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Aurigemma I, Lanzetta O, Cirino A, Allegretti S, Lania G, Ferrentino R, Poondi Krishnan V, Angelini C, Illingworth E, Baldini A. Endothelial gene regulatory elements associated with cardiopharyngeal lineage differentiation. Commun Biol 2024; 7:351. [PMID: 38514806 PMCID: PMC10957928 DOI: 10.1038/s42003-024-06017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and branchiomeric muscles. The enhancers activated during endothelial differentiation within the cardiopharyngeal mesoderm are not completely known. Here, we use a cardiogenic mesoderm differentiation model that activates an endothelial transcription program to identify endothelial regulatory elements activated in early cardiogenic mesoderm. Integrating chromatin remodeling and gene expression data with available single-cell RNA-seq data from mouse embryos, we identify 101 putative regulatory elements of EC genes. We then apply a machine-learning strategy, trained on validated enhancers, to predict enhancers. Using this computational assay, we determine that 50% of these sequences are likely enhancers, some of which are already reported. We also identify a smaller set of regulatory elements of well-known EC genes and validate them using genetic and epigenetic perturbation. Finally, we integrate multiple data sources and computational tools to search for transcriptional factor binding motifs. In conclusion, we show EC regulatory sequences with a high likelihood to be enhancers, and we validate a subset of them using computational and cell culture models. Motif analyses show that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC regulation in cardiopharyngeal mesoderm.
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Affiliation(s)
- Ilaria Aurigemma
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Olga Lanzetta
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Andrea Cirino
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Sara Allegretti
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
| | - Gabriella Lania
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Rosa Ferrentino
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Claudia Angelini
- Istituto Applicazioni del Calcolo, National Research Council, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Elizabeth Illingworth
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Antonio Baldini
- PhD program in Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
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Cirino A, Aurigemma I, Franzese M, Lania G, Righelli D, Ferrentino R, Illingworth E, Angelini C, Baldini A. Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells. Front Cell Dev Biol 2020; 8:571501. [PMID: 33015063 PMCID: PMC7505952 DOI: 10.3389/fcell.2020.571501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
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 type-specific, 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.
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Affiliation(s)
- Andrea Cirino
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Ilaria Aurigemma
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Department of Chemistry and Biology, University of Salerno, Fisciano, Italy
| | - Monica Franzese
- Institute Applicazioni del Calcolo, National Research Council, Naples, Italy
| | - Gabriella Lania
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Dario Righelli
- Department of Chemistry and Biology, University of Salerno, Fisciano, Italy
| | - Rosa Ferrentino
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | - Claudia Angelini
- Institute Applicazioni del Calcolo, National Research Council, Naples, Italy
| | - Antonio Baldini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
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