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

Abstract

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 ...

Impact of experience-dependent and -independent factors on gene expression in songbird brain

“…gives the designated number of each experiment, and the other columns show the species, number of birds (n), number of treatment groups (g), age, sex, brain regions, and contrasts evaluated by each experiment. We provide both rigorous Bonferroni-corrected P values and a more liberal empirical standard (raw P < 0.001) derived from previous analyses of individual experiments in this dataset (23)(24)(25)(26)(27). We compared the numbers of significant probes based on raw P values instead of FDR-corrected P values because a cDNA could have the same raw P value in two experiments yet have vastly different FDR P values depending on how many other cDNAs have expression differences in each experiment.…”

“…Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA). Independent analyses of seven of the individual experiments have already been published (23)(24)(25)(26)(27), but all data were reanalyzed here under uniform procedures. The data from all 488 arrays, each representing one contributed sample (SI Appendix, Table S2), were first standardized and then assessed for relationships between the samples using principal components analysis (PCA) (SI Appendix, Fig.…”

“…Through a set of structured collaborations, this array was used to assess variations in gene expression in brain tissue samples contributed by multiple laboratories and representing a diversity of songbird species, brain subregions, developmental stages, and physiological or behavioral states. These collaborations were organized so that individual datasets could be analyzed independently, as shown in several reports to date (23)(24)(25)(26)(27). However, a unique opportunity was anticipated for an integrated global This paper results from the Arthur M. Sackler Colloquium of the National Academy of Sciences, "Biological Embedding of Early Social Adversity: From Fruit Flies to Kindergartners," held December 9-10, 2011, at the Arnold and Mabel Beckman Center of the National Academies of Sciences and Engineering in Irvine, CA.…”

What can whole genome expression data tell us about the ecology and evolution of personality?

“…Without a priori knowledge about the time course of the transcriptomic response, it can be difficult to know when, following an experimental treatment, to sample for gene expression. Because gene expression is dynamic, one might get very different results from sampling individuals 30 min after a stimulus, for example, compared with 1 day after a stimulus (Dong et al 2009). Different genes are likely to be involved in the initiation of the plastic response, the response itself, and the maintenance of it, and all of those could be interesting and relevant to understanding behavioural plasticity (Aubin-Horth & Renn 2009).…”

The singing genome

“…In all 17 475 genes were predicted, which is slightly less than what is often considered for mammalian genomes. A set of these genes is differentially expressed in the auditory forebrain in song experiments (Dong et al, 2009) and are thus candidates for involvement in vocalization and learning functions. Moreover, differentially expressed transcripts include a large number of non-coding RNAs, indicating that other types of sequences than protein-coding genes might mediate complex cognitive behaviours, for example, microRNAs.…”