TATA box forkhead family: Difference between revisions

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|url=https://www.ncbi.nlm.nih.gov/gene/668
|url=https://www.ncbi.nlm.nih.gov/gene/668
|accessdate=24 July 2024 }}</ref> This gene does not have a TATA box in its promoter, but it does have a MTE+.<ref name=Jin/>
|accessdate=24 July 2024 }}</ref> This gene does not have a TATA box in its promoter, but it does have a MTE+.<ref name=Jin/>
===Gene ID: 1112===
"This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms."<ref name=RefSeq1112>{{ cite web
|author=RefSeq
|title=FOXN3 forkhead box N3 [ Homo sapiens (human) ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=July 2008
|url=https://www.ncbi.nlm.nih.gov/gene/1112
|accessdate=24 July 2024 }}</ref> There's no TATA box in its core promoter but it does contain a BRE+ and a MTE-.<ref name=Jin/>
===Gene ID: 2297===
"This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. Studies of the orthologous mouse protein indicate that it functions in kidney development by promoting nephron progenitor differentiation, and it also functions in the development of the retina and optic chiasm. It may also regulate inflammatory reactions and prevent autoimmunity."<ref name=RefSeq2297>{{ cite web
|author=RefSeq
|title=FOXD1 forkhead box D1 [ Homo sapiens (human) ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=April 2014
|url=https://www.ncbi.nlm.nih.gov/gene/2297
|accessdate=24 July 2024 }}</ref> The "TATA box" in the core promoter has the nucleotides -32 "TATAAGC" -26 and a MTE+.<ref name=Jin/>


===Gene ID: 2305===
===Gene ID: 2305===
Line 160: Line 182:
|url=http://www.ncbi.nlm.nih.gov/gene/3171
|url=http://www.ncbi.nlm.nih.gov/gene/3171
|accessdate=2024-06-26 }}</ref>
|accessdate=2024-06-26 }}</ref>
===Gene ID: 4303===
"This gene encodes a member of the O class of winged helix/forkhead transcription factor family. Proteins encoded by this class are regulated by factors involved in growth and differentiation indicating they play a role in these processes. A translocation involving this gene on chromosome X and the homolog of the Drosophila trithorax gene, encoding a DNA binding protein, located on chromosome 11 is associated with leukemia. Multiple transcript variants encoding different isoforms have been found for this gene."<ref name=RefSeq4303>{{ cite web
|author=RefSeq
|title=FOXO4 forkhead box O4 [ Homo sapiens ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=January 2010
|url=http://www.ncbi.nlm.nih.gov/gene/4303
|accessdate=2024-07-24 }}</ref> At the approximate location of a TATA box in version CR596165, -36 to -30, has the nucleotides "AGCAACT" as a TATA-, also a MTE+ and a DPE+.<ref name=Jin/> In version X93996, there is no TATA box but there are an INR- and a MTE+.<ref name=Jin/>
===Gene ID: 22887===
"Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus."<ref name=AllianceofGenomeResources22887>{{ cite web
|author=Alliance of Genome Resources
|title=FOXJ3 forkhead box J3 [ Homo sapiens ]
|publisher=ncbi.nlm.nih
|location=Bethsda, Maryland, USA
|date=April 2022
|url=http://www.ncbi.nlm.nih.gov/gene/22887
|accessdate=2024-07-02 }}</ref> The apparent TATA- box in the core promoter is -27 "TCTAAAC" -21 with an INR-.<ref name=Jin/>


===Gene ID: 50943===
===Gene ID: 50943===
Line 171: Line 215:
|url=http://www.ncbi.nlm.nih.gov/gene/50943
|url=http://www.ncbi.nlm.nih.gov/gene/50943
|accessdate=2024-07-01 }}</ref>
|accessdate=2024-07-01 }}</ref>
===Gene ID: 55743===
"This gene encodes an E3 ubiquitin-protein ligase required for the maintenance of the antephase checkpoint that regulates cell cycle entry into mitosis and, therefore, may play a key role in cell cycle progression and tumorigenesis. The encoded protein has an N-terminal forkhead-associated domain, a central RING-finger domain, and a cysteine-rich C-terminal region. Alternatively spliced transcript variants that encode different protein isoforms have been described."<ref name=RefSeq55743>{{ cite web
|author=RefSeq
|title=CHFR checkpoint with forkhead and ring finger domains [ Homo sapiens (human) ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=March 2014
|url=https://www.ncbi.nlm.nih.gov/gene/55743
|accessdate=24 July 2024 }}</ref> This gene does not have a TATA box in its promoter, but it does have a BRE- and an INR-.<ref name=Jin/>


