Coexpression analysis identifies nuclear reprogramming barriers of somatic cell nuclear transfer embryos

Abstract

The success of cloned animal “Dolly Sheep” demonstrated the somatic cell nuclear transfer (SCNT) technique holds huge potentials for mammalian asexual reproduction. However, the extremely poor development of SCNT embryos indicates their molecular mechanism remain largely unexplored. Deciphering the spatiotemporal patterns of gene expression in SCNT embryos is a crucial step toward understanding the mechanisms associated with nuclear reprogramming. In this study, a valuable transcriptome recourse of SCNT embryos was firstly established, which derived from different inter-/intra donor cells. The gene co-expression analysis identified 26 cell-specific modules, and a series of regulatory pathways related to reprogramming barriers were further enriched. Compared to the intra-SCNT embryos, the inter-SCNT embryos underwent only complete partially reprogramming. As master genome trigger genes, the transcripts related to TFIID subunit, RNA polymerase and mediators were incomplete activated in inter-SCNT embryos. The inter-SCNT embryos only wasted the stored maternal mRNA of master regulators, but failed to activate their self-sustained pathway of RNA polymerases. The KDM family of epigenetic regulator also seriously delayed in inter-SCNT embryo reprogramming process. Our study provided new insight into understanding of the mechanisms of nuclear reprogramming.

Identification of immune‐enhanced molecular subtype associated with BRCA1 mutations, immune checkpoints and clinical outcome in ovarian carcinoma

“…The expression profile data of 871 immune genes for the 4 subtypes were obtained to further mine the prognostic markers related to the immune microenvironment of ovarian carcinoma. The distance between transcripts was then calculated, and the weighted co‐expression network was constructed using WGCNA in the R software package . Finally, the co‐expression modules were screened with the soft threshold of 2.…”

Peer Review #2 of "Exploring regulatory networks in plants: transcription factors of starch metabolism (v0.1)"

“…Regulatory complexity becomes most evident at the tissue culture level: plant cloning can be simply done with almost any pre-differentiated vegetative cell with a mixture of auxins (roots) and cytokinin's (shoots), while regeneration and cloning of animals is harder because it requires a protected environment and a precise mixture of epigenetic, cytosolic, nuclear and membranal factors (Zuo et al 2017). Coexpression analysis identified several barriers of animal cloning during somatic cell nuclear transfer (Zuo et al 2017). Transcription factors and epigenetic regulators hampered the embryo reprogramming process (Zuo et al 2017).…”

“…Coexpression analysis identified several barriers of animal cloning during somatic cell nuclear transfer (Zuo et al 2017). Transcription factors and epigenetic regulators hampered the embryo reprogramming process (Zuo et al 2017). In comparison, plant cells have less barriers of transcriptional reprogramming.…”

“…For example, dessert plants adapt to diurnal variations of temperature from 5° C in the morning to 55° C at noon, while mammalian cells stop working if temperatures drop or rise a few degrees from 37° C. Animals form complex organs through multiple cell layers that have a predefined cell lineage (fixed transcriptional fate). They are non-totipotent due to hierarchical restrictions by cytosolic and nuclear factors (Zuo et al 2017). Animal transcription networks are more hierarchical because they react strongly to cell lineage, growth factors and cell-to-cell communication (Fig 4d).…”

Peer Review #1 of "Exploring regulatory networks in plants: transcription factors of starch metabolism (v0.1)"

“…For example, dessert plants adapt to diurnal variations of temperature from 5° C in the morning 197 to 55° C at noon, while mammalian cells stop working if temperatures drop or rise a few degrees 198 from 37° C. Animals form complex organs through multiple cell layers that have a predefined cell lineage (fixed transcriptional fate). They are non-totipotent due to hierarchical restrictions by 200 cytosolic and nuclear factors (Zuo et al 2017). Animal transcription networks are more 201 hierarchical because they react strongly to cell lineage, growth factors and cell-to-cell 202 communication (Fig 4d).…”