ATA box gene transcriptions: Difference between revisions

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==Consensus sequences==
==Consensus sequences==
{{main|Gene transcriptions/Consensus sequences|Consensus sequences}}
{{main|Consensus sequence gene transcriptions|Consensus sequences}}
"The 3' flanking area contained the highly conserved hexanucleotide sequence A-A-T-A-A-A found in eukaryotic messages between the terminator codon and the polyadenylylation site (44)."<ref name=Liebhaber>{{ cite journal
"The 3' flanking area contained the highly conserved hexanucleotide sequence A-A-T-A-A-A found in eukaryotic messages between the terminator codon and the polyadenylylation site (44)."<ref name=Liebhaber>{{ cite journal
|author=Stephen A. Liebhaber, Michel J. Goossens, and Yuet Wai Kan
|author=Stephen A. Liebhaber, Michel J. Goossens, and Yuet Wai Kan
Line 145: Line 145:
==Hypotheses==
==Hypotheses==
{{main|Hypotheses}}
{{main|Hypotheses}}
# A1BG has no ATA boxes in either promoter.
# A1BG is not transcribed by an ATA box.
# A1BG is not transcribed by an ATA box.
{{seealso|Control groups|Proof of concept|Proof of technology}}
# AGCE1 does not participate in the transcription of A1BG.
 
==Samplings==
 
For the Basic programs (starting with SuccessablesATA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:
# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesATA--.bas, looking for 3'-AATAAA-5', 1, 3'-AATAAA-5', 1726,
# negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesATA-+.bas, looking for 3'-AATAAA-5', 0,
# positive strand in the negative direction is SuccessablesATA+-.bas, looking for 3'-AATAAA-5', 3, 3'-AATAAA-5', 3014, 3'-AATAAA-5', 3335, 3'-AATAAA-5', 4072,
# positive strand in the positive direction is SuccessablesATA++.bas, looking for 3'-AATAAA-5', 0,
# complement, negative strand, negative direction is SuccessablesATAc--.bas, looking for 3'-TTATTT-5', 3, 3'-TTATTT-5', 3014, 3'-TTATTT-5', 3335, 3'-TTATTT-5', 4072,
# complement, negative strand, positive direction is SuccessablesATAc-+.bas, looking for 3'-TTATTT-5', 0,
# complement, positive strand, negative direction is SuccessablesATAc+-.bas, looking for 3'-TTATTT-5', 1, 3'-TTATTT-5', 1726,
# complement, positive strand, positive direction is SuccessablesATAc++.bas, looking for 3'-TTATTT-5', 0,
# inverse complement, negative strand, negative direction is SuccessablesATAci--.bas, looking for 3'-TTTATT-5', 5, 3'-TTTATT-5', 3013, 3'-TTTATT-5', 3334, 3'-TTTATT-5', 4071, 3'-TTTATT-5', 4075, 3'-TTTATT-5', 4221,
# inverse complement, negative strand, positive direction is SuccessablesATAci-+.bas, looking for 3'-TTTATT-5', 1, 3'-TTTATT-5', 703,
# inverse complement, positive strand, negative direction is SuccessablesATAci+-.bas, looking for 3'-TTTATT-5', 1, 3'-TTTATT-5', 4537,
# inverse complement, positive strand, positive direction is SuccessablesATAci++.bas, looking for 3'-TTTATT-5', 0,
# inverse, negative strand, negative direction, is SuccessablesATAi--.bas, looking for 3'-AAATAA-5', 1, 3'-AAATAA-5', 4537,
# inverse, negative strand, positive direction, is SuccessablesATAi-+.bas, looking for 3'-AAATAA-5', 0,
# inverse, positive strand, negative direction, is SuccessablesATAi+-.bas, looking for 3'-AAATAA-5', 5, 3'-AAATAA-5', 3013, 3'-AAATAA-5', 3334, 3'-AAATAA-5', 4071, 3'-AAATAA-5', 4075, 3'-AAATAA-5', 4221,
# inverse, positive strand, positive direction, is SuccessablesATAi++.bas, looking for 3'-AAATAA-5', 1, 3'-AAATAA-5', 703.
 
