Downstream TFIIB recognition element gene transcriptions

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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 BREd,[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

Main article: Consensus sequence gene transcriptions

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

Main article: 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

Main article: 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 BREd."[1]

General transcription factor II Bs

Main articles: General transcription factor II B gene transcriptions and 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 (BREu) and 5 nucleotides downstream (BREd) of the TATA box.[4]"[5]

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

Transcription start sites

Main articles: Start site gene transcriptions and 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

Main article: Hypotheses
  1. The dBRE is not involved in the transcription of A1BG.

dBRE samplings

For the Basic programs (starting with SuccessablesdBRE.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 (+) expanded to 4445 nts from 958, the programs are, are looking for, and found:

  1. Negative strand, negative direction: GTAGGTG at 4458, GTGGGGT at 4446, GTTTTTT at 4378, GTTTTTT at 4218, ATGTTTT at 4216, GTTGTGT at 4196, GTTTTTT at 4068, ATGTTTT at 4066, GTGTTTT at 3767, ATGGTGG at 3740, GTAGTTG at 3523, ATTTGGT at 3484, ATTTGGT at 3365, ATTTGTT at 3338, GTTTTTG at 3328, GTATTTT at 3171, ATTTTTG at 3165, GTGGGTT at 3136, ATTTTTT at 3026, GTAGTTT at 2890, ATATTTG at 2875, GTTGGGT at 2846, GTGGGGT at 2764, ATGTTTT at 2644, ATATGTT at 2642, GTTTGTT at 2488, GTTTGTT at 2484, GTGTGGT at 2419, GTTTTTT at 2309, ATGTTTT at 2307, GTTTTTT at 2184, ATGTTTT at 2182, GTTTTTT at 2038, GTTTTTT at 1882, ATGTTTT at 1880, GTTTGTG at 1540, GTTGGGT at 1516, GTTGGGT at 1409, GTTTTTT at 1396, GTTTGTT at 1392, GTTTTTG at 1386, GTTTTTT at 1230, ATGTTTT at 1228, GTTTTTT at 1094, GTTTTTT at 928, GTGTGGT at 883, GTTTTTT at 773, ATGTTTT at 771, GTTTTTT at 639, ATGTTTT at 637, ATTGGGG at 616, GTTTTTT at 487, ATGTTTT at 485, GTTTTGG at 259, ATATTTT at 222, ATATTTT at 183, GTTTTGT at 166, ATATGTT at 113, ATTTTGT at 68.
  2. Positive strand, negative direction: ATGGTGG at 4110, GTTGGTT at 3944, GTGTTGG at 3942, ATGTGGT at 3811, ATGGGGT at 3802, GTGGTTG at 3605, ATTGGTT at 3531, GTGGGTG at 3195, GTGGTGG at 3192, GTGGTGG at 3189, GTGTGGT at 3187, GTGGTGG at 3050, ATATTTT at 2853, GTGGTGG at 2661, GTGTGGT at 2659, GTGGGTG at 2332, GTGGTGG at 1903, GTGGTGG at 1900, GTGGTGT at 1477, GTGGTGG at 1247, GTGGGTG at 1163, ATTGGGT at 1047, GTGGTGT at 793, GTGGTGG at 790, ATGTGGT at 788, ATGGTGT at 608, ATATGGT at 606, ATGTTTT at 215, ATGGGGT at 204, ATATGGG at 78, ATATGTT at 43.
  3. Negative strand, positive direction: GTGGGGT at 4397, ATGGGGG at 4225, ATTGTTG at 4173, GTGGTTT at 4108, GTGGTGT at 3969, GTGTGGT at 3967, GTGGTGG at 3816, ATGTTTG at 3339, GTGTTGG at 2816, ATTTTTT at 2451, GTGGGGG at 56.
  4. Positive strand, positive direction: GTGGGGT at 4328, GTGGGGT at 4286, GTTTGTG at 4257, GTGTGGT at 3825, GTAGGGT at 3631, ATAGGGT at 3386, GTGTGGG at 2965, ATGGTGG at 2759, GTGTGGT at 2603, ATGGTGT at 2600, ATATGGT at 2591, GTTGGTG at 2122, GTGGGGG at 2020, GTTGGGT at 2015, ATGGGGT at 1891, GTGGTGG at 704, GTAGGTG at 700, GTAGGTG at 631, GTGGGTG at 72.
  5. inverse complement, Negative strand, negative direction: AACCAAC at 3945, CCACTAC at 3798, CACCAAC at 3605, AACCAAC at 3532, CCAAAAT at 3350, CCCACAC at 3185, ACACCAC at 2660, CACCCAC at 2332, CCACCAC at 1902, ACCACAC at 1478, AAAAAAC at 1433, CACCCAC at 1163, AACCCAC at 1048, ACACCAC at 789, ACCACAC at 609, CAAAAAT at 217.
  6. inverse complement, Positive strand, negative direction: AACCCAT at 4454, AAAAAAT at 4219, AAAAAAT at 4069, CCAACAC at 3981, CCCATAC at 3857, ACAAAAT at 3768, CAACTAT at 3526, AAAACAC at 3512, AAACCAC at 3366, CAAAAAC at 3328, AAAACAT at 3167, ACCCCAT at 3152, ACCCAAC at 3137, AAAAAAC at 3027, AAACCAC at 2972, AAAAAAT at 2930, AAAATAT at 2869, AAACAAC at 2843, CAAAAAT at 2646, CCAACAT at 2612, CCAACAC at 2549, AACAAAC at 2511, AACAAAC at 2486, ACACCAC at 2420, AAAATAC at 2303, ACCCCAT at 2288, AAAAAAT at 2185, CCAACAT at 2150, AAAAAAT at 2061, AAAATAC at 1876, ACCCCAT at 1861, AAAATAT at 1740, AACAAAC at 1587, AAAATAC at 1564, CAAACAC at 1540, CAAAAAC at 1386, AAAAAAT at 1231, CCAACAT at 1205, ACACCAT at 884, AAAATAC at 767, AAAATAC at 633, AAAAAAT at 488, AAAACAT at 361, AAACAAT at 230.
  7. inverse complement, Negative strand, positive direction: ACCCCAC at 4287, CAAACAC at 4257, ACCCCAT at 4220, ACCCCAC at 3941, ACACCAT at 3826, ACCAAAC at 3176, AACACAC at 3097, AAACCAC at 2633, ACCACAC at 2601, CAACCAC at 2122, AACCCAC at 2016, AACCTAC at 1283, CCACCAC at 703, CACCCAC at 72.
  8. inverse complement, Positive strand, positive direction: ACCCCAC at 4398, CCAAAAT at 4110, ACACCAC at 3968, AAACCAC at 3949, ACACCAC at 3644, CCAATAC at 3026, CCACAAC at 2815, CACCTAC at 2714, CCAAAAC at 2688, CCCCTAT at 2659, AAAAAAC at 2452, ACCCTAC at 2409, AAAAAAC at 2282, AACCCAC at 1802, ACAAAAT at 148, CCCCTAC at 59.

