Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors.
Ruben DriesAgata StryjewskaKathleen CoddensSatoshi OkawaTineke NotelaersJudith BirkhoffMike DekkerCatherine M VerfaillieAntonio Del SolEskeatnaf MulugetaAndrea ConidiFrank G GrosveldDanny HuylebroeckPublished in: Stem cells (Dayton, Ohio) (2019)
Cooperative actions of extrinsic signals and cell-intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell-type specific and context-dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system's actions during development, we selected 95 of its components and investigated their mRNA-expression dynamics, gene-gene interactions, and single-cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA-based perturbation of each individual component and documented the effect on steady-state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene-gene interactions display a marked cell-stage specific behavior. Furthermore, single-cell RNA-profiling at individual stages demonstrated the presence of detailed co-expression modules and subpopulations showing stable co-expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.
Keyphrases
- single cell
- embryonic stem cells
- transforming growth factor
- genome wide identification
- transcription factor
- genome wide
- rna seq
- cell fate
- copy number
- poor prognosis
- epithelial mesenchymal transition
- gene expression
- high throughput
- blood pressure
- genome wide analysis
- cell therapy
- stem cells
- long non coding rna
- induced apoptosis
- mesenchymal stem cells
- squamous cell carcinoma
- radiation therapy
- lymph node
- neoadjuvant chemotherapy
- cell proliferation
- oxidative stress
- signaling pathway
- bone regeneration
- atomic force microscopy
- human health
- high resolution
- bioinformatics analysis