LOC689986, a unique gene showing specific expression in restricted areas of the rodent neocortex

BMC Neuroscience

Vidar M Steen¹  Christine Stansberg¹  Vidar Gundersen²  Johanne Egge Rinholm³  Bjarte Håvik¹  Kari M Ersland¹ 

[1]KG Jebsen Centre for Psychosis Research, Oslo, Norway

[2]Department of Neurology, Oslo University Hospital, Oslo, Norway

[3]Department of Anatomy and Centre for Molecular Biology and Neuroscience, University of Oslo, Oslo, Norway

关键词: Somatosensory;    Enriched expression;    Cortex;    Conservation;    Cerebellum;   

Others  :  1140218
DOI  :  10.1186/1471-2202-14-68

 received in 2012-12-14, accepted in 2013-07-01,  发布年份 2013

【 摘 要 】

Background

The neocortex is a highly specialised and complex brain structure, involved in numerous tasks, ranging from processing and interpretation of somatosensory information, to control of motor functions. The normal function linked to distinct neocortical areas might involve control of highly specific gene expression, and in order to identify such regionally enriched genes, we previously analysed the global gene expression in three different cortical regions (frontomedial, temporal and occipital cortex) from the adult rat brain. We identified distinct sets of differentially expressed genes. One of these genes, namely the hypothetical protein LOC689986 (LOC689986), was of particular interest, due to an almost exclusive expression in the temporal cortex.

Results

Detailed analysis of LOC689986 in the adult rat brain confirmed the expression in confined areas of parieto-temporal cortex, and revealed highly specific expression in layer 4 of the somatosensory cortex, with sharp borders towards the neighbouring motor cortex. In addition, LOC689986 was found to be translated in vivo, and was detected in the somatosensory cortex and in the Purkinje cells of the cerebellar cortex. The protein was present in neuronal dendrites and also in astrocyte cells. Finally, this unique gene is apparently specific for, and highly conserved in, the vertebrate lineage.

Conclusions

In this study, we have partially characterised the highly conserved LOC689986 gene, which is specific to the vertebrate linage. The gene displays a distinct pattern of expression in layer 4 of the somatosensory cortex, and areas of the parieto-temporal cortex in rodents.

【 授权许可】

   
2013 Ersland et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Rakic P: Specification of cerebral cortical areas. Science 1988, 241(4862):170-176.
• [2]Rash BG, Grove EA: Area and layer patterning in the developing cerebral cortex. Curr Opin Neurobiol 2006, 16(1):25-34.
• [3]O'Leary DD, Sahara S: Genetic regulation of arealization of the neocortex. Curr Opin Neurobiol 2008, 18(1):90-100.
• [4]Bishop KM, Goudreau G, O'Leary DD: Regulation of area identity in the mammalian neocortex by Emx2 and Pax6. Science 2000, 288(5464):344-349.
• [5]Mallamaci A, Muzio L, Chan CH, Parnavelas J, Boncinelli E: Area identity shifts in the early cerebral cortex of Emx2-/- mutant mice. Nat Neurosci 2000, 3(7):679-686.
• [6]O'Leary DD, Chou SJ, Sahara S: Area patterning of the mammalian cortex. Neuron 2007, 56(2):252-269.
• [7]Sansom SN, Livesey FJ: Gradients in the brain: the control of the development of form and function in the cerebral cortex. Cold Spring Harb Perspect Biol 2009, 1(2):a002519.
• [8]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.
• [9]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]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. BioMed Central Full Text
• [11]Stansberg C, Ersland KM, van der Valk P, Steen VM: Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex. BMC Neurosci 2011, 12:15. BioMed Central Full Text
• [12]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.
• [13]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. BioMed Central Full Text
• [14]Ferno J, Raeder MB, Vik-Mo AO, Skrede S, Glambek M, Tronstad KJ, Breilid H, Lovlie R, Berge RK, Stansberg C, et al.: Antipsychotic drugs activate SREBP-regulated expression of lipid biosynthetic genes in cultured human glioma cells: a novel mechanism of action? Pharmacogenomics J 2005, 5(5):298-304.
• [15]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.
• [16]Wibrand K, Messaoudi E, Havik B, Steenslid V, Lovlie R, Steen VM, Bramham CR: Identification of genes co-upregulated with Arc during BDNF-induced long-term potentiation in adult rat dentate gyrus in vivo. Eur J Neurosci 2006, 23(6):1501-1511.
• [17]Rain JC, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schachter V, et al.: The protein-protein interaction map of Helicobacter pylori. Nature 2001, 409(6817):211-215.
• [18]Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, et al.: Ensembl 2011. Nucleic Acids Res 2011, 39(Database issue):D800-D806.
• [19]Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al.: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948.
• [20]Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R: A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 2010, 38(Web Server issue):W695-W699.
• [21]Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al.: InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37(Database issue):D211-D215.
• [22]Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340(4):783-795.
• [23]Nielsen H, Engelbrecht J, Brunak S, von Heijne G: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997, 10(1):1-6.
• [24]Nielsen H, Krogh A: Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol 1998, 6:122-130.
• [25]Paxinos G, Watson C: The Rat Brain in Stereotaxic coordinates. 5th edition. Burlington (MA), San Diego (CA), London (UK): Elsevier Academic Press; 2005.
• [26]Fox K: Barrel cortex. New York (NY): Cambridge University Press; 2008.
• [27]Belgard TG, Marques AC, Oliver PL, Abaan HO, Sirey TM, Hoerder-Suabedissen A, Garcia-Moreno F, Molnar Z, Margulies EH, Ponting CP: A transcriptomic atlas of mouse neocortical layers. Neuron 2011, 71(4):605-616.
• [28]Valles A, Boender AJ, Gijsbers S, Haast RA, Martens GJ, de Weerd P: Genomewide analysis of rat barrel cortex reveals time- and layer-specific mRNA expression changes related to experience-dependent plasticity. J Neurosci 2011, 31(16):6140-6158.
• [29]Paxinos G (Ed): The Rat Nervous System. Third edition. San Diego (CA), London (UK): Elsevier Academic Press; 2004.
• [30]Ghazalpour A, Bennett B, Petyuk VA, Orozco L, Hagopian R, Mungrue IN, Farber CR, Sinsheimer J, Kang HM, Furlotte N, et al.: Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet 2011, 7(6):e1001393.
• [31]Fisher SE, Scharff C: FOXP2 as a molecular window into speech and language. Trends Genet 2009, 25(4):166-177.
• [32]Wade PA, Jones PL, Vermaak D, Wolffe AP: A multiple subunit Mi-2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. Curr Biol 1998, 8(14):843-846.
• [33]Zhang Y, LeRoy G, Seelig HP, Lane WS, Reinberg D: The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 1998, 95(2):279-289.
• [34]Xue Y, Wong J, Moreno GT, Young MK, Cote J, Wang W: NURD, a novel complex with both ATP-dependent chromatin-remodeling and histone deacetylase activities. Mol Cell 1998, 2(6):851-861.
• [35]Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL: Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature 1998, 395(6705):917-921.
• [36]Bowen NJ, Fujita N, Kajita M, Wade PA: Mi-2/NuRD: multiple complexes for many purposes. Biochim Biophys Acta 2004, 1677(1–3):52-57.