TATA box basic helix-loop-helix family

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

"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: 3280

"This protein belongs to the basic helix-loop-helix family of transcription factors. It is a transcriptional repressor of genes that require a bHLH protein for their transcription. The protein has a particular type of basic domain that contains a helix interrupting protein that binds to the N-box rather than the canonical E-box."^[7]

Gene ID: 3397

"The protein encoded by this gene is a helix-loop-helix (HLH) protein that can form heterodimers with members of the basic HLH family of transcription factors. The encoded protein has no DNA binding activity and therefore can inhibit the DNA binding and transcriptional activation ability of basic HLH proteins with which it interacts. This protein may play a role in cell growth, senescence, and differentiation. Two transcript variants encoding different isoforms have been found for this gene."^[8]

Gene ID: 4618

"The protein encoded by this gene is a probable basic helix-loop-helix (bHLH) DNA binding protein involved in muscle differentiation. The encoded protein likely acts as a heterodimer with another bHLH protein. Defects in this gene are a cause of autosomal dominant centronuclear myopathy (ADCNM)."^[9]

Gene ID: 9421

"The protein encoded by this gene belongs to the basic helix-loop-helix family of transcription factors. This gene product is one of two closely related family members, the HAND proteins, which are asymmetrically expressed in the developing ventricular chambers and play an essential role in cardiac morphogenesis. Working in a complementary fashion, they function in the formation of the right ventricle and aortic arch arteries, implicating them as mediators of congenital heart disease. In addition, it has been suggested that this transcription factor may be required for early trophoblast differentiation."^[10]

Gene ID: 10215

"This gene encodes a basic helix-loop-helix transcription factor which is expressed in oligodendroglial tumors of the brain. The protein is an essential regulator of ventral neuroectodermal progenitor cell fate. The gene is involved in a chromosomal translocation t(14;21)(q11.2;q22) associated with T-cell acute lymphoblastic leukemia. Its chromosomal location is within a region of chromosome 21 which has been suggested to play a role in learning deficits associated with Down syndrome."^[11]

Families of TATA box genes

Acknowledgements

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

References

↑ 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.
↑ 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.
↑ 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.
↑ ^4.0 ^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.
↑ ^5.0 ^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.
↑ ^6.0 ^6.1 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.
↑ RefSeq (July 2008). "HES1 hes family bHLH transcription factor 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-20.
↑ RefSeq (July 2008). "ID1 inhibitor of DNA binding 1 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-06-27.
↑ RefSeq (May 2010). "MYF6 myogenic factor 6 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-02.
↑ RefSeq (July 2008). "HAND1 heart and neural crest derivatives expressed 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-10.
↑ RefSeq (July 2008). "OLIG2 oligodendrocyte transcription factor 2 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-11.

External links

[Lifton-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.

[Smale03-2] 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.

[Yang2007-3] 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.

[Yang2006-4] 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.

[Xu-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.

[Jin-6] 6.0 ^6.1 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.

[RefSeq3280-7] RefSeq (July 2008). "HES1 hes family bHLH transcription factor 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-06-20.

[RefSeq3397-8] RefSeq (July 2008). "ID1 inhibitor of DNA binding 1 [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2024-06-27.

[RefSeq4618-9] RefSeq (May 2010). "MYF6 myogenic factor 6 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-02.

[RefSeq9421-10] RefSeq (July 2008). "HAND1 heart and neural crest derivatives expressed 1 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-10.

[RefSeq10215-11] RefSeq (July 2008). "OLIG2 oligodendrocyte transcription factor 2 [ Homo sapiens ]". Bethsda, Maryland, USA: ncbi.nlm.nih. Retrieved 2024-07-11.

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transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Families of TATA box genes F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General 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 Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene 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 actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family 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