuron and interneuron specification. Neuron 31 : 743–755.
15. HelmsAW, JohnsonJE (2003) Specification of dorsal spinal cord interneurons. Curr Opin Neurobiol 13 : 42–49.
16. GouldingMD, ChalepakisG, DeutschU, ErseliusJR, GrussP (1991) Pax-3, a novel murine DNA binding protein expressed during early neurogenesis. EMBO J 10 : 1135–1147.
17. JostesB, WaltherC, GrussP (1990) The murine paired box gene, Pax7, is expressed specifically during the development of the nervous and muscular system. Mech Dev 33 : 27–37.
18. BangAG, PapalopuluN, GouldingMD, KintnerC (1999) Expression of Pax-3 in the lateral neural plate is dependent on a Wnt-mediated signal from posterior nonaxial mesoderm. Dev Biol 212 : 366–380.
19. LiemKFJr, TremmlG, RoelinkH, JessellTM (1995) Dorsal differentiation of neural plate cells induced by BMP-mediated signals from epidermal ectoderm. Cell 82 : 969–979.
20. GouldingMD, LumsdenA, GrussP (1993) Signals from the notochord and floor plate regulate the region-specific expression of two Pax genes in the developing spinal cord. Development 117 : 1001–1016.
21. LitingtungY, ChiangC (2000) Specification of ventral neuron types is mediated by an antagonistic interaction between Shh and Gli3. Nat Neurosci 3 : 979–985.
22. DegenhardtKR, MilewskiRC, PadmanabhanA, MillerM, SinghMK, et al. (2010) Distinct enhancers at the Pax3 locus can function redundantly to regulate neural tube and neural crest expressions. Dev Biol 339 : 519–527.
23. MilewskiRC, ChiNC, LiJ, BrownC, LuMM, et al. (2004) Identification of minimal enhancer elements sufficient for Pax3 expression in neural crest and implication of Tead2 as a regulator of Pax3. Development 131 : 829–837.
24. NatoliTA, EllsworthMK, WuC, GrossKW, PruittSC (1997) Positive and negative DNA sequence elements are required to establish the pattern of Pax3 expression. Development 124 : 617–626.
25. PruittSC, BussmanA, MaslovAY, NatoliTA, HeinamanR (2004) Hox/Pbx and Brn binding sites mediate Pax3 expression in vitro and in vivo. Gene Expr Patterns 4 : 671–685.
26. GarnettAT, SquareTA, MedeirosDM (2012) BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border. Development 139 : 4220–4231.
27. EnglekaKA, GitlerAD, ZhangM, ZhouDD, HighFA, et al. (2005) Insertion of Cre into the Pax3 locus creates a new allele of Splotch and identifies unexpected Pax3 derivatives. Dev Biol 280 : 396–406.
28. ErskineL, PatelK, ClarkeJD (1998) Progenitor dispersal and the origin of early neuronal phenotypes in the chick embryo spinal cord. Dev Biol 199 : 26–41.
29. LeberSM, BreedloveSM, SanesJR (1990) Lineage, arrangement, and death of clonally related motoneurons in chick spinal cord. J Neurosci 10 : 2451–2462.
30. LeberSM, SanesJR (1995) Migratory paths of neurons and glia in the embryonic chick spinal cord. J Neurosci 15 : 1236–1248.
31. Moran-RivardL, KagawaT, SaueressigH, GrossMK, BurrillJ, et al. (2001) Evx1 is a postmitotic determinant of v0 interneuron identity in the spinal cord. Neuron 29 : 385–399.
32. SeoHC, SaetreBO, HavikB, EllingsenS, FjoseA (1998) The zebrafish Pax3 and Pax7 homologues are highly conserved, encode multiple isoforms and show dynamic segment-like expression in the developing brain. Mech Dev 70 : 49–63.
33. ViselA, BlowMJ, LiZ, ZhangT, AkiyamaJA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457 : 854–858.
34. 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.
35. MoroE, Ozhan-KizilG, MongeraA, BeisD, WierzbickiC, et al. (2012) In vivo Wnt signaling tracing through a transgenic biosensor fish reveals novel activity domains. Dev Biol 366 : 327–340.
36. DorskyRI, SheldahlLC, MoonRT (2002) A transgenic Lef1/beta-catenin-dependent reporter is expressed in spatially restricted domains throughout zebrafish development. Dev Biol 241 : 229–237.
37. CurrierN, CheaK, HlavacovaM, SussmanDJ, SeldinDC, et al. (2010) Dynamic expression of a LEF-EGFP Wnt reporter in mouse development and cancer. Genesis 48 : 183–194.
38. MarettoS, CordenonsiM, DupontS, BraghettaP, BroccoliV, et al. (2003) Mapping Wnt/beta-catenin signaling during mouse development and in colorectal tumors. Proc Natl Acad Sci U S A 100 : 3299–3304.
39. MohamedOA, ClarkeHJ, DufortD (2004) Beta-catenin signaling marks the prospective site of primitive streak formation in the mouse embryo. Dev Dyn 231 : 416–424.
40. MuhrJ, AnderssonE, PerssonM, JessellTM, EricsonJ (2001) Groucho-mediated transcriptional repression establishes progenitor cell pattern and neuronal fate in the ventral neural tube. Cell 104 : 861–873.
41. BergslandM, RamskoldD, ZaouterC, KlumS, SandbergR, et al. (2011) Sequentially acting Sox transcription factors in neural lineage development. Genes Dev 25 : 2453–2464.
