Homogentisate 1,2-dioxygenase (HGD) is involved in the catabolism of the amino acids tyrosine and phenylalanine. Mutations of HGD are the cause of the autosomal recessive metabolism disorder alkaptonuria.
This gene encodes a protein that binds to the hepatocyte growth factor receptor to regulate cell growth, cell motility and morphogenesis in numerous cell and tissue types. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate alpha and beta chains, which form the mature heterodimer. This protein is secreted by mesenchymal cells and acts as a multi-functional cytokine on cells of mainly epithelial origin. This protein also plays a role in angiogenesis, tumorogenesis, and tissue regeneration. Although the encoded protein is a member of the peptidase S1 family of serine proteases, it lacks peptidase activity. Mutations in this gene are associated with nonsyndromic hearing loss.
The hypoxia-inducible transcription factor 1 alpha (HIF-1 alpha ) is the regulated member of the transcription factor heterodimer HIF-1. HIF-1 binds to hypoxia-response elements (HREs) in the promoters of many genes involved in adapting to an environment of insufficient oxygen or hypoxia. Hypoxic tissue environments occur in vascular and pulmonary diseases as well as cancer, which illustrates the broad impact of gene regulation by HIF-1 alpha.
Hypoxia-inducible factor 1 (HIF1) is a heterodimeric transcription factor that plays a critical role in the cellular response to hypoxia (1). The HIF1 complex consists of two subunits, HIF-1α and HIF-1β, which are basic helix-loop-helix proteins of the PAS (Per, ARNT, Sim) family (2). HIF1 regulates the transcription of a broad range of genes that facilitate responses to the hypoxic environment, including genes regulating angiogenesis, erythropoiesis, cell cycle, metabolism and apoptosis. The widely expressed HIF-1α is typically degraded rapidly in normoxic cells by the ubiquitin/proteasomal pathway. Under normoxic conditions, HIF-1α is proline hydroxylated leading to a conformational change that promotes binding to the von Hippel Lindau protein (VLH) E3 ligase complex; ubiquitination and proteasomal degradation follows (3,4). Both hypoxic conditions and chemical hydroxylase inhibitors (such as desferrioxamine and cobalt) inhibit HIF-1α degradation and lead to its stabilization. In addition, HIF-1α can be induced in an oxygen-independent manner by various cytokines through the PI3K-AKT-mTOR pathway (5-7).HIF-1β is also known as AhR nuclear translocator (ARNT) due to its ability to partner with the aryl hydrocarbon receptor (AhR) to form a heterodimeric transcription factor complex (8). Together with AhR, HIF-1β plays an important role in xenobiotics metabolism (8).
Huntingtin-interacting protein 2 (HIP2/LIG), is a E2 ubiquitin-conjugating enzyme, which accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro, HIP2/LIG catalyzes the synthesis of 'Lys-48'-linked polyubiquitin chains in the presence or in the absence of BRCA1-BARD1 E3 ubiquitin-protein ligase complex, while it does not transfer ubiquitin directly to but elongates monoubiquitinated substrate protein. Moreover, HIP2/LIG mediates the selective degradation of short-lived and abnormal proteins, such as the endoplasmic reticulum-associated degradation (ERAD) of misfolded lumenal proteins.
Histone post-translational modifications (PTMs) are key mechanisms of epigenetics that modulate chromatin structures, termed as “histone code”. The PTMs on histone including acetylation, methylation,phosphorylation and novel acylations directly affect the accessibility of chromatin to transcription factors and other epigenetic regulators, altering genome stability, gene transcription, etc. Histone methylation occurs primarily at lysine and arginine residues on the amino terminal of core histones. Methylation of histones can either increase or decrease transcription of genes, depending on which amino acids (Lys or Arg) in the histones are methylated and how many methyl groups are attached (mono-, di-, trimethylation on Lys, mono-di-symmetric/asymmetric methylation on Arg). Mostly, lysine methylation occurs primarily on histone H3 Lys4, 9, 27, 36, 79 and H4 Lys20,while Arginine methylation occurs primarily on histone H3 Arg2, 8, 17, 26 and H4 Arg3. histone methyltransferases (HMTs) and histone demethylases (HDMs) are major regulating factors.
Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation.
Histone post-translational modifications (PTMs), known as the “histone code”, are key mechanisms of epigenetics that modulate chromatin structures. The PTMs on histone including acetylation, methylation, phosphorylation, and novel acylations directly affect the accessibility of chromatin to transcription factors and other epigenetic regulators, altering genome stability and gene transcription. Histone acetylation, tightly controlled by the opposing action of histone acetyltransferases (HATs) and histone deacetylases (HDACs), occurs primarily at lysine residues on the N-terminal tails of histones H2A (Lys5, 9, and 15), H2B (Lys5, 12, 15, 16, and 20), H3 (Lys4, 9, 14, 18, 23, 27, and 36), and H4 (Lys5, 8, 12, 16, and 20), and plays vital roles in the regulation of gene expression, DNA damage repair, chromatin dynamics, etc.
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