==Core promoters==
{{main|Core promoter gene transcriptions}}
Negative direction: 3'-AAATAA-5', 4537 and complements.
 
==Proximal promoters==
{{main|Proximal promoter gene transcriptions}}
Negative direction: 3'-AAATAA-5' at 4221 and complements.
 
==Distal promoters==
{{main|Distal promoter gene transcriptions}}
Negative direction: 3'-AAATAA-5' at 4075, 3'-AATAAA-5' at 4072, 3'-AAATAA-5' at 4071, 3'-AATAAA-5' at 3335, 3'-AAATAA-5' at 3334, 3'-AATAAA-5' at 3014, 3'-AAATAA-5' at 3013, 3'-AATAAA-5' at 1726 and complements.
 
Positive direction: 3'-AAATAA-5' at 703 and complements.


==Acknowledgements==
==Acknowledgements==
Line 158: Line 193:
* [[A1BG gene transcriptions]]
* [[A1BG gene transcriptions]]
* [[ATA box gene transcription laboratory]]
* [[ATA box gene transcription laboratory]]
* [[Complex locus A1BG and ZNF497]]
* [[TATA box gene transcriptions]]
* [[TATA box gene transcriptions]]
{{Div col end}}
{{Div col end}}
Line 165: Line 201:


==External links==
==External links==
* [http://www.bing.com/search?q=&go=&qs=n&sk=&sc=8-15&qb=1&FORM=AXRE Bing Advanced search]
* [http://www.genome.jp/ GenomeNet KEGG database]
* [http://www.genome.jp/ GenomeNet KEGG database]
* [http://books.google.com/ Google Books]
* [http://scholar.google.com/advanced_scholar_search?hl=en&lr= Google scholar Advanced Scholar Search]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
* [http://www.jstor.org/ JSTOR]
* [http://www.lycos.com/ Lycos search]
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
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* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search]
* [http://www.osti.gov/ Office of Scientific & Technical Information]
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database]
* [http://www.questia.com/ Questia - The Online Library of Books and Journals]
* [http://online.sagepub.com/ SAGE journals online]
* [http://www.scirus.com/srsapp/advanced/index.jsp?q1= Scirus for scientific information only advanced search]
* [http://www.springerlink.com/ SpringerLink]
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Revision as of 18:49, 7 October 2020

Editor-In-Chief: Henry A. Hoff

The ATA box is a variant of the TATA box that appears in the globin and other genes. Instead of a sequence TATA as in the TATA box, the ATA box lacks the first thymine (T) and may be tissue specific.

Consensus sequences

Main articles: Consensus sequence gene transcriptions and Consensus sequences

"The 3' flanking area contained the highly conserved hexanucleotide sequence A-A-T-A-A-A found in eukaryotic messages between the terminator codon and the polyadenylylation site (44)."[1]

"ATA boxes [AATAAA] can be clearly identified in the chicken αA- and αD-globin genes about 70 bp upstream from the initiator ATG codon [...] The sequences of the proposed cap sites agree with those determined for other globin genes (Fig. 6A; Refs. 15, 24, and 32) as do their positions relative to the ATA boxes"[2]

An ATA box may have the sequence AAATAT.[3] The CArG box has the sequence CCTATTATGG.[3]

"The [Sminthopsis crassicaudata putative embryonic β-globin gene] ATA box, located 30 bp 5' to the putative cap site, is of the form AAATAAAA typically found in eutherian embryonic β-like globin genes. In sequence comparisons with ATA boxes from human, mouse, and [Didelphis virginiana] adult and embryonic β-like globin genes, the S.c-ε ATA box was found to most closely resemble that found in the D. virginiana ε-globin gene (Fig 4)."[4]

This suggests a consensus sequence of 3'-AAATA(A/T)A-5' on the template strand, or perhaps 3'-(A/C/G/T)AATA(A/T)A-5'.

