MYB recognition element gene transcriptions

Jump to navigation Jump to search

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, looking for AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. negative strand, positive direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

ACE random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

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

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

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

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

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

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

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

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

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

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

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

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 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
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 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are 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, looking for A(A/C)C(A/T)A(A/C)C, 2, ACCAACC at 3946, ACCAACC at 3606.
  2. positive strand, negative direction, looking for A(A/C)C(A/T)A(A/C)C, 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, looking for A(A/C)C(A/T)A(A/C)C, 1, ACCAAAC at 3176.
  5. complement, negative strand, negative direction, looking for T(G/T)G(A/T)T(G/T)G, 5, TTGTTGG at 2844, TTGTTTG at 2511, TTGTTTG at 2486, TTGTTTG at 1587, TTGTTTG at 1390.
  6. complement, positive strand, negative direction, looking for T(G/T)G(A/T)T(G/T)G, 2, TGGTTGG at 3946, TGGTTGG at 3606.
  7. complement, positive strand, positive direction, looking for T(G/T)G(A/T)T(G/T)G, 1, TGGTTTG at 3176.
  8. complement, negative strand, positive direction, looking for T(G/T)G(A/T)T(G/T)G, 0.
  9. inverse complement, negative strand, negative direction, looking for G(G/T)T(A/T)G(G/T)T, 5, GGTAGGT at 4457, GGTTGTT at 3139, GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392.
  10. inverse complement, positive strand, negative direction, looking for G(G/T)T(A/T)G(G/T)T, 0.
  11. inverse complement, positive strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 1, GGTAGGT at 3109.
  12. inverse complement, negative strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 0.
  13. inverse negative strand, negative direction, looking for C(A/C)A(A/T)C(A/C)A, 0.
  14. inverse positive strand, negative direction, looking for C(A/C)A(A/T)C(A/C)A, 5, CCATCCA at 4457, CCAACAA at 3139, CAAACAA at 2488, CAAACAA at 2484, CAAACAA at 1392.
  15. inverse positive strand, positive direction, looking for C(A/C)A(A/T)C(A/C)A, 0.
  16. inverse negative strand, positive direction, looking for C(A/C)A(A/T)C(A/C)A, 1, CCATCCA at 3109.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

MRE UTR gene transcriptions

Main article: UTR promoter gene transcriptions

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

MRE core promoters

Main article: Core promoter gene transcriptions

Positive strand, negative direction: AACAACC at 2844.

MRE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392.

Positive strand, negative direction: AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390.

Positive strand, positive direction: GGTAGGT at 3109.

Negative strand, positive direction: ACCAAAC at 3176.

MRE random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

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

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

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

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

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

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

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

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

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

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

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

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 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
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 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences 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 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
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 2 2 1 1
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 2 2 1 1
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences 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

Retrieved from "https://www.wikidoc.org/index.php?title=MYB_recognition_element_gene_transcriptions&oldid=1728076"