===Gene ID: 93986===
===Gene ID: 93986===
Line 182: Line 237:
|url=http://www.ncbi.nlm.nih.gov/gene/93986
|url=http://www.ncbi.nlm.nih.gov/gene/93986
|accessdate=2024-07-24 }}</ref> This gene does not have a TATA box in its core promoter but it does have a MTE+.<ref name=Jin/>
|accessdate=2024-07-24 }}</ref> This gene does not have a TATA box in its core promoter but it does have a MTE+.<ref name=Jin/>
===Gene ID: 399823===
"Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anatomical structure morphogenesis; cell differentiation; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of chromatin."<ref name=AllianceofGenomeResources399823>{{ cite web
|author=Alliance of Genome Resources
|title=FOXI2 forkhead box I2 [ Homo sapiens ]
|publisher=ncbi.nlm.nih
|location=Bethsda, Maryland, USA
|date=April 2022
|url=http://www.ncbi.nlm.nih.gov/gene/399823
|accessdate=2024-07-24 }}</ref> This gene does not have a TATA box in its core promoter but it does have an INR+ and a DPE-.<ref name=Jin/>


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

Latest revision as of 06:32, 25 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: 668

"This gene encodes a forkhead transcription factor. The protein contains a fork-head DNA-binding domain and may play a role in ovarian development and function. Expansion of a polyalanine repeat region and other mutations in this gene are a cause of blepharophimosis syndrome and premature ovarian failure 3."[7] This gene does not have a TATA box in its promoter, but it does have a MTE+.[6]

Gene ID: 1112

"This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms."[8] There's no TATA box in its core promoter but it does contain a BRE+ and a MTE-.[6]

Gene ID: 2297

"This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. Studies of the orthologous mouse protein indicate that it functions in kidney development by promoting nephron progenitor differentiation, and it also functions in the development of the retina and optic chiasm. It may also regulate inflammatory reactions and prevent autoimmunity."[9] The "TATA box" in the core promoter has the nucleotides -32 "TATAAGC" -26 and a MTE+.[6]

Gene ID: 2305

"The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene."[10] This gene does not have a TATA box in its promoter, but it does have an INR- and a MTE+.[6]

Gene ID: 2308

"This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in myogenic growth and differentiation. Translocation of this gene with PAX3 has been associated with alveolar rhabdomyosarcoma."[11]

Gene ID: 2309

"This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. This gene likely functions as a trigger for apoptosis through expression of genes necessary for cell death. Translocation of this gene with the MLL gene is associated with secondary acute leukemia. Alternatively spliced transcript variants encoding the same protein have been observed."[12] This gene does not have a TATA box in its core promoter but does have a DPE- in version NM_001455 or a BRE+, INR+ and MTE+ in version AJ001590.[6]

Gene ID: 3169

"This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver."[13] This gene does not have a TATA box in its core promoter but does have a MTE-.[6]

Gene ID: 3170

"This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific genes such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. This gene has been linked to sporadic cases of maturity-onset diabetes of the young. Transcript variants encoding different isoforms have been identified for this gene."[14] This gene has the following nucleotides "TTGAAAC" at the TATA box location in its core promoter as well as an INR+ and a MTE+.[6]

Gene ID: 3171

"This gene encodes a member of the forkhead class of DNA-binding proteins. These hepatocyte nuclear factors are transcriptional activators for liver-specific transcripts such as albumin and transthyretin, and they also interact with chromatin. Similar family members in mice have roles in the regulation of metabolism and in the differentiation of the pancreas and liver. The crystal structure of a similar protein in rat has been resolved."[15]

