RNA polymerase synthesizes RNA from a DNA template. For transcription to begin, RNA polymerase must attach to a specific DNA region at the beginning of a gene, known as promoter. Transcription factors control access of and frequently recruit RNA polymerases to promoter regions. Promoters can additionally function together with other more distant regulatory DNA regions, such as enhancers or repressors to further control the level of transcription of a given gene. Insulator regions in the genome protect genes from influences from regulation of neighboring genes. Multiple enhancer sites may tune the transcription of one gene, and each enhancer may be bound by more than one transcription factor, increasing the complexity of transcriptional regulation. Enhancers are often the major determinant of transcription of developmental genes in the differing lineages and stages of hematopoiesis. Genes can have more than one transcription start site, giving rise to RNA molecules starting with distinct sequences.

RNA is heterogeneous and stretches of genomic DNA may encode for more than one RNA or more than one type of RNA. Most eukaryotic RNA genes, especially messenger RNAs (mRNAs), contain a basic structure consisting of alternating coding exons and noncoding introns, subsequently dealt with in the splicing process.

While most RNAs in the cell are encoded by chromosomes in the nucleus, several mitochondrial proteins are encoded by the mitochondrial genome, often referred to as mtDNA. Transcription of the different classes of RNAs in eukaryotes is carried out by three different RNA polymerase enzymes. RNA polymerase I synthesizes the ribosomal RNAs (rRNAs), except for the 5 S species. RNA polymerase II synthesizes the mRNAs and some small nuclear RNAs (snRNAs) involved in RNA splicing. RNA polymerase III synthesizes 5 S rRNA and transfer RNAs (tRNAs). Transcription levels are finely tuned by the binding strength of the RNA polymerase to the promoter region at the beginning of a given gene, the interaction between activating and inhibiting transcription factors that bind to the given promoter, and transcriptional regulatory domains such as the enhancers or silencers mentioned previously.

Gene-specific transcription factors are sequence-specific DNA binding proteins that can be modified by cell signals. Numerous genetic diseases are associated with mutations in a gene’s coding region, promoter, or enhancers. In β-thalassemia, mutations can occur in the promoter region, the enhancer region, or the coding region of the gene. Mutations can involve single nucleotide substitutions, small deletions, or insertions and can heavily affect transcription, RNA splicing or stability, translation, and ultimately protein availability or functionality. Regulation of transcription is fundamental during T-lymphocyte differentiation, which requires binding of multiple activating transcription factors, such as lymphocyte enhancer factor (LEF)-1, GATA binding protein 3 (GATA)-3, and ETS proto-onco gene (ETS)-1, to the T-cell receptor alpha (TCRA) gene enhancer.

Mutations in promoter sequences that result in decreased transcription factor binding, and therefore less RNA polymerase binding, ultimately lead to decreased gene expression. One of the best examples of a mutation in a transcription factor binding site associated with a human disease is in the factor IX gene. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4α) is required to bind to the factor IX promoter before this gene can be transcribed.[1] Patients with a mutation in the HNF4α binding site can develop hemophilia B, an X-linked recessive bleeding disorder primarily affecting males (Fig. 1).

Fig1. ROLE OF TRANSCRIPTION FACTORS IN THE REGULATION OF EUKARYOTIC GENE EXPRESSION. Upper panel: schematic diagram of the DNA region containing the locus of the coagulation factor IX gene and its promoter, containing a binding site for the HNFα transcription factor. Lower panel: mutations in either the promoter region or in the HNFα transcription factor reduce the expression of factor IX, leading to bleeding disorders such as hemophilia B.

Many transcription factors, such as signal transducer and activator of transcription (STAT) proteins, require phosphorylation to bind DNA. Since transcription factors can be targeted by kinases and phosphatases, phosphorylation can effectively integrate information carried by multiple signal transduction pathways, thus providing versatility and flexibility in gene regulation. For example, the Janus kinase (JAK) STAT pathway is widely used by members of the cytokine receptor superfamily, including those for granulocyte colony-stimulating factor (G-CSF), erythropoietin, thrombopoietin, interferons, and interleukins. Normally, ligand-bound growth factor receptors lead to JAK2 phosphorylation, which then activates STAT, also by phosphorylation. Activated STAT then dimerizes, translocates to the hematopoietic cell nucleus, binds DNA, and promotes transcription of genes for hematopoiesis. Alteration of JAK2, such as a V617F mutation, results in a constitutively active kinase capable of driving STAT activation. This leads to constitutive transcription of STAT target genes and results in myeloproliferative disorders such as polycythemia vera.

References

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[1] Funnell APW, Crossley M. Hemophilia B Leyden and once mysterious cis regulatory mutations. Trends Genet. 2014;30(1):18–23.