Regulation of terminal differentiation programs in the nervous system

Annual Review of Cell and Developmental Biology

Volumn 27, Issue , 2011, Pages 681-696

  Hobert, Oliver ^a  

^a NewYork Presbyterian Hospital   (United States)

Author keywords

Neuronal identity; Regulon; Terminal selector; Transcriptional regulation

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CAENORHABDITIS ELEGANS; CHROMATIN IMMUNOPRECIPITATION; DOWNSTREAM PROCESSING; GENE EXPRESSION; GENE TARGETING; INVERTEBRATE; NERVE CELL DIFFERENTIATION; NERVE ENDING; NERVOUS SYSTEM; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; VERTEBRATE;

ANIMALS; CELL DIFFERENTIATION; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HOMEODOMAIN PROTEINS; HUMANS; NERVOUS SYSTEM; NEURONS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

INVERTEBRATA; VERTEBRATA;

EID: 80054051689     PISSN: 10810706     EISSN: 15308995     Source Type: Book Series    
DOI: 10.1146/annurev-cellbio-092910-154226     Document Type: Article

References (72)

1. Alon U. 2007. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8:450-61 (Pubitemid 46789247)
2. Altun-Gultekin Z, Andachi Y, Tsalik EL, PilgrimD, Kohara Y, Hobert O. 2001. A regulatory cascade of three homeobox genes, ceh-10, ttx-3 and ceh-23, controls cell fate specification of a defined interneuron class in C. elegans. Development 128:1951-69 (Pubitemid 32600460)
3. Armstrong KR, Chamberlin HM. 2010. Coordinate regulation of gene expression in the C. elegans excretory cell by the POU domain protein CEH-6. Mol. Genet. Genomics 283:73-87
4. Bertrand V, Hobert O. 2009. Linking asymmetric cell division to the terminal differentiation program of postmitotic neurons in C. elegans. Dev. Cell 16:563-75
5. Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. 2001. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell 107:579-89 (Pubitemid 34014860)
6. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, et al. 2004. Genomic analysis of mouse retinal development. PLoS Biol. 2:e247
7. Cave JW, Akiba Y, Banerjee K, Bhosle S, Berlin R, Baker H. 2010. Differential regulation of dopaminergic gene expression by Er81. J. Neurosci. 30:4717-24
8. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. 1994. Green fluorescent protein as a marker for gene expression. Science 263:802-5 (Pubitemid 24093206)
9. Chang S, Johnston RJ Jr, Hobert O. 2003. A transcriptional regulatory cascade that controls left/right asymmetry in chemosensory neurons of C. elegans. Genes Dev. 17:2123-37 (Pubitemid 37052292)
10. Chanut-Delalande H, Fernandes I, Roch F, Payre F, Plaza S. 2006. Shavenbaby couples patterning to epidermal cell shape control. PLoS Biol. 4:e290
11. Cheng L, Arata A, Mizuguchi R, Qian Y, Karunaratne A, et al. 2004. Tlx3 and Tlx1 are post-mitotic selector genes determining glutamatergic over GABAergic cell fates. Nat. Neurosci. 7:510-17 (Pubitemid 38544590)
12. Cobaleda C, Schebesta A, Delogu A, Busslinger M. 2007. Pax5: the guardian of B cell identity and function. Nat. Immunol. 8:463-70 (Pubitemid 46605911)
13. Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, et al. 2010. CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Genome Res. 20:1512-25
14. Davidson EH. 2006. The Regulatory Genome:Gene Regulatory Networks in Development and Evolution. Burlington, MA: Academic
15. Duggan A, Ma C, Chalfie M. 1998. Regulation of touch receptor differentiation by the Caenorhabditis elegans mec-3 and unc-86 genes. Development 125:4107-19 (Pubitemid 28515448)
16. EastmanC, Horvitz HR, Jin Y. 1999. Coordinated transcriptional regulation of the unc-25 glutamic acid decarboxylase and the unc-47 GABA vesicular transporter by the Caenorhabditis elegans UNC-30 homeodomain protein. J. Neurosci. 19:6225-34 (Pubitemid 29347423)
17. Erwin DH, Davidson EH. 2009. The evolution of hierarchical gene regulatory networks. Nat. Rev. Genet. 10:141-48
18. Etchberger JF, Flowers EB, Poole RJ, Bashllari E, Hobert O. 2009. Cis-regulatory mechanisms of left/right asymmetric neuron-subtype specification in C. elegans. Development 136:147-60
19. Etchberger JF, Lorch A, Sleumer MC, Zapf R, Jones SJ, et al. 2007. Themolecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes Dev. 21:1653-74 (Pubitemid 47026369)
20. Flames N, Hobert O. 2009. Gene regulatory logic of dopamine neuron differentiation. Nature 458:885-89
21. Fox RM, Von Stetina SE, Barlow SJ, Shaffer C, Olszewski KL, et al. 2005. A gene expression fingerprint of C. elegans embryonic motor neurons. BMC Genomics 6:42
22. Fujimoto E, Stevenson TJ, Chien CB, Bonkowsky JL. 2011. Identification of a dopaminergic enhancer indicates complexity in vertebrate dopamine neuron phenotype specification. Dev. Biol. 352(2):393-404
23. Gaudet J, Mango SE. 2002. Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4. Science 295:821-25 (Pubitemid 34118356)
24. Guillemot F. 2007. Spatial and temporal specification of neural fates by transcription factor codes. Development 134:3771-80 (Pubitemid 350187336)
25. Hadley D, Murphy T, Valladares O, Hannenhalli S, Ungar L, et al. 2006. Patterns of sequence conservation in presynaptic neural genes. Genome Biol. 7:R105
26. Hamanaka Y, Park D, Yin P, Annangudi SP, Edwards TN, et al. 2010. Transcriptional orchestration of the regulated secretory pathway in neurons by the bHLH protein DIMM. Curr. Biol. 20:9-18
27. Hamburger V. 1981. Historical landmarks in neurogenesis. Trends Neurosci. 4:151-55
28. Hendricks T, Francis N, Fyodorov D, Deneris ES. 1999. The ETS domain factor Pet-1 is an early and precisemarker of central serotonin neurons and interacts with a conserved element in serotonergic genes. J. Neurosci. 19:10348-56 (Pubitemid 30228042)
29. Hendricks TJ, Fyodorov DV, Wegman LJ, Lelutiu NB, Pehek EA, et al. 2003. Pet-1 ETS gene plays a critical role in 5-HT neuron development and is required for normal anxiety-like and aggressive behavior. Neuron 37:233-47 (Pubitemid 36143819)
30. Hobert O. 2006. Architecture of a microRNA-controlled gene regulatory network that diversifies neuronal cell fates. Cold Spring Harb. Symp. Quant. Biol. 71:181-88
31. Hobert O. 2008. Regulatory logic of neuronal diversity: terminal selector genes and selector motifs. Proc. Natl. Acad. Sci. USA 105:20067-71
32. Hobert O. 2010. Neurogenesis in the nematode Caenorhabditis elegans. In WormBook, ed. C. elegans Res. Community. http://www. wormbook.org/chapters/www- specnervsys. 2/neurogenesis. html
33. Hobert O, Carrera I, Stefanakis N. 2010. The molecular and gene regulatory signature of a neuron. Trends Neurosci. 33(10):435-45
34. Hsiau TH, Diaconu C, Myers CA, Lee J, Cepko CL, Corbo JC. 2007. The cis-regulatory logic of the mammalian photoreceptor transcriptional network. PLoS ONE 2:e643
