Old and new functions of proneural factors revealed by the genome-wide characterization of their transcriptional targets

References

• Edlund T, Jessell TM. Progression from extrinsic to intrinsic signaling in cell fate specification: a view from the nervous system. Cell 1999; 96:211 - 224; PMID: 9988216; http://dx.doi.org/10.1016/S0092-8674(00)80561-9
   PubMed Web of Science ®Google Scholar
• Marín O, Valiente M, Ge X, Tsai LH. Guiding neuronal cell migrations. Cold Spring Harb Perspect Biol 2010; 2:1834; PMID: 20182622; http://dx.doi.org/10.1101/cshperspect.a001834
   PubMed Web of Science ®Google Scholar
• Bertrand N, Castro DS, Guillemot F. Proneural genes and the specification of neural cell types. Nat Rev Neurosci 2002; 3:517 - 530; PMID: 12094208; http://dx.doi.org/10.1038/nrn874
   PubMed Web of Science ®Google Scholar
• Powell LM, Jarman AP. Context dependence of proneural bHLH proteins. Curr Opin Genet Dev 2008; 18:411 - 417; PMID: 18722526; http://dx.doi.org/10.1016/j.gde.2008.07.012
   PubMed Web of Science ®Google Scholar
• Ge W, He F, Kim KJ, Blanchi B, Coskun V, Nguyen L, et al. Coupling of cell migration with neurogenesis by proneural bHLH factors. Proc Natl Acad Sci USA 2006; 103:1319 - 1324; PMID: 16432194; http://dx.doi.org/10.1073/pnas.0510419103
   PubMed Web of Science ®Google Scholar
• Heng JI, Nguyen L, Castro DS, Zimmer C, Wildner H, Armant O, et al. Neurogenin 2 controls cortical neuron migration through regulation of Rnd2. Nature 2008; 455:114 - 118; PMID: 18690213; http://dx.doi.org/10.1038/nature07198
   PubMed Web of Science ®Google Scholar
• Johnson JE, Birren SJ, Anderson DJ. Two rat homologues of Drosophila achaete-scute specifically expressed in neuronal precursors. Nature 1990; 346:858 - 861; PMID: 2392153; http://dx.doi.org/10.1038/346858a0
   PubMed Web of Science ®Google Scholar
• Casarosa S, Fode C, Guillemot F. Mash1 regulates neurogenesis in the ventral telencephalon. Development 1999; 126:525 - 534; PMID: 9876181
   PubMed Web of Science ®Google Scholar
• Fode C, Ma Q, Casarosa S, Ang SL, Anderson DJ, Guillemot F. A role for neural determination genes in specifying the dorsoventral identity of telencephalic neurons. Genes Dev 2000; 14:67 - 80; PMID: 10640277
   PubMed Web of Science ®Google Scholar
• Parras CM, Schuurmans C, Scardigli R, Kim J, Anderson DJ, Guillemot F. Divergent functions of the proneural genes Mash1 and Ngn2 in the specification of neuronal subtype identity. Genes Dev 2002; 16:324 - 338; PMID: 11825874; http://dx.doi.org/10.1101/gad.940902
   PubMed Web of Science ®Google Scholar
• Castro DS, Martynoga B, Parras C, Ramesh V, Pacary E, Johnston C, et al. A novel function of the proneural factor Ascl1 in progenitor proliferation identified by genome-wide characterization of its targets. Genes Dev 2011; 25:930 - 945; PMID: 21536733; http://dx.doi.org/10.1101/gad.627811
   PubMed Web of Science ®Google Scholar
• Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 2004; 5:101; PMID: 15575967; http://dx.doi.org/10.1186/gb-2004-5?12-r101
   PubMed Web of Science ®Google Scholar
• Castro DS, Skowronska-Krawczyk D, Armant O, Donaldson IJ, Parras C, Hunt C, et al. Proneural bHLH and Brn proteins coregulate a neurogenic program through cooperative binding to a conserved DNA motif. Dev Cell 2006; 11:831 - 844; PMID: 17141158; http://dx.doi.org/10.1016/j.devcel.2006.10.006
   PubMed Web of Science ®Google Scholar
