TATA box solute carrier family

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The TATA box (also called Goldberg-Hogness box)[1] is a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes;[2] approximately 24% of human genes contain a TATA box within the core promoter.[3]

Human genes

Main article: Human genes

"TATA-containing genes are more often highly regulated, such as by biotic or stress stimuli."[4] Only "∼10% of these TATA-containing promoters have the canonical TATA box (TATAWAWR)."[4]

"SRF-regulated genes of the actin/cytoskeleton/contractile family tend to have a TATA box."[5]

Different "TATA box sequences have different abilities to convey the activating signals of certain enhancers and activators in mammalian cells [...] and in yeast [...]."[5]

"SRF is a well established master regulator of the specific family of genes encoding the actin cytoskeleton and contractile apparatus [...], and we found that ~40% of the core promoters for these genes contain a TATA box, which is a significant enrichment compared to the low overall frequency of TATA-containing promoters in human and mouse genomes (...)."[5] "Global frequencies of core promoter types for human [9010 orthologous mouse-human promoter pairs with 1848 TATA-containing or 7162 TATA-less][6] genes with experimentally validated transcription start sites [are known from 2006]."[5] "The TATA box [...] has a consensus sequence of TATAWAAR [...]."[5] W = A or T and R = A or G. We "estimate that ~17% of promoters contain a TATA box".[6]

Gene ID: 292

"This gene is a member of the mitochondrial carrier subfamily of solute carrier protein genes. The product of this gene functions as a gated pore that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm. The protein forms a homodimer embedded in the inner mitochondria membrane. Suppressed expression of this gene has been shown to induce apoptosis and inhibit tumor growth. The human genome contains several non-transcribed pseudogenes of this gene."[7]

Gene ID: 1811

The DRA gene (colon mucosa-associated gene) has a TATA box.[8]

"The protein encoded by this gene is a transmembrane glycoprotein that transports chloride ions across the cell membrane in exchange for bicarbonate ions. It is localized to the mucosa of the lower intestinal tract, particularly to the apical membrane of columnar epithelium and some goblet cells. The protein is essential for intestinal chloride absorption, and mutations in this gene have been associated with congenital chloride diarrhea."[9]

Gene ID: 2542

"This gene regulates glucose-6-phosphate transport from the cytoplasm to the lumen of the endoplasmic reticulum, in order to maintain glucose homeostasis. It also plays a role in ATP-mediated calcium sequestration in the lumen of the endoplasmic reticulum. Mutations in this gene have been associated with various forms of glycogen storage disease. Alternative splicing in this gene results in multiple transcript variants."[10]

Gene ID: 6513

"This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia."[11]

Gene ID: 6518

"The protein encoded by this gene is a fructose transporter responsible for fructose uptake by the small intestine. The encoded protein also is necessary for the increase in blood pressure due to high dietary fructose consumption."[12] It has a TATA box (TATAAAA) from -33 to -27 nts from the TSS, Code score: 1.00; Matrix score: 0.92.[6]

Gene ID: 6519

"This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associated with cystinuria. Alternatively spliced transcript variants have been described, but their biological validity has not been determined."[13]

Gene ID: 6548

"This gene encodes a Na+/H+ antiporter that is a member of the solute carrier family 9. The encoded protein is a plasma membrane transporter that is expressed in the kidney and intestine. This protein plays a central role in regulating pH homeostasis, cell migration and cell volume. This protein may also be involved in tumor growth."[14] It has a TATA box (TATAAGT) from -32 to -26 nts from the TSS, Code score: 0.91; Matrix score: 0.84.[6]

Gene ID: 6559

"This gene encodes a renal thiazide-sensitive sodium-chloride cotransporter that is important for electrolyte homeostasis. This cotransporter mediates sodium and chloride reabsorption in the distal convoluted tubule. Mutations in this gene cause Gitelman syndrome, a disease similar to Bartter's syndrome, that is characterized by hypokalemic alkalosis combined with hypomagnesemia, low urinary calcium, and increased renin activity associated with normal blood pressure. This cotransporter is the target for thiazide diuretics that are used for treating high blood pressure. Multiple transcript variants encoding different isoforms have been found for this gene."[15]