dBRE UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: GTAGGTG at 4458, GTGGGGT at 4446, GTTTTTT at 4378, GTTTTTT at 4218, ATGTTTT at 4216, GTTGTGT at 4196, GTTTTTT at 4068, ATGTTTT at 4066, AACCAAC at 3945, CCACTAC at 3798, GTGTTTT at 3767, ATGGTGG at 3740, CACCAAC at 3605, AACCAAC at 3532, GTAGTTG at 3523, ATTTGGT at 3484, ATTTGGT at 3365, CCAAAAT at 3350, ATTTGTT at 3338, GTTTTTG at 3328, CCCACAC at 3185, GTATTTT at 3171, ATTTTTG at 3165, GTGGGTT at 3136, ATTTTTT at 3026, GTAGTTT at 2890, ATATTTG at 2875, GTTGGGT at 2846.

Positive strand, negative direction: AACCCAT at 4454, AAAAAAT at 4219, ATGGTGG at 4110, AAAAAAT at 4069, CCAACAC at 3981, GTTGGTT at 3944, GTGTTGG at 3942, CCCATAC at 3857, ATGTGGT at 3811, ATGGGGT at 3802, ACAAAAT at 3768, GTGGTTG at 3605, ATTGGTT at 3531, CAACTAT at 3526, AAAACAC at 3512, AAACCAC at 3366, CAAAAAC at 3328, GTGGGTG at 3195, GTGGTGG at 3192, GTGGTGG at 3189, GTGTGGT at 3187, AAAACAT at 3167, ACCCCAT at 3152, ACCCAAC at 3137, GTGGTGG at 3050, AAAAAAC at 3027, AAACCAC at 2972, AAAAAAT at 2930, AAAATAT at 2869. ATATTTT at 2853.

dBRE core promoters

Main article: Core promoter gene transcriptions

Positive strand, negative direction: AAACAAC at 2843.

Negative strand, positive direction: GTGGGGT at 4397, ACCCCAC at 4287.

Positive strand, positive direction: ACCCCAC at 4398, GTGGGGT at 4328, GTGGGGT at 4286.

dBRE proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: GTGGGGT at 2764, ACACCAC at 2660, ATGTTTT at 2644, ATATGTT at 2642.

