Chromatin and transcriptional response to loss of TBX1 in early differentiation of mouse cells

Abstract

The T-box transcription factor TBX1 has critical roles in the cardiopharyngeal lineage and the gene is haploinsufficient in DiGeorge syndrome, a typical developmental anomaly of the pharyngeal apparatus. Despite almost two decades of research, if and how TBX1 function triggers chromatin remodeling is not known.Here, we explored genome-wide gene expression and chromatin remodeling in two independent cellular models of Tbx1 loss of function, mouse embryonic carcinoma cells P19Cl6, and mouse embryonic stem cells (mESCs). The results of our study revealed that the loss or knockdown of TBX1 caused extensive transcriptional changes, some of which were cell typespecific, some were in common between the two models. However, unexpectedly we observed only limited chromatin changes in both systems. In P19Cl6 cells, differentially accessible regions (DARs) were not enriched in T-BOX binding motifs; in contrast, in mESCs, 34% (n=47) of all DARs included a T-BOX binding motif and almost all of them gained accessibility in Tbx1 -/cells. In conclusion, despite a clear transcriptional response of our cell models to loss of TBX1 in early cell differentiation, chromatin changes were relatively modest. G. (2011). Stage-specific optimization of activin/nodal and BMP signaling promotes cardiac differentiation of mouse and human pluripotent stem cell lines. Cell Stem Cell 8, 228-240. , et al. (2015). 22q11.2 deletion syndrome. Nat. Rev. Dis. Primer 1, 15071. Mueller, I., Kobayashi, R., Nakajima, T., Ishii, M. and Ogawa, K. (2010). Effective and steady differentiation of a clonal derivative of P19CL6 embryonal carcinoma cell line into beating cardiomyocytes. J Biomed Biotechnol 2010, 380561. Okubo, T., Kawamura, A., Takahashi, J., Yagi, H., Morishima, M., Matsuoka, R. and Takada, S. (2011). Ripply3, a Tbx1 repressor, is required for development of the pharyngeal apparatus and its derivatives in mice. Dev. Camb. Engl. 138, 339-348. Quinlan, A. R. and Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinforma. Oxf. Engl. 26, 841-842. Raudvere, U., Kolberg, L., Kuzmin, I., Arak, T., Adler, P., Peterson, H. and Vilo, J. (2019). g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 47, W191-W198. . In vitro modeling of paraxial and lateral mesoderm differentiation reveals early reversibility. Stem Cells Dayt. Ohio 24, 575-586.

Application of CRISPR-Cas9 gene editing for congenital heart disease

“…CRISPR-Cas9 knockout of Tbx1 in murine stem cells (E14-Tg2a) enabled chromatin remodeling studies and transcriptome analyses to understand the pathogenesis of this syndrome. 105) Similarly, the putative adhesion receptor protein DGCR2, which has shown muscular defects as well as the risk for developing schizophrenia in DiGeorge syndrome, was deleted in mouse TT2…”

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells

“… Funding. This manuscript has been released as a pre-print at Biorxiv ( Cirino et al, 2020 ). This work was funded in part by grants from the Italian Ministry of Research PRIN 20179J2P9J (to AB, EI, GL, and CA), the Campania SATIN Project (to AB), the Jerome Lejeune Foundation project #1685 (to EI), and the Fondation Leducq grant 15CVD01 (to AB and EI).…”