Forebrain-enriched RNAs of the canary: a population analysis using hybridization kinetics

Expression of the GABA(A) receptor gamma4-subunit gene in discrete nuclei within the zebra finch song system

The acquisition, production and maintenance of song by oscine birds is a form of audition-dependent learning that, in many ways, resembles the process by which humans learn to speak. In songbirds, the generation of structured song is determined by the activity of two interconnected neuronal pathways (the anterior forebrain pathway and the vocal motor pathway), each of which contains a number of discrete nuclei that together form the song system. It is becoming increasingly evident that inhibitory GABAergic mechanisms are indispensable in counterbalancing the excitatory actions of glutamate and, thus, likely shape the neuronal firing patterns of neurons within this network. Furthermore, there is compelling evidence for the involvement of GABA(A) receptors, although the molecular composition of these has, to date, remained elusive. Here we describe the isolation of a complementary DNA for the zebra finch GABA(A) receptor gamma4 subunit, and map the expression pattern of the corresponding gene within the zebra finch (Taeniopygia guttata) brain. Our findings show, remarkably, that the gamma4-subunit transcript is highly enriched in the major nuclei of the song system, including the lateral magnocellular nucleus of the anterior nidopallium (LMAN), the medial magnocellular nucleus of the anterior nidopallium (MMAN), Area X, the robust nucleus of the arcopallium (RA) and the HVC (used as the proper name), as well as Field L, which innervates the area surrounding HVC. In summary, we have demonstrated the presence of the mRNA for the gamma4 subunit of the GABA(A) receptor, the major inhibitory receptor in brain, in most of the nuclei of the two neural circuits that mediate song production in the zebra finch. This not only marks the beginning of the characterization of the GABA(A) receptor subtype(s) that mediates the actions of GABA in the song system but it also provides a robust molecular marker with which to distinguish song system-specific brain structures.

The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution

BACKGROUND

Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts.

RESULTS

We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing approximately 22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations.

CONCLUSION

Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.

A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes

Songbirds have one of the most accessible neural systems for the study of brain mechanisms of behavior. However, neuroethological studies in songbirds have been limited by the lack of high-throughput molecular resources and gene-manipulation tools. To overcome these limitations, we constructed 21 regular, normalized, and subtracted full-length cDNA libraries from brains of zebra finches in 57 developmental and behavioral conditions in an attempt to clone as much of the brain transcriptome as possible. From these libraries, approximately 14,000 transcripts were isolated, representing an estimated 4,738 genes. With the cDNAs, we created a hierarchically organized transcriptome database and a large-scale songbird brain cDNA microarray. We used the arrays to reveal a set of 33 genes that are regulated in forebrain vocal nuclei by singing behavior. These genes clustered into four anatomical and six temporal expression patterns. Their functions spanned a large range of cellular and molecular categories, from signal transduction, trafficking, and structural, to synaptically released molecules. With the full-length cDNAs and a lentiviral vector system, we were able to overexpress, in vocal nuclei, proteins of representative singing-regulated genes in the absence of singing. This publicly accessible resource http://songbirdtranscriptome.net can now be used to study molecular neuroethological mechanisms of behavior.

Songbird Genomics: Methods, Mechanisms, Opportunities, and Pitfalls

The biology of songbirds poses fundamental questions about the interplay between gene, brain, and behavior. New tools of genomic analysis will be invaluable in pursuing answers to these questions. This review begins with a summary of the broad properties of the songbird genome and how songbird brain gene expression has been measured in past studies. Four key problems in songbird biology are then considered from a genomics perspective: What role does differential gene expression play in the development, maintenance, and functional organization of the song control circuit? Does gene regulation set boundaries on the process of juvenile song learning? What is the purpose of song-induced gene activity in the adult brain? How does the genome underlie the profound sexual differentiation of the song control circuit? Finally, the range of genomic technologies currently or soon to be available to songbird researchers is briefly reviewed. These technologies include online databases of expressed genes ("expressed sequence tags" or ESTs); a complete library of the zebra finch genome maintained as a bacterial artificial chromosome (BAC) library; DNA microarrays for simultaneous measurement of many genes in a single experiment; and techniques for gene manipulation in the organism. Collectively, these questions and techniques define the field of songbird neurogenomics.

The canary androgen receptor mRNA is localized in the song control nuclei of the brain and is rapidly regulated by testosterone

Singing in canaries is an androgen-inducible behavior, under the control of an identified motor pathway, which includes several discrete "song nuclei" in the telencephalon. To determine whether the mRNA for the canary androgen receptor (cAR) is expressed in these song control nuclei, we synthesized probes from the recently cloned cAR cDNA and used in situ hybridization to examine spring male canary brain sections. Concentrations of cAR mRNA are detectable in several of the song control nuclei of the forebrain, including high vocal center (HVC), lateral magnocellular nucleus of the anterior neostriatum and robust nucleus of the archistriatum. In addition, we also show that testosterone treatment rapidly induces a significant reduction of cAR mRNA levels in nucleus HVC of females. Since the effects of androgen on singing behavior occur much more slowly, the behavioral effects are probably a secondary or independent result of androgen's primary and immediate action on target gene transcription.

Differential regulation in the avian song control circuit of an mRNA predicting a highly conserved protein related to protein kinase C and the bcr oncogene

An RNA identified by differential cDNA cloning (HAT-2) is highly enriched in canary forebrain in areas associated with the control of complex learned behaviors and higher perceptual processes. The nucleotide sequence predicts a protein that is 96% identical to the product of the n-chimaerin gene isolated from human brain and contains two identifiable domains suggesting a novel role in signal transduction processes. One domain is similar to the sequence in protein kinase C which mediates diacylglycerol binding and regulation. The second domain is similar to a portion of BCR, a GTPase-activating protein encoded by the breakpoint cluster region gene. In male canaries examined during the song season, HAT-2 RNA shows variable expression within the song control circuit, and is notably less abundant in the three nuclei which concentrate androgens (HVC, RA and L-MAN). A fundamental function in the vertebrate forebrain and a possible role in the regulation of neural plasticity are suggested by the conserved structure and pattern of expression of this gene in the brain.