Identification of highly conserved putative developmental enhancers bound by SOX3 in neural progenitors using ChIP-Seq

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  McAninch, Dale ^a   Thomas, Paul ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

E1A ASSOCIATED P300 PROTEIN; NESTIN; TRANSCRIPTION FACTOR SOX; TRANSCRIPTION FACTOR SOX3;

ANIMAL CELL; ARTICLE; BINDING SITE; BRAIN DEVELOPMENT; CENTRAL NERVOUS SYSTEM; CONSENSUS SEQUENCE; CONTROLLED STUDY; DEVELOPMENTAL GENE; EMBRYO DEVELOPMENT; ENHANCER REGION; GENETIC CONSERVATION; GENOME ANALYSIS; INTRON; MOUSE; NERVOUS SYSTEM DEVELOPMENT; NESTIN GENE; NEURAL STEM CELL; NEURODEVELOPMENTAL GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN MOTIF; SCORING SYSTEM; ANIMAL; CELL CULTURE; CHEMISTRY; CHROMATIN IMMUNOPRECIPITATION; CYTOLOGY; DNA SEQUENCE; GENE REGULATORY NETWORK; GENETICS; METABOLISM;

ANIMALS; BASE SEQUENCE; BINDING SITES; CELLS, CULTURED; CHROMATIN IMMUNOPRECIPITATION; ENHANCER ELEMENTS, GENETIC; GENE REGULATORY NETWORKS; MICE; NEURAL STEM CELLS; SEQUENCE ANALYSIS, DNA; SOXB1 TRANSCRIPTION FACTORS;

EID: 84912076325     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113361     Document Type: Article

References (45)