35. Hwang SB, Lee J. 2003. Neuron cell type-specific SNAP-25 expression driven by multiple regulatory elements in the nematode Caenorhabditis elegans. J. Mol. Biol. 333:237-47 (Pubitemid 37188569)
36. Jacobs FM, Smits SM, Noorlander CW, von Oerthel L, Van der Linden AJ, et al. 2007. Retinoic acid counteracts developmental defects in the substantia nigra caused by Pitx3 deficiency. Development 134:2673-84 (Pubitemid 47225963)
37. Jacobs FM, Van der Linden AJ, Wang Y, vonOerthel L, Sul HS, et al. 2009a. Identification ofDlk1, Ptpru and Klhl1 as novel Nurr1 target genes in meso-diencephalic dopamine neurons. Development 136:2363-73
38. Jacobs FM, Van Erp S, Van der Linden AJ, von Oerthel L, Burbach JP, Smidt MP. 2009b. Pitx3 potentiates Nurr1 in dopamine neuron terminal differentiation through release of SMRT-mediated repression. Development 136:531-40
39. Jessell TM. 2000. Neuronal specification in the spinal cord: inductive signals and transcriptional codes. Nat. Rev. Genet. 1:20-29
40. Jin Y, Hoskins R, Horvitz HR. 1994. Control of type-D GABAergic neuron differentiation by C. elegans UNC-30 homeodomain protein. Nature 372:780-83
41. Johnston RJ Jr, Hobert O. 2003. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426:845-49 (Pubitemid 38056870)
42. Kadkhodaei B, Ito T, Joodmardi E, Mattsson B, Rouillard C, et al. 2009. Nurr1 is required for maintenance of maturing and adult midbrain dopamine neurons. J. Neurosci. 29:15923-32
43. Kala K, Haugas M, Lillevali K, Guimera J, Wurst W, et al. 2009. Gata2 is a tissue-specific post-mitotic selector gene for midbrain GABAergic neurons. Development 136:253-62
44. Kim K, Kim R, Sengupta P. 2010. TheHMX/NKX homeodomain proteinMLS-2 specifies the identity of the AWC sensory neuron type via regulation of the ceh-36 Otx gene in C. elegans. Development 137:963-74
45. Lanjuin A, Sengupta P. 2004. Specification of chemosensory neuron subtype identities in Caenorhabditis elegans. Curr. Opin. Neurobiol. 14:22-30 (Pubitemid 38264568)
46. Liu C, Maejima T, Wyler SC, Casadesus G, Herlitze S, Deneris ES. 2010. Pet-1 is required across different stages of life to regulate serotonergic function. Nat. Neurosci. 13:1190-98
47. Liu R, Hannenhalli S, Bucan M. 2009. Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. Genome Biol. 10:R72
48. Liu Y, Ma Q. 2011. Generation of somatic sensory neuron diversity and implications on sensory coding. Curr. Opin. Neurobiol. 21(1):52-60
49. Livesey FJ, Cepko CL. 2001. Vertebrate neural cell-fate determination: lessons from the retina. Nat. Rev. Neurosci. 2:109-18 (Pubitemid 33673365)
50. Mah AK, Tu DK, Johnsen RC, Chu JS, Chen N, Baillie DL. 2010. Characterization of the octamer, a cisregulatory element that modulates excretory cell gene-expression in Caenorhabditis elegans. BMC Mol. Biol. 11:19
51. Martinat C, Bacci JJ, Leete T, Kim J, Vanti WB, et al. 2006. Cooperative transcription activation by Nurr1 and Pitx3 induces embryonic stem cell maturation to the midbrain dopamine neuron phenotype. Proc. Natl. Acad. Sci. USA 103:2874-79
52. McGregor AP,Orgogozo V, Delon I, Zanet J, Srinivasan DG, et al. 2007. Morphological evolution through multiple cis-regulatory mutations at a single gene. Nature 448:587-90 (Pubitemid 47206931)
