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B recognition element
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<h2 id="binding">Binding</h2> <p>The <a href="/facts/Transcription_factor_II_B/t575UD5e">transcription factor II B</a> (TFIIB) recognizes either BRE and binds to it. Both BREs work in conjunction with the TATA box (and <a href="/facts/TATA_box_binding_protein/3paQrYHT">TATA box binding protein</a>), and have various effects on levels of transcription.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> </p><p>TFIIB uses the <a href="/facts/Cyclin/XtodJmQa">cyclin</a>-like repeats to recognize DNA. The C-terminal <a href="/facts/Alpha_helix/7CESPIYJ">alpha helices</a> of TFIIB intercalate with the <a href="/facts/DNA/nB89Iauz">major groove</a> of the DNA at the BREu. The N-terminal helices bind to the minor groove at BREd. TFIIB is one part of the <a href="/facts/Transcription_preinitiation_complex/gsma64bU">preinitiation complex</a> that helps <a href="/facts/RNA_polymerase_II/MK2kgybw">RNA polymerase II</a> bind to the DNA.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> </p><p>In addition to the human TFIIB-BRE structure, structures from many other organisms have been solved. Among those are <a href="/facts/Archaeal_transcription_factor_B/DvN81KPS">transcription factor B</a> (TFB) from the <a href="/facts/Archaeon/Adxh0aHw">archaeon</a> <i><a href="/facts/Pyrococcus_woesei/XTdRINR4">Pyrococcus woesei</a></i> which presents an inverted orientation<a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> and a TFIIB from the parasite <i><a href="/facts/Trypanosoma_brucei/nNTY1A0A">Trypanosoma brucei</a></i> which despite some specific insertions show a similar fold.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/CAAT_box/TI8BJIsn">CAAT box</a></li> <li><a href="/facts/Enhancer_(genetics)/E5NU74sw">Enhancer (genetics)</a></li> <li><a href="/facts/Initiator_element/NHCD44wg">Initiator element</a></li> <li><a href="/facts/Insulator_(genetics)/tNovBWhd">Insulator (genetics)</a></li> <li><a href="/facts/Promoter_(biology)/YDYBzLfg">Promoter (biology)</a></li> <li><a href="/facts/Transcription_start_site/bDgp9HDN">Transcription start site</a></li></ul> <h2 id="notes">Notes</h2> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH (1998). "New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB". Genes & Development. 12 (1): 34–44. doi:10.1101/gad.12.1.34. PMC 316406. PMID 9420329. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC316406" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC316406</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Littlefield O, Korkhin Y, Sigler PB (1999). "The structural basis for the oriented assembly of a TBP/TFB/promoter complex". Proceedings of the National Academy of Sciences of the USA. 96 (24): 13668–13673. Bibcode:1999PNAS...9613668L. doi:10.1073/pnas.96.24.13668. PMC 24122. PMID 10570130. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC24122" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC24122</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>In nucleic acid notation for DNA, R (puRine) stands for A/G (adenine or guanine, which are both purines); S (Strong) stands for C/G (cytosine or guanine, which base-pair to form three hydrogen bonds); K (Keto) stands for G/T; D (not C) stands for A/T/G. <a href="/wiki/Nucleic_acid_notation" target="_blank">/wiki/Nucleic_acid_notation</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Wilson, David B. "Drosophila Core Promoter Motifs". gander.wustl.edu. Retrieved 2 April 2019. <a href="http://gander.wustl.edu/~wilson/core_promoter_motifs.html" target="_blank">http://gander.wustl.edu/~wilson/core_promoter_motifs.html</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Juven-Gershon, T; Kadonaga, JT (15 March 2010). "Regulation of gene expression via the core promoter and the basal transcriptional machinery". Developmental Biology. 339 (2): 225–9. doi:10.1016/j.ydbio.2009.08.009. PMC 2830304. PMID 19682982. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830304" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830304</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH (1998). "New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB". Genes & Development. 12 (1): 34–44. doi:10.1101/gad.12.1.34. PMC 316406. PMID 9420329. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC316406" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC316406</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Deng, W; Roberts, SG (15 October 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. PMC 1257396. PMID 16230532. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1257396" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1257396</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Tsai, FT; Sigler, PB (4 January 2000). "Structural basis of preinitiation complex assembly on human pol II promoters". The EMBO Journal. 19 (1): 25–36. doi:10.1093/emboj/19.1.25. PMC 1171774. PMID 10619841. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1171774" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1171774</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Juven-Gershon, T; Kadonaga, JT (15 March 2010). "Regulation of gene expression via the core promoter and the basal transcriptional machinery". Developmental Biology. 339 (2): 225–9. doi:10.1016/j.ydbio.2009.08.009. PMC 2830304. PMID 19682982. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830304" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830304</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Tsai, FT; Sigler, PB (4 January 2000). "Structural basis of preinitiation complex assembly on human pol II promoters". The EMBO Journal. 19 (1): 25–36. doi:10.1093/emboj/19.1.25. PMC 1171774. PMID 10619841. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1171774" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1171774</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Kosa, PF; Ghosh, G; DeDecker, BS; Sigler, PB (10 June 1997). "The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box". Proceedings of the National Academy of Sciences of the United States of America. 94 (12): 6042–7. doi:10.1073/pnas.94.12.6042. PMC 20997. PMID 9177165. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20997" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC20997</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Ibrahim, BS; Kanneganti, N; Rieckhof, GE; Das, A; Laurents, DV; Palenchar, JB; Bellofatto, V; Wah, DA (11 August 2009). "Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei". Proceedings of the National Academy of Sciences of the United States of America. 106 (32): 13242–7. Bibcode:2009PNAS..10613242I. doi:10.1073/pnas.0904309106. PMC 2726365. PMID 19666603. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726365" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726365</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> </ol>