Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Dabrowski, Michal ^a   Aerts, Stein ^b   Kaminska, Bozena ^a  

^a NENCKI INSTITUTE OF EXPERIMENTAL BIOLOGY   (Poland)

^b UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

EXPRESSION PATTERNS; EXPRESSION VECTORS; GENE EXPRESSION PROFILES; MESENCHYMAL CELLS; NEURONAL DIFFERENTIATION; REGULATORY MECHANISM; REGULATORY SEQUENCES; TEMPORAL EXPRESSIONS;

BRAIN; GENE EXPRESSION; MAMMALS; NEURONS; SINGULAR VALUE DECOMPOSITION; VECTORS;

GENE EXPRESSION REGULATION;

BIOLOGICAL FACTOR; CHICKEN OVALBUMIN UPSTREAM PROMOTER TRANSCRIPTION FACTOR; HEPATOCYTE NUCLEAR FACTOR 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CDE; TRANSCRIPTION FACTOR CHR; TRANSCRIPTION FACTOR E2F; TRANSCRIPTION FACTOR NR2F; UNCLASSIFIED DRUG; PROTEIN BINDING;

ARTICLE; BINDING SITE; BRAIN DEVELOPMENT; CELL DIFFERENTIATION; DATA ANALYSIS; DOWN REGULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SEQUENCE; HIPPOCAMPUS; MYOBLAST; NERVE CELL DIFFERENTIATION; PREDICTION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN MOTIF; REGULATORY MECHANISM; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STEM CELL; UPREGULATION; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; CYTOLOGY; GENETICS; GROWTH, DEVELOPMENT AND AGING; HUMAN; METABOLISM; MOUSE; PROCEDURES;

MAMMALIA;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CELL DIFFERENTIATION; COMPUTATIONAL BIOLOGY; COUP TRANSCRIPTION FACTORS; DOWN-REGULATION; E2F TRANSCRIPTION FACTORS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HIPPOCAMPUS; HUMANS; MICE; MYOBLASTS; PROTEIN BINDING; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 33748623792     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-367     Document Type: Article

References (50)

