Functional characterization of mesenchymal stem cell-derived lncRNAs

• Applicant: Dr. Philipp Maass
• Subject Area: Human Genetics
• Term: from 2014 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 267068313

Long non-coding RNAs (lncRNAs) are important transcriptional regulators that are involved in many biological processes. We identified the chondrogenic lncRNA, CISTR-ACT, on chromosome 12 that impacts PTHLH in cis and pinpoints the non-homologous chromosome 17 in trans, interacting on chondrogenesis genes to regulate cartilage development. However, the fine-regulatory functions of lncRNAs including that of CISTR-ACT, with their associated proteins, remain poorly understood, particularly the mysterious in trans interactions. We used multi-potent human mesenchymal stem cells (MSCs) to derive chondrocytes for further mechanistic insights. With this model, we are identifying lncRNAs that correlate with the expression of chondrogenesis genes. We employ chromatin isolation by RNA purification (ChIRP), to determine in trans acting lncRNAs. To shed light on the interaction of lncRNAs with the nuclear architecture and chromatin organization, the nuclear habitat of potential in trans acting chondrogenic lncRNAs, we employ single-molecule RNA-FISH (smRNA-FISH). When validated in trans, lncRNAs will be subject to mass spectrometric analysis to determine novel RNA-binding proteins (RBPs). By identifying specific contacts between non-homologous chromosomes and interacting lncRNAs and their associated proteins, we will broaden the general understanding of genome organization and epigenetic regulation.

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Professor John L. Rinn, Ph.D.