Gene ID: 6566

"The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene."[16] It has a TATA box (TATAAGG) from -31 to -25 nts from the TSS, Code score: 0.91; Matrix score: 0.78.[6]

Gene ID: 84889

"This gene encodes a member of the solute carrier family 7. The encoded protein is a sodium-independent cationic amino acid transporter. Alternate splicing results in multiple transcripts that encoded the same protein."[17]

Families of TATA box genes

Main article: Families of TATA box genes

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

References

  1. ↑ R. P. Lifton, M. L. Goldberg, R. W. Karp, and D. S. Hogness (1978). "The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications". Cold Spring Harbor Symposia on Quantitative Biology. 42: 1047–51. doi:10.1101/SQB.1978.042.01.105. PMID 98262.
  2. ↑ Stephen T. Smale and James T. Kadonaga (July 2003). "The RNA Polymerase II Core Promoter" (PDF). Annual Review of Biochemistry. 72 (1): 449–79. doi:10.1146/annurev.biochem.72.121801.161520. PMID 12651739. Retrieved 2012-05-07.
  3. ↑ C Yang, E Bolotin, T Jiang, FM Sladek, E Martinez (March 2007). "Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. PMID 17123746.
  4. ↑ 4.0 4.1 Chuhu Yang, Eugene Bolotin, Tao Jiang, Frances M. Sladek, and Ernest Martinez (10 October 2006). "Prevalence of the Initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters". Gene. 389 (1): 52–65. doi:10.1016/j.gene.2006.09.029. PMID 17123746. Retrieved 2024-06-07.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 Muyu Xu, Elsie Gonzalez-Hurtado, and Ernest Martinez (April 2016). "Core promoter-specific gene regulation: TATA box selectivity and Initiator-dependent bi-directionality of serum response factor-activated transcription". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (4): 553–563. doi:10.1016/j.bbagrm.2016.01.005. Retrieved 2024-06-08.
  6. ↑ 6.0 6.1 6.2 6.3 6.4 Victor X Jin, Gregory AC Singer, Francisco J Agosto-Pérez, Sandya Liyanarachchi, and Ramana V Davuluri (2006). "Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs". BMC Bioinformatics. 7: 114. doi:10.1186/1471-2105-7-114. Retrieved 2024-06-09.
  7. ↑ RefSeq (June 2013). "SLC25A5 solute carrier family 25 member 5 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-18.
  8. ↑ Yutaka Suzuki, Tatsuhiko Tsunoda, Jun Sese, Hirotoshi Taira, Junko Mizushima-Sugano, Hiroko Hata, Toshio Ota, Takao Isogai, Toshihiro Tanaka, Yusuke Nakamura, Akira Suyama, Yoshiyuki Sakaki, Shinichi Morishita, Kousaku Okubo, and Sumio Sugano (11 April 2001). "Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes". Genome Research. 11 (5): 677-684. doi:10.1101/gr.164001.
  9. ↑ RefSeq (October 2008). "SLC26A3 solute carrier family 26 member 3 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-19.
  10. ↑ RefSeq (August 2009). "SLC37A4 solute carrier family 37 member 4 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-06-26.
  11. ↑ RefSeq (April 2013). "SLC2A1 solute carrier family 2 member 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-09.
  12. ↑ RefSeq (June 2016). "SLC2A5 solute carrier family 2 member 5 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-06-11.
  13. ↑ RefSeq (July 2008). "SLC3A1 solute carrier family 3 member 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-09.
  14. ↑ RefSeq (September 2011). "SLC9A1 solute carrier family 9 member A1 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-06-11.
  15. ↑ RefSeq (July 2008). "SLC12A3 solute carrier family 12 member 3 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-09.
  16. ↑ RefSeq (October 2009). "SLC16A1 solute carrier family 16 member 1 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-06-11.
  17. ↑ RefSeq (May 2010). "SLC7A3 solute carrier family 7 member 3 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-23.

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