Table 5 Genes dysregulated after early RAR inhibition associated with organ development and differentiation. Genes shown in Fig. 5 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 | ||
 CALCINEURIN A (PPP3CA) | Protein phosphatase 3 catalytic subunit alpha | Calcium-dependent phosphatase that is activated by calmodulin and involved in CAMKII signaling |
 CAMKIIG | Calcium/Calmodulin Dependent Protein Kinase II Gamma | Serine/threonine protein kinase, activated by calcium and/or calmodulin with several roles in development, particularly in neurodevelopment |
 CHFR | Checkpoint With Forkhead And Ring Finger Domains | E3 ubiquitin-protein ligase required for the maintenance of the G2/M checkpoint, may play a key role in cell cycle progression |
 ERM (ETV5) | ETS variant 5 | Transcription factor that binds to DNA with consensus sequence 5-GGAA-3, may be disregulated in cancer. |
 GCLC | Glutamate-Cysteine Ligase, Catalytic Subunit | Glutamate-cysteine ligase, rate-limiting enzyme of glutathione synthesis. |
 NFACTC1 | Nuclear Factor Of Activated T-Cells 1 | A component of the NFAT DNA-binding complex. Members of this family play central roles in inducible gene transcription during immune response. |
 RDX | Radixin | Cytoskeletal protein that important in linking actin to the plasma membrane. |
 SPTBN2 | Spectrin Beta, Non-Erythrocytic 2 | Component of spectrin, important in securing glutamate transporter EEAT4 to the plasma membrane and regulating glutamatergic signaling. |
 ZNF292 | Zinc Finger Protein 292 | Growth hormone-dependent transcription regulator. |
Increased | ||
 AK1 | Adenylate Kinase 1 | Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP |
 BET | Bromodomain containing, BET | Family of genes that contain 110 amino acid domains that recognize acetylated lysine residues and translate the acetylation signal into various phenotypes depending on the family member’s location and expression. |
 BHLHE40 | Basic Helix-Loop-Helix Family Member E40 | Basic helix-loop-helix protein expressed in various tissues and is believed to be involved in the control of circadian rhythm and cell differentiation. |
 BRD4 | Bromodomain Containing 4 | Protein with a conserved sequence motif involved in chromatin targeting and binds acetylated lysine residues. |
 CKMT1A/CKMT1B | Creatine Kinase, Mitochondrial 1A, Creatine Kinase, Mitochondrial 1B | Serine/threonine kinases that play a central role in energy transduction in tissues with large, fluctuating energy demands, such as skeletal muscle, heart, brain and spermatozoa. |
 COL2A1 | Collagen Type II Alpha 1 Chain | Alpha-1 chain of type II collagen, a fibrillar collagen found in cartilage |
 DYRK1A | Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A | Located on the Down’s Syndrome Critical Region, this gene product is involved in cell survival, proliferation, quiescence, and differentiation. |
 FOS | Fos Proto-Oncogene, AP-1 Transcription Factor Subunit | Leucine zipper protein that dimerizes with proteins of the JUN family to form the transcription factor AP-1; regulates cell proliferation, differentiation, and transformation. |
 FOXD1 | Forkhead Box D1 | Member of the forkhead family of transcription factors, functions in the differentiation of nephron progenitors and the development of the retina. |
 GATA5 | GATA Binding Protein 5 | Transcription factor containing 2 GATA-type zinc fingers, involved in establishment of cardiac smooth muscle diversity. |
 GLTSCR1 (BICRA) | BRD4-interacting chromatin domain remodeling complex associated protein | Plays a role in BRD4-mediated transcription. |
 GPSM1 | G Protein Signaling Modulator 1 | A receptor-independent activator of G protein signaling, regulates spindle orientation and cortical neuronal cell fate. May also be involved in macroautophagy in the intestine. |
 HOXA11 | Homeobox A11 | Transcription factor that provides cells with specific positional identities on the anterior-posterior axis. |
 HOXD11 | Homeobox D11 | Transcription factor that provides cells with specific positional identities on the anterior-posterior axis. |
 ID2 | Inhibitor Of DNA Binding 2 | Basic helix-loop-helix transcription regulator that binds to other HLH transcription regulators and inhibits their activity; important for glial differentiation and chondrocyte development. |
 PP2A (PPP2CA) | Protein phosphatase 2 catalytic subunit alpha | Catalytic subunit of serine/threonine phosphatase involved in the negative regulation of cell growth. |
 PPARG | Peroxisome Proliferator Activated Receptor Gamma | Forms heterodimers with retinoid X receptors (RXRs) to regulate transcription. |
 PPP1R3C | Protein Phosphatase 1 Regulatory Subunit 3C | Carbohydrate binding protein subunit of the protein phosphatase 1 (PP1) complex. Involved in the maintenance of glycogen levels by activating/inhibiting synthesis and breakdown enzymes. |
 PPP2C | Protein Phosphatase 2 Catalytic Subunit | Catalytic subunit of serine/threonine phosphatase involved in the negative regulation of cell growth. |
 PRKAR1A | Protein Kinase cAMP-Dependent Type I Regulatory Subunit Alpha | Regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells including GPCR signal transduction. |
 SRF | Serum Response Factor | Ubiquitous transcription factor that stimulates proliferation and differentiation. |
 TAL1 | TAL BHLH Transcription Factor 1, Erthyroid Differentiation Factor | Basic helix-loop-helix transcription factor that plays a role in hematopoietic and erthyroid differentiation. |
UNCHANGED | ||
 ITPR | Inositol 1,4,5 triphosphate receptor family | Family of membrane glycoproteins that act as calcium channels to regulate several cellular processes including proliferation, learning, and memory. |