Expression data from embryonic chicken feather and scale skins
ABSTRACT: Epithelial appendages are the product of epithelial – mesenchymal interactions. Tissue recombination experiments showed that in general, the dermis determines the phenotype of the epithelial appendage. Chicken dorsal skin epithelium interacts with its underlying mesenchyme to form feathers beginning at E7 (H&H stage 31), while metatarsal scale epithelium interacts with its mesenchyme to form scales beginning at E9 (H&H stage 35) which stabilize around E12 (H&H stage 38). We sought to evaluate the molecular differences of tissues with different competence and inductive abilities to form feathers and scales. Chicken embryos were selected to obtain competent E7 and non-competent at E9 feather forming skin from dorsal. The competent E9 and non-competent E11 meta-tarsal scale forming skin from metatarsal were selected for examing the differences in regional specificity. Epithelium and mesenchyme from each skin were prepared separately. Samples were prepared for RNA extraction and hybridization on Affymetrix microarrays. We gathered 8 sets of samples for the analysis: undifferentiated E7 feather skin epithelium (E7fe) and mesenchyme (E7fm); differentiated E9 feather skin epithelium (E9fe) and mesenchyme (E9fm); undifferentiated E9 scale skin epithelium (E9se) and mesenchyme (E9sm); and differentiated E11 scale skin epithelium (E11se) and mesenchyme (E11sm)
Project description:Feather branching morphogenesis is a complex process which is likely to be regulated by many genes. Also, feathers from different body regions are drastically different in their morphology, thus suggesting differential gene expression. To understand the feather epithelial branching process, we profiled gene expression in the ramogenic feather epithelium in adult chicken where branching begins. Feathers from the neck, wing, and tail regions in their actively growing phase were each profiled. Overall design: Feathers from the neck, wing, leg regions in adult chicken in their actively growing phase were plucked. Feathers were dissected under a stereo dissection microscope. The mesenchymal pulp were discarded. The ramogenic feather epithelium was pooled from five feathers. Total RNAs were extracted from the feather epithelium, and processed for RNA-seq.
Project description:Transcriptome profiles of skin and feather follicle from two body parts at three physiological stages were constructed to understand the molecular network and excavate the candidate genes associated with the plumulaceous and flight feathers structure. The key series-clusters, many candidate biological processes and genes were identified for the morphogenesis, growth and development of two feather types. Through comparing the results of developmental transcritpomes from plumulaceous and flight feather, we found that DEGs belonging to the family of WNT, FGF and BMP have certain differences; even the consistent DEGs of skin and feather follicle transcriptomes from abdomen and wing have the different expression patterns. Overall design: A total of twelve libraries were sequenced from skin and feather follicle tissues of six groups (n=2 for each; control samples), including the early growth plumulaceous feathers (EP), middle growth plumulaceous feathers (MP), late growth plumulaceous feathers (LP), early growth flight feathers (EF), middle growth flight feathers (MF) and late growth flight feathers (LF).
Project description:Study of H3K4me3 profile patterns during early feather development Overall design: H3K4me3 ChIP-seq was performed to document E7 (H&H 31) and E9 (H&H 35) feather development. There are 2 replicates for each sample group.
Project description:Many animals can change their coats in response to different ages, sexes, or seasonal environmental changes. The hormones can also alter the size, shape, texture and color of the regenerated coat. Here we propose feather core branching morphogenesis module can be modulated by sex hormone or other environmental factors to change the form, texture or colors, thus generate a large spectrum of complexity for adaptation. We use sexual dimorphisms of the feather coat to explore the role of hormones in in coat morphogenesis and regeneration. A long-standing question is whether the sex-dependent feather morphologies are autonomously controlled by the male or female cell types, or extrinsically controlled and reversible. We have recently identified core feather branching molecular modules which control the anterior-posterior (BMP, Wnt gradient), medio-lateral (retinoic signaling, gremlin), and proximo-distal (sprouty, BMP) patterning of feathers. We hypothesize that modulatory signaling modules can be added upon these core branching modules to topologically tune the dimension of each parameter. Here we explore the involvement of hormones in generating sexual dimorphisms using exogenously delivered hormones. Our strategy is to mimic androgen levels by applying exogenous dihydrotestosterone and aromatase inhibitors to adult females and injecting exogenous estradiol to adult males. We also examine differentially expressed genes in the feathers of wildtype male and female chickens to identify potential downstream modifiers of feather morphogenesis. The data show male and female feather morphology and their color patterns can be modified extrinsically through molting and reseting the stem cell niche during regeneration. Overall design: Six kinds of adult chicken sickle feather tissues between male (M) and female (F), including lower follicle sheath (LFS), upper follicle sheath (UFS), pulp (PP), epithelium (EPi), papilla ectoderm (PE), and dermal papilla (DP)