1. Diaz E, Ge Y, Yang YH, Loh KC, Serafini TA, Okazaki Y, Hayashizaki Y, Speed TP, Ngai J, Scheiffele P: Molecular analysis of gene expression in the developing pontocerebellar projection system. Neuron 2002, 36:417-434.
2. Mody M, Cao Y, Cui Z, Tay KY, Shyong A, Shimizu E, Pham K, Schultz P, Welsh D, Tsien JZ: Genome-wide gene expression profiles of the developing mouse hippocampus. Proc Natl Acad Sci U S A 2001, 98:8862-8867.
3. Gurok U, Steinhoff C, Lipkowitz B, Ropers HH, Scharff C, Nuber UA: Gene expression changes in the course of neural progenitor cell differentiation. J Neurosci 2004, 24:5982-6002.
4. Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M: Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet 2003, 19:570-577.
5. Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13:97-102.
6. Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, Ukkonen E, Taipale J: Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity. Cell 2006, 124:47-59.
7. Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet 2001, 27:167-171.
8. Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell 2004, 117:185-198.
9. Bulyk ML: Computational prediction of transcription-factor binding site locations. Genome Biol 2003, 5:201.
10. Ludwig MZ, Bergman C, Patel NH, Kreitman M: Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 2000, 403:564-567.
11. Dieterich C, Rahmann S, Vingron M: Functional inference from non-random distributions of conserved predicted transcription factor binding, sites. Bioinformatics 2004, 20 Suppl 1:1109-1115.
12. Kel OV, Romaschenko AG, Kel AE, Wingender E, Kolchanov NA: A compilation of composite regulatory elements affecting gene transcription in vertebrates. Nucleic Acids Res 1995, 23:4097-4103.
13. Kel-Margoulis OV, Romashchenko AG, Kolchanov NA, Wingender E, Kell AE: COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res 2000, 28:311-315.
14. Davidson EH: Genomic Regulatory Systems. San Diego CA, Academic Press; 2001.
15. Michelson AM: Deciphering genetic regulatory codes: a challenge for functional genomics. Proc Natl Acad Sci U S A 2002, 99:546-548.
16. Yuh CH, Bolouri H, Davidson EH: Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 1998, 279:1896-1902.
17. Laybourn PJ, Kadonaga JT: Threshold phenomena and long-distance activation of transcription by RNA polymerase II. Science 1992, 257:1682-1685.
18. Strang G: Introduction to linear algebra. Wellesley MA, Wellesley-Cambridge Press; 1993.
19. Alter O, Brown PO, Botstein D: Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 2000, 97:10101-10106.
20. Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV: Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci U S A 2000, 97:8409-8414.
21. Goslin K, Banker G: Rat Hippocampal Neurons in Low-Density Culture. In Culturing Nerve Cells Edited by: Goslin K. Cambrige, Massachusetts, The MIT Press; 1991:251-282.
22. Dabrowski M, Aerts S, Van Hummelen P, Craessaerts K, De Moor B, Annaert W, Moreau Y, De Strooper B: Gene profiling of hippocampal neuronal culture. J Neurochem 2003, 85:1279-1288.
23. Dityateva G, Hammond M, Thiel C, Ruonala MO, Delling M, Siebenkotten G, Nix M, Dityatev A: Rapid and efficient electroporation-based gene transfer into primary dissociated neurons. J Neurosci Methods 2003, 130:65-73.
24. Mabuchi T, Kitagawa K, Kuwabara K, Takasawa K, Ohtsuki T, Xia Z, Storm D, Yanagihara T, Hori M, Matsumoto M: Phosphorylation of cAMP response element-binding protein in hippocampal neurons as a protective response after exposure to glutamate in vitro and ischernia in vivo. J Neurosci 2001, 21:9204-9213.
25. Dabrowski M, Adach A, Aerts S, Moreau Y, Kaminska B: Identification of conserved modes of expression during hippocampal development and neuronal differentiation in vitro. J Neurochem 2006, 97:87-91.
26. Pickert L, Reuter I, Klawonn F, Wingender E: Transcription regulatory region analysis using signal detection and fuzzy clustering. Bioinformatics 1998, 14:244-251.
27. Chan WK, Yao G, Gu YZ, Bradfield CA: Cross-talk between the aryl hydrocarbon receptor and hypoxia inducible factor signaling pathways. Demonstration of competition and compensation. J Biol Chem 1999, 274:12115-12123.
28. Boesch JS, Miskimins R, Miskimins WK, Lindahl R: The same xenobiotic response element is required for constitutive and inducible expression of the mammalian aldehyde dehydrogenase-3 gene. Arch Biochem Biophys 1999, 361:223-230.
29. Tomczak KK, Marinescu VD, Ramoni MF, Sanoudou D, Montanaro F, Han M, Kunkel LM, Kohane IS, Beggs AH: Expression profiling and identification of novel genes involved in myogenic differentiation. Faseb J 2004, 18:403-405.
30. Dabrowski M, Adach A, Aerts S, Moreau Y, Kaminska B: Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro. J Neurochem 2006, 97 Suppl 1:87-91.
31. Zwicker J, Lucibello FC, Wolfraim LA, Gross C, Truss M, Engeland K, Muller R: Cell cycle regulation of the cyclin A, cdc25C and cdc2 genes is based on a common mechanism of transcriptional repression. Embo J 1995, 14:4514-4522.
32. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I: The transcriptional program of sporulation in budding yeast. Science 1998, 282:699-705.
33. Chiang DY, Brown PO, Eisen MB: Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles. Bioinformatics 2001, 17 Suppl 1:S49-55.
34. Alter O, Brown PO, Botstein D: Processing and modeling genome-wide expression data using singular value decomposition. Proc SPIE 2001, 4266:171-186.
35. Keles S, van der Laan M, Eisen MB: Identification of regulatory elements using a feature selection method. Bioinformatics 2002, 18:1167-1175.
36. Weinberg RA: The retinoblastoma protein and cell cycle control. Cell 1995, 81:323-330.
37. Frisen J, Johansson CB, Lothian C, Lendahl U: Central nervous system stem cells in the embryo and adult. Cell Mol Life Sci 1998, 54:935-945.
38. Maurer MH, Feldmann REJ, Futterer CD, Butlin J, Kuschinsky W: Comprehensive proteome expression profiling of undifferentiated versus differentiated neural stem cells from adult rat hippocampus. Neurochem Res 2004, 29:1129-1144.
39. Liu DX, Nath N, Chellappan SP, Greene LA: Regulation of neuron survival and death by p130 and associated chromatin modifiers. Genes Dev 2005, 19:719-732.
40. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002, 99:757-762.
41. Ait-Si-Ali S, Guasconi V, Fritsch L, Yahi H, Sekhri R, Naguibneva I, Robin P, Cabon F, Polesskaya A, Harel-Bellan A. A Suv39h-dependent mechanism for silencing S-phase genes in differentiating but not in cycling cells. Embo J 2004, 23:605-615.
42. Gauchat D, Escriva H, Miljkovic-Licina M, Chera S, Langlois MC, Begue A, Laudet V, Galliot B. The orphan COUP-TF nuclear receptors are markers for neurogenesis from cnidarians to vertebrates. Dev Biol 2004, 275:104-123.
43. Lothian C, Prakash N, Lendahl U, Wahlstrom GM: Identification of both general and region-specific embryonic CNS enhancer elements in the nestin promoter. Exp Cell Res 1999, 248:509-519.
44. Connor H, Nornes H, Neuman T: Expression screening reveals an orphan receptor chick ovalbumin upstream promoter transcription factor I as a regulator of neurite/substrate-cell contacts and cell aggregation. J Biol Chem 1995, 270:15066-15070.
45. Jonk LJ, de Jonge ME, Vervaart JM, Wissink S, Kruijer W: Isolation and developmental expression of retinoic-acid-induced genes. Dev Biol 1994, 161:604-614.
46. Rohr O, Aunis D, Schaeffer E: COUP-TF and Sp I interact and cooperate in the transcriptional activation of the human immunodeficiency virus type I long terminal repeat in human microglial cells. J Biol Chem 1997, 272:31149-31155.
47. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, Lancet D, Shmueli O: Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics; 2005, 21:650-659.
48. Clamp M, Andrews D, Barker D, Bevan P, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Hubbard T, Kasprzyk A, Keefe D, Lehvaslaiho H, Iyer V, Melsopp C, Mongin E, Pettett R, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Birney E: Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res 2003, 31:38-42.
49. Quandt K, Frech K, Karas H, Wingender E, Werner T: MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res 1995, 23:4878-4884.
50. Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T: MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005, 21:2933-2942.