The effects of parity and maternal behavior on gene expression in the medial preoptic area and the medial amygdala in postpartum and virgin female rats: A microarray study.

To determine the pattern of gene expression in brains associated with mothering during the postpartum period, in the present study we assessed gene expression through microarrays in four groups of female rats: two groups of new mothers that were experiencing the hormonal and neurochemical changes associated with pregnancy and parturition, and two groups of virgin females that were not. Within each of these parity groups we assessed one group of animals that was exposed to and responded to pups and engaged in maternal behavior, and one group left without any exposure to pups and therefore had no maternal experience. We explored the pattern of expression of genes related to the hormones, neurotransmitters, and modulatory neuropeptides associated with maternal behavior within the medial preoptic area (MPOA) and the medial amygdala (MeA) in the rat. Within the MPOA there were significant main effects of pup exposure for the dopamine-related genes (DRD4 and dopamine transporter, DAT), the glucocorticoid-related gene (CYPX1B1a), the opioid receptor µ-1 gene (OPRM1) and the gamma-aminobutyric acid (GABA) receptor gene (GABAbRid). OPRM1 and the serotonin-related gene that regulates biosynthesis of serotonin (5HTR2A) showed a main effect of parity. For both sets of analyses, higher gene expression was associated with pup exposure and parity. Genes expressed in the MeA tended to reside in the glucocorticoid family. The microarrays were able to identify, on a transcriptional level, a list of candidate genes involved in maternal behavior and the factors that surround it.

Prediction of Drosophila melanogaster gene function using Support Vector Machines.

BACKGROUND: While the genomes of hundreds of organisms have been sequenced and good approaches exist for finding protein encoding genes, an important remaining challenge is predicting the functions of the large fraction of genes for which there is no annotation. Large gene expression datasets from microarray experiments already exist and many of these can be used to help assign potential functions to these genes. We have applied Support Vector Machines (SVM), a sigmoid fitting function and a stratified cross-validation approach to analyze a large microarray experiment dataset from Drosophila melanogaster in order to predict possible functions for previously un-annotated genes. A total of approximately 5043 different genes, or about one-third of the predicted genes in the D. melanogaster genome, are represented in the dataset and 1854 (or 37%) of these genes are un-annotated. RESULTS: 39 Gene Ontology Biological Process (GO-BP) categories were found with precision value equal or larger than 0.75, when recall was fixed at the 0.4 level. For two of those categories, we have provided additional support for assigning given genes to the category by showing that the majority of transcripts for the genes belonging in a given category have a similar localization pattern during embryogenesis. Additionally, by assessing the predictions using a confidence score, we have been able to provide a putative GO-BP term for 1422 previously un-annotated genes or about 77% of the un-annotated genes represented on the microarray and about 19% of all of the un-annotated genes in the D. melanogaster genome. CONCLUSIONS: Our study successfully employs a number of SVM classifiers, accompanied by detailed calibration and validation techniques, to generate a number of predictions for new annotations for D. melanogaster genes. The applied probabilistic analysis to SVM output improves the interpretability of the prediction results and the objectivity of the validation procedure.

Identification of heat shock factor 1 molecular and cellular targets during embryonic and adult female meiosis.

Heat shock factor 1 (HSF1), while recognized as the major regulator of the heat shock transcriptional response, also exerts important functions during mammalian embryonic development and gametogenesis. In particular, HSF1 is required for oocyte maturation, the adult phase of meiosis preceding fertilization. To identify HSF1 target genes implicated in this process, comparative transcriptomic analyses were performed with wild-type and HSF-deficient oocytes. This revealed a network of meiotic genes involved in cohesin and synaptonemal complex (SC) structures, DNA recombination, and the spindle assembly checkpoint (SAC). All of them were found to be regulated by HSF1 not only during adult but also in embryonic phases of female meiosis. Additional investigations showed that SC, recombination nodules, and DNA repair were affected in Hsf1(-/-) oocytes during prenatal meiotic prophase I. However, targeting Hsf1 deletion to postnatal oocytes (using Zp3 Cre; Hsf1(loxP/loxP)) did not fully rescue the chromosomal anomalies identified during meiotic maturation, which possibly caused a persistent SAC activation. This would explain the metaphase I arrest previously described in HSF1-deficient oocytes since SAC inhibition circumvented this block. This work provides new insights into meiotic gene regulation and points out potential links between cellular stress and the meiotic anomalies frequently observed in humans.

Whole-genome analysis reveals that active heat shock factor binding sites are mostly associated with non-heat shock genes in Drosophila melanogaster.