• Farah MH, Olson JM, Sucic HB, Hume RI, Tapscott SJ, Turner DL. Generation of neurons by transient expression of neural bHLH proteins in mammalian cells. Development 2000; 127:693 - 702; PMID: 10648228
   PubMed Web of Science ®Google Scholar
• Nakada Y, Hunsaker TL, Henke RM, Johnson JE. Distinct domains within Mash1 and Math1 are required for function in neuronal differentiation versus neuronal cell-type specification. Development 2004; 131:1319 - 1330; PMID: 14993186; http://dx.doi.org/10.1242/dev.01008
   PubMed Web of Science ®Google Scholar
• DeGregori J, Johnson DG. Distinct and Overlapping Roles for E2F Family Members in Transcription, Proliferation and Apoptosis. Curr Mol Med 2006; 6:739 - 748; PMID: 17100600
   PubMed Web of Science ®Google Scholar
• McClellan KA, Ruzhynsky VA, Douda DN, Vanderluit JL, Ferguson KL, Chen D, et al. Unique requirement for Rb/E2F3 in neuronal migration: evidence for cell cycle-independent functions. Mol Cell Biol 2007; 27:4825 - 4843; PMID: 17452454; http://dx.doi.org/10.1128/MCB.02100-06
   PubMed Web of Science ®Google Scholar
• Schüller U, Zhao Q, Godinho SA, Heine VM, Medema RH, Pellman D, et al. Forkhead transcription factor FoxM1 regulates mitotic entry and prevents spindle defects in cerebellar granule neuron precursors. Mol Cell Biol 2007; 27:8259 - 8270; PMID: 17893320; http://dx.doi.org/10.1128/MCB.00707-07
   PubMed Web of Science ®Google Scholar
• Cao X, Pfaff SL, Gage FH. YAP regulates neural progenitor cell number via the TEA domain transcription factor. Genes Dev 2008; 22:3320 - 3334; PMID: 19015275; http://dx.doi.org/10.1101/gad.1726608
   PubMed Web of Science ®Google Scholar
• Ball DW. Achaete-scute homolog-1 and Notch in lung neuroendocrine development and cancer. Cancer Lett 2004; 204:159 - 169; PMID: 15013215; http://dx.doi.org/10.1016/S0304-3835(03)00452-X
   PubMed Web of Science ®Google Scholar
• Jiang T, Collins BJ, Jin N, Watkins DN, Brock MV, Matsui W, et al. Achaete-scute complex homologue 1 regulates tumor-initiating capacity in human small cell lung cancer. Cancer Res 2009; 69:845 - 854; PMID: 19176379; http://dx.doi.org/10.1158/0008-5472.CAN-08-2762
   PubMed Web of Science ®Google Scholar
• Linnoila RI, Zhao B, DeMayo JL, Nelkin BD, Baylin SB, DeMayo FJ, et al. Constitutive achaete-scute homologue-1 promotes airway dysplasia and lung neuroendocrine tumors in transgenic mice. Cancer Res 2000; 60:4005 - 4009; PMID: 10945598
   PubMed Web of Science ®Google Scholar
• Southall TD, Brand AH. Neural stem cell transcriptional networks highlight genes essential for nervous system development. EMBO J 2009; 28:3799 - 3807; PMID: 19851284; http://dx.doi.org/10.1038/emboj.2009.309
   PubMed Web of Science ®Google Scholar
• Anderson D, JaJ YN. Cowan WM. The determination of the neuronal phenotype. Molecular and cellular approaches to neural development 1997; New York Oxford University Press 26 - 63
   Google Scholar
• Brunet JF, Ghysen A. Deconstructing cell determination: proneural genes and neuronal identity. Bioessays 1999; 21:313 - 318; PMID: 10377893; http://dx.doi.org/10.1002/(SICI)1521-1878(199904)21:4<313::AIDBIES7>3.0.CO;2-C
   PubMed Web of Science ®Google Scholar
• Klisch TJ, Xi Y, Flora A, Wang L, Li W, Zoghbi HY. In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development. Proc Natl Acad Sci USA 2011; 108:3288 - 3293; PMID: 21300888; http://dx.doi.org/10.1073/pnas.1100230108
   PubMed Web of Science ®Google Scholar
