Understanding the role of divergent lncRNA-TF pairs in regulating embryonic cell-fate decisions

• Applicant: Professor Leo Kurian, Ph.D.
• Subject Area: Developmental Biology
• Term: from 2018 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 400875225

Embryonic organogenesis requires precise timing and coordinated activity of core transcriptional networks that drive developmental progression. Understanding the mechanisms by which these transcriptional networks program developmental decisions is pivotal in devising ways to engineer specialized cell types or to re-engineer them for regenerative repair. Yet, our knowledge of the mechanisms that regulate and coordinate developmental progression of a tissue/organ is far from complete. Using a near synchronous human pluripotent stem cell based differentiation system recapitulating embryonic cardiac development, we discovered that a significant proportion of the key transcription factors (TF) governing developmental cell fate decisions are accompanied by a divergently transcribed long non-coding RNAs (dlncRNA). Importantly, this phenomenon is evolutionarily conserved. Our preliminary loss-of-function analysis revealed that dlncRNAs are essential for the cell-fate transitions at which they are expressed by potentially regulating the accompanying TF and other co-expressed regulators of lineage decisions. Based on these observations, we hypothesize that dlncRNA-TF pairs program the transcriptional code that facilitates cell-fate transitions at key developmental crossroads. Using the novel dlncRNA transcribed from the Brachyury locus (dlncT) that we identified, here we aim to understand: I) The physiological role of dlncT in mediating mesoderm commitment. II) The direct targets of dlncT and the molecular partners that enable its function. III) The modular rules and molecular mechanism by which dlncT communicate with its targets in the chromatin 3D space. Our genome wide analysis both in vivo and in vitro suggests that dlncRNA-TF pairs is a prevalent developmental phenomenon. This study will allow us to understand the relevance of this class of divergent lncRNAs and provide insights into their mode of action. We envision that this will uncover a new regulatory layer in developmental gene regulation.

• DFG Programme: Research Grants