1. Bylund M, Andersson E, Novitch BG, Muhr J (2003) Vertebrate neurogenesis is counteracted by Sox1-3 activity. Nat Neurosci 6: 1162-1168.
2. Bergsland M, Ramskold D, Zaouter C, Klum S, Sandberg R, et al. (2011) Sequentially acting Sox transcription factors in neural lineage development. Genes Dev 25: 2453-2464.
3. Bowles J, Schepers G, Koopman P (2000) Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol 227: 239-255.
4. Remenyi A, Lins K, Nissen LJ, Reinbold R, Scholer HR, et al. (2003) Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev 17: 2048-2059.
5. Yoshida M, Uchikawa M, Rizzoti K, Lovell-Badge R, Takemoto T, et al. (2014) Regulation of mesodermal precursor production by low-level expression of B1 Sox genes in the caudal lateral epiblast. Mech Dev 132: 59-68.
6. Rogers N, Cheah PS, Szarek E, Banerjee K, Schwartz J, et al. (2013) Expression of the murine transcription factor SOX3 during embryonic and adult neurogenesis. Gene Expr Patterns 13: 240-248.
7. Graham V, Khudyakov J, Ellis P, Pevny L (2003) SOX2 functions to maintain neural progenitor identity. Neuron 39: 749-765.
8. Shih YH, Kuo CL, Hirst CS, Dee CT, Liu YR, et al. (2010) SoxB1 transcription factors restrict organizer gene expression by repressing multiple events downstream of Wnt signalling. Development 137: 2671-2681.
9. Holmberg J, Hansson E, Malewicz M, Sandberg M, Perlmann T, et al. (2008) SoxB1 transcription factors and Notch signaling use distinct mechanisms to regulate proneural gene function and neural progenitor differentiation. Development 135: 1843-1851.
10. Rizzoti K, Brunelli S, Carmignac D, Thomas PQ, Robinson IC, et al. (2004) SOX3 is required during the formation of the hypothalamo-pituitary axis. Nat Genet 36: 247-255.
11. Rizzoti K, Lovell-Badge R (2005) Early development of the pituitary gland: induction and shaping of Rathke's pouch. Rev Endocr Metab Disord 6: 161-172.
12. Favaro R, Valotta M, Ferri AL, Latorre E, Mariani J, et al. (2009) Hippocampal development and neural stem cell maintenance require Sox2-dependent regulation of Shh. Nat Neurosci 12: 1248-1256.
13. Miyagi S, Masui S, Niwa H, Saito T, Shimazaki T, et al. (2008) Consequence of the loss of Sox2 in the developing brain of the mouse. FEBS Lett 582: 2811-2815.
14. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) Highresolution profiling of histone methylations in the human genome. Cell 129: 823-837.
15. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
16. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. (2007) Genomewide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657.
17. Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, et al. (2013) Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504: 306-310.
18. Krivega I, Dean A (2012) Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev 22: 79-85.
19. Consortium EP, Bernstein BE, Birney E, Dunham I, Green ED, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
20. Ying QL, Smith AG (2003) Defined conditions for neural commitment and differentiation. Methods Enzymol 365: 327-341.
21. Rogers N, McAninch D, Thomas P (2014) Dbx1 Is a Direct Target of SOX3 in the Spinal Cord. PLoS One 9: e95356.
22. Hughes J, Piltz S, Rogers N, McAninch D, Rowley L, et al. (2013) Mechanistic insight into the pathology of polyalanine expansion disorders revealed by a mouse model for X linked hypopituitarism. PLoS Genet 9: e1003290.
23. Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, et al. (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42: D142-147.
24. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
25. Fan R, Bonde S, Gao P, Sotomayor B, Chen C, et al. (2012) Dynamic HoxB4-regulatory network during embryonic stem cell differentiation to hematopoietic cells. Blood 119: e139-147.
26. Kawaguchi A, Miyata T, Sawamoto K, Takashita N, Murayama A, et al. (2001) Nestin-EGFP transgenic mice: visualization of the self-renewal and multipotency of CNS stem cells. Mol Cell Neurosci 17: 259-273.
27. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858.
28. Kondoh H, Kamachi Y (2010) SOX-partner code for cell specification: Regulatory target selection and underlying molecular mechanisms. Int J Biochem Cell Biol 42: 391-399.
29. Kamachi Y, Uchikawa M, Kondoh H (2000) Pairing SOX off: with partners in the regulation of embryonic development. Trends Genet 16: 182-187.
30. Spitz F, Furlong EE (2012) Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13: 613-626.
31. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202-208.
32. Bery A, Martynoga B, Guillemot F, Joly JS, Retaux S (2013) Characterization of Enhancers Active in the Mouse Embryonic Cerebral Cortex Suggests Sox/Pou cis-Regulatory Logics and Heterogeneity of Cortical Progenitors. Cereb Cortex.
33. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499-502.
34. Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, et al. (2008) Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet 40: 158-160.
35. Oosterveen T, Kurdija S, Enstero M, Uhde CW, Bergsland M, et al. (2013) SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals. Proc Natl Acad Sci U S A 110: 7330-7335.
36. Cooper SJ, Trinklein ND, Nguyen L, Myers RM (2007) Serum response factor binding sites differ in three human cell types. Genome Res 17: 136-144.
37. Conboy CM, Spyrou C, Thorne NP, Wade EJ, Barbosa-Morais NL, et al. (2007) Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS One 2: e1061.
38. Stuebner S, Faus-Kessler T, Fischer T, Wurst W, Prakash N (2010) Fzd3 and Fzd6 deficiency results in a severe midbrain morphogenesis defect. Dev Dyn 239: 246-260.
39. Kamachi Y, Kondoh H (2013) Sox proteins: regulators of cell fate specification and differentiation. Development 140: 4129-4144.
40. Lee KE, Seo J, Shin J, Ji EH, Roh J, et al. (2014) Positive feedback loop between Sox2 and Sox6 inhibits neuronal differentiation in the developing central nervous system. Proc Natl Acad Sci U S A 111: 2794-2799.
41. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
42. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
43. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, et al. (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28:495-501.
44. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
45. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.