B recognition element
The B recognition element (BRE) is a DNA sequence found in the promoter region of most{{clarify|date=April 2019}} genes in eukaryotes and Archaea.{{cite journal| vauthors=Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH| year=1998 |journal=Genes & Development| volume=12 |issue=1 |pages=34–44 |title=New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB |pmid=9420329| doi=10.1101/gad.12.1.34| pmc=316406}}{{cite journal| journal=Proceedings of the National Academy of Sciences of the USA| title=The structural basis for the oriented assembly of a TBP/TFB/promoter complex |year=1999 |vauthors=Littlefield O, Korkhin Y, Sigler PB |volume=96 |issue=24 |pages=13668–13673 |pmid=10570130| doi=10.1073/pnas.96.24.13668| pmc=24122| bibcode=1999PNAS...9613668L | doi-access=free }} 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.{{efn|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.}}{{cite web |last1=Wilson |first1=David B. |title=Drosophila Core Promoter Motifs |url=http://gander.wustl.edu/~wilson/core_promoter_motifs.html |website=gander.wustl.edu |accessdate=2 April 2019}}{{cite journal |last1=Juven-Gershon |first1=T |last2=Kadonaga |first2=JT |title=Regulation of gene expression via the core promoter and the basal transcriptional machinery. |journal=Developmental Biology |date=15 March 2010 |volume=339 |issue=2 |pages=225–9 |doi=10.1016/j.ydbio.2009.08.009 |pmid=19682982 |pmc=2830304}}
The BREu was discovered in 1998 by Richard Ebright and co-workers. The BREd was named in 2005 by Deng and Roberts;{{cite journal |last1=Deng |first1=W |last2=Roberts |first2=SG |title=A core promoter element downstream of the TATA box that is recognized by TFIIB. |journal=Genes & Development |date=15 October 2005 |volume=19 |issue=20 |pages=2418–23 |doi=10.1101/gad.342405 |pmid=16230532|pmc=1257396 }} such a downstream recognition was reported earlier in 2000 in Tsai and Sigler's crystal structure.
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.
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.{{cite journal |last1=Tsai |first1=FT |last2=Sigler |first2=PB |title=Structural basis of preinitiation complex assembly on human pol II promoters. |journal=The EMBO Journal |date=4 January 2000 |volume=19 |issue=1 |pages=25–36 |doi=10.1093/emboj/19.1.25 |pmid=10619841|pmc=1171774 }}
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{{cite journal |last1=Kosa |first1=PF |last2=Ghosh |first2=G |last3=DeDecker |first3=BS |last4=Sigler |first4=PB |title=The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=10 June 1997 |volume=94 |issue=12 |pages=6042–7 |pmid=9177165|pmc=20997 |doi=10.1073/pnas.94.12.6042 |doi-access=free }} and a TFIIB from the parasite Trypanosoma brucei which despite some specific insertions show a similar fold.{{cite journal |last1=Ibrahim |first1=BS |last2=Kanneganti |first2=N |last3=Rieckhof |first3=GE |last4=Das |first4=A |last5=Laurents |first5=DV |last6=Palenchar |first6=JB |last7=Bellofatto |first7=V |last8=Wah |first8=DA |title=Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=11 August 2009 |volume=106 |issue=32 |pages=13242–7 |doi=10.1073/pnas.0904309106 |pmid=19666603|pmc=2726365 |bibcode=2009PNAS..10613242I |doi-access=free }}
See also
Notes
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