AGCE gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

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This is a restored image of a group of Ainu men between 1863 and early 1870s. Credit: Felice Beato.

Angiotensinogen core promoter element 1 (AGCE1) is an example of a core promoter element that may occur in a DNA sequence for only one gene (the human angiotensinogen gene angiotensin).

"[T]he core promoter element 1 (AGCE1) of the human angiotensinogen gene (AGT) ... acts as a critical regulator of AGT transcription".[1]

Human genes

Main article: Human genes

Gene ID: 183 is angiotensinogen (serpin peptidase inhibitor, clade A, member 8) [ Homo sapiens ] has the official symbol AGT.[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

The consensus sequence is (A/C)T(C/T).[1] By convention, this is MTY on the mRNA, with T replaced by uracil (U).

The core nucleotides for AGCE1 include (A/C)T(C/T)GTG, "located between the TATA box and transcription initiation site (positions −25 to −1) is an authentic regulator of human AG transcription."[3]

AGCE1 can occur upstream from -25 to -1 base pairs (bp)s of the transcription start site.[1]

A1BG gene transcriptions

Main article: A1BG gene transcriptions

An AGCE1 occurs at ATC, in the nucleotides before the transcription start site for the transcription of A1BG, which ends 5 bp upstream from the TSS and is the only AGCE1 within -25 and -1 bp of the TSS. Usually, the AGCE1 spans -20 to -18 bp, when a TATA box is present.[1]

However, for the transcription of A1BG, there is no TATA box and the core nucleotides GTG do not occur on either side of ATC.

Hypotheses

Main article: Hypotheses
  1. AGCE1 does not participate in the transcription of A1BG.

AGCE samplings

Main article: Angiotensinogen core promoter element gene transcriptions
  1. AGCE, negative strand, negative direction, looking for (A/C)T(C/T)GTG: CTCGTG at 3914, CTTGTG at 3669, ATCGTG at 2096, ATTGTG at 340.
  2. AGCE, negative strand, positive direction, looking for (A/C)T(C/T)GTG: 2, CTCGTG at 4376, ATTGTG at 2679.
  3. AGCE, positive strand, negative direction, looking for (A/C)T(C/T)GTG: 0.
  4. AGCE, positive strand, positive direction, looking for (A/C)T(C/T)GTG: 6, CTCGTG at 3739, CTTGTG at 3095, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855.
  5. AGCEci, negative strand, negative direction, looking for CAC(A/G)A(G/T): 2, CACGAG at 4403, CACGAT at 336.
  6. AGCEci, negative strand, positive direction, looking for CAC(A/G)A(G/T): 1, CACGAG at 243.
  7. AGCEci, positive strand, negative direction, looking for CAC(A/G)A(G/T): 10, CACGAG at 4472, CACAAG at 3634, CACAAT at 3515, CACGAG at 3232, CACAAG at 2244, CACAAT at 1721, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.
  8. AGCEci, positive strand, positive direction, looking for CAC(A/G)A(G/T): 3, CACGAG at 3152, CACGAG at 2090, CACAAG at 107.

AGCE (4560-2846) UTRs

  1. Negative strand, negative direction: CACGAG at 4403, CTCGTG at 3914, CTTGTG at 3669.
  2. Positive strand, negative direction: CACGAG at 4472, CACAAG at 3634, CACAAT at 3515, CACGAG at 3232.

AGCE positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: CTCGTG at 4376.

AGCE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATCGTG at 2096, ATTGTG at 340, CACGAT at 336.
  2. Positive strand, negative direction: CACAAG at 2244, CACAAT at 1721, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.

AGCE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: ATTGTG at 2679, CACGAG at 243.
  2. Positive strand, positive direction: CTCGTG at 3739, CACGAG at 3152, CTTGTG at 3095, CACGAG at 2090, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855, CACAAG at 107.

