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Characterization of the gene regulatory network controled by Coup-TFII in cardiomyocytes derived from embryonic stem cells

Abstract

Gene regulatory Networks (GRN) controlled by transcription factors are the main molecular component acting on the maintenance or alteration of cell states. Among the GRNs described so far, the GRN controlling heart development is of great interest, due to its potential application for human health. The role of many genes and gene interactions have been characterized during cardiac differentiation, but very little is known about the genes controlling steps such as the patterning of the heart tube antero-posterior axis. This step is controlled by a Retinoic Acid gradient that, in short, will subdivide the heart tube into an anterior region, the future conus and ventricles, and a posterior region, that will become the sinoatrial compartment. The transcription factor Coup-TFII (chicken ovalbumin promoter-transcription factor II) has an important role in patterning the posterior region of the heart and is considered an important modulator of the Retinoic Acid signaling during heart development. As a transcription factor, Coup-TFII plays an important role in regulating directly, or indirectly, the expression of target genes. The aim of this project is to characterize the complete GRN controlled by Coup-TFII during heart development, using mice embryonic hearts as well as heart cells (cardiomyocytes) derived in vitro from mouse embryonic stem cells. Although many target genes have been described for Coup-TFII in different cellular contexts, this will be the first attempt to characterize all possible binding sites and target genes in a genome-wide context. To this aim, the cardiac cells expressing Coup-TFII will be processed for chromatin imunoprecipitation followed by deep sequencing (ChIP-seq). At first, this approach will reveal all the genomic regions where Coup-TFII bindings, revealing as well all the genes surrounding these regions as potential Coup-TFII target genes. With the use of loss-of-function strategies, such as gene silencing via RNAi, the expression of these potential target genes will be analyzed, revealing which one of these genes are indeed regulated directly by Coup-TFII. As a result, the genes that are misexpressed in the loss-of-function analysis but are not bound by Coup-TFII, will be considered indirect targets of Coup-TFII. (AU)

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
DIEHL, OTAVIO J.; ASSANO, PATRICIA K.; DA COSTA, THIAGO RONCINI G.; OLIVEIRA, RHAUL; MARQUES-SOUZA, HENRIQUE; UMBUZEIRO, GISELA DE A. Antenna regeneration as an ecotoxicological endpoint in a marine amphipod: a proof of concept using dimethyl sulfoxide and diflubenzuron. ECOTOXICOLOGY, v. 30, n. 4, p. 751-755, MAY 2021. Web of Science Citations: 0.
DIEHL, OTAVIO J.; ASSANO, PATRICIA K.; DA COSTA, THIAGO RONCINI G.; OLIVEIRA, RHAUL; MARQUES-SOUZA, HENRIQUE; UMBUZEIRO, GISELA DE A. Antenna regeneration as an ecotoxicological endpoint in a marine amphipod: a proof of concept using dimethyl sulfoxide and diflubenzuron. ECOTOXICOLOGY, v. 30, n. 4 MAR 2021. Web of Science Citations: 0.
SENSIATE, L. A.; MARQUES-SOUZA, H. Bone growth as the main determinant of mouse digit tip regeneration after amputation. SCIENTIFIC REPORTS, v. 9, JUL 4 2019. Web of Science Citations: 2.

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