Profiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing

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dc.contributor.authorDudakovic, Amel
dc.contributor.authorGluscevic, Martina
dc.contributor.authorParadise, Christopher R.
dc.contributor.authorDudakovic, Halil
dc.contributor.authorKhani, Farzaneh
dc.contributor.authorThaler, Roman
dc.contributor.authorAhmed, Farah S.
dc.contributor.authorLi, Xiaodong
dc.contributor.authorDietz, Allan B.
dc.contributor.authorStein, Gary S.
dc.contributor.authorMontecino, Martin A.
dc.contributor.authorDeyle, David R.
dc.contributor.authorWestendorf, Jennifer J.
dc.date.accessioned2024-06-18T18:57:23Z
dc.date.available2024-06-18T18:57:23Z
dc.date.issued2017-04
dc.descriptionIndexación: Scopus
dc.description.abstractEpigenetic mechanisms control phenotypic commitment of mesenchymal stromal/stem cells (MSCs) into osteogenic, chondrogenic or adipogenic lineages. To investigate enzymes and chromatin binding proteins controlling the epigenome, we developed a hybrid expression screening strategy that combines semi-automated real-time qPCR (RT-qPCR), next generation RNA sequencing (RNA-seq), and a novel data management application (FileMerge). This strategy was used to interrogate expression of a large cohort (n > 300) of human epigenetic regulators (EpiRegs) that generate, interpret and/or edit the histone code. We find that EpiRegs with similar enzymatic functions are variably expressed and specific isoforms dominate over others in human MSCs. This principle is exemplified by analysis of key histone acetyl transferases (HATs) and deacetylases (HDACs), H3 lysine methyltransferases (e.g., EHMTs) and demethylases (KDMs), as well as bromodomain (BRDs) and chromobox (CBX) proteins. Our results show gender-specific expression of H3 lysine 9 [H3K9] demethylases (e.g., KDM5D and UTY) as expected and upregulation of distinct EpiRegs (n > 30) during osteogenic differentiation of MSCs (e.g., HDAC5 and HDAC7). The functional significance of HDACs in osteogenic lineage commitment of MSCs was functionally validated using panobinostat (LBH-589). This pan-deacetylase inhibitor suppresses osteoblastic differentiation as evidenced by reductions in bone-specific mRNA markers (e.g., ALPL), alkaline phosphatase activity and calcium deposition (i.e., Alizarin Red staining). Thus, our RT-qPCR platform identifies candidate EpiRegs by expression screening, predicts biological outcomes of their corresponding inhibitors, and enables manipulation of the human epigenome using molecular or pharmacological approaches to control stem cell differentiation. © 2017 Elsevier B.V.
dc.description.urihttps://www-sciencedirect-com.recursosbiblioteca.unab.cl/science/article/pii/S0378111917300410?via%3Dihub
dc.identifier.citationGene Volume 609, Pages 28 - 3720 April 2017
dc.identifier.doi10.1016/j.gene.2017.01.019
dc.identifier.issn0378-1119
dc.identifier.urihttps://repositorio.unab.cl/handle/ria/57736
dc.language.isoen
dc.publisherElsevier B.V.
dc.rights.licenseATRIBUCIÓN-NOCOMERCIAL-SINDERIVADAS 4.0 INTERNACIONAL CC BY-NC-ND 4.0 Deed
dc.rights.urihttps://v2.sherpa.ac.uk/id/publication/16823
dc.subjectAdipose-tissue derived stromal cells
dc.subjectDeacetylase
dc.subjectEpigenetic regulators
dc.subjectEpigenetics
dc.subjectHistone
dc.subjectMesenchymal stem cell
dc.subjectMethyltransferase
dc.titleProfiling of human epigenetic regulators using a semi-automated real-time qPCR platform validated by next generation sequencing
dc.typeArtículo
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