AGCE random dataset samplings

  1. AGCEr0: 1, CTTGTG at 4106.
  2. AGCEr1: 8, ATTGTG at 3974, ATTGTG at 2904, CTCGTG at 2548, ATCGTG at 2338, ATCGTG at 2253, CTCGTG at 1377, CTTGTG at 871, CTTGTG at 44.
  3. AGCEr2: 2, ATCGTG at 3539, CTTGTG at 3505.
  4. AGCEr3: 1, CTCGTG at 3114.
  5. AGCEr4: 1, ATCGTG at 4271.
  6. AGCEr5: 4, CTTGTG at 2854, ATTGTG at 2836, ATCGTG at 531, ATCGTG at 513.
  7. AGCEr6: 2, ATTGTG at 2421, CTTGTG at 1745.
  8. AGCEr7: 4, CTCGTG at 3824, ATCGTG at 3591, ATTGTG at 2153, CTCGTG at 1007.
  9. AGCEr8: 2, CTCGTG at 3664, CTCGTG at 1212.
  10. AGCEr9: 0.
  11. AGCEr0ci: 4, CACAAT at 3576, CACGAG at 2462, CACGAG at 1070, CACGAG at 443.
  12. AGCEr1ci: 5, CACAAG at 4525, CACGAT at 4040, CACGAG at 3665, CACAAT at 2698, CACGAT at 1229.
  13. AGCEr2ci: 5, CACAAG at 4090, CACAAT at 2222, CACAAG at 2028, CACGAG at 1005, CACAAT at 511.
  14. AGCEr3ci: 3, CACAAT at 2703, CACGAT at 1356, CACGAT at 885.
  15. AGCEr4ci: 3, CACAAG at 4396, CACGAT at 4032, CACAAT at 238.
  16. AGCEr5ci: 2, CACAAG at 3418, CACAAT at 391.
  17. AGCEr6ci: 1, CACAAT at 4198.
  18. AGCEr7ci: 2, CACGAT at 1467, CACGAG at 1241.
  19. AGCEr8ci: 2, CACAAT at 3964, CACGAG at 2995.
  20. AGCEr9ci: 2, CACAAT at 1676, CACAAT at 1098.

AGCEr arbitrary (evens) (4560-2846) UTRs

  1. AGCEr0: CTTGTG at 4106.
  2. AGCEr2: ATCGTG at 3539, CTTGTG at 3505.
  3. AGCEr4: ATCGTG at 4271.
  4. AGCEr8: CTCGTG at 3664.
  5. AGCEr0ci: CACAAT at 3576.
  6. AGCEr2ci: CACAAG at 4090.
  7. AGCEr4ci: CACAAG at 4396, CACGAT at 4032.
  8. AGCEr6ci: CACAAT at 4198.
  9. AGCEr8ci: CACAAT at 3964, CACGAG at 2995.

AGCEr alternate (odds) (4560-2846) UTRs

  1. AGCEr1: ATTGTG at 3974, ATTGTG at 2904.
  2. AGCEr3: CTCGTG at 3114.
  3. AGCEr5: CTTGTG at 2854.
  4. AGCEr7: CTCGTG at 3824, ATCGTG at 3591.
  5. AGCEr1ci: CACAAG at 4525, CACGAT at 4040, CACGAG at 3665.
  6. AGCEr5ci: CACAAG at 3418.

AGCEr alternate negative direction (odds) (2846-2811) core promoters

  1. AGCEr5: ATTGTG at 2836.

AGCEr alternate positive direction (evens) (4445-4265) core promoters

  1. AGCEr4: ATCGTG at 4271.
  2. AGCEr4ci: CACAAG at 4396.

AGCEr alternate negative direction (odds) (2811-2596) proximal promoters

  1. AGCEr1ci: CACAAT at 2698.
  2. AGCEr3ci: CACAAT at 2703.

AGCEr alternate positive direction (evens) (4265-4050) proximal promoters

  1. AGCEr0: CTTGTG at 4106.
  2. AGCEr2ci: CACAAG at 4090.
  3. AGCEr6ci: CACAAT at 4198.

AGCEr arbitrary negative direction (evens) (2596-1) distal promoters

  1. AGCEr6: ATTGTG at 2421, CTTGTG at 1745.
  2. AGCEr8: CTCGTG at 1212.
  3. AGCEr0ci: CACGAG at 2462, CACGAG at 1070, CACGAG at 443.
  4. AGCEr2ci: CACAAT at 2222, CACAAG at 2028, CACGAG at 1005, CACAAT at 511.
  5. AGCEr4ci: CACAAT at 238.

AGCEr alternate negative direction (odds) (2596-1) distal promoters

  1. AGCEr1: CTCGTG at 2548, ATCGTG at 2338, ATCGTG at 2253, CTCGTG at 1377, CTTGTG at 871, CTTGTG at 44.
  2. AGCEr5: ATCGTG at 531, ATCGTG at 513.
  3. AGCEr7: ATTGTG at 2153, CTCGTG at 1007.
  4. AGCEr1ci: CACGAT at 1229.
  5. AGCEr3ci: CACGAT at 1356, CACGAT at 885.
  6. AGCEr5ci: CACAAT at 391.
  7. AGCEr7ci: CACGAT at 1467, CACGAG at 1241.
  8. AGCEr9ci: CACAAT at 1676, CACAAT at 1098.

AGCEr arbitrary positive direction (odds) (4050-1) distal promoters

  1. AGCEr1: ATTGTG at 3974, ATTGTG at 2904, CTCGTG at 2548, ATCGTG at 2338, ATCGTG at 2253, CTCGTG at 1377, CTTGTG at 871, CTTGTG at 44.
  2. AGCEr3: CTCGTG at 3114.
  3. AGCEr5: CTTGTG at 2854, ATTGTG at 2836, ATCGTG at 531, ATCGTG at 513.
  4. AGCEr7: CTCGTG at 3824, ATCGTG at 3591, ATTGTG at 2153, CTCGTG at 1007.
  5. AGCEr1ci: CACGAT at 4040, CACGAG at 3665, CACAAT at 2698, CACGAT at 1229.
  6. AGCEr3ci: CACAAT at 2703, CACGAT at 1356, CACGAT at 885.
  7. AGCEr5ci: CACAAG at 3418, CACAAT at 391.
  8. AGCEr7ci: CACGAT at 1467, CACGAG at 1241.
  9. AGCEr9ci: CACAAT at 1676, CACAAT at 1098.

AGCEr alternate positive direction (evens) (4050-1) distal promoters

  1. AGCEr2: ATCGTG at 3539, CTTGTG at 3505.
  2. AGCEr6: ATTGTG at 2421, CTTGTG at 1745.
  3. AGCEr8: CTCGTG at 3664, CTCGTG at 1212.
  4. AGCEr0ci: CACAAT at 3576, CACGAG at 2462, CACGAG at 1070, CACGAG at 443.
  5. AGCEr2ci: CACAAT at 2222, CACAAG at 2028, CACGAG at 1005, CACAAT at 511.
  6. AGCEr4ci: CACGAT at 4032, CACAAT at 238.
  7. AGCEr8ci: CACAAT at 3964, CACGAG at 2995.

AGCE analysis and results

Main article: Complex locus A1BG and ZNF497 § AGCEs

The core nucleotides for AGCE1 include (A/C)T(C/T)GTG, "located between the TATA box and transcription initiation site (positions −25 to −1) is an authentic regulator of human AG transcription."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 7 2 3.5 3.5 ± 0.5 (--3,+-4)
Randoms UTR arbitrary negative 12 10 1.2 1.1
Randoms UTR alternate negative 10 10 1.0 1.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0.05
Randoms Core alternate negative 1 10 0.1 0.05
Reals Core positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Core arbitrary positive 0 10 0 0.1
Randoms Core alternate positive 2 10 0.2 0.1
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0.1
Randoms Proximal alternate negative 2 10 0.2 0.1
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0.15
Randoms Proximal alternate positive 3 10 0.3 0.15
Reals Distal negative 9 2 4.5 4.5 ± 1.5 (--3,+-6)
Randoms Distal arbitrary negative 11 10 1.1 1.45
Randoms Distal alternate negative 18 10 1.8 1.45
Reals Distal positive 11 2 5.5 5.5 ± 3.5 (-+2,++9)
Randoms Distal arbitrary positive 30 10 3.0 2.4
Randoms Distal alternate positive 18 10 1.8 2.4

Comparison:

The occurrences of real AGCE UTRs, positive direction cores, and distals are greater than the randoms, but low occurrences of positive direction distals overlaps randoms. This suggests that the real AGCEs are likely active or activable.

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 Noriyuki Sato; Tomohiro Katsuya; Hiromi Rakugi; Seiju Takami; Yukiko Nakata; Tetsuro Miki; Jitsuo Higaki; Toshio Ogihara (September 1997). "Association of Variants in Critical Core Promoter Element of Angiotensinogen Gene With Increased Risk of Essential Hypertension in Japanese". Hypertension. 30 (3 Pt 1): 321–5. doi:10.1161/01.HYP.30.3.321. PMID 9314411. Retrieved 2012-02-20.
  2. ↑ HGNC (February 7, 2013). "AGT angiotensinogen (serpin peptidase inhibitor, clade A, member 8) [ Homo sapiens ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-02-10.
  3. ↑ 3.0 3.1 Kazuyuki Yanai, Tomoko Saito, Keiko Hirota, Hideyuki Kobayashi, Kazuo Murakami and Akiyoshi Fukamizu (28 November 1997). "Molecular Variation of the Human Angiotensinogen Core Promoter Element Located between the TATA Box and Transcription Initiation Site Affects Its Transcriptional Activity". The Journal of Biological Chemistry. 272 (48): 30558–62. PMID 9374551. Retrieved 2012-02-20.

External links

{{Phosphate biochemistry}}


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