53. O'Meara MM, Bigelow H, Flibotte S, Etchberger JF, Moerman DG, Hobert O. 2009. Cis-regulatory mutations in the Caenorhabditis elegans homeobox gene locus cog-1 affect neuronal development. Genetics 181:1679-86
54. Ortiz CO, Faumont S, Takayama J, Ahmed HK, Goldsmith AD, et al. 2009. Lateralized gustatory behavior of C. elegans is controlled by specific receptor-type guanylyl cyclases. Curr. Biol. 19:996-1004
55. Piasecki BP, Burghoorn J, Swoboda P. 2010. Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals. Proc. Natl. Acad. Sci. USA 107:12969-74
56. Raḿon y Cajal S. 1911. Histologie du Syst̀eme Nerveux de l'Homme et des Vert́ebŕes. Paris: Maloine
57. Ruvinsky I, Ohler U, Burge CB, RuvkunG. 2007. Detection of broadly expressed neuronal genes in C. elegans. Dev. Biol. 302:617-26 (Pubitemid 46216257)
58. Sardiello M, Palmieri M, di Ronza A, Medina DL, ValenzaM, et al. 2009. A gene network regulating lysosomal biogenesis and function. Science 325:473-77
59. Sarin S, O'Meara MM, Flowers EB, AntonioC, Poole RJ, et al. 2007. Genetic screens for Caenorhabditis elegans mutants defective in left/right asymmetric neuronal fate specification. Genetics 176:2109-30 (Pubitemid 47360646)
60. Smidt MP, Burbach JP. 2009. Terminal differentiation of mesodiencephalic dopaminergic neurons: the role of Nurr1 and Pitx3. Adv. Exp. Med. Biol. 651:47-57
61. Smith CJ, Watson JD, Spencer WC, O'Brien T, Cha B, et al. 2010. Time-lapse imaging and cell-specific expression profiling reveal dynamic branching and molecular determinants of amulti-dendritic nociceptor in C. elegans. Dev. Biol. 345:18-33
62. Stern DL,Orgogozo V. 2008. The loci of evolution:How predictable is genetic evolution? Evolution 62:2155-77
63. Sucena E, Delon I, Jones I, Payre F, Stern DL. 2003. Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism. Nature 424:935-38 (Pubitemid 37051683)
64. Suzuki H, Thiele TR, Faumont S, Ezcurra M, Lockery SR, Schafer WR. 2008. Functional asymmetry in Caenorhabditis elegans taste neurons and its computational role in chemotaxis. Nature 454:114-17 (Pubitemid 351931968)
65. Swaroop A, Kim D, Forrest D. 2010. Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina. Nat. Rev. Neurosci. 11:563-76
66. Swoboda P, Adler HT, Thomas JH. 2000. The RFX-type transcription factor DAF-19 regulates sensory neuron cilium formation in C. elegans. Mol. Cell 5:411-21
67. Uchida O, Nakano H, Koga M, Ohshima Y. 2003. The C. elegans che-1 gene encodes a zinc finger transcription factor required for specification of the ASE chemosensory neurons. Development 130:1215-24 (Pubitemid 36410771)
68. Way JC, Chalfie M. 1989. The mec-3 gene of Caenorhabditis elegans requires its own product for maintained expression and is expressed in three neuronal cell types. Genes Dev. 3:1823-33 (Pubitemid 20023210)
69. Wenick AS, Hobert O. 2004. Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. Dev. Cell 6:757-70 (Pubitemid 38745411)
70. Xue D, Tu Y, Chalfie M. 1993. Cooperative interactions between the Caenorhabditis elegans homeoproteins UNC-86 and MEC-3. Science 261:1324-28 (Pubitemid 24081169)
71. Yoshida K, Yamaguchi H, Kinehara M, Ohki YH, Nakaura Y, Fujita Y. 2003. Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. Mol. Microbiol. 49:157-65 (Pubitemid 36792011)
72. Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, et al. 2002. Identification of genes expressed in C. elegans touch receptor neurons. Nature 418:331-35 (Pubitemid 34790684)