42. FrostV, GrocottT, EcclesMR, ChantryA (2008) Self-regulated Pax gene expression and modulation by the TGFbeta superfamily. Crit Rev Biochem Mol Biol 43 : 371–391.
43. EpsteinJ, CaiJ, GlaserT, JepealL, MaasR (1994) Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes. J Biol Chem 269 : 8355–8361.
44. AdamsB, DorflerP, AguzziA, KozmikZ, UrbanekP, et al. (1992) Pax-5 encodes the transcription factor BSAP and is expressed in B lymphocytes, the developing CNS, and adult testis. Genes Dev 6 : 1589–1607.
45. TreismanJ, HarrisE, DesplanC (1991) The paired box encodes a second DNA-binding domain in the paired homeo domain protein. Genes Dev 5 : 594–604.
46. JunS, DesplanC (1996) Cooperative interactions between paired domain and homeodomain. Development 122 : 2639–2650.
47. XuW, RouldMA, JunS, DesplanC, PaboCO (1995) Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. Cell 80 : 639–650.
48. XuHE, RouldMA, XuW, EpsteinJA, MaasRL, et al. (1999) Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. Genes Dev 13 : 1263–1275.
49. CzernyT, SchaffnerG, BusslingerM (1993) DNA sequence recognition by Pax proteins: bipartite structure of the paired domain and its binding site. Genes Dev 7 : 2048–2061.
50. VoganKJ, GrosP (1997) The C-terminal subdomain makes an important contribution to the DNA binding activity of the Pax-3 paired domain. J Biol Chem 272 : 28289–28295.
51. RelaixF, MontarrasD, ZaffranS, Gayraud-MorelB, RocancourtD, et al. (2006) Pax3 and Pax7 have distinct and overlapping functions in adult muscle progenitor cells. J Cell Biol 172 : 91–102.
52. SegerC, HargraveM, WangX, ChaiRJ, ElworthyS, et al. (2011) Analysis of Pax7 expressing myogenic cells in zebrafish muscle development, injury, and models of disease. Dev Dyn 240 : 2440–2451.
53. BergerMF, BadisG, GehrkeAR, TalukderS, PhilippakisAA, et al. (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133 : 1266–1276.
54. JolmaA, YanJ, WhitingtonT, ToivonenJ, NittaKR, et al. (2013) DNA-binding specificities of human transcription factors. Cell 152 : 327–339.
55. HutchinsonSA, CheesmanSE, HaleLA, BooneJQ, EisenJS (2007) Nkx6 proteins specify one zebrafish primary motoneuron subtype by regulating late islet1 expression. Development 134 : 1671–1677.
56. MoriyamaA, KiiI, SunaboriT, KuriharaS, TakayamaI, et al. (2007) GFP transgenic mice reveal active canonical Wnt signal in neonatal brain and in adult liver and spleen. Genesis 45 : 90–100.
57. FrankelN, DavisGK, VargasD, WangS, PayreF, et al. (2010) Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature 466 : 490–493.
58. HongJW, HendrixDA, LevineMS (2008) Shadow enhancers as a source of evolutionary novelty. Science 321 : 1314.
59. PerryMW, BoettigerAN, BothmaJP, LevineM (2010) Shadow enhancers foster robustness of Drosophila gastrulation. Curr Biol 20 : 1562–1567.
60. PerryMW, BoettigerAN, LevineM (2011) Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A 108 : 13570–13575.
61. OvcharenkoI, LootsGG, GiardineBM, HouM, MaJ, et al. (2005) Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res 15 : 184–194.
62. LarkinMA, BlackshieldsG, BrownNP, ChennaR, McGettiganPA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23 : 2947–2948.
63. BaileyTL, BodenM, BuskeFA, FrithM, GrantCE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208.
64. GuptaS, StamatoyannopoulosJA, BaileyTL, NobleWS (2007) Quantifying similarity between motifs. Genome Biol 8: R24.
65. HamburgerV, HamiltonHL (1992) A series of normal stages in the development of the chick embryo. 1951. Dev Dyn 195 : 231–272.
66. RelaixF, PolimeniM, RocancourtD, PonzettoC, SchaferBW, et al. (2003) The transcriptional activator PAX3-FKHR rescues the defects of Pax3 mutant mice but induces a myogenic gain-of-function phenotype with ligand-independent activation of Met signaling in vivo. Genes Dev 17 : 2950–2965.
67. FriedrichG, SorianoP (1991) Promoter traps in embryonic stem cells: a genetic screen to identify and mutate developmental genes in mice. Genes Dev 5 : 1513–1523.
68. ThisseC, ThisseB (2008) High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat Protoc 3 : 59–69.
69. DavisGK, D'AlessioJA, PatelNH (2005) Pax3/7 genes reveal conservation and divergence in the arthropod segmentation hierarchy. Dev Biol 285 : 169–184.
70. HammondCL, HinitsY, OsbornDP, MinchinJE, TettamantiG, et al. (2007) Signals and myogenic regulatory factors restrict pax3 and pax7 expression to dermomyotome-like tissue in zebrafish. Dev Biol 302 : 504–521.
71. MinchinJE, HughesSM (2008) Sequential actions of Pax3 and Pax7 drive xanthophore development in zebrafish neural crest. Dev Biol 317 : 508–522.
72. HoldenNS, TaconCE (2011) Principles and problems of the electrophoretic mobility shift assay. J Pharmacol Toxicol Methods 63 : 7–14.
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