AFFISH-RC - Applied and Fundamental FISH Research Center - ULiège FOCUS - Freshwater and OCeanic science Unit of reSearch - ULiège
Disciplines :
Zoology
Author, co-author :
Derycke, Sofie
Kever, Loïc ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Morphologie fonctionnelle et évolutive
Van den Berge, K
Van Steenberge, M
Van Houdt, J
Clement, L
Poncin, Pascal ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Biologie du comportement - Ethologie et psychologie animale
Parmentier, Eric ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Morphologie fonctionnelle et évolutive
Verheyen, Erik
Language :
English
Title :
Neurogenomic profiling reveals distinct gene expression profiles between brain parts that are consistent in Ophthalmotilapia cichlids
Albert, F. W., Somel, M., Carneiro, M., Aximu-Petri, A., Halbwax, M., Thalmann, O., et al. (2012). A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genet. 8:e1002962. doi: 10.1371/journal.pgen.1002962
Ampatzis, K., and Dermon, C. R. (2016). Sexual dimorphisms in swimming behavior, cerebral metabolic activity and adrenoceptors in adult zebrafish (Danio rerio). Behav. Brain Res. 312, 385-393. doi: 10.1016/j.bbr.2016.06.047
Anders, S., Pyl, P. T., and Huber, W. (2015). HTSeq-a python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169. doi: 10.1093/bioinformatics/btu638
Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate-a practical and powerful approach to multiple testing J. R. Stat. Soc. Ser. B-Methodol. 57, 289-300
Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120. doi: 10.1093/bioinformatics/btu170
Bosch, O. J. (2013). Maternal aggression in rodents: brain oxytocin and vasopressin mediate pup defence. Philos. Trans. R. Soc. B Biol. Sci. 368:20130085. doi: 10.1098/rstb.2013.0085
Bshary, R., Gingins, S., and Vail, A. L. (2014). Social cognition in fishes. Trends Cogn. Sci. 18, 465-471. doi: 10.1016/j.tics.2014.04.005
Burmeister, S. S., Jarvis, E. D., and Fernald, R. D. (2005). Rapid behavioral and genomic responses to social opportunity. PLoS Biol. 3:e363. doi: 10.1371/journal.pbio.0030363
Cardoso, S. D., Teles, M. C., and Oliveira, R. F. (2015). Neurogenomic mechanisms of social plasticity. J. Exp. Biol. 218, 140-149. doi: 10.1242/jeb.106997
Cummings, M. E. (2015). The mate choice mind: studying mate preference, aversion and social cognition in the female poeciliid brain. Anim. Behav. 103, 249-258. doi: 10.1016/j.anbehav.2015.02.021
Cummings, M. E., Larkins-Ford, J., Reilly, C. R., Wong, R. Y., Ramsey, M., and Hofmann, H. A. (2008). Sexual and social stimuli elicit rapid and contrasting genomic responses. Proc. R. Soc. B Biol. Sci. 275, 393-402. doi: 10.1098/rspb.2007.1454
Dean, C., and Dresbach, T. (2006). Neuroligins and neurexins: linking cell adhesion, synapse formation and cognitive function. Trends Neurosci. 29, 21-29. doi: 10.1016/j.tins.2005.11.003
Di Poi, C., Bélanger, D., Amyot, M., Rogers, S., and Aubin-Horth, N. (2016). Receptors rather than signals change in expression in four physiological regulatory networks during evolutionary divergence in threespine stickleback. Mol. Ecol. 25, 3416-3427. doi: 10.1111/mec.13690
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., et al. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21. doi: 10.1093/bioinformatics/bts635
Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., et al. (2005). BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439-3440. doi: 10.1093/bioinformatics/bti525