Gene ID: 4303

"This gene encodes a member of the O class of winged helix/forkhead transcription factor family. Proteins encoded by this class are regulated by factors involved in growth and differentiation indicating they play a role in these processes. A translocation involving this gene on chromosome X and the homolog of the Drosophila trithorax gene, encoding a DNA binding protein, located on chromosome 11 is associated with leukemia. Multiple transcript variants encoding different isoforms have been found for this gene."[16] At the approximate location of a TATA box in version CR596165, -36 to -30, has the nucleotides "AGCAACT" as a TATA-, also a MTE+ and a DPE+.[6] In version X93996, there is no TATA box but there are an INR- and a MTE+.[6]

Gene ID: 22887

"Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus."[17] The apparent TATA- box in the core promoter is -27 "TCTAAAC" -21 with an INR-.[6]

Gene ID: 50943

"The protein encoded by this gene is a member of the forkhead/winged-helix family of transcriptional regulators. Defects in this gene are the cause of immunodeficiency polyendocrinopathy, enteropathy, X-linked syndrome (IPEX), also known as X-linked autoimmunity-immunodeficiency syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified."[18]

Gene ID: 55743

"This gene encodes an E3 ubiquitin-protein ligase required for the maintenance of the antephase checkpoint that regulates cell cycle entry into mitosis and, therefore, may play a key role in cell cycle progression and tumorigenesis. The encoded protein has an N-terminal forkhead-associated domain, a central RING-finger domain, and a cysteine-rich C-terminal region. Alternatively spliced transcript variants that encode different protein isoforms have been described."[19] This gene does not have a TATA box in its promoter, but it does have a BRE- and an INR-.[6]

Gene ID: 93986

"This gene encodes a member of the forkhead/winged-helix (FOX) family of transcription factors. It is expressed in fetal and adult brain as well as in several other organs such as the lung and gut. The protein product contains a FOX DNA-binding domain and a large polyglutamine tract and is an evolutionarily conserved transcription factor, which may bind directly to approximately 300 to 400 gene promoters in the human genome to regulate the expression of a variety of genes. This gene is required for proper development of speech and language regions of the brain during embryogenesis, and may be involved in a variety of biological pathways and cascades that may ultimately influence language development. Mutations in this gene cause speech-language disorder 1 (SPCH1), also known as autosomal dominant speech and language disorder with orofacial dyspraxia. Multiple alternative transcripts encoding different isoforms have been identified in this gene."[20] This gene does not have a TATA box in its core promoter but it does have a MTE+.[6]

Gene ID: 399823

"Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anatomical structure morphogenesis; cell differentiation; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of chromatin."[21] This gene does not have a TATA box in its core promoter but it does have an INR+ and a DPE-.[6]

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. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 6.14 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 (July 2016). "FOXL2 forkhead box L2 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 July 2024.
  8. ↑ RefSeq (July 2008). "FOXN3 forkhead box N3 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 July 2024.
  9. ↑ RefSeq (April 2014). "FOXD1 forkhead box D1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 July 2024.
  10. ↑ RefSeq (July 2011). "FOXM1 forkhead box M1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 July 2024.
  11. ↑ RefSeq (July 2008). "FOXO1 forkhead box O1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 3 December 2020.
  12. ↑ RefSeq (July 2008). "FOXO3 forkhead box O3 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 July 2024.
  13. ↑ RefSeq (July 2008). "FOXA1 forkhead box A1 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-07-23.
  14. ↑ RefSeq (October 2008). "FOXA2 forkhead box A2 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-07-23.
  15. ↑ RefSeq (July 2008). "FOXA3 forkhead box A3 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-06-26.
  16. ↑ RefSeq (January 2010). "FOXO4 forkhead box O4 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-07-24.
  17. ↑ Alliance of Genome Resources (April 2022). "FOXJ3 forkhead box J3 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-02.
  18. ↑ RefSeq (July 2008). "FOXP3 forkhead box P3 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-01.
  19. ↑ RefSeq (March 2014). "CHFR checkpoint with forkhead and ring finger domains [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 July 2024.
  20. ↑ RefSeq (February 2010). "FOXP2 forkhead box P2 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-24.
  21. ↑ Alliance of Genome Resources (April 2022). "FOXI2 forkhead box I2 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-24.

External links


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