Gene expression in the rat brain: High similarity but unique differences between frontomedial-, temporal- and occipital cortex

BMC Neuroscience

Volumn 12, Issue , 2011, Pages

  Stansberg, Christine ^a,b   Ersland, Kari M ^a,b   van der Valk, Paul ^c   Steen, Vidar M ^a,b  

^a UNIVERSITY OF BERGEN   (Norway)

^b HAUKELAND UNIVERSITY HOSPITAL   (Norway)

^c VU UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

RETINOID RELATED ORPHAN RECEPTOR BETA;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BRAIN; BRAIN CORTEX; CELL TYPE; CONTROLLED STUDY; DIFFERENTIAL DISPLAY; GENE EXPRESSION; MAMMAL; NEOCORTEX; NONHUMAN; OCCIPITAL CORTEX; RAT; RODENT; SIGNAL TRANSDUCTION; ANIMAL; COMPARATIVE STUDY; FRONTAL LOBE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; OCCIPITAL LOBE; PHYSIOLOGY; TEMPORAL LOBE;

ANIMALS; FRONTAL LOBE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; OCCIPITAL LOBE; RATS; TEMPORAL LOBE;

EID: 79251576489     PISSN: None     EISSN: 14712202     Source Type: Journal    
DOI: 10.1186/1471-2202-12-15     Document Type: Article

References (48)

