Factor II B recognition element gene transcriptions
The B recognition element (BRE) is a DNA sequence found in the promoter region of most genes in eukaryotes and Archaea.
The BRE is a cis-regulatory element that is found immediately upstream of the TATA box, and consists of 7 nucleotides.
In the archaean from the Dead Sea imaged at the right, "We have completely fragmented their DNA. I mean we have completely destroyed it by bombarding it with . And they can reassemble their entire chromosome and put it back into working order within several hours."

# Consensus sequences
The consensus sequence is 5-G/C G/C G/A C G C C-3.
The general consensus sequence using degenerate nucleotides is 5-SSRCGCC-3, where S = G or C and R = A or G.
"The transcription factor II B recognition elements BREu "CGACGCA" and BREd "ATGGTTG" were upstream ( 279 to  273 of the transcript) and downstream ( 165 to  159 of the transcript) of the TATA box, respectively."

# Transcription start sites
"The position in nucleotides (nt) relative to the transcription start site (TSS, +1)" is -35 for the BRE. Of human promoters, some "22-25%  BRE containing promoters ... the functional consensus sequences for BRE ... motif  still poorly defined."

# General transcription factor II Bs
The Transcription Factor IIB (TFIIB) recognizes this sequence in the DNA, and binds to it. The fourth and fifth alpha helices of TFIIB intercalate with the major groove of the DNA at the BRE. TFIIB is one part of the preinitiation complex that helps RNA Polymerase II bind to the DNA.

# Core promoters
The core promoter is approximately -34 nts upstream from the TSS.
From the first nucleotide just after ZSCAN22 to the first nucleotide just before A1BG are 4460 nucleotides. The core promoter on this side of A1BG extends from approximately 4425 to the possible transcription start site at nucleotide number 4460.
To extend the analysis from inside and just on the other side of ZNF497 some 3340 nts have been added to the data. This would place the core promoter some 3340 nts further away from the other side of ZNF497. The TSS would be at about 4300 nts with the core promoter starting at 4266.
Def. "the factors, including RNA polymerase II itself, that are minimally essential for transcription in vitro from an isolated core promoter" is called the basal machinery, or basal transcription machinery.

# Hypotheses
- B recognition factor is not involved in the transcription of A1BG.
- If involved it assists transcription by other TFs.

# BREu samplings
For the Basic programs (starting with SuccessablesBRE.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- Negative strand, negative direction: 4, CCACGCC at 3047, CCACGCC at 2197, CCGCGCC at 1762, CCACGCC at 380.
- Negative strand, positive direction: 3, GGGCGCC at 1769, GGACGCC at 1672, GCACGCC at 1302.
- Positive strand, negative direction: 1, GGACGCC at 1153.
- Positive strand, positive direction: 3, CCACGCC at 1764, CGACGCC at 1033, CCACGCC at 489.
- inverse complement, negative strand, negative direction: 0.
- inverse complement, negative strand, positive direction: 1, GGCGCCC at 1770.
- inverse complement, positive strand, negative direction: 3, GGCGTGG at 1897, GGCGTGG at 1244.
- inverse complement, positive strand, positive direction: 4, GGCGTGG at 2566, GGCGCCG at 1438, GGCGCCG at 1338, GGCGCGC at 682.

## BREu (4560-2846) UTRs
- Negative strand, negative direction: CCGCACC at 3047.

## BREu negative direction (2596-1) distal promoters
- Negative strand, negative direction: CCACGCC at 2197, CCGCGCC at 1762, CCACGCC at 380.
- Positive strand, negative direction: GGCGTGG at 1897, GGCGTGG at 1244, GGACGCC at 1153.

## BREu positive direction (4050-1) distal promoters
- Negative strand, positive direction: GGCGCCC at 1770, GGGCGCC at 1769, GGACGCC at 1672, GCACGCC at 1302.
- Positive strand, positive direction: GGCGTGG at 2566, CCACGCC at 1764, GGCGCCG at 1438, GGCGCCG at 1338, CGACGCC at 1033, GGCGCGC at 682, CCACGCC at 489.

