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

Replogle, Kirstin; Arnold, Arthur P.; Ball, Gregory F.; Band, Mark; Bensch, Staffan; Brenowitz, Eliot A.; Dong, Shu; Drnevich, Jenny; Ferris, Margaret; George, Julia M.; Gong, George; Hasselquist, Dennis; Hernández, Álvaro Gonzalez; Kim, Ryan; Lewin, Harris A.; Liu, Lei; Lovell, Peter V.; Mello, Claudio V.; Naurin, Sara; Rodriguez-Zas, Sandra L.; Thimmapuram, Jyothi; Wade, Juli; Clayton, David F.

doi:10.1186/1471-2164-9-131

Cited by 128 publications

(156 citation statements)

References 71 publications

(70 reference statements)

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“…For RNA analysis we used the microarray resources of the Songbird Neurogenomics Initiative to measure the RNAs that hybridize to Ϸ18,000 cDNA probes (see Table 4 in ref. 17). These are ''nonredundant'' in that their sequences are nonoverlapping, although we have estimated that 15Ϫ35% may derive from genes in common (e.g., different splice forms or different segments of long transcripts).…”

Section: Microarray Analysis Distinguishes Eachmentioning

confidence: 99%

“…To tease out the larger functional significance of these molecular differences, we applied a statistical analysis (23) based on the Gene Ontology (GO) annotation terms associated with each expression profile. GO annotations were derived primarily from the annotations of apparent chicken orthologs as described (17). Overall, 72% of the regulated sequences had some degree of annotation.…”

Section: The Habituated Profile Is a Slow Response To Habituation Tramentioning

confidence: 99%

“…S3, Table S2, and Table S3. Clone ID: ESTIMA sequence ID for the cDNA spotted on the array (17). Gene ID (common protein names): based on the SoNG Initiative annotation (17).…”

Section: Novel Song Suppresses Putative Noncoding and Ion Channel Rnasmentioning

confidence: 99%

“…With new resources available for comprehensive analysis of zebra finch genes and proteins (17), we now address these questions experimentally. To increase the power and depth of our analysis, in our primary experiment we measured both RNAs (via microarray hybridizations) and proteins (via 2-dimensional gel electrophoresis followed by mass-spectroscopy-based sequencing of individual spots).…”

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confidence: 99%

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Discrete molecular states in the brain accompany changing responses to a vocal signal

Dong¹,

Replogle

Hasadsri³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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New experiences can trigger changes in gene expression in the brain. To understand this phenomenon better, we studied zebra finches hearing playbacks of birdsong. Earlier research had shown that initial playbacks of a novel song transiently increase the ZENK (ZIF-268, EGR1, NGFIA, KROX-24) mRNA in the auditory forebrain, but the response selectively habituates after repetition of the stimulus. Here, using DNA microarray analysis, we show that novel song exposure induces rapid changes in thousands of RNAs, with even more RNAs decreasing than increasing. Habituation training leads to the emergence of a different gene expression profile a day later, accompanied by loss of essentially all of the rapid ''novel'' molecular responses. The novel molecular profile is characterized by increases in genes involved in transcription and RNA processing and decreases in ion channels and putative noncoding RNAs. The ''habituated'' profile is dominated by changes in genes for mitochondrial proteins. A parallel proteomic analysis [2-dimensional difference gel electrophoresis (2D-DIGE) and sequencing by mass spectrometry] also detected changes in mitochondrial proteins, and direct enzyme assay demonstrated changes in both complexes I and IV in the habituated state. Thus a natural experience, in this case hearing the sound of birdsong, can lead to major shifts in energetics and macromolecular metabolism in higher centers in the brain.habituation ͉ microarray ͉ mitochondria ͉ proteomic ͉ songbird T he genome was once regarded as a passive agent in brain function, directing brain development but having little role in the moment-to-moment operation of the mature brain. Through the widespread application of technologies for measuring gene expression in experimental model systems, however, it now appears that changing social conditions, perceptual experience, and behavioral activity can all result in rapid changes in the expression of specific genes in the brain (1, 2). The challenge ahead is to understand the links between gene expression and natural experience, behavior, and cognition.A striking example for study is the phenomenon of song response habituation in songbirds (3). In one of the first demonstrations of brain gene activation in response to a natural experience, Mello and colleagues (4) showed that the sound of another bird singing triggers a transient increase in expression of the ZENK gene EGR1, NGFIA, in an auditory/associative region of the songbird forebrain. This was not simply a sensory or an auditory response, as its magnitude showed clear categorical discrimination (conspecific song Ͼ heterospecific song Ͼ noise Ͼ pure tones). Further research showed that the same song stimulus would either activate ZENK expression or not, depending on the recent history of exposure to the stimulus and its context. After the stimulus was repeated for a few hours the ZENK RNA declined back to its initial starting level (5, 6). Subsequent presentations no longer elicited a response, but presentation of a different song (6) or even of ...

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Section: Microarray Analysis Distinguishes Eachmentioning

confidence: 99%

Section: The Habituated Profile Is a Slow Response To Habituation Tramentioning

confidence: 99%

“…S3, Table S2, and Table S3. Clone ID: ESTIMA sequence ID for the cDNA spotted on the array (17). Gene ID (common protein names): based on the SoNG Initiative annotation (17).…”

Section: Novel Song Suppresses Putative Noncoding and Ion Channel Rnasmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Discrete molecular states in the brain accompany changing responses to a vocal signal

Dong¹,

Replogle

Hasadsri³

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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100

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“…Various molecular tools for exploring these issues in songbirds are available, including a sequenced cDNA library and microarrays of genes expressed in the zebra finch brain (27)(28)(29)(30), the sequence of the zebra finch genome (Songbird Genomics Organization; http://songbirdgenome.org. ), and a zebra finch BAC library (31).…”

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confidence: 99%