Downstream TFIIB recognition element gene transcriptions: Difference between revisions

Associate Editor(s)-in-Chief: Henry A. Hoff

File:Loris lydekkerianus nordicus 003.jpg

This image is of a gray slender loris (Loris lydekkerianus nordicus) from Northern Sri Lanka. Credit: Dr. K.A.I. Nekaris.

The downstream B recognition element designated as the BRE^d,^[1] or dBRE, is an additional core promoter element that occurs downstream of the TATA box and is recognized by general transcription factor II B.^[1]

Consensus sequences

A consensus sequence is 5'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-3' or in the transcription direction on the template strand 3'-A/G-T-A/G/T-G/T-G/T-G/T-G/T-5'.^[1]

Eukaryote genes

Of 140 promoters from the eukaryotic promoter database, "[S]ix percent ... [contain] at least six out of seven bases of the consensus sequence, 18% contain at least five of seven bases and 37% contain at least four of seven".^[1]

Human genes

GeneID: 9555 H2A histone family, member Y (H2AFY)^[2] "contains a poor TATA element, but both a consensus Inr and DPE in addition to a six/seven match BRE^d."^[1]

General transcription factor II Bs

A TFIIB recognition element (BRE) functions to determine the orientation of the TFIIB-TBP-TATA complex that projects the zinc ribbon of TFIIB toward the TSS.^[3]

General transcription factor II B can recognize two distinct sequence elements that flank the TATA box.^[1] "The selected sequences contain a strong representation of [ guanine (G) and thymine (T)] bases and a striking preference against [ adenine (A)] (especially between bases -17 and -20)."^[1]

"[T]here are ... some weakly conserved features including the TFIIB-Recognition Element (BRE), approximately 5 nucleotides upstream (BRE^u) and 5 nucleotides downstream (BRE^d) of the TATA box.^[4]"^[5]

The TFIIB-DNA contact with the BRE^d takes place via the minor groove, while that with the upstream B recognition element (BRE^u) takes place through the major groove.^[1]

Transcription start sites

dBRE is cis-TATA box, between the TATA box and the Inr or transcription start site (TSS) and trans-TSS.^[1]

Hypotheses

The dBRE is not involved in the transcription of A1BG.

Acknowledgements

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

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

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Wensheng Deng, Stefan G.E. Roberts (October 15, 2005). "A core promoter element downstream of the TATA box that is recognized by TFIIB". Genes & Development. 19 (20): 2418–23. doi:10.1101/gad.342405. PMID 16230532.
↑ HGNC (February 10, 2013). "H2AFY H2A histone family, member Y [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-11.
↑ Tsai FTP, Sigler PB (2000). "Structural basis of preinitiation complex assembly on human Pol II promoters". EMBO J. 19: 25–36.
↑ "Polymerase II".
↑ "RNA polymerase II holoenzyme, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. January 19, 2013. Retrieved 2013-02-11.

External links

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Downstream promoter element gene transcriptions Downstream TFIIB recognition element gene transcriptions DREB box gene transcriptions E2 box gene 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 Heat shock elements 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 M-CAT boxes Mcm1 regulatory factor gene transcriptions Met3 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 Nanos/Pumilio response element 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 Shue boxes Sip4p gene transcriptions Smp1p gene transcriptions Sp1 (Berberich) elements 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 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transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream repressor site 1 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

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 {{AE}} Henry A. Hoff
 [[Image:Loris lydekkerianus nordicus 003.jpg|thumb|right|250px|This image is of a gray slender loris (''Loris lydekkerianus nordicus'') from Northern Sri Lanka. Credit: Dr. K.A.I. Nekaris.]]
-{{TOCright}}
 The '''downstream B recognition element''' designated as the BRE<sup>d</sup>,<ref name=Deng/> or dBRE, is an additional core promoter element that occurs downstream of the [[TATA box]] and is recognized by general transcription factor II B.<ref name=Deng>{{ cite journal
 |author=Wensheng Deng, Stefan G.E. Roberts
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Downstream TFIIB recognition element gene transcriptions: Difference between revisions

Revision as of 21:51, 13 December 2020

Contents