Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency
Stem Cell Research(2020)
摘要
Pluripotent stem cells (PSCs) have been observed to occur in two distinct states — naive and primed. Both naive and primed state PSCs can give rise to tissues of all the three germ layers in vitro but differ in their potential to generate germline chimera in vivo. Understanding the molecular mechanisms that govern these two states of pluripotency in human can open up a plethora of opportunities for studying early embryonic development and in biomedical applications. In this work, we use weighted gene co-expression network (WGCN) approach to identify the key molecular makers and their interactions that define the two distinct pluripotency states. Signed-hybrid WGCN was reconstructed from transcriptomic data (RNA-seq) of naive and primed state pluripotent samples. Our analysis revealed two sets of genes that are involved in establishment and maintenance of naive (4791 genes) and primed (5066 genes) states. The naive state genes were found to be enriched for biological processes and pathways related to metabolic processes while primed state genes were associated with system development. Further, we identified the top 10% genes by intra-modular connectivity as hubs and the hub transcription factors for each group, thus providing a three-tier list of genes associated with naive and primed states of pluripotency in human.
HIGHLIGHTS
### Competing Interest Statement
The authors have declared no competing interest.
* CPM
: Count Per Million
ENA
: European Nucleotide Archive
FDR
: False Discovery Rate
GO
: Gene Ontology
hESC
: Human Embryonic Stem Cell
mESC
: Mouse Embryonic Stem Cell
PSC
: Pluripotent Stem Cell
TF
: Transcription Factor
TOM
: Topological Overlap Measure
WGCNA
: Weighted Gene Co-expression Network Analysis
ZNF
: Zinc Finger Protein
更多查看译文
AI 理解论文
溯源树
样例
生成溯源树,研究论文发展脉络
Chat Paper
正在生成论文摘要