B recognition element

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The B recognition element (BRE) is a DNA sequence found in the promoter region of most[clarification needed] genes in eukaryotes and Archaea.[1][2] The BRE is a cis-regulatory element that is found immediately near TATA box, and consists of 7 nucleotides. There are two sets of BREs: one (BREu) found immediately upstream of the TATA box, with the consensus SSRCGCC; the other (BREd) found around 7 nucleotides downstream, with the consensus RTDKKKK.[a][3][4]

The BREu was discovered in 1998 by Richard Ebright and co-workers.[1] The BREd was named in 2005 by Deng and Roberts;[5] such a downstream recognition was reported earlier in 2000 in Tsai and Sigler's crystal structure.[6]

Binding

The transcription factor II B (TFIIB) recognizes either BRE and binds to it. Both BREs work in conjunction with the TATA box (and TATA box binding protein), and have various effects on levels of transcription.[4]

TFIIB uses the cyclin-like repeats to recognize DNA. The C-terminal alpha helices of TFIIB intercalate with the major groove of the DNA at the BREu. The N-terminal helices bind to the minor groove at BREd. TFIIB is one part of the preinitiation complex that helps RNA polymerase II bind to the DNA.[6]

In addition to the human TFIIB-BRE structure, structures from many other organisms have been solved. Among those are transcription factor B (TFB) from the archaeon Pyrococcus woesei which presents an inverted orientation[7] and a TFIIB from the parasite Trypanosoma brucei which despite some specific insertions show a similar fold.[8]

See also

Notes

  1. ^ 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.

References

  1. ^ a b 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.
  2. ^ 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.
  3. ^ Wilson, David B. "Drosophila Core Promoter Motifs". gander.wustl.edu. Retrieved 2 April 2019.
  4. ^ a b 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.
  5. ^ 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.
  6. ^ a b 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.
  7. ^ 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.
  8. ^ 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.


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