TATA box HMG-CoA synthase family: Difference between revisions

Jump to navigation Jump to search
VisualWikitext
(Created page with "The '''TATA box''' (also called '''Goldberg-Hogness box''')<ref name=Lifton>{{ cite journal | author = R. P. Lifton, M. L. Goldberg, R. W. Karp, and D. S. Hogness | year = 1978 | title = The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications | url = https://symposium.cshlp.org/content/42/1047.extract | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 42 | issue = | pages = 1047–51 | doi = 10.11...")
 
Line 83: Line 83:
|pmid=
|pmid=
|accessdate=2024-06-09 }}</ref> genes with experimentally validated transcription start sites [are known from 2006]."<ref name=Xu/> "The TATA box [...] has a consensus sequence of TATAWAAR [...]."<ref name=Xu/> W = A or T and R = A or G. We "estimate that ~17% of promoters contain a TATA box".<ref name=Jin/>
|accessdate=2024-06-09 }}</ref> genes with experimentally validated transcription start sites [are known from 2006]."<ref name=Xu/> "The TATA box [...] has a consensus sequence of TATAWAAR [...]."<ref name=Xu/> W = A or T and R = A or G. We "estimate that ~17% of promoters contain a TATA box".<ref name=Jin/>
===Gene ID: 3157===
"Enables protein homodimerization activity. Predicted to be involved in acetyl-CoA metabolic process and farnesyl diphosphate biosynthetic process, mevalonate pathway. Predicted to be located in cytoplasm. Predicted to be active in cytosol."<ref name=AllianceofGenomeResources3157>{{ cite web
|author=Alliance of Genome Resources
|title=HMGCS1 3-hydroxy-3-methylglutaryl-CoA synthase 1 [ Homo sapiens ]
|publisher=ncbi.nlm.nih
|location=Bethsda, Maryland, USA
|date=April 2022
|url=http://www.ncbi.nlm.nih.gov/gene/3157
|accessdate=2024-06-10 }}</ref> This gene is not included,<ref name=Jin/> suggesting it does not contain a TATA box in its core promoter.<ref name=Jin/>


===Gene ID: 3158===
===Gene ID: 3158===
Line 93: Line 104:
|date=October 2009
|date=October 2009
|url=http://www.ncbi.nlm.nih.gov/gene/3158
|url=http://www.ncbi.nlm.nih.gov/gene/3158
|accessdate=2024-06-10 }}</ref> It has a TATA box (TATAAAG) from -30 to -24 nts from the TSS.<ref name=Jin/>
|accessdate=2024-06-10 }}</ref> It has a TATA box (TATAAAG) from -30 to -24 nts from the TSS.<ref name=Jin/> Transcription initiation by eukaryotic [[RNA polymerase II]] involves the following GTFs:<ref name="pmid11092823"/><ref name="pmidc">{{cite journal | last1 = Orphanides|first1= George|last2=Lagrange|first2=Thierry|last3=Reinberg|first3= Danny| title = The general transcription factors of RNA polymerase II | journal = [[Genes & Development]] | volume = 10 | issue = 21 | pages = 2657–83 | date = November 1996 | pmid = 8946909 | doi = 10.1101/gad.10.21.2657 | doi-access = free }}{{open access}}</ref>
* [[TFIIA]] – stabilizes the interaction between the TATA box and TFIID/TATA binding protein (TBP)


==Families of TATA box genes==
==Families of TATA box genes==

Revision as of 06:50, 23 July 2024

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: 3157

"Enables protein homodimerization activity. Predicted to be involved in acetyl-CoA metabolic process and farnesyl diphosphate biosynthetic process, mevalonate pathway. Predicted to be located in cytoplasm. Predicted to be active in cytosol."[7] This gene is not included,[6] suggesting it does not contain a TATA box in its core promoter.[6]

Gene ID: 3158

"The protein encoded by this gene belongs to the [3-hydroxy-3-methylglutaryl (HMG)] HMG-CoA synthase family. It is a mitochondrial enzyme that catalyzes the first reaction of ketogenesis, a metabolic pathway that provides lipid-derived energy for various organs during times of carbohydrate deprivation, such as fasting. Mutations in this gene are associated with HMG-CoA synthase deficiency. Alternatively spliced transcript variants encoding different isoforms have been found for this gene."[8] It has a TATA box (TATAAAG) from -30 to -24 nts from the TSS.[6] Transcription initiation by eukaryotic RNA polymerase II involves the following GTFs:[9][10]

  • TFIIA – stabilizes the interaction between the TATA box and TFIID/TATA binding protein (TBP)

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. ↑ Alliance of Genome Resources (April 2022). "HMGCS1 3-hydroxy-3-methylglutaryl-CoA synthase 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-10.
  8. ↑ RefSeq (October 2009). "HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-10.
  9. ↑
  10. ↑ Orphanides, George; Lagrange, Thierry; Reinberg, Danny (November 1996). "The general transcription factors of RNA polymerase II". Genes & Development. 10 (21): 2657–83. doi:10.1101/gad.10.21.2657. PMID 8946909.open access publication – free to read

External links


Retrieved from "https://www.wikidoc.org/index.php?title=TATA_box_HMG-CoA_synthase_family&oldid=1738995"