• Nieto M, Schuurmans C, Britz O, Guillemot F. Neural bHLH genes control the neuronal versus glial fate decision in cortical progenitors. Neuron 2001; 29:401 - 413; PMID: 11239431; http://dx.doi.org/10.1016/S0896-6273(01)00214-8
   PubMed Web of Science ®Google Scholar
• Seo S, Lim JW, Yellajoshyula D, Chang LW, Kroll KL. Neurogenin and NeuroD direct transcriptional targets and their regulatory enhancers. EMBO J 2007; 26:5093 - 5108; PMID: 18007592; http://dx.doi.org/10.1038/sj.emboj.7601923
   PubMed Web of Science ®Google Scholar
• Berninger B, Guillemot F, Gotz M. Directing neurotransmitter identity of neurones derived from expanded adult neural stem cells. Eur J Neurosci 2007; 25:2581 - 2590; PMID: 17561834; http://dx.doi.org/10.1111/j.1460-9568.2007.05509.x
   PubMed Web of Science ®Google Scholar
• Geoffroy CG, Critchley JA, Castro DS, Ramelli S, Barraclough C, Descombes P, et al. Engineering of dominant active basic helix-loop-helix proteins that are resistant to negative regulation by postnatal central nervous system antineurogenic cues. Stem Cells 2009; 27:847 - 856; PMID: 19350686; http://dx.doi.org/10.1002/stem.17
   PubMed Web of Science ®Google Scholar
• Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Sudhof TC, Wernig M. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 2010; 463:1035 - 1041; PMID: 20107439; http://dx.doi.org/10.1038/nature08797
   PubMed Web of Science ®Google Scholar
• Chien CT, Hsiao CD, Jan LY, Jan YN. Neuronal type information encoded in the basic-helix-loop-helix domain of proneural genes. Proc Natl Acad Sci USA 1996; 93:13239 - 13244; PMID: 8917575; http://dx.doi.org/10.1073/pnas.93.23.13239
   PubMed Web of Science ®Google Scholar
• Cachero S, Simpson TI, Zur Lage PI, Ma L, Newton FG, Holohan EE, et al. The gene regulatory cascade linking proneural specification with differentiation in Drosophila sensory neurons. PLoS Biol 2011; 9:1000568; PMID: 21283833; http://dx.doi.org/10.1371/journal.pbio.1000568
   PubMed Web of Science ®Google Scholar
• Thomas J, Morle L, Soulavie F, Laurencon A, Sagnol S, Durand B. Transcriptional control of genes involved in ciliogenesis: a first step in making cilia. Biol Cell 2010; 102:499 - 513; PMID: 20690903; http://dx.doi.org/10.1042/BC20100035
   PubMed Web of Science ®Google Scholar
• Orkin SH. Diversification of haematopoietic stem cells to specific lineages. Nat Rev Genet 2000; 1:57 - 64; PMID: 11262875; http://dx.doi.org/10.1038/35049577
   PubMed Web of Science ®Google Scholar
• Tapscott SJ, Bennett GS, Holtzer H. Neuronal precursor cells in the chick neural tube express neurofilament proteins. Nature 1981; 292:836 - 838; PMID: 6791030; http://dx.doi.org/10.1038/292836a0
   PubMed Web of Science ®Google Scholar
• Guillemot F. Spatial and temporal specification of neural fates by transcription factor codes. Development 2007; 134:3771 - 3780; PMID: 17898002; http://dx.doi.org/10.1242/dev.006379
   PubMed Web of Science ®Google Scholar
• Lai HC, Klisch TJ, Roberts R, Zoghbi HY, Johnson JE. In vivo neuronal subtype-specific targets of Atoh1 (Math1) in dorsal spinal cord. J Neurosci 2011; 31:10859 - 10871; PMID: 21795538; http://dx.doi.org/10.1523/JNEUROSCI.0445-11.2011
   PubMed Web of Science ®Google Scholar
• Aerts S, Quan XJ, Claeys A, Naval Sanchez M, Tate P, Yan J, et al. Robust target gene discovery through transcriptome perturbations and genomewide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification. PLoS Biol 2010; 8:1000435; PMID: 20668662; http://dx.doi.org/10.1371/journal.pbio.1000435
   PubMed Web of Science ®Google Scholar