1. O'Leary DD, Sahara S. Genetic regulation of arealization of the neocortex. Curr Opin Neurobiol 2008, 18(1):90-100. 2677555, 18524571.
2. Rakic P. Specification of cerebral cortical areas. Science 1988, 241(4862):170-176. 10.1126/science.3291116, 3291116.
3. Rash BG, Grove EA. Area and layer patterning in the developing cerebral cortex. Curr Opin Neurobiol 2006, 16(1):25-34. 10.1016/j.conb.2006.01.004, 16426837.
4. O'Leary DD, Chou SJ, Sahara S. Area patterning of the mammalian cortex. Neuron 2007, 56(2):252-269.
5. Funatsu N, Inoue T, Nakamura S. Gene expression analysis of the late embryonic mouse cerebral cortex using DNA microarray: identification of several region- and layer-specific genes. Cereb Cortex 2004, 14(9):1031-1044. 10.1093/cercor/bhh063, 15142957.
6. Kudo LC, Karsten SL, Chen J, Levitt P, Geschwind DH. Genetic analysis of anterior posterior expression gradients in the developing mammalian forebrain. Cereb Cortex 2007, 17(9):2108-2122. 10.1093/cercor/bhl118, 17150988.
7. Watakabe A, Sugai T, Nakaya N, Wakabayashi K, Takahashi H, Yamamori T, Nawa H. Similarity and variation in gene expression among human cerebral cortical subregions revealed by DNA macroarrays: technical consideration of RNA expression profiling from postmortem samples. Brain Res Mol Brain Res 2001, 88(1-2):74-82. 10.1016/S0169-328X(01)00019-5, 11295233.
8. Sansom SN, Hebert JM, Thammongkol U, Smith J, Nisbet G, Surani MA, McConnell SK, Livesey FJ. Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap. Development 2005, 132(17):3947-3961. 10.1242/dev.01968, 16079153.
9. Semeralul MO, Boutros PC, Likhodi O, Okey AB, Van Tol HH, Wong AH. Microarray analysis of the developing cortex. J Neurobiol 2006, 66(14):1646-1658. 10.1002/neu.20302, 17013924.
10. Stead JD, Neal C, Meng F, Wang Y, Evans S, Vazquez DM, Watson SJ, Akil H. Transcriptional profiling of the developing rat brain reveals that the most dramatic regional differentiation in gene expression occurs postpartum. J Neurosci 2006, 26(1):345-353. 10.1523/JNEUROSCI.2755-05.2006, 16399705.
11. Abrahams BS, Tentler D, Perederiy JV, Oldham MC, Coppola G, Geschwind DH. Genome-wide analyses of human perisylvian cerebral cortical patterning. Proc Natl Acad Sci USA 2007, 104(45):17849-17854. 10.1073/pnas.0706128104, 2077018, 17978184.
12. Leamey CA, Glendining KA, Kreiman G, Kang ND, Wang KH, Fassler R, Sawatari A, Tonegawa S, Sur M. Differential gene expression between sensory neocortical areas: potential roles for Ten_m3 and Bcl6 in patterning visual and somatosensory pathways. Cereb Cortex 2008, 18(1):53-66. 10.1093/cercor/bhm031, 17478416.
13. Muhlfriedel S, Kirsch F, Gruss P, Chowdhury K, Stoykova A. Novel genes differentially expressed in cortical regions during late neurogenesis. Eur J Neurosci 2007, 26(1):33-50. 10.1111/j.1460-9568.2007.05639.x, 17614941.
14. Sun T, Patoine C, Abu-Khalil A, Visvader J, Sum E, Cherry TJ, Orkin SH, Geschwind DH, Walsh CA. Early asymmetry of gene transcription in embryonic human left and right cerebral cortex. Science 2005, 308(5729):1794-1798. 10.1126/science.1110324, 2756725, 15894532.
15. O'Leary DD. Do cortical areas emerge from a protocortex?. Trends Neurosci 1989, 12(10):400-406.
16. Watakabe A, Komatsu Y, Nawa H, Yamamori T. Gene expression profiling of primate neocortex: molecular neuroanatomy of cortical areas. Genes Brain Behav 2006, 5(Suppl 1):38-43. 10.1111/j.1601-183X.2006.00193.x, 16417616.
17. Caceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, Geschwind DH, Lockhart DJ, Preuss TM, Barlow C. Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci USA 2003, 100(22):13030-13035. 10.1073/pnas.2135499100, 240739, 14557539.
18. Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do HH, Weiss G, Enard W, et al. Regional patterns of gene expression in human and chimpanzee brains. Genome Res 2004, 14(8):1462-1473. 10.1101/gr.2538704, 509255, 15289471.
19. Roth RB, Hevezi P, Lee J, Willhite D, Lechner SM, Foster AC, Zlotnik A. Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics 2006, 7(2):67-80. 10.1007/s10048-006-0032-6, 16572319.
20. Stansberg C, Vik-Mo AO, Holdhus R, Breilid H, Srebro B, Petersen K, Jorgensen HA, Jonassen I, Steen VM. Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation. BMC Genomics 2007, 8:94. 10.1186/1471-2164-8-94, 1853090, 17408481.
21. Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, et al. The functional landscape of mouse gene expression. J Biol 2004, 3(5):21. 10.1186/jbiol16, 549719, 15588312.
22. Dysvik B, Jonassen I. J-Express: exploring gene expression data using Java. Bioinformatics 2001, 17(4):369-370. 10.1093/bioinformatics/17.4.369, 11301307.
23. Winer J, Jung CK, Shackel I, Williams PM. Development and validation of real-time quantitative reverse transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal Biochem 1999, 270(1):41-49. 10.1006/abio.1999.4085, 10328763.
24. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34(2):374-378.
25. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98(9):5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
26. Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, et al. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 2005, (33 Database):D284-288. 540032, 15608197.
27. Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucl Acids Res 2006, 34(suppl_2):W645-650. 10.1093/nar/gkl229, 1538848, 16912992.
28. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, Xing Y, Lubischer JL, Krieg PA, Krupenko SA, et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 2008, 28(1):264-278. 10.1523/JNEUROSCI.4178-07.2008, 18171944.
29. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, et al. A survey of genetic human cortical gene expression. Nat Genet 2007, 39(12):1494-1499. 10.1038/ng.2007.16, 17982457.
30. Sugino K, Hempel CM, Miller MN, Hattox AM, Shapiro P, Wu C, Huang ZJ, Nelson SB. Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat Neurosci 2006, 9(1):99-107. 10.1038/nn1618, 16369481.
31. Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics 2000, 2(3):143-147.
32. Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature 2007, 445(7124):168-176. 10.1038/nature05453, 17151600.
33. Arimatsu Y. Latexin: a molecular marker for regional specification in the neocortex. Neurosci Res 1994, 20(2):131-135. 10.1016/0168-0102(94)90030-2, 7808696.
34. Hirokawa J, Watakabe A, Ohsawa S, Yamamori T. Analysis of Area-Specific Expression Patterns of RORbeta, ER81 and Nurr1 mRNAs in Rat Neocortex by Double In Situ Hybridization and Cortical Box Method. PLoS ONE 2008, 3(9):e3266. 10.1371/journal.pone.0003266, 2533703, 18815614.
35. Li H, Bishop KM, O'Leary DD. Potential target genes of EMX2 include Odz/Ten-M and other gene families with implications for cortical patterning. Mol Cell Neurosci 2006, 33(2):136-149. 10.1016/j.mcn.2006.06.012, 16919471.
36. Strand AD, Aragaki AK, Baquet ZC, Hodges A, Cunningham P, Holmans P, Jones KR, Jones L, Kooperberg C, Olson JM. Conservation of regional gene expression in mouse and human brain. PLoS Genet 2007, 3(4):e59. 10.1371/journal.pgen.0030059, 1853119, 17447843.
37. Yamamori T, Rockland KS. Neocortical areas, layers, connections, and gene expression. Neurosci Res 2006, 55(1):11-27. 10.1016/j.neures.2006.02.006, 16546282.
38. Zapala MA, Hovatta I, Ellison JA, Wodicka L, Del Rio JA, Tennant R, Tynan W, Broide RS, Helton R, Stoveken BS, et al. Adult mouse brain gene expression patterns bear an embryologic imprint. Proc Natl Acad Sci USA 2005, 102(29):10357-10362. 10.1073/pnas.0503357102, 1173363, 16002470.
39. Liu Q, Dwyer ND, O'Leary DD. Differential expression of COUP-TFI, CHL1, and two novel genes in developing neocortex identified by differential display PCR. J Neurosci 2000, 20(20):7682-7690.
40. Armentano M, Chou SJ, Tomassy GS, Leingartner A, O'Leary DD, Studer M. COUP-TFI regulates the balance of cortical patterning between frontal/motor and sensory areas. Nat Neurosci 2007, 10(10):1277-1286. 10.1038/nn1958, 17828260.
41. Kashani AH, Qiu Z, Jurata L, Lee S-K, Pfaff S, Goebbels S, Nave K-A, Ghosh A. Calcium Activation of the LMO4 Transcription Complex and Its Role in the Patterning of Thalamocortical Connections. J Neurosci 2006, 26(32):8398-8408. 10.1523/JNEUROSCI.0618-06.2006, 16899735.
42. Wadman IA, Osada H, Grutz GG, Agulnick AD, Westphal H, Forster A, Rabbitts TH. The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins. EMBO J 1997, 16(11):3145-3157. 10.1093/emboj/16.11.3145, 1169933, 9214632.
43. Lee SK, Jurata LW, Nowak R, Lettieri K, Kenny DA, Pfaff SL, Gill GN. The LIM domain-only protein LMO4 is required for neural tube closure. Mol Cell Neurosci 2005, 28(2):205-214. 10.1016/j.mcn.2004.04.010, 15691703.
44. Huang Z, Kawase-Koga Y, Zhang S, Visvader J, Toth M, Walsh CA, Sun T. Transcription factor Lmo4 defines the shape of functional areas in developing cortices and regulates sensorimotor control. Dev Biol 2009, 327(1):132-142. 10.1016/j.ydbio.2008.12.003, 2771174, 19111533.
45. Santo-Yamada Y, Yamada K, Wada E, Goto Y, Wada K. Blockade of bombesin-like peptide receptors impairs inhibitory avoidance learning in mice. Neurosci Lett 2003, 340(1):65-68. 10.1016/S0304-3940(03)00077-6, 12648760.
46. Arimatsu Y, Ishida M, Takiguchi-Hayashi K, Uratani Y. Cerebral cortical specification by early potential restriction of progenitor cells and later phenotype control of postmitotic neurons. Development 1999, 126(4):629-638.
47. Krubitzer L. The organization of neocortex in mammals: are species differences really so different?. Trends Neurosci 1995, 18(9):408-417. 10.1016/0166-2236(95)93938-T, 7482807.
48. Northcutt RG, Kaas JH. The emergence and evolution of mammalian neocortex. Trends Neurosci 1995, 18(9):373-379. 10.1016/0166-2236(95)93932-N, 7482801.