Edgar, R., Domrachev, M., and Lash, A. E. (2002). Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210. doi: 10.1093/nar/30.1.207
Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., et al. (2002). Intra-and interspecific variation in primate gene expression patterns. Science 296, 340-343. doi: 10.1126/science.1068996
Fernald, R. D., and Maruska, K. P. (2012). Social information changes the brain. Proc. Natl. Acad. Sci. U.S.A. 109, 17194-17199. doi: 10.1073/pnas.1202552109
Godwin, J., and Thompson, R. (2012). Nonapeptides and social behavior in fishes. Horm. Behav. 61, 230-238. doi: 10.1016/j.yhbeh.2011.12.016
Gonzalez-Martinez, D., Madigou, T., Zmora, N., Anglade, I., Zanuy, S., Zohar, Y., et al. (2001). Differential expression of three different prepro-GnRH (gonadotrophin-releasing hormone) messengers in the brain of the European sea bass (Dicentrarchus labrax). J. Comp. Neurol. 429, 144-155. doi: 10.1002/1096-9861(20000101)429:1<144::AID-CNE11>3.0.CO;2-B
Gopurappilly, R., Ogawa, S., and Parhar, I. S. (2013). Functional significance of GnRH and kisspeptin, and their cognate receptors in teleost reproduction. Front. Endocrinol. 4:24. doi: 10.3389/fendo.2013.00024
Greenwood, A. K., and Peichel, C. L. (2015). Social regulation of gene expression in threespine sticklebacks. PLoS ONE 10:e0137726. doi: 10.1371/journal.pone.0137726
Hanssens, M., Snoeks, J., and Verheyen, E. (1999). A morphometric revision of the genus Ophthalmotilapia (Teleostei, Cichlidae) from Lake Tanganyika (East Africa). Zool. J. Linn. Soc. 125, 487-512. doi: 10.1111/j.1096-3642.1999.tb00602.x
Hein, L., and Kobilka, B. K. (1997). Adrenergic receptors-from molecular structure to in vivo function. Trends Cardiovasc. Med. 7, 137-145. doi: 10.1016/S1050-1738(97)00034-0
Heller, R., Manduchi, E., Grant, G. R., and Ewens, W. J. (2009). A flexible two-stage procedure for identifying gene sets that are differentially expressed. Bioinformatics 25, 1019-1025. doi: 10.1093/bioinformatics/btp076
Herdegen, T., and Leah, J. D. (1998). Inducible and constitutive transcription factors in the mammalian nervous system: control of gene expression by Jun, Fos and Krox, and CREB/ATF proteins. Brain Res. Rev. 28, 370-490. doi: 10.1016/S0165-0173(98)00018-6
Heyne, H. O., Lautenschlager, S., Nelson, R., Besnier, F., Rotival, M., Cagan, A., et al. (2014). Genetic influences on brain gene expression in rats selected for tameness and aggression. Genetics 198, 1277-1290. doi: 10.1534/genetics.114.168948
Holm, S. (1979). A simple sequentially rejective mulitple test procedure. Scand. J. Stat. 6, 65-70
Kéver, L., Parmentier, E., Derycke, S., Verheyen, E., Snoeks, J., and Van Steenberge, M. (2017). Limited possibilities for prezygotic barriers in the reproductive behaviour of sympatric Ophthalmotilapia species (Teleostei, Cichlidae). Zoology. doi: 10.1016/j.zool.2017.12.001. [Epub ahead of print]
Khaitovich, P., Muetzel, B., She, X. W., Lachmann, M., Hellmann, I., Dietzsch, J., et al. (2004). Regional patterns of gene expression in human and chimpanzee brains. Genome Res. 14, 1462-1473. doi: 10.1101/gr.2538704
Konings, A. (2014). Featherfins in their Natural Habitat. Cichlid Press
Kuenzel, W. J., McCune, S. K., Talbot, R. T., Sharp, P. J., and Hill, J. M. (1997). Sites of gene expression for vasoactive intestinal polypeptide throughout the brain of the chick (Gallus domesticus). J. Comp. Neurol. 381, 101-118. doi: 10.1002/(SICI)1096-9861(19970428)381:1<101::AID-CNE8>3.0.CO;2-5;2-5
Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168-176. doi: 10.1038/nature05453
Li, H. (2011). A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993. doi: 10.1093/bioinformatics/btr509
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079. doi: 10.1093/bioinformatics/btp352
Lund, S. P., Nettleton, D., McCarthy, D. J., and Smyth, G. K. (2012). Detecting differential expression in RNA-sequence data using Quasi-likelihood with shrunken dispersion Estimates. Stat. Appl. Genet. Mol. Biol. 11. doi: 10.1515/1544-6115.1826
McCarthy, D. J., and Smyth, G. K. (2009). Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 25, 765-771. doi: 10.1093/bioinformatics/btp053
Mello, C. V., Vicario, D. S., and Clayton, D. F. (1992). Song presentation induces gene-expression in the songbird forebrain. Proc. Natl. Acad. Sci. U.S.A. 89, 6818-6822. doi: 10.1073/pnas.89.15.6818
Miranda, E., and Lomas, D. A. (2006). Neuroserpin: a serpin to think about. Cell. Mol. Life Sci. 63, 709-722. doi: 10.1007/s00018-005-5077-4
Moll, P., Ante, M., Seitz, A., and Reda, T. (2014). QuantSeq 3' mRNA sequencing for RNA quantification. Nat. Meth. 11. doi: 10.1038/nmeth.f.376
Myers, E. M., Bartlett, C. W., Machiraju, R., and Bohland, J. W. (2015). An integrative analysis of regional gene expression profiles in the human brain. Methods 73, 54-70. doi: 10.1016/j.ymeth.2014.12.010
Nevado, B., Fazalova, V., Backeljau, T., Hanssens, M., and Verheyen, E. (2011). Repeated unidirectional introgression of nuclear and mitochondrial DNA between four congeneric Tanganyikan Cichlids. Mol. Biol. Evol. 28, 2253-2267. doi: 10.1093/molbev/msr043
Newman, S. W. (1999). The Medial Extended Amygdala in Male Reproductive Behavior A Node in the Mammalian Social Behavior Network. Ann. N. Y. Acad. Sci. 877, 242-257. doi: 10.1111/j.1749-6632.1999.tb09271.x
Northcutt, R. G. (2002). Understanding vertebrate brain evolution. Integr. Comp. Biol. 42, 743-756. doi: 10.1093/icb/42.4.743
O'Connell, L. A., and Hofmann, H. A. (2011). The vertebrate mesolimbic reward system and social behavior network: a comparative synthesis. J. Comp. Neurol. 519, 3599-3639. doi: 10.1002/cne.22735
Oliveira, R. F. (2012). Social plasticity in fish: integrating mechanisms and function. J. Fish Biol. 81, 2127-2150. doi: 10.1111/j.1095-8649.2012.03477.x
Prasad, P., Ogawa, S., and Parhar, I. S. (2015). Role of serotonin in fish reproduction. Front. Neurosci. 9:195. doi: 10.3389/fnins.2015.00195
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y. F., Law, C. W., Shi, W., et al. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43:e47. doi: 10.1093/nar/gkv007
Roberts, B. L., Vanrossem, A., and Dejager, S. (1992). The influence of cerebellar lesions on the swimming performance of the trout. J. Exp. Biol. 167, 171-178
Robinson, G. E., Fernald, R. D., and Clayton, D. F. (2008). Genes and social behavior. Science 322, 896-900. doi: 10.1126/science.1159277
Robinson, M. D., McCarthy, D. J., and Smyth, G. K. (2010). Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. doi: 10.1093/bioinformatics/btp616
Robinson, M. D., and Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11:R25. doi: 10.1186/gb-2010-11-3-r25
Rotta, L. N., Valle, S. C., Schweigert, I., Dei Ricardi, L., Ferronatto, M. E., da Silva, L., et al. (2002). Utilization of energy nutrients by cerebellar slices. Neurochem. Res. 27, 201-206. doi: 10.1023/A:1014828419900
