Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3′ untranslated region (3′UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3′UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3′ end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3′ end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3′UTR lengths, especially for chicken, and APADB provides necessary information to close this gap.Database URL: http://tools.genxpro.net/apadb/

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In recent decades the embryo of Gallus g. domesticus has been widely used as a model for the study of early sexual development and the potential impact of substances affecting development, including endocrine disrupting chemicals (EDCs). Since there is no standardized procedure available for experiments with the chicken embryo, the objective of our project is to expedite the protocol to assess the potential effects of EDCs on early sexual differentiation. The main aim of the present study was to systematically investigate the natural variability of individual developmental and histological key parameters in untreated and solvent-treated control groups, since this has been insufficiently addressed so far. A further aim was to provide robust values for all parameters investigated in control and substance experiments, using two known estrogenic compounds, bisphenol A (75/150/300 μg/g egg) and 17α-ethinylestradiol (20 ng/g egg). On embryonic day 1 eggs were injected with the estrogenic compounds. On embryonic day 19 histological gonadal data as well as morphological parameters were noted. In baseline experiments with control groups the selected endpoints showed reproducible results with low variabilities. Furthermore, gonadal endpoints responded sensitively to the treatment with the two model EDCs. Thus, these endpoints are recommended for the assessment of suspected EDCs in which the values provided for all parameters can serve as validity criteria in future experiments. The embryo of G. domesticus has shown to be a suitable alternative to currently accepted mammalian bioassays for the impact assessment of EDCs on reproductive tissues.

In chicken, the left and right female gonads undergo a completely different program during development. To learn more about the molecular factors underlying side-specific development and to identify potential sex- and side-specific genes in developing gonads, we separately performed next-generation sequencing-based deepSuperSAGE transcription profiling from left and right, female and male gonads of 19-day-old chicken embryos. A total of 836 transcript variants were significantly differentially expressed (p < 10^-5) between combined male and female gonads. Left-right comparison revealed 1,056 and 822 differentially (p < 10^-5) expressed transcript variants for male and female gonads, respectively, of which 72 are side-specific in both sexes. At least some of these may represent key players for lateral development in birds. Additionally, several genes with laterally differential expression in the ovaries seem to determine female gonads for growth or regression, whereas right-left differences in testes are mostly limited to the differentially expressed genes present in both sexes. With a few exceptions, side-specific genes are not located on the sex chromosomes. The large differences in lateral gene expression in the ovaries in almost all metabolic pathways suggest that the regressing right gonad might have undergone a change of function during evolution.

Since it is known that environmental contaminants have the potential to cause endocrine disorders in humans and animals, there is an urgent need for in vivo tests to assess possible effects of these endocrine disrupting chemicals (EDCs). Although there is no standardized guideline, the avian embryo has proven to be particularly promising as it responds sensitively to a number of EDCs preferentially impacting the reproductive axis. In the present study we examined the effects of in ovo exposure to fulvestrant and tamoxifen as antiestrogenic model compounds and co-exposure to both substances and the potent estrogen 17α-ethinylestradiol (EE2) regarding sex differentiation and embryonic development of the domestic fowl (Gallus gallus domesticus). The substances were injected into the yolk of fertilized eggs on embryonic day 1. On embryonic day 19 sex genotype and phenotype were determined, followed by gross morphological and histological examination of the gonads. Sole EE2-treatment (20 ng/g egg) particularly affected male gonads and resulted in an increased formation of female-like gonadal cortex tissue and a reduction of seminiferous tubules. In ovo exposure to tamoxifen (0.1/1/10 µg/g egg) strongly impaired the differentiation of female gonads, led to a significant size reduction of the left ovary and induced malformations of the ovarian cortex, while fulvestrant (0.1/1/10 µg/g egg) did not affect sexual differentiation. However, both antiestrogens were able to antagonize the feminizing effects of EE2in genetic males when administered simultaneously. Since both estrogens and antiestrogens induce concentration-dependent morphological alterations of the sex organs, the chick embryo can be regarded as a promising model for the identification of chemicals with estrogenic and antiestrogenic activity.