Gene transcriptions/Boxes/V and Ps

"REV-ERBα and RORa are nuclear receptors rather than bZIP transcription factors like VRI [target gene: vrille (VRI)] and PDP1ϵ, and they regulate transcription by binding RORE elements rather than V/P-boxes (Bell-Pedersen et al., 2005)."

"A delayed accumulation of PDP1 leads to a replacement of VRI from P/V (PDP1 and VRI) boxes and restimulates clk transcription."

"For VRI to be a direct repressor of Clk, the 8.0 kb Clk genomic fragment should contain binding sites for VRI. The consensus binding site for VRI has not been determined; however, the basic (DNA binding) domain shares >85% homology with that of mammalian E4BP4, and hence, VRI should bind similar DNA sequences as E4BP4 (George and Terracol, 1997). The optimal binding site for E4BP4 has been determined as 5′-(A/G): (A/G)T(A/C)A(A/T/C)-3′ (Cowell et al., 1992)."

Consensus sequences
"As VRI accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."

Human genes
Gene ID: 54704 is PDP1 pyruvate dehyrogenase phosphatase catalytic subunit 1. "Pyruvate dehydrogenase (E1) is one of the three components (E1, E2, and E3) of the large pyruvate dehydrogenase complex. Pyruvate dehydrogenase kinases catalyze phosphorylation of serine residues of E1 to inactivate the E1 component and inhibit the complex. Pyruvate dehydrogenase phosphatases catalyze the dephosphorylation and activation of the E1 component to reverse the effects of pyruvate dehydrogenase kinases. Pyruvate dehydrogenase phosphatase is a heterodimer consisting of catalytic and regulatory subunits. Two catalytic subunits have been reported; one is predominantly expressed in skeletal muscle and another one is is much more abundant in the liver. The catalytic subunit, encoded by this gene, is the former, and belongs to the protein phosphatase 2C (PP2C) superfamily. Along with the pyruvate dehydrogenase complex and pyruvate dehydrogenase kinases, this enzyme is located in the mitochondrial matrix. Mutation in this gene causes pyruvate dehydrogenase phosphatase deficiency. Multiple alternatively spliced transcript variants encoding different isoforms have been identified."


 * 1) NP_001155251.1 pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 2 (variant 2).
 * 2) NP_001155252.1 pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 2 (variant 3).
 * 3) NP_001155253.1 pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 3 (variant 4).
 * 4) NP_060914.2 pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform 3 (variant 5).
 * 5) XP_016869077.1 pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X1.
 * 6) XP_011515437.1 pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X2.
 * 7) XP_011515438.1 pyruvate dehyrogenase phosphatase catalytic subunit 1 isoform X3.