Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo

Abstract

Background The transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo. Results In the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified. Conclusion Our findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.

A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors

“…Bioinformatics tools improve experimental validations by According to Mackeh et al (2018), 3% of human genes refer to C2H2 zinc-finger proteins, totalizing more than seven hundred proteins described [43]. In chicken embryos, a species well-established as an animal model of thalidomide embryopathy, C2H2 was suggested as one of the most dominant types of TFs in embryogenesis [44]. Despite the fact that the role of human C2H2 proteins is yet to be fully explained, most of the 17 C2H2 TFs suggested here were involved in embryonic development [45][46][47].…”

Deep Proteome of the Developing Chick Midbrain

“…13 The species has also aided protein expression studies in the context of a neural crest-derived cell line. 14 However, while transcriptomics has characterized the expression of 14,536 genes at embryonic day (E)1 in whole chick embryos, 15 deep HRMS-based proteomics has not been used to assess early embryonic development, with the earliest existing study starting at E3. 16 Moreover, most proteomics studies in the chick embryo have utilized one-or two-dimensional gel electrophoresis separation in combination with downstream MS analysis, detecting up to ∼1500 proteins, 10 though some data sets were limited to only tens 17 to hundreds 16 of proteins.…”