Human genes

Main articles: Genes/Human and Human genes

GeneID: 3043 HBB hemoglobin subunit beta, "The alpha (HBA) and beta (HBB) loci determine the structure of the 2 types of polypeptide chains in adult hemoglobin, Hb A. The normal adult hemoglobin tetramer consists of two alpha chains and two beta chains. Mutant beta globin causes sickle cell anemia. Absence of beta chain causes beta-zero-thalassemia. Reduced amounts of detectable beta globin causes beta-plus-thalassemia. The order of the genes in the beta-globin cluster is 5'-epsilon -- gamma-G -- gamma-A -- delta -- beta--3'."[5]

Cystatin genes

The "four cystatin genes [GeneID: 1469 CST1, GeneID: 1470 CST2, GeneID: 1471 CST3, and GeneID: 1472 CST4] contain the ATA-box sequence (ATAAA) in their 5'-flanking regions; however, the CAT-box sequence (CAT), a binding site of the transcription factor, CTF, is found only in the 5'-flanking region of the S-type cystatin genes."[6]

β-thalassemia

"DNA sequence analysis of a cloned β-globin gene from a Chinese patient with β-thalassemia revealed a single nucleotide substitution (A→ G) within the ATA box homology and 28 base pairs upstream from the cap site."[7]

"Comparison of the level of β-globin transcripts in a variety of deletion mutants shows that for efficient transcription, both the ATA or Goldberg–Hogness box, and a region between 100 and 58 base pairs in front of the site at which transcription is initiated, are required. Deletion of either of these regions results in a decrease in the level of β-globin transcripts by an order of magnitude; deletion of the ATA box causes an additional loss in the specificity of the site of initiation of RNA synthesis. The DNA sequences downstream from the ATA box, including the natural β-globin mRNA cap site, are dispensable for transcription in vivo."[8]

"The first is a sequence rich in the nucleic acids adenine and thymine (the Goldberg-Hogness, "TATA," or "ATA" box) which is located 20-30 base pairs upstream from the RNA initiation site (the cap site which is the transcriptional start site for the mRNA) and is characterized by a concensus sequence (5'-TATAA-ATA-3')."[9]

Hypotheses

Main article: Hypotheses
  1. A1BG has no ATA boxes in either promoter.
  2. A1BG is not transcribed by an ATA box.
  3. AGCE1 does not participate in the transcription of A1BG.

Samplings

For the Basic programs (starting with SuccessablesATA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesATA--.bas, looking for 3'-AATAAA-5', 1, 3'-AATAAA-5', 1726,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesATA-+.bas, looking for 3'-AATAAA-5', 0,
  3. positive strand in the negative direction is SuccessablesATA+-.bas, looking for 3'-AATAAA-5', 3, 3'-AATAAA-5', 3014, 3'-AATAAA-5', 3335, 3'-AATAAA-5', 4072,
  4. positive strand in the positive direction is SuccessablesATA++.bas, looking for 3'-AATAAA-5', 0,
  5. complement, negative strand, negative direction is SuccessablesATAc--.bas, looking for 3'-TTATTT-5', 3, 3'-TTATTT-5', 3014, 3'-TTATTT-5', 3335, 3'-TTATTT-5', 4072,
  6. complement, negative strand, positive direction is SuccessablesATAc-+.bas, looking for 3'-TTATTT-5', 0,
  7. complement, positive strand, negative direction is SuccessablesATAc+-.bas, looking for 3'-TTATTT-5', 1, 3'-TTATTT-5', 1726,
  8. complement, positive strand, positive direction is SuccessablesATAc++.bas, looking for 3'-TTATTT-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesATAci--.bas, looking for 3'-TTTATT-5', 5, 3'-TTTATT-5', 3013, 3'-TTTATT-5', 3334, 3'-TTTATT-5', 4071, 3'-TTTATT-5', 4075, 3'-TTTATT-5', 4221,
  10. inverse complement, negative strand, positive direction is SuccessablesATAci-+.bas, looking for 3'-TTTATT-5', 1, 3'-TTTATT-5', 703,
  11. inverse complement, positive strand, negative direction is SuccessablesATAci+-.bas, looking for 3'-TTTATT-5', 1, 3'-TTTATT-5', 4537,
  12. inverse complement, positive strand, positive direction is SuccessablesATAci++.bas, looking for 3'-TTTATT-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesATAi--.bas, looking for 3'-AAATAA-5', 1, 3'-AAATAA-5', 4537,
  14. inverse, negative strand, positive direction, is SuccessablesATAi-+.bas, looking for 3'-AAATAA-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesATAi+-.bas, looking for 3'-AAATAA-5', 5, 3'-AAATAA-5', 3013, 3'-AAATAA-5', 3334, 3'-AAATAA-5', 4071, 3'-AAATAA-5', 4075, 3'-AAATAA-5', 4221,
  16. inverse, positive strand, positive direction, is SuccessablesATAi++.bas, looking for 3'-AAATAA-5', 1, 3'-AAATAA-5', 703.