# BREu random dataset samplings
- BREur0: 3, GCGCGCC at 3886, GCGCGCC at 3239, GGGCGCC at 2770.
- BREur1: 2, GGGCGCC at 2824, GGGCGCC at 628.
- BREur2: 2, CCGCGCC at 1536, GCACGCC at 1468.
- BREur3: 3, CCGCGCC at 2378, GGACGCC at 1330, GCGCGCC at 651.
- BREur4: 4, GGGCGCC at 3103, GGGCGCC at 2628, GGACGCC at 1280, CCGCGCC at 19.
- BREur5: 8, CCGCGCC at 4413, GGGCGCC at 4265, GGGCGCC at 3775, CGGCGCC at 3755, GCACGCC at 3472, GGACGCC at 2908, CCACGCC at 1789, GCACGCC at 78.
- BREur6: 4, CCGCGCC at 4276, CGACGCC at 3410, GGACGCC at 3227, CCGCGCC at 1282.
- BREur7: 5, CCGCGCC at 4216, CCGCGCC at 2992, CGGCGCC at 2497, GGACGCC at 923, CGGCGCC at 777.
- BREur8: 0.
- BREur9: 3, GGGCGCC at 4516, GGACGCC at 870, CGACGCC at 53.
- BREur0ci: 5, GGCGCGC at 3238, GGCGCGG at 3116, GGCGCGG at 2069, GGCGTCG at 1351, GGCGTGC at 1077.
- BREur1ci: 3, GGCGCCC at 2825, GGCGTCC at 2107, GGCGTCG at 591.
- BREur2ci: 4, GGCGCCC at 4504, GGCGTCC at 979, GGCGCCC at 690, GGCGTCC at 629.
- BREur3ci: 1, GGCGCGC at 650.
- BREur4ci: 6, GGCGCCG at 4344, GGCGTGG at 3733, GGCGCCC at 3104, GGCGCCC at 2987, GGCGCCG at 2629, GGCGTGG at 958.
- BREur5ci: 3, GGCGCCC at 4266, GGCGTGG at 3956, GGCGCCC at 3756.
- BREur6ci: 0.
- BREur7ci: 4, GGCGCCG at 1966, GGCGTGG at 1790, GGCGCCC at 778, GGCGTGG at 453.
- BREur8ci: 1, GGCGTCC at 1390.
- BREur9ci: 2, GGCGCCG at 3882, GGCGTGG at 1431.

## BREur arbitrary (evens) (4560-2846) UTRs
- BREur0: GCGCGCC at 3886, GCGCGCC at 3239.
- BREur4: GGGCGCC at 3103.
- BREur6: CCGCGCC at 4276, CGACGCC at 3410, GGACGCC at 3227.
- BREur0ci: GGCGCGC at 3238, GGCGCGG at 3116.
- BREur2ci: GGCGCCC at 4504.
- BREur4ci: GGCGCCG at 4344, GGCGTGG at 3733, GGCGCCC at 3104, GGCGCCC at 2987.

## BREur alternate (odds) (4560-2846) UTRs
- BREur5: CCGCGCC at 4413, GGGCGCC at 4265, GGGCGCC at 3775, CGGCGCC at 3755, GCACGCC at 3472, GGACGCC at 2908.
- BREur7: CCGCGCC at 4216, CCGCGCC at 2992.
- BREur9: GGGCGCC at 4516.
- BREur5ci: GGCGCCC at 4266, GGCGTGG at 3956, GGCGCCC at 3756.
- BREur9ci: GGCGCCG at 3882.

## BREur alternate negative direction (odds) (2846-2811) core promoters
- BREur1: GGGCGCC at 2824.
- BREur1ci: GGCGCCC at 2825.

## BREur arbitrary positive direction (odds) (4445-4265) core promoters
- BREur5: CCGCGCC at 4413, GGGCGCC at 4265.
- BREur5ci: GGCGCCC at 4266.

## BREur alternate positive direction (evens) (4445-4265) core promoters
- BREur6: CCGCGCC at 4276.
- BREur4ci: GGCGCCG at 4344.

## BREur arbitrary negative direction (evens) (2811-2596) proximal promoters
- BREur0: GGGCGCC at 2770.
- BREur4: GGGCGCC at 2628.
- BREur4ci: GGCGCCG at 2629.

## BREur arbitrary positive direction (odds) (4265-4050) proximal promoters
- BREur5: GGGCGCC at 4265.
- BREur7: CCGCGCC at 4216.

## BREur arbitrary negative direction (evens) (2596-1) distal promoters
- BREur0: GGGCGCC at 2770.
- BREur2: CCGCGCC at 1536, GCACGCC at 1468.
- BREur4: GGACGCC at 1280, CCGCGCC at 19.
- BREur6: CCGCGCC at 1282.
- BREur0ci: GGCGCGG at 2069, GGCGTCG at 1351, GGCGTGC at 1077.
- BREur2ci: GGCGTCC at 979, GGCGCCC at 690, GGCGTCC at 629.
- BREur4ci: GGCGTGG at 958.
- BREur8ci: GGCGTCC at 1390.

## BREur alternate negative direction (odds) (2596-1) distal promoters
- BREur1: GGGCGCC at 628.
- BREur3: CCGCGCC at 2378, GGACGCC at 1330, GCGCGCC at 651.
- BREur5: CCACGCC at 1789, GCACGCC at 78.
- BREur7: CGGCGCC at 2497, GGACGCC at 923, CGGCGCC at 777.
- BREur0ci: GGCGCGG at 2069, GGCGTCG at 1351, GGCGTGC at 1077.
- BREur1ci: GGCGTCC at 2107, GGCGTCG at 591.
- BREur3ci: GGCGCGC at 650.
- BREur7ci: GGCGCCG at 1966, GGCGTGG at 1790, GGCGCCC at 778, GGCGTGG at 453.
- BREur9ci: GGCGTGG at 1431.

