Table 3 Genes dysregulated after early RAR inhibition associated with transcriptional regulation. Genes shown in Fig. 3 along with their general function (adapted from genecards.org)
From: Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function
Gene | Gene Name | General Protein Function |
|---|---|---|
Decreased | ||
 ATRX | α-thalassemia mental retardation X-linked protein | A SWI/SNF family member protein involved in chromatin remodeling. |
 CHD1 | Chromodomain Helicase DNA Binding Protein 1 | An ATP-dependent chromatin-remodeling factor. |
 CHD2 | Chromodomain Helicase DNA Binding Protein 2 | An ATP-dependent chromatin-remodeling factor. |
 ESR1 | Estrogen Receptor 1 | A nuclear receptor for the estrogen ligand. |
 EZH2 | Enhancer Of Zeste 2 Polycomb Repressive Complex 2 Subunit | A polycomb group family member that methylates Lys-9 and Lys-27 of histone H3, leading to transcriptional repression. |
 HDAC1 | Histone Deacetylase 1 | A histone deacetylase that targets lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4) which is necessary for transcriptional repression. |
 SMARCAD1 | SWI/SNF-Related, Matrix-Associated Actin-Dependent Regulator Of Chromatin, Subfamily A, Containing DEAD/H Box 1 | A SNF subfamily of helicase proteins that mediates histone H3/H4 deacetylation that is necessary for restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication. |
 SUPT6H | SPT6 Homolog, Histone Chaperone | A transcription elongation factor which binds to histone H3 and plays a key role in the regulation of transcriptional elongation and mRNA processing. |
 SUZ12 | SUZ12 Polycomb Repressive Complex 2 Subunit | A Polycomb group protein that methylates Lys-9 and Lys-27 of histone H3, leading to transcriptional repression. |
 UHRF1 | Ubiquitin Like With PHD And Ring Finger Domains 1 | A protein that bridges DNA methylation and chromatin modification. |
Increased | ||
 AKT1 | AKT Serine/Threonine Kinase 1 | A serine/threonine-protein kinase |
 BAG6 | BCL2 Associated Athanogene 6 | A nuclear protein that forms a complex with E1A binding protein p300 and is required for the acetylation of p53 in response to DNA damage. |
 BRD4 | Bromodomain Containing 4 | A chromatin reader protein that recognizes and binds acetylated histones and plays a key role in transmission of epigenetic memory across cell divisions and transcription regulation. |
 CEBPB | CCAAT/Enhancer Binding Protein Beta | A transcription factor that contains a basic leucine zipper (bZIP) domain. |
 FOS | Fos Proto-Oncogene, AP-1 Transcription Factor Subunit | A leucine zipper protein that can dimerize JUN and together form part of the AP-1 transcription factor complex. |
 GATA3 | GATA Binding Protein 3 | A protein that belongs to the GATA family of transcription factors. |
 JUN | Jun Proto-Oncogene, AP-1 Transcription Factor Subunit | A protein that can dimerize FOS and together form part of the AP-1 transcription factor complex. |
 MTA2 | Metastasis Associated 1 Family Member 2 | A component of NuRD complex which is a deacetylase that is required for remodeling nucleosomes. |
 NCOA3 | Nuclear Receptor Coactivator 3 | A histone acetyltransferase that recruits p300/CBP as well as CREB binding proteins to form a transcriptional coactivation complex. |
 NCOR1 | Nuclear Receptor Corepressor 1 | A protein that is associated with thyroid-hormone and retinoic-acid receptors and promotes chromatin condensation and transcriptional repression. |
 OTUB1 | OTU Deubiquitinase, Ubiquitin Aldehyde Binding 1 | A hydrolase that can specifically remove Lys-48-linked conjugated ubiquitin from proteins and thereby prevents protein degradation. |
 PAX7 | Paired Box 7 | A member of the paired box (PAX) family of transcription factors. |
 PBRM1 | Polybromo 1 | A protein necessary for ligand-dependent transcriptional activation by nuclear hormone receptors. |
 WBP2 | WW Domain Binding Protein 2 | A WW domain binding protein that is a transcriptional coactivator of the estrogen and progesterone receptor. |
Unchanged | ||
 SMAD3 | SMAD Family Member 3 | An intracellular signal transducer and transcriptional modulator activated by TGF-beta family receptor kinases. |