Sanogo, Y. O., Band, M., Blatti, C., Sinha, S., and Bell, A. M. (2012). Transcriptional regulation of brain gene expression in response to a territorial intrusion. Proc. R. Soc. B Biol. Sci. 279, 4929-4938. doi: 10.1098/rspb.2012.2087
Sanogo, Y. O., and Bell, A. M. (2016). Molecular mechanisms and the conflict between courtship and aggression in three-spined sticklebacks. Mol. Ecol. 25, 4368-4376. doi: 10.1111/mec.13766
Schuirmann, D. J. (1987). A comparison of the two one-sided tests procedure and the power approach for assessing equivalence of average bioavailability. J. Pharmacokin. Biopharm. 15, 657-680. doi: 10.1007/BF01068419
Sih, A., Bell, A., and Johnson, J. C. (2004). Behavioral syndromes: an ecological and evolutionary overview. Trends Ecol. Evol. (Amst). 19, 372-378. doi: 10.1016/j.tree.2004.04.009
Simões, J. M., Teles, M. C., Oliveira, R. F., Van der Linden, A., and Verhoye, M. (2012). A three-dimensional stereotaxic MRI brain atlas of the cichlid fish Oreochromis mossambicus. PLoS ONE 7:e44086. doi: 10.1371/journal.pone.0044086
Srinivasan, M., Sedmak, D., and Jewell, S. (2002). Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am. J. Pathol. 161, 1961-1971. doi: 10.1016/S0002-9440(10)64472-0
Sukhov, R. R., Walker, L. C., Rance, N. E., Price, D. L., and Young, W. S. (1993). Vasopressin and oxytocin gene-expression in the human hypothalamus. J. Comp. Neurol. 337, 295-306. doi: 10.1002/cne.903370210
Van den Berge, K., Soneson, C., Robinson, M. D., and Clement, L. (2017). stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biol. 18:151. doi: 10.1186/s13059-017-1277-0
van Maldegem, F., de Wit, M., Morsink, F., Musler, A., Weegenaar, J., and van Noesel, C. J. M. (2008). Effects of processing delay, formalin fixation, and immunohistochemistry on RNA recovery from formalin-fixed paraffin-embedded tissue sections. Diagn. Mol. Pathol. 17, 51-58. doi: 10.1097/PDM.0b013e31814b8866
Warnes, G. R., Bolker, B., Bonebakker, L., Gentleman, R., Liaw, W. H. A., Lumley, T., et al. (2016). Gplots: Various R Programming Tools for Plotting Data. R package version 3.0.1. (Online). Available online at: https://CRAN.R-project.org/package=gplots
Wencke, W., Sanchez-Cabo, F., and Ricote, M. (2015). GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics 31, 2912-2914. doi: 10.1093/bioinformatics/btv300
Whitehead, A., and Crawford, D. L. (2005). Variation in tissue-specific gene expression among natural populations. Genome Biol. 6:R13. doi: 10.1186/gb-2005-6-2-r13
Wong, R. Y., and Hofmann, H. A. (2010). 'Behavioural Genomics: an organismic perspective'. in Encyclopedia of Life Sciences. (Chichester: John Wiley & Sons, Ltd.)
Wood, L. S., Desjardins, J. K., and Fernald, R. D. (2011). Effects of stress and motivation on performing a spatial task. Neurobiol. Learn. Mem. 95, 277-285. doi: 10.1016/j.nlm.2010.12.002
Wu, D., and Smyth, G. (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res. 40:e133. doi: 10.1093/nar/gks461
Yoshida, M., Okamura, I., and Uematsu, K. (2004). Involvement of the cerebellum in classical fear conditioning in goldfish. Behav. Brain Res. 153, 143-148. doi: 10.1016/j.bbr.2003.11.008
Zapala, M. A., Hovatta, I., Ellison, J. A., Wodicka, L., Del Rio, J. A., Tennant, R., et al. (2005). Adult mouse brain gene expression patterns bear an embryologic imprint. Proc. Natl. Acad. Sci. U.S.A. 102, 10357-10362. doi: 10.1073/pnas.0503357102
Zohar, Y., Munoz-Cueto, J. A., Elizur, A., and Kah, O. (2010). Neuroendocrinology of reproduction in teleost fish. Gen. Comp. Endocrinol. 165, 438-455. doi: 10.1016/j.ygcen.2009.04.017