## BREur arbitrary positive direction (odds) (4050-1) distal promoters
- BREur1: GGGCGCC at 2824, GGGCGCC at 628.
- BREur3: CCGCGCC at 2378, GGACGCC at 1330, GCGCGCC at 651.
- BREur5: GGGCGCC at 3775, CGGCGCC at 3755, GCACGCC at 3472, GGACGCC at 2908, CCACGCC at 1789, GCACGCC at 78.
- BREur7: CCGCGCC at 2992, CGGCGCC at 2497, GGACGCC at 923, CGGCGCC at 777.
- BREur9: GGACGCC at 870, CGACGCC at 53.
- BREur1ci: GGCGCCC at 2825, GGCGTCC at 2107, GGCGTCG at 591.
- BREur3ci: GGCGCGC at 650.
- BREur5ci: GGCGTGG at 3956, GGCGCCC at 3756.
- BREur7ci: GGCGCCG at 1966, GGCGTGG at 1790, GGCGCCC at 778, GGCGTGG at 453.
- BREur9ci: GGCGCCG at 3882, GGCGTGG at 1431.

## BREur alternate positive direction (evens) (4050-1) distal promoters
- BREur0: GCGCGCC at 3886, GCGCGCC at 3239, GGGCGCC at 2770.
- BREur2: CCGCGCC at 1536, GCACGCC at 1468.
- BREur4: GGGCGCC at 3103, GGGCGCC at 2628, GGACGCC at 1280, CCGCGCC at 19.
- BREur6: CGACGCC at 3410, GGACGCC at 3227, CCGCGCC at 1282.
- BREur0ci: GGCGCGC at 3238, GGCGCGG at 3116, GGCGCGG at 2069, GGCGTCG at 1351, GGCGTGC at 1077.
- BREur2ci: GGCGTCC at 979, GGCGCCC at 690, GGCGTCC at 629.
- BREur4ci: GGCGTGG at 3733, GGCGCCC at 3104, GGCGCCC at 2987, GGCGCCG at 2629, GGCGTGG at 958.
- BREur8ci: GGCGTCC at 1390.

# BREu analysis and results
The consensus sequence is G/C G/C G/A C G C C.
Comparison:
The occurrences of real BREu distals are greater than the randoms, but the UTRs are less than the randoms. This suggests that the real BREus are likely active or activable.

# Regarding hypothesis 2
The BRE is likely involved in and assists transcription by these other TFs when they are present.
The diagram on the right shows an overview of the four core promoter elements: B recognition element (BRE), TATA box, initiator element (Inr), and downstream promoter element (DPE), with their respective consensus sequences and their distance from the transcription start site.
On the left is a more comprehensive diagram of a promoter. "The best known core promoter element is the TATA-box, consisting of an AT-rich sequence located ~27 bp upstream of the TSS, but several other core promoter elements exist, including initiator element (Inr) and X core promoter element 1 (XCPE1) localized around the TSS, the TFIIB recognition elements (BRE) that are positioned upstream of the TSS, and downstream promoter element (DPE), motif ten element (MTE) and downstream core element (DCE) that are situated downstream of TSS. The distal regulatory elements include locus control regions (LCR), enhancers, silencers and insulators. The enhancers and silencers have sites for binding multiple transcription factors and they function in activating and repressing transcription, respectively. Insulators operate by blocking genes from being affected by the regulatory elements of neighbouring genes. The LCR consists of multiple transcription regulatory elements that function together to provide proper expression regulation to a cluster of genes."

# Transcribed BREs
"One of the major discoveries in large-scale detection of promoters was the existence of different classes of core promoters, for which there are common features across the metazoan lineage. The number of main classes has not been settled, but the current evidence points towards three main functional classes ."
"In D. melanogaster, a number of different promoter types have been suggested based on motif content. An exhaustive analysis of motif composition in D. melanogaster and human promoters14 revealed extensive differences in the type and directionality of motifs found in different promoters and their association with gene function. In parallel, five principal motif-based classes of D. melanogaster promoters were proposed15, which could be further grouped into three general functional classes16."
"Type I consists of the tissue-specific promoters, which are similar to the low-CpG class in mammals with respect to motif composition, stage of development at which they are expressed and tissue specificity, and they are characterized by a high enrichment for a TATA box at an appropriate distance from an initiator element (Inr element). Type II promoters are associated with housekeeping genes and genes that are regulated at the level of individual cells; they have either a DNA recognition element (DRE) or a combination of novel motifs15. Finally, type III promoters have an Inr element only or an Inr element plus a downstream promoter element (DPE). These promoters are preferentially associated with developmentally regulated genes, the expression of which is precisely coordinated across different cells in a tissue or anatomical structure16."

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Initial content for this page in some instances came from Wikiversity.