Project description:The genetic and developmental mechanisms that control the decision between scale and feather growth – two profoundly different epidermal appendages, and an important developmental shift in the evolution of birds from their dinosaurian ancestors – remain poorly understood. Domestic pigeons display dramatic variation in foot epidermal appendages within a single species, and classical studies suggest that a small number of genes control much of this variation; thus pigeons provide a tractable model to understand skin appendage specification and variation. Here we show that feathered feet in pigeons are the consequence of a partial transformation of limb-type identity mediated by cis-regulatory changes in the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also demonstrate that ectopic hindlimb expression of Tbx5 is associated with the development of foot feathers in domestic chickens, suggesting that similar developmental mechanisms underlie phenotypic convergence in avian lineages that diverged over 100 MYA. These results show how qualitative and quantitative changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide a viable molecular mechanism for the evolution of hindlimb scale and feather distribution in dromaeosaurs. Examination of H3K27ac status in embryonic limb buds from two domestic pigeon breeds, racing homer and Indian fantail
Project description:Purpose: The goals of this study is to identify crucial genes associated with narrow and wide vane sizes in feather epithelium and mesenchyme (pulp) Overall design: proximal follicles of 3 primary remiges from Spafas white leghorn chickens into the lateral and medial halves and separated the epithelium from the mesenchyme in 2xCMF solution. For dorsal plumes and breast plumes, 25 proximal follicles were used, respectively. Total RNA was extracted using Trizol reagent. 4 µg RNA was used for library construction by TruSeq RNA Sample Prep Kit Version2 (Illumina). Two biological replicates were sent for sequencing (50bp, single end) with Illumina HiSeq 2000 in the USC Epigenome Center.
Project description:The quality and yield of duck feathers are very important economic traits that might be controlled by miRNA regulation. The aim of the present study was to investigate the mechanism underlying the crosstalk between individual miRNAs and the activity of signaling pathways that control the growth of duck feathers during different periods. Overall design: We conducted a comprehensive investigation using Solexa sequencing technology on the Pekin duck microRNAome over six stages of feather development at days 11, 15, and 20 of embryonic development (during the hatching period), and at 1 day and 4 and 10 weeks posthatch.
Project description:Complex multicellular organisms have evolved numerous cell types with many different functions. Comparative transcriptomic data yields valuable insights into cell type, tissue, and organ evolution. However, interpreting this data requires understanding how transcriptomes evolve. A particularly difficult problem is that cell type transcriptomes may not evolve independently, a key assumption of most evolutionary analyses. Non-independence of cell types can occur when cell types share regulatory mechanisms. This leads to concerted evolution in gene expression across different cell types, confounding efforts to unravel the history of cell type evolution, and identify cell type-specific patterns of expression. Here we present a statistical model to estimate the level of concerted transcriptome evolution and apply it to published and new data. The results indicate that tissues undergo pervasive concerted evolution in gene expression. Tissues related by morphology or developmental lineage exhibit higher levels of concerted evolution. Concerted evolution also causes tissues from the same species to be more similar in gene expression to each other than to homologous tissues in another species. This result may explain why some tissue transcriptomes cluster by species rather than homology. Our analysis of bird skin appendages data suggests levels of concerted evolution also varies with phylogenetic age of the tissue. Our study illustrates the importance of accounting for concerted evolution when interpreting comparative transcriptome data, and should serve as a foundation for future investigations of cell type evolution. Overall design: We sampled epidermis from 4 different tracts of developing bird skin appendages in chicken and emu embryos: feather placodes, scutate scale placodes, reticulate scale placodes, and claw placodes. In chicken we sampled two biological replicates for each skin appendages. In emu we sampled 2 biological replicates for feathers and scutate scales, and 1 biological replicate for reticulate scales and claw (due to limitations in available material).
Project description:The feather follicle is a “professional” regenerative organ that undergoes natural cycling and, regeneration after wound plucking. Similar to mammalian hair follicle, dermal papilla (DP) controls feather regeneration, shape, size, and axis. Here we report gene expression profiling for feather DP at different growth stages. For growth phase, we compared gene expression of DP, the ramogenic zone of feather branching epithelium (Erz) and the mesenchymal pulp (Pp). We also compared gene expression of DP at resting phase. To characterize the feather regeneration process, we further profiled gene expression at Day-2 and Day-4 post wound. Our results provide a resource for investigating feather growth and regeneration. Examination of gene expression in dermal papilla (DP) at growth phase and resting phase feather follicle, and during feather regeneration.
Project description:Comparison of H3K27ac profile patterns between feather- and scale-forming regions. Overall design: H3K27ac ChIP-seq was performed to compare the feather-forming and scale-forming regions. There are 2 replicates for each sample group.