During heat shock (HS) and other stresses, HS gene transcription in eukaryotes is up-regulated by the transcription factor heat shock factor (HSF). While the identities of the major HS genes have been known for more than 30 years, it has been suspected that HSF binds to numerous other genes and potentially regulates their transcription. In this study, we have used a chromatin immunoprecipitation and microarray (ChIP-chip) approach to identify 434 regions in the Drosophila genome that are bound by HSF. We have also performed a transcript analysis of heat shocked Kc167 cells and third instar larvae and compared them to HSF binding sites. The heat-induced transcription profiles were quite different between cells and larvae and surprisingly only about 10% of the genes associated with HSF binding sites show changed transcription. There were also genes that showed changes in transcript levels that did not appear to correlate with HSF binding sites. Analysis of the locations of the HSF binding sites revealed that 57% were contained within genes with approximately 2/3rds of these sites being in introns. We also found that the insulator protein, BEAF, has enriched binding prior to HS to promoters of genes that are bound by HSF upon HS but that are not transcriptionally induced during HS. When the genes associated with HSF binding sites in promoters were analyzed for gene ontology terms, categories such as stress response and transferase activity were enriched whereas analysis of genes having HSF binding sites in introns identified those categories plus ones related to developmental processes and reproduction. These results suggest that Drosophila HSF may be regulating many genes besides the known HS genes and that some of these genes may be regulated during non-stress conditions.

Chronic alcohol exposure induced gene expression changes in the zebrafish brain.

Chronic alcohol exposure affects the central nervous system, influences behavior, and induces neuroadaptive changes in vertebrate species including our own. The molecular mechanisms responsible for chronic alcohol effects have not been fully elucidated due to the complexity of alcohol's actions. Here we use zebrafish, a novel tool in alcohol research, to reveal a large number of genes that respond to chronic alcohol treatment. We demonstrate differential gene expression in response to chronic alcohol treatment using full genome DNA microarrays and find a total of 1914 genes to show a minimum of 2-fold and significant expression level change (1127 were up- and 787 were down-regulated). Approximately two-thirds of these genes had no known previous functional annotation. The results of the microarray analyses correlated well with those obtained on a selected subset of genes analyzed by quantitative real-time RT-PCR. Analyses of the differentially expressed genes with known annotations were enriched for a variety of molecular functions. Only a fraction of these known genes has been reported in the literature to be alcohol related. We conclude that the zebrafish is an excellent tool for the analysis of genes associated with alcohol's actions in vertebrates, one which may facilitate the discovery and better understanding of the mechanisms of alcohol abuse.

Microarray analysis of gene expression by skeletal muscle of three mouse models of Kennedy disease/spinal bulbar muscular atrophy.

BACKGROUND: Emerging evidence implicates altered gene expression within skeletal muscle in the pathogenesis of Kennedy disease/spinal bulbar muscular atrophy (KD/SBMA). We therefore broadly characterized gene expression in skeletal muscle of three independently generated mouse models of this disease. The mouse models included a polyglutamine expanded (polyQ) AR knock-in model (AR113Q), a polyQ AR transgenic model (AR97Q), and a transgenic mouse that overexpresses wild type AR solely in skeletal muscle (HSA-AR). HSA-AR mice were included because they substantially reproduce the KD/SBMA phenotype despite the absence of polyQ AR. METHODOLOGY/PRINCIPAL FINDINGS: We performed microarray analysis of lower hindlimb muscles taken from these three models relative to wild type controls using high density oligonucleotide arrays. All microarray comparisons were made with at least 3 animals in each condition, and only those genes having at least 2-fold difference and whose coefficient of variance was less than 100% were considered to be differentially expressed. When considered globally, there was a similar overlap in gene changes between the 3 models: 19% between HSA-AR and AR97Q, 21% between AR97Q and AR113Q, and 17% between HSA-AR and AR113Q, with 8% shared by all models. Several patterns of gene expression relevant to the disease process were observed. Notably, patterns of gene expression typical of loss of AR function were observed in all three models, as were alterations in genes involved in cell adhesion, energy balance, muscle atrophy and myogenesis. We additionally measured changes similar to those observed in skeletal muscle of a mouse model of Huntington's Disease, and to those common to muscle atrophy from diverse causes. CONCLUSIONS/SIGNIFICANCE: By comparing patterns of gene expression in three independent models of KD/SBMA, we have been able to identify candidate genes that might mediate the core myogenic features of KD/SBMA.