Genomic resources for songbird research and their use in characterizing gene expression during brain development

Vocal learning and neuronal replacement have been studied extensively in songbirds, but until recently, few molecular and genomic tools for songbird research existed. Here we describe new molecular/genomic resources developed in our laboratory. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11,000 cDNA clones from these libraries, representing 5,866 unique gene transcripts, were randomly picked and sequenced from the 3′ ends. A web-based database was established for clone tracking, sequence analysis, and functional annotations. Our cDNA libraries were not normalized. Sequencing ESTs without normalization produced many developmental stage-specific sequences, yielding insights into patterns of gene expression at different stages of brain development. In particular, the cDNA library made from brains at posthatching day 30–50, corresponding to the period of rapid song system development and song learning, has the most diverse and richest set of genes expressed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the high vocal center of both adult male zebra finches and canaries (Serinus canaria). Genes differentially expressed in the high vocal center were identified from the microarray hybridization results. Selected genes were validated by in situ hybridization. Networks among the regulated genes were also identified. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis.

[1]  D. Wilkin,et al.  Neuron , 2001, Brain Research.

[2]  P. Crino,et al.  Preparation of cDNA from single cells and subcellular regions. , 1999, Methods in enzymology.

[3]  V. Ambros,et al.  Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation , 2004, Genome Biology.

[4]  F. Nottebohm,et al.  Fate of new neurons in adult canary high vocal center during the first 30 days after their formation , 1999, The Journal of comparative neurology.

[5]  Gabriel Kreiman,et al.  Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex , 2006, Nature Neuroscience.

[6]  Fernando Nottebohm,et al.  Migration of young neurons in adult avian brain , 1988, Nature.

[7]  F. Nottebohm,et al.  Direct evidence for loss and replacement of projection neurons in adult canary brain , 1993, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[8]  Robert J. Tempelman,et al.  A cDNA microarray from the telencephalon of juvenile male and female zebra finches , 2004, Journal of Neuroscience Methods.

[9]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[10]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[11]  Fernando Nottebohm,et al.  The Neural Basis of Birdsong , 2005, PLoS biology.

[12]  T. Tuschl,et al.  Identification of Tissue-Specific MicroRNAs from Mouse , 2002, Current Biology.

[13]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[14]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[15]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[16]  Masakazu Konishi,et al.  Neuronal growth, atrophy and death in a sexually dimorphic song nucleus in the zebra finch brain , 1985, Nature.

[17]  R. Mooney,et al.  Calcium‐binding proteins define interneurons in HVC of the zebra finch (Taeniopygia guttata) , 2005, The Journal of comparative neurology.

[18]  Richard Hans Robert Hahnloser,et al.  An ultra-sparse code underliesthe generation of neural sequences in a songbird , 2002, Nature.

[19]  L. Maffei,et al.  BDNF Regulates the Maturation of Inhibition and the Critical Period of Plasticity in Mouse Visual Cortex , 1999, Cell.

[20]  F. Nottebohm.  Why Are Some Neurons Replaced in Adult Brain? , 2002, The Journal of Neuroscience.

[21]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[22]  Konstantin Khrapko,et al.  A microRNA array reveals extensive regulation of microRNAs during brain development. , 2003, RNA.

[23]  Richard P Lifton,et al.  Disruption of Contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome. , 2004, American journal of human genetics.

[24]  F. Nottebohm,et al.  Central control of song in the canary, Serinus canarius , 1976, The Journal of comparative neurology.

[25]  T Gaasterland,et al.  Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture. , 1996, Biochimie.

[26]  Jörg Böhner,et al.  Early acquisition of song in the zebra finch, Taeniopygia guttata , 1990, Animal Behaviour.

[27]  F. Nottebohm,et al.  Cell death and neuronal recruitment in the high vocal center of adult male canaries are temporally related to changes in song. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[28]  U. Rutishauser.  Defining a Role and Mechanism for Igcam Function in Vertebrate Axon Guidance , 2000, The Journal of cell biology.

[29]  A. Steven,et al.  Transgenic Mice Expressing a Mutant Form of Loricrin Reveal the Molecular Basis of the Skin Diseases, Vohwinkel Syndrome and Progressive Symmetric Erythrokeratoderma , 2000, The Journal of cell biology.

[30]  Piero Carninci,et al.  A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes , 2006, Proceedings of the National Academy of Sciences.

[31]  B. Ranscht,et al.  Sequence of contactin, a 130-kD glycoprotein concentrated in areas of interneuronal contact, defines a new member of the immunoglobulin supergene family in the nervous system , 1988, The Journal of cell biology.

[32]  Felix Naef,et al.  Freedom and Rules: The Acquisition and Reprogramming of a Bird's Learned Song , 2005, Science.

[33]  Kenneth S. Kosik,et al.  The Elegance of the MicroRNAs: A Neuronal Perspective , 2005, Neuron.

[34]  M. Soares,et al.  Construction and characterization of a normalized cDNA library. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[35]  E. Nordeen,et al.  Projection neurons within a vocal motor pathway are born during song learning in zebra finches , 1988, Nature.

[36]  Fernando Nottebohm,et al.  High Levels of New Neuron Addition Persist When the Sensitive Period for Song Learning Is Experimentally Prolonged , 2006, The Journal of Neuroscience.

[37]  F. Nottebohm,et al.  A relationship between behavior, neurotrophin expression, and new neuron survival. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[38]  F. Nottebohm,et al.  The Road We Travelled: Discovery, Choreography, and Significance of Brain Replaceable Neurons , 2004, Annals of the New York Academy of Sciences.