Core promoters

Main article: Core promoter gene transcriptions

Negative direction: 3'-AAATAA-5', 4537 and complements.

Proximal promoters

Main article: Proximal promoter gene transcriptions

Negative direction: 3'-AAATAA-5' at 4221 and complements.

Distal promoters

Main article: Distal promoter gene transcriptions

Negative direction: 3'-AAATAA-5' at 4075, 3'-AATAAA-5' at 4072, 3'-AAATAA-5' at 4071, 3'-AATAAA-5' at 3335, 3'-AAATAA-5' at 3334, 3'-AATAAA-5' at 3014, 3'-AAATAA-5' at 3013, 3'-AATAAA-5' at 1726 and complements.

Positive direction: 3'-AAATAA-5' at 703 and complements.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ Stephen A. Liebhaber, Michel J. Goossens, and Yuet Wai Kan (December 1980). "Cloning and complete nucleotide sequence of human 5'-α-globin gene" (PDF). Proceedings of the National Academy of Science USA. 77 (12): 7054–8. Retrieved 2013-06-28.
  2. ↑ Jerry B. Dodgson and James Douglas Engel (10 April 1983). "The nucleotide sequence of the adult chicken alpha-globin genes" (PDF). The Journal of Biological Chemistry. 258 (7): 4623–9. Retrieved 2017-02-04.
  3. ↑ 3.0 3.1 Shigemi Kimura, Kuniya Abe, Misao Suzuki, Masakatsu Ogawa, Kowashi Yoshioka, Tadasi Kaname, Teruhisa Miike and Ken-ichi Yamamura (June 1997). "A 900 bp genomic region from the mouse dystrophin promoter directs lacZ reporter expression only to the right heart of transgenic mice". Development, Growth & Differentiation. 39 (3): 257–65. doi:10.1046/j.1440-169X.1997.t01-2-00001.x. Retrieved 2013-06-28.
  4. ↑ Steven J.B. Cooper and Rory M.HOPE (December 1993). "Evolution and expression of a beta-like globin gene of the Australian marsupial Sminthopsis crassicaudata" (PDF). Proceedings of the National Academy of Sciences USA. 90: 11777–81. Retrieved 2017-02-04.
  5. ↑ RefSeq (July 2008). HBB hemoglobin subunit beta [ Homo sapiens (human) ]. 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2017-02-04.
  6. ↑ Eiichi Saitoh and Satoko Isemura (January 1, 1993). "Molecular Biology of Human Salivary Cysteine Proteinase Inhibitors" (PDF). Critical Reviews in Oral Biology and Medicine. 4 (3/4): 487–93. doi:10.1177/10454411930040033301. Retrieved 2013-06-28.
  7. ↑ Stuart H. Orkin, Julianne P. Sexton, Tu-chen Cheng, Sabra C. Goff, Patricia J. V. Giardina, I. Lee Joseph and Haig H. Hazazian Jr. (1983). "ATA box transcription mutation in β-thalassemia". Nucleic Acids Research. 11 (14): 4727–34. doi:10.1093/nar/11.14.4727. Retrieved 2014-05-29.
  8. ↑ G. C. Grosveld, E. De Boer, C. K. Shewmaker, & R. A. Flavell (January 14, 1982). "DNA sequences necessary for transcription of the rabbit β-globin gene in vivo". Nature. 295 (5845): 120–6. doi:10.1038/295120a0. Retrieved 2014-05-29.
  9. ↑ GE Smith, MD Summers (1988). "Method for producing a recombinant baculovirus expression vector". US Patent (4, 745, 051). Retrieved 2014-05-29.

External links

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