Positive strand, negative direction: GTGGTGG at 2661, GTGTGGT at 2659, CAAAAAT at 2646, CCAACAT at 2612.

Negative strand, positive direction: CAAACAC at 4257, ATGGGGG at 4225, ACCCCAT at 4220, ATTGTTG at 4173, GTGGTTT at 4108.

Positive strand, positive direction: GTTTGTG at 4257, CCAAAAT at 4110.

dBRE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: GTTTGTT at 2488, GTTTGTT at 2484, GTGTGGT at 2419, CACCCAC at 2332, GTTTTTT at 2309, ATGTTTT at 2307, GTTTTTT at 2184, ATGTTTT at 2182, GTTTTTT at 2038, CCACCAC at 1902, GTTTTTT at 1882, ATGTTTT at 1880, GTTTGTG at 1540, GTTGGGT at 1516, ACCACAC at 1478, AAAAAAC at 1433, GTTGGGT at 1409, GTTTTTT at 1396, GTTTGTT at 1392, GTTTTTG at 1386, GTTTTTT at 1230, ATGTTTT at 1228, CACCCAC at 1163, GTTTTTT at 1094, AACCCAC at 1048, GTTTTTT at 928, GTGTGGT at 883, ACACCAC at 789, GTTTTTT at 773, ATGTTTT at 771, GTTTTTT at 639, ATGTTTT at 637, ATTGGGG at 616, ACCACAC at 609, GTTTTTT at 487, ATGTTTT at 485, GTTTTGG at 259, ATATTTT at 222, CAAAAAT at 217, ATATTTT at 183, GTTTTGT at 166, ATATGTT at 113, ATTTTGT at 68.

Positive strand, negative direction: CCAACAC at 2549, AACAAAC at 2511, AACAAAC at 2486, ACACCAC at 2420, GTGGGTG at 2332, AAAATAC at 2303, ACCCCAT at 2288, AAAAAAT at 2185, CCAACAT at 2150, AAAAAAT at 2061, GTGGTGG at 1903, GTGGTGG at 1900, AAAATAC at 1876, ACCCCAT at 1861, AAAATAT at 1740, AACAAAC at 1587, AAAATAC at 1564, CAAACAC at 1540, GTGGTGT at 1477, CAAAAAC at 1386, GTGGTGG at 1247, AAAAAAT at 1231, CCAACAT at 1205, GTGGGTG at 1163, ATTGGGT at 1047, ACACCAT at 884, GTGGTGT at 793, GTGGTGG at 790, ATGTGGT at 788, AAAATAC at 767, AAAATAC at 633, ATGGTGT at 608, ATATGGT at 606, AAAAAAT at 488, AAAACAT at 361, AAACAAT at 230 ATGTTTT at 215, ATGGGGT at 204, ATATGGG at 78, ATATGTT at 43.

Negative strand, positive direction: GTGGTGT at 3969, GTGTGGT at 3967, ACCCCAC at 3941, ACACCAT at 3826, GTGGTGG at 3816, ATGTTTG at 3339, ACCAAAC at 3176, AACACAC at 3097, GTGTTGG at 2816, AAACCAC at 2633, ACCACAC at 2601, ATTTTTT at 2451, CAACCAC at 2122, AACCCAC at 2016, AACCTAC at 1283, CCACCAC at 703, CACCCAC at 72, GTGGGGG at 56.

Positive strand, positive direction: ACACCAC at 3968, AAACCAC at 3949, GTGTGGT at 3825, ACACCAC at 3644, GTAGGGT at 3631, ATAGGGT at 3386, CCAATAC at 3026, GTGTGGG at 2965, CCACAAC at 2815, ATGGTGG at 2759, CACCTAC at 2714, CCAAAAC at 2688, CCCCTAT at 2659, GTGTGGT at 2603, ATGGTGT at 2600, ATATGGT at 2591, AAAAAAC at 2452, ACCCTAC at 2409, AAAAAAC at 2282, GTTGGTG at 2122, GTGGGGG at 2020, GTTGGGT at 2015, ATGGGGT at 1891, AACCCAC at 1802, GTGGTGG at 704, GTAGGTG at 700, GTAGGTG at 631, ACAAAAT at 148, GTGGGTG at 72, CCCCTAC at 59.

Acknowledgements

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

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

See also

References

  1. ↑ 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.
  2. ↑ 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.
  3. ↑ Tsai FTP, Sigler PB (2000). "Structural basis of preinitiation complex assembly on human Pol II promoters". EMBO J. 19: 25–36.
  4. ↑ "Polymerase II".
  5. ↑ "RNA polymerase II holoenzyme, In: Wikipedia". San Francisco, California: Wikimedia Foundation, Inc. January 19, 2013. Retrieved 2013-02-11.

Further reading

External links

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