ATA box gene transcriptions: Difference between revisions

Revision as of 05:01, 13 October 2019

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

"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 α^A- and α^D-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

GeneID: 3043 HBB hemoglobin subunit beta [ Homo sapiens (human) ] "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

A1BG is not transcribed by an ATA box.

Template:Seealso

References

↑ Stephen A. Liebhaber, Michel J. Goossens, and Yuet Wai Kan (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. Unknown parameter |month= ignored (help)
↑ Jerry B. Dodgson and James Douglas Engel (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. Unknown parameter |month= ignored (help)
↑ ^3.0 ^3.1 Shigemi Kimura, Kuniya Abe, Misao Suzuki, Masakatsu Ogawa, Kowashi Yoshioka, Tadasi Kaname, Teruhisa Miike and Ken-ichi Yamamura (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. Unknown parameter |month= ignored (help)
↑ Steven J.B. Cooper and Rory M.HOPE (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. Unknown parameter |month= ignored (help)
↑ 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.
↑ Eiichi Saitoh and Satoko Isemura (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. Unknown parameter |month= ignored (help)
↑ 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.
↑ G. C. Grosveld, E. De Boer, C. K. Shewmaker, & R. A. Flavell (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. Unknown parameter |month= ignored (help)
↑ GE Smith, MD Summers (1988). "Method for producing a recombinant baculovirus expression vector". US Patent (4, 745, 051). Retrieved 2014-05-29.

External links

Template:Sisterlinks

[Liebhaber-1] Stephen A. Liebhaber, Michel J. Goossens, and Yuet Wai Kan (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. Unknown parameter |month= ignored (help)

[Dodgson-2] Jerry B. Dodgson and James Douglas Engel (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. Unknown parameter |month= ignored (help)

[Kimura-3] 3.0 ^3.1 Shigemi Kimura, Kuniya Abe, Misao Suzuki, Masakatsu Ogawa, Kowashi Yoshioka, Tadasi Kaname, Teruhisa Miike and Ken-ichi Yamamura (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. Unknown parameter |month= ignored (help)

[Cooper-4] Steven J.B. Cooper and Rory M.HOPE (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. Unknown parameter |month= ignored (help)

[RefSeq2008-5] 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.

[Saitoh-6] Eiichi Saitoh and Satoko Isemura (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. Unknown parameter |month= ignored (help)

[Orkin-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.

[Grosveld-8] G. C. Grosveld, E. De Boer, C. K. Shewmaker, & R. A. Flavell (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. Unknown parameter |month= ignored (help)

[Smith-9] GE Smith, MD Summers (1988). "Method for producing a recombinant baculovirus expression vector". US Patent (4, 745, 051). Retrieved 2014-05-29.

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transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes 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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions