MYB recognition element gene transcriptions

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

File:Arabidopsisthaliana.JPG
A rosette of Arabidopsis thaliana with the inflourescence just emerging at the centre is imaged. Credit: Quentin Groom.{{free media}}

"Another class of cis-acting elements is represented by Boxes P and L from the parsley phenylalanine ammonia-lyase (PAL) and 4-coumarate:CoA ligase (4CL) genes and the H-box from the bean chalcone synthase gene Chs15 [23,24]."[1]

"The combination of an [ACGT-containing element] ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."[2]

Human genes

Main article: Human genes

Gene ID: 4602 is MYB [myeloblastosis] MYB proto-oncogene, transcription factor on 6q23.3: "This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants."[3]

Gene expressions

Main article: Gene expressions

"Chalcone synthase (CHS), chalcone flavanone isomerase (CFI), flavanone 3-hydroxylase (F3H) and flavonol synthase (FLS) catalyze successive steps in the biosynthetic pathway leading to the production of flavonols."[2]

In "Arabidopsis thaliana all four corresponding genes are coordinately expressed in response to light, and are spatially coexpressed in siliques, flowers and leaves."[2]

"Light regulatory units (LRUs) sufficient for light responsiveness were identified in all four promoters."[2]

A "R response element (RRE) was identified in the CHS promoter."[2]

"Only the ACE from the CFI promoter shows flanking sequences giving rise to a symmetrical G-box (Foster et al., 1994; Menkens et al., 1995) that also fits the consensus of the R motif (CANNTG; Blackwell and Weintraub, 1990; Bodeau and Walbot, 1996) which is recognized by [basic helix-loop-helix] BHLH factors."[2]

The gain-of-function for the FLS gene (MRE, ACE) lies between -97 and -42.[2]

For the F3H gene the ACE lies between -463 and -382 and the MRE lies between -99 and -63.[2]

For the CFI gene the ACE, MRE lie between -99 and -39.[2]

For the CHS gene the ACE, RRE, MRE lie between -106 and -69.[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"These elements fit the type II MYB consensus sequence A(A/C)C(A/T)A(A/C)C, suggesting that they are MYB recognition elements (MREs)."[1]

The consensus sequence for the RRE is 5'-CATCTG-3'.[2]

The consensus sequence for the ACE is 5'-CACGT-3'.[2]

Hypotheses

Main article: Hypotheses
  1. A1BG has no MYB recognition elements (MRE) in either promoter.
  2. A1BG is not transcribed by a MRE.
  3. No MRE participates in the transcription of A1BG.

ACE samplings

Copying a responsive elements consensus sequence CACGT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CACGT (starting with SuccessablesACE.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:

  1. Negative strand, negative direction: 5, CACGT at 3429, CACGT at 2863, CACGT at 2081, CACGT at 1535, CACGT at 1470.
  2. Positive strand, negative direction: 3, CACGT at 1772, CACGT at 531, CACGT at 342.
  3. Negative strand, positive direction: 2, CACGT at 3254, CACGT at 569.
  4. Positive strand, positive direction: 13, CACGT at 3960, CACGT at 3883, CACGT at 3464, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, CACGT at 1786, CACGT at 1218, CACGT at 783, CACGT at 546.
  5. inverse complement, negative strand, negative direction: 8, ACGTG at 4339, ACGTG at 3288, ACGTG at 2760, ACGTG at 2425, ACGTG at 1999, ACGTG at 1718, ACGTG at 1346, ACGTG at 1338.
  6. inverse complement, positive strand, negative direction: 1, ACGTG at 4237.
  7. inverse complement, negative strand, positive direction: 1, ACGTG at 570.
  8. inverse complement, positive strand, positive direction: 10, ACGTG at 4342, ACGTG at 3884, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, ACGTG at 1821, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, ACGTG at 547.

ACE (4560-2846) UTRs

  1. Negative strand, negative direction: ACGTG at 4339, CACGT at 3429, ACGTG at 3288, CACGT at 2863.
  2. Positive strand, negative direction: ACGTG at 4237.

ACE positive direction (4445-4265) core promoters

  1. Positive strand, positive direction: ACGTG at 4342.

ACE negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: ACGTG at 2760.

ACE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ACGTG at 2425, CACGT at 2081, ACGTG at 1999, ACGTG at 1718, CACGT at 1535, CACGT at 1470, ACGTG at 1346, ACGTG at 1338.
  2. Positive strand, negative direction: CACGT at 1772, CACGT at 531, CACGT at 342.

ACE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CACGT at 3254, ACGTG at 570, CACGT at 569.
  2. Positive strand, positive direction: CACGT at 3960, ACGTG at 3884, CACGT at 3883, CACGT at 3464, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, ACGTG at 1821, CACGT at 1786, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, CACGT at 1218, CACGT at 783, ACGTG at 547, CACGT at 546.

ACE random dataset samplings

  1. ACEr0: 5, CACGT at 4342, CACGT at 2592, CACGT at 2168, CACGT at 1356, CACGT at 419.
  2. ACEr1: 4, CACGT at 3788, CACGT at 3428, CACGT at 3298, CACGT at 191.
  3. ACEr2: 2, CACGT at 3409, CACGT at 3194.
  4. ACEr3: 4, CACGT at 4080, CACGT at 3768, CACGT at 2750, CACGT at 1482.
  5. ACEr4: 4, CACGT at 4410, CACGT at 4365, CACGT at 3507, CACGT at 2286.
  6. ACEr5: 3, CACGT at 4067, CACGT at 843, CACGT at 58.
  7. ACEr6: 4, CACGT at 3433, CACGT at 2925, CACGT at 2904, CACGT at 653.
  8. ACEr7: 3, CACGT at 1855, CACGT at 1391, CACGT at 944.
  9. ACEr8: 3, CACGT at 3750, CACGT at 2984, CACGT at 897.
  10. ACEr9: 5, CACGT at 2965, CACGT at 2698, CACGT at 1858, CACGT at 1186, CACGT at 874.
  11. ACEr0ci: 5, ACGTG at 4343, ACGTG at 3209, ACGTG at 2399, ACGTG at 1935, ACGTG at 841.
  12. ACEr1ci: 3, ACGTG at 4030, ACGTG at 1857, ACGTG at 496.
  13. ACEr2ci: 4, ACGTG at 1697, ACGTG at 1594, ACGTG at 484, ACGTG at 99.
  14. ACEr3ci: 2, ACGTG at 3769, ACGTG at 1437.
  15. ACEr4ci: 4, ACGTG at 2287, ACGTG at 1453, ACGTG at 660, ACGTG at 386.
  16. ACEr5ci: 3, ACGTG at 1587, ACGTG at 712, ACGTG at 59.
  17. ACEr6ci: 3, ACGTG at 2905, ACGTG at 2529, ACGTG at 654.
  18. ACEr7ci: 3, ACGTG at 3534, ACGTG at 1856, ACGTG at 850.
  19. ACEr8ci: 1, ACGTG at 914.
  20. ACEr9ci: 2, ACGTG at 1187, ACGTG at 797.

ACEr arbitrary (evens) (4560-2846) UTRs

  1. ACEr0: CACGT at 4342.
  2. ACEr2: CACGT at 3409, CACGT at 3194.
  3. ACEr4: CACGT at 4410, CACGT at 4365, CACGT at 3507.
  4. ACEr6: CACGT at 3433, CACGT at 2925, CACGT at 2904.
  5. ACEr8: CACGT at 3750, CACGT at 2984, CACGT at 897.
  6. ACEr0ci: ACGTG at 4343, ACGTG at 3209.
  7. ACEr6ci: ACGTG at 2905.

ACEr alternate (odds) (4560-2846) UTRs

  1. ACEr1: CACGT at 3788, CACGT at 3428, CACGT at 3298.
  2. ACEr3: CACGT at 4080, CACGT at 3768.
  3. ACEr5: CACGT at 4067.
  4. ACEr9: CACGT at 2965.
  5. ACEr1ci: ACGTG at 4030.
  6. ACEr3ci: ACGTG at 3769.
  7. ACEr7ci: ACGTG at 3534.

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

  1. ACEr0: CACGT at 4342.
  2. ACEr4: CACGT at 4410, CACGT at 4365.
  3. ACEr0ci: ACGTG at 4343.

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

  1. ACEr3: CACGT at 2750.
  2. ACEr9: CACGT at 2698.

ACEr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ACEr3: CACGT at 4080.
  2. ACEr5: CACGT at 4067.

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

  1. ACEr0: CACGT at 2592, CACGT at 2168, CACGT at 1356, CACGT at 419.
  2. ACEr4: CACGT at 2286.
  3. ACEr6: CACGT at 653.
  4. ACEr8: CACGT at 897.
  5. ACEr0ci: ACGTG at 2399, ACGTG at 1935, ACGTG at 841.
  6. ACEr2ci: ACGTG at 1697, ACGTG at 1594, ACGTG at 484, ACGTG at 99.
  7. ACEr4ci: ACGTG at 2287, ACGTG at 1453, ACGTG at 660, ACGTG at 386.
  8. ACEr6ci: ACGTG at 2529, ACGTG at 654.
  9. ACEr8ci: ACGTG at 914.

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

  1. ACEr1: CACGT at 191.
  2. ACEr3: CACGT at 1482.
  3. ACEr5: CACGT at 843, CACGT at 58.
  4. ACEr7: CACGT at 1855, CACGT at 1391, CACGT at 944.
  5. ACEr9: CACGT at 1858, CACGT at 1186, CACGT at 874.
  6. ACEr1ci:ACGTG at 1857, ACGTG at 496.
  7. ACEr3ci: ACGTG at 1437.
  8. ACEr5ci: ACGTG at 1587, ACGTG at 712, ACGTG at 59.
  9. ACEr7ci: ACGTG at 1856, ACGTG at 850.
  10. ACEr9ci: ACGTG at 1187, ACGTG at 797.

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

  1. ACEr1: CACGT at 3788, CACGT at 3428, CACGT at 3298, CACGT at 191.
  2. ACEr3: CACGT at 3768, CACGT at 2750, CACGT at 1482.
  3. ACEr5: CACGT at 843, CACGT at 58.
  4. ACEr7: CACGT at 1855, CACGT at 1391, CACGT at 944.
  5. ACEr9: CACGT at 2965, CACGT at 2698, CACGT at 1858, CACGT at 1186, CACGT at 874.
  6. ACEr1ci: ACGTG at 4030, ACGTG at 1857, ACGTG at 496.
  7. ACEr3ci: ACGTG at 3769, ACGTG at 1437.
  8. ACEr5ci: ACGTG at 1587, ACGTG at 712, ACGTG at 59.
  9. ACEr7ci: ACGTG at 3534, ACGTG at 1856, ACGTG at 850.
  10. ACEr9ci: ACGTG at 1187, ACGTG at 797.

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

  1. ACEr0: CACGT at 2592, CACGT at 2168, CACGT at 1356, CACGT at 419.
  2. ACEr2: CACGT at 3409, CACGT at 3194.
  3. ACEr4: CACGT at 3507, CACGT at 2286.
  4. ACEr6: CACGT at 3433, CACGT at 2925, CACGT at 2904, CACGT at 653.
  5. ACEr8: CACGT at 3750, CACGT at 2984, CACGT at 897.
  6. ACEr0ci: ACGTG at 3209, ACGTG at 2399, ACGTG at 1935, ACGTG at 841.
  7. ACEr2ci: ACGTG at 1697, ACGTG at 1594, ACGTG at 484, ACGTG at 99.
  8. ACEr4ci: ACGTG at 2287, ACGTG at 1453, ACGTG at 660, ACGTG at 386.
  9. ACEr6ci: ACGTG at 2905, ACGTG at 2529, ACGTG at 654.
  10. ACEr8ci: ACGTG at 914.

ACE analysis and results

Main article: Complex locus A1BG and ZNF497 § ACEs

The consensus sequence for the ACE is CACGT.[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5 ± 1.5 (--4,+-1)
Randoms UTR arbitrary negative 15 10 1.5 1.25
Randoms UTR alternate negative 10 10 1.0 1.25
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Core arbitrary positive 0 10 0 0.2
Randoms Core alternate positive 4 10 0.4 0.2
Reals Proximal negative 1 2 0.5 0.5 ± 0.5 (--1,+-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 2 10 0.2 0.1
Randoms Proximal alternate positive 0 10 0 0.1
Reals Distal negative 11 2 5.5 5.5 ± 2.5 (--8,+-3)
Randoms Distal arbitrary negative 21 10 2.1 2.05
Randoms Distal alternate negative 20 10 2.0 2.05
Reals Distal positive 25 2 12.5 12.5 ± 9.5 (-+3,++22)
Randoms Distal arbitrary positive 30 10 3.0 3.05
Randoms Distal alternate positive 31 10 3.1 3.05

Comparison:

The occurrences of real ACE UTRs are greater than the randoms and overlap high randoms, positive ACE cores, proximals, and negative distals greater than the randoms, positive direction distals are greater than the randoms and overlap high randoms. This suggests that the real ACEs are generally likely active or activable.

MRE samplings

Main article: Model samplings

Copying an apparent core consensus sequence for the MYBRE of AACAAAC or TAACTG and putting it in "⌘F" finds none located between ZSCAN22 and none or one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence A(A/C)C(A/T)A(A/C)C (starting with SuccessablesMYB.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:

  1. Negative strand, negative direction: 2, ACCAACC at 3946, ACCAACC at 3606.
  2. Positive strand, negative direction: 5, AACAACC at 2844, AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390.
  3. Positive strand, positive direction, looking for A(A/C)C(A/T)A(A/C)C, 0.
  4. Negative strand, positive direction: 1, ACCAAAC at 3176.
  5. inverse complement, negative strand, negative direction: 5, GGTAGGT at 4457, GGTTGTT at 3139, GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392.
  6. inverse complement, positive strand, negative direction, looking for G(G/T)T(A/T)G(G/T)T, 0.
  7. inverse complement, positive strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 1, GGTAGGT at 3109.
  8. inverse complement, negative strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 0.

MRE (4560-2846) UTRs

  1. Negative strand, negative direction: GGTAGGT at 4457, ACCAACC at 3946, ACCAACC at 3606, GGTTGTT at 3139.

MRE negative direction (2846-2811) core promoters

  1. Positive strand, negative direction: AACAACC at 2844.

MRE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392.
  2. Positive strand, negative direction: AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390.

MRE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: ACCAAAC at 3176.
  2. Positive strand, positive direction: GGTAGGT at 3109.

MRE random dataset samplings

  1. MYBr0: 2, ACCTAAC at 3804, ACCAAAC at 1086.
  2. MYBr1: 3, AACAACC at 4321, ACCAACC at 3539, AACAAAC at 614.
  3. MYBr2: 4, ACCTAAC at 3319, ACCAAAC at 3175, AACAAAC at 3170, AACAACC at 2193.
  4. MYBr3: 6, AACTACC at 3788, ACCAACC at 3391, AACAAAC at 2925, AACTACC at 1855, AACTAAC at 1802, AACTACC at 1293.
  5. MYBr4: 3, ACCAAAC at 2135, AACAAAC at 533, AACAACC at 421.
  6. MYBr5: 2, AACAAAC at 1377, AACTAAC at 1373.
  7. MYBr6: 1, AACTAAC at 2918.
  8. MYBr7: 2, ACCAACC at 4433, AACAACC at 2550.
  9. MYBr8: 3, ACCAACC at 4296, AACAACC at 2105, ACCAACC at 812.
  10. MYBr9: 4, AACAAAC at 3457, AACTAAC at 3071, AACAAAC at 3067, AACAAAC at 1093.
  11. MYBr0ci: 1, GTTTGTT at 3180.
  12. MYBr1ci: 2, GGTAGTT at 559, GTTTGGT at 414.
  13. MYBr2ci: 1, GTTAGTT at 2043.
  14. MYBr3ci: 5, GGTTGTT at 4514, GTTTGTT at 2269, GTTAGTT at 997, GGTTGTT at 530, GTTTGTT at 452.
  15. MYBr4ci: 5, GGTTGTT at 3531, GTTTGTT at 3208, GGTTGTT at 2436, GGTAGTT at 2397, GTTTGGT at 430.
  16. MYBr5ci: 4, GGTAGGT at 3891, GTTAGTT at 3264, GTTAGGT at 304, GGTTGGT at 255.
  17. MYBr6ci: 1, GTTTGTT at 4533.
  18. MYBr7ci: 3, GTTAGGT at 2810, GGTAGTT at 2117, GGTTGTT at 1884.
  19. MYBr8ci: 3, GTTAGTT at 4396, GGTTGTT at 2381, GTTTGTT at 43.
  20. MYBr9ci: 3, GGTAGTT at 1877, GTTAGGT at 603, GTTTGTT at 95.

MYBr arbitrary (evens) (4560-2846) UTRs

  1. MYBr0: ACCTAAC at 3804.
  2. MYBr2: ACCTAAC at 3319, ACCAAAC at 3175, AACAAAC at 3170.
  3. MYBr6: AACTAAC at 2918.
  4. MYBr8: ACCAACC at 4296.
  5. MYBr0ci: GTTTGTT at 3180.
  6. MYBr4ci: GGTTGTT at 3531, GTTTGTT at 3208.
  7. MYBr6ci: GTTTGTT at 4533.

MYBr alternate (odds) (4560-2846) UTRs

  1. MYBr1: AACAACC at 4321, ACCAACC at 3539.
  2. MYBr3: AACTACC at 3788, ACCAACC at 3391, AACAAAC at 2925.
  3. MYBr7: ACCAACC at 4433.
  4. MYBr9: AACAAAC at 3457, AACTAAC at 3071, AACAAAC at 3067.
  5. MYBr3ci: GGTTGTT at 4514.
  6. MYBr5ci: GGTAGGT at 3891, GTTAGTT at 3264.

MYBr arbitrary positive direction (odds) (4445-4265) core promoters

  1. MYBr1: AACAACC at 4321.
  2. MYBr7: ACCAACC at 4433.

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

  1. MYBr8: ACCAACC at 4296.

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

  1. MYBr7ci: GTTAGGT at 2810.

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

  1. MYBr0: ACCAAAC at 1086.
  2. MYBr2: AACAACC at 2193.
  3. MYBr4: ACCAAAC at 2135, AACAAAC at 533, AACAACC at 421.
  4. MYBr8: AACAACC at 2105, ACCAACC at 812.
  5. MYBr2ci: GTTAGTT at 2043.
  6. MYBr4ci: GGTTGTT at 2436, GGTAGTT at 2397, GTTTGGT at 430.

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

  1. MYBr1: AACAAAC at 614.
  2. MYBr3: AACTACC at 1855, AACTAAC at 1802, AACTACC at 1293.
  3. MYBr5: AACAAAC at 1377, AACTAAC at 1373.
  4. MYBr7: AACAACC at 2550.
  5. MYBr9: AACAAAC at 1093.
  6. MYBr1ci: GGTAGTT at 559, GTTTGGT at 414.
  7. MYBr3ci: GTTTGTT at 2269, GTTAGTT at 997, GGTTGTT at 530, GTTTGTT at 452.
  8. MYBr5ci: GTTAGGT at 304, GGTTGGT at 255.
  9. MYBr7ci: GTTAGGT at 2810, GGTAGTT at 2117, GGTTGTT at 1884.
  10. MYBr9ci: GGTAGTT at 1877, GTTAGGT at 603, GTTTGTT at 95.

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

  1. MYBr1: ACCAACC at 3539, AACAAAC at 614.
  2. MYBr3: AACTACC at 3788, ACCAACC at 3391, AACAAAC at 2925, AACTACC at 1855, AACTAAC at 1802, AACTACC at 1293.
  3. MYBr5: AACAAAC at 1377, AACTAAC at 1373.
  4. MYBr7: AACAACC at 2550.
  5. MYBr9: AACAAAC at 3457, AACTAAC at 3071, AACAAAC at 3067, AACAAAC at 1093.
  6. MYBr1ci: GGTAGTT at 559, GTTTGGT at 414.
  7. MYBr3ci: GTTTGTT at 2269, GTTAGTT at 997, GGTTGTT at 530, GTTTGTT at 452.
  8. MYBr5ci: GGTAGGT at 3891, GTTAGTT at 3264, GTTAGGT at 304, GGTTGGT at 255.
  9. MYBr7ci: GTTAGGT at 2810, GGTAGTT at 2117, GGTTGTT at 1884.
  10. MYBr9ci: GGTAGTT at 1877, GTTAGGT at 603, GTTTGTT at 95.

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

  1. MYBr0: ACCTAAC at 3804, ACCAAAC at 1086.
  2. MYBr2: ACCTAAC at 3319, ACCAAAC at 3175, AACAAAC at 3170, AACAACC at 2193.
  3. MYBr4: ACCAAAC at 2135, AACAAAC at 533, AACAACC at 421.
  4. MYBr6: AACTAAC at 2918.
  5. MYBr8: AACAACC at 2105, ACCAACC at 812.
  6. MYBr0ci: GTTTGTT at 3180.
  7. MYBr2ci: GTTAGTT at 2043.
  8. MYBr4ci: GGTTGTT at 3531, GTTTGTT at 3208, GGTTGTT at 2436, GGTAGTT at 2397, GTTTGGT at 430.

MRE analysis and results

Main article: Complex locus A1BG and ZNF497 § MREs

"These elements fit the type II MYB consensus sequence A(A/C)C(A/T)A(A/C)C, suggesting that they are MYB recognition elements (MREs)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 4 2 2 2 ± 2 (--4,+-0)
Randoms UTR arbitrary negative 10 10 1 1.1
Randoms UTR alternate negative 12 10 1.2 1.1
Reals Core negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 2 10 0.2 0.15
Randoms Core alternate positive 1 10 0.1 0.15
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 7 2 3.5 3.5 ± 0.5 (--3,+-4)
Randoms Distal arbitrary negative 11 10 1.1 1.15
Randoms Distal alternate negative 22 10 2.2 1.15
Reals Distal positive 2 2 1 1 ± 0 (-+1,++1)
Randoms Distal arbitrary positive 31 10 3.1 2.6
Randoms Distal alternate positive 21 10 2.1 2.6

Comparison:

The occurrences of real MYB recognition elements are greater than the randoms, the positive distals are less than the randoms. This suggests that the real MYB recognition elements are likely active or activable.

RRE samplings

Copying the apparent consensus sequence for the RRE (CATCTG) and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CATCTG (starting with SuccessablesRRE.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:

  1. negative strand, negative direction, looking for CATCTG, 0.
  2. positive strand, negative direction, looking for CATCTG, 0.
  3. positive strand, positive direction, looking for CATCTG, 0.
  4. negative strand, positive direction, looking for CATCTG, 1, CATCTG at 3404.
  5. inverse complement, negative strand, negative direction, looking for CAGATG, 4, CAGATG at 4212, CAGATG at 2988, CAGATG at 1224, CAGATG at 481.
  6. inverse complement, positive strand, negative direction, looking for CAGATG, 3, CAGATG at 3919, CAGATG at 3627, CAGATG at 3620.
  7. inverse complement, positive strand, positive direction, looking for CAGATG, 0.
  8. inverse complement, negative strand, positive direction, looking for CAGATG, 1, CAGATG at 3475.

RRE (4560-2846) UTRs

  1. Negative strand, negative direction: CAGATG at 4212, CAGATG at 2988.
  2. Positive strand, negative direction: CAGATG at 3919, CAGATG at 3627, CAGATG at 3620.

RRE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CAGATG at 1224, CAGATG at 481.

RRE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CAGATG at 3475, CATCTG at 3404.

RRE random dataset samplings

  1. RREr0: 0.
  2. RREr1: 1, CATCTG at 1131.
  3. RREr2: 1, CATCTG at 203.
  4. RREr3: 2, CATCTG at 3286, CATCTG at 1770.
  5. RREr4: 1, CATCTG at 2584.
  6. RREr5: 0.
  7. RREr6: 0.
  8. RREr7: 1, CATCTG at 1159.
  9. RREr8: 1, CATCTG at 1711.
  10. RREr9: 0.
  11. RREr0ci: 0.
  12. RREr1ci: 0.
  13. RREr2ci: 1, CAGATG at 1826.
  14. RREr3ci: 1, CAGATG at 298.
  15. RREr4ci: 1, CAGATG at 4202.
  16. RREr5ci: 0.
  17. RREr6ci: 0.
  18. RREr7ci: 0.
  19. RREr8ci: 2, CAGATG at 3821, CAGATG at 2726.
  20. RREr9ci: 2, CAGATG at 4485, CAGATG at 4027.

RREr arbitrary (evens) (4560-2846) UTRs

  1. RREr4ci: CAGATG at 4202.
  2. RREr8ci: CAGATG at 3821.

RREr alternate (odds) (4560-2846) UTRs

  1. RREr3: CATCTG at 3286.
  2. RREr9ci: CAGATG at 4485, CAGATG at 4027.

RREr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. RREr8ci: CAGATG at 2726.

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

  1. RREr4ci: CAGATG at 4202.

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

  1. RREr2: CATCTG at 203.
  2. RREr4: CATCTG at 2584.
  3. RREr8: CATCTG at 1711.
  4. RREr2ci: CAGATG at 1826.
  5. RREr8ci: CAGATG at 2726.

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

  1. RREr1: CATCTG at 1131.
  2. RREr3: CATCTG at 1770.
  3. RREr7: CATCTG at 1159.
  4. RREr3ci: CAGATG at 298.

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

  1. RREr1: CATCTG at 1131.
  2. RREr3: CATCTG at 3286, CATCTG at 1770.
  3. RREr7: CATCTG at 1159.
  4. RREr3ci: CAGATG at 298.
  5. RREr9ci: CAGATG at 4027.

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

  1. RREr2: CATCTG at 203.
  2. RREr4: CATCTG at 2584.
  3. RREr8: CATCTG at 1711.
  4. RREr2ci: CAGATG at 1826.
  5. RREr8ci: CAGATG at 3821, CAGATG at 2726.

RRE analysis and results

Main article: Complex locus A1BG and ZNF497 § RREs

The consensus sequence for the RRE is CATCTG.[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5 ± 0.5
Randoms UTR arbitrary negative 2 10 0.2 0.25
Randoms UTR alternate negative 3 10 0.3 0.25
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 1 10 0.1 0.05
Randoms Proximal alternate negative 0 10 0 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0.05
Randoms Proximal alternate positive 1 10 0.1 0.05
Reals Distal negative 2 2 1 1 ± 1 (--2,+-0)
Randoms Distal arbitrary negative 5 10 0.5 0.45
Randoms Distal alternate negative 4 10 0.4 0.45
Reals Distal positive 2 2 1 1 ± 1 (-+2,++0)
Randoms Distal arbitrary positive 6 10 0.6 0.6
Randoms Distal alternate positive 6 10 0.6 0.6

Comparison:

The occurrences of real RREs are greater than the randoms. This suggests that the real RREs 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.

Initial content for this page in some instances incorporates text from the United States National Library of Medicine.

See also

References

  1. ↑ 1.0 1.1 1.2 Paul J Rushton and Imre E Somssich (August 1998). "Transcriptional control of plant genes responsive to pathogens" (PDF). Current Opinion in Plant Biology. 1 (4): 311–5. doi:10.1016/1369-5266(88)80052-9. Retrieved 5 November 2018.
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 Ulrike Hartmann, Martin Sagasser, Frank Mehrtens, Ralf Stracke and Bernd Weisshaar (January 2005). "Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes" (PDF). Plant Molecular Biology. 57 (2): 155–171. doi:10.1007/s11103-004-6910-0. Retrieved 10 November 2018.
  3. ↑ RefSeq (January 2016). "MYB MYB proto-oncogene, transcription factor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 7 February 2021.

External links

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