Homeobox gene transcriptions

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

"Transcription factors Pax-4 and Pax-6 are known to be key regulators of pancreatic cell differentiation and development. [...] The gene-targeting experiments revealed that Pax-4 and Pax-6 cannot substitute for each other in tissue with overlapping expression of both genes. [The] DNA-binding specificities of Pax-4 and Pax-6 are similar. The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."[1]

The "crucial difference between the binding sites of Antennapedia class and TTF-1 HDs is in the motifs 5'-TAAT-3', recognized by Antennapedia [a Hox gene, a subset of homeobox genes, first discovered in Drosophila which controls the formation of legs during development], and 5'-CAAG-3', preferentially bound by TTF-1. [The] binding of wild type and mutants TTF-1 HD to oligonucleotides containing either 5'-TAAT-3' or 5'-CAAG-3' indicate that only in the presence of the latter motif the Gln50 in TTF-1 HD is utilized for DNA recognition."[2]

Human genes

Main article: Human genes

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

An apparent consensus sequence is 5'-CAAG-3'.[2]

Hypotheses

Main article: Hypotheses
  1. A1BG has no homeoboxes in either promoter.
  2. A1BG is not transcribed by a homeobox.
  3. No homeobox participates in the transcription of A1BG.

Homeobox samplings

Copying a portion of the homeobox motif of CAAG and putting it in "⌘F" finds eight located between ZSCAN22 and A1BG and 21 between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CAAG (starting with SuccessablesHome.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 CAAG, 8, CAAG at 4417, CAAG at 4175, CAAG at 4024, CAAG at 1177, CAAG at 719, CAAG at 344, CAAG at 253, CAAG at 44.
  2. negative strand, positive direction, looking for CAAG, 21, CAAG at 2692, CAAG at 2615, CAAG at 2593, CAAG at 2508, CAAG at 2398, CAAG at 2189, CAAG at 1947, CAAG at 1525, CAAG at 1510, CAAG at 1426, CAAG at 1326, CAAG at 1258, CAAG at 1006, CAAG at 922, CAAG at 822, CAAG at 754, CAAG at 670, CAAG at 586, CAAG at 502, CAAG at 338, CAAG at 177.
  3. positive strand, negative direction, looking for CAAG, 24, CAAG at 4183, CAAG at 4178, CAAG at 4027, CAAG at 4019, CAAG at 3844, CAAG at 3758, CAAG at 3634, CAAG at 3373, CAAG at 3339, CAAG at 3306, CAAG at 3273, CAAG at 3140, CAAG at 2963, CAAG at 2244, CAAG at 2022, CAAG at 1817, CAAG at 1496, CAAG at 874, CAAG at 692, CAAG at 556, CAAG at 454, CAAG at 419, CAAG at 114, CAAG at 70.
  4. positive strand, positive direction, looking for CAAG, 14, CAAG at 4200, CAAG at 4073, CAAG at 3624, CAAG at 3351, CAAG at 2954, CAAG at 2933, CAAG at 2922, CAAG at 1987, CAAG at 1926, CAAG at 1489, CAAG at 1389, CAAG at 508, CAAG at 305, CAAG at 107.
  5. complement, negative strand, negative direction, looking for GTTC, 24, GTTC at 4183, GTTC at 4178, GTTC at 4027, GTTC at 4019, GTTC at 3844, GTTC at 3758, GTTC at 3634, GTTC at 3373, GTTC at 3339, GTTC at 3306, GTTC at 3273, GTTC at 3140, GTTC at 2963, GTTC at 2244, GTTC at 2022, GTTC at 1817, GTTC at 1496, GTTC at 874, GTTC at 692, GTTC at 556, GTTC at 454, GTTC at 419, GTTC at 114, GTTC at 70.
  6. complement, negative strand, positive direction, looking for GTTC, 14, GTTC at 4200, GTTC at 4073, GTTC at 3624, GTTC at 3351, GTTC at 2954, GTTC at 2933, GTTC at 2922, GTTC at 1987, GTTC at 1926, GTTC at 1489, GTTC at 1389, GTTC at 508, GTTC at 305, GTTC at 107.
  7. complement, positive strand, negative direction, looking for GTTC, 8, GTTC at 4417, GTTC at 4175, GTTC at 4024, GTTC at 1177, GTTC at 719, GTTC at 344, GTTC at 253, GTTC at 44.
  8. complement, positive strand, positive direction, looking for GTTC, 21, GTTC at 2692, GTTC at 2615, GTTC at 2593, GTTC at 2508, GTTC at 2398, GTTC at 2189, GTTC at 1947, GTTC at 1525, GTTC at 1510, GTTC at 1426, GTTC at 1326, GTTC at 1258, GTTC at 1006, GTTC at 922, GTTC at 822, GTTC at 754, GTTC at 670, GTTC at 586, GTTC at 502, GTTC at 338, GTTC at 177.
  9. inverse complement, negative strand, negative direction, looking for CTTG, 15, CTTG at 4450, CTTG at 3783, CTTG at 3723, CTTG at 3667, CTTG at 3459, CTTG at 3244, CTTG at 2716, CTTG at 2381, CTTG at 1955, CTTG at 1684, CTTG at 1551, CTTG at 1302, CTTG at 1011, CTTG at 845, CTTG at 286.
  10. inverse complement, negative strand, positive direction, looking for CTTG, 13, CTTG at 4388, CTTG at 4299, CTTG at 4130, CTTG at 4015, CTTG at 3373, CTTG at 3001, CTTG at 2741, CTTG at 2418, CTTG at 1798, CTTG at 1578, CTTG at 654, CTTG at 526, CTTG at 129.
  11. inverse complement, positive strand, negative direction, looking for CTTG, 24, CTTG at 4293, CTTG at 4267, CTTG at 4187, CTTG at 4011, CTTG at 3792, CTTG at 3570, CTTG at 3400, CTTG at 3241, CTTG at 3102, CTTG at 2920, CTTG at 2713, CTTG at 2579, CTTG at 2378, CTTG at 2126, CTTG at 1972, CTTG at 1926, CTTG at 1648, CTTG at 1618, CTTG at 1606, CTTG at 1299, CTTG at 1008, CTTG at 842, CTTG at 327, CTTG at 280.
  12. inverse complement, positive strand, positive direction, looking for CTTG, 13, CTTG at 4443, CTTG at 4067, CTTG at 4047, CTTG at 3936, CTTG at 3855, CTTG at 3837, CTTG at 3093, CTTG at 2775, CTTG at 2578, CTTG at 2224, CTTG at 1950, CTTG at 1810, CTTG at 362.
  13. inverse negative strand, negative direction, looking for GAAC, 24, GAAC at 4293, GAAC at 4267, GAAC at 4187, GAAC at 4011, GAAC at 3792, GAAC at 3570, GAAC at 3400, GAAC at 3241, GAAC at 3102, GAAC at 2920, GAAC at 2713, GAAC at 2579, GAAC at 2378, GAAC at 2126, GAAC at 1972, GAAC at 1926, GAAC at 1648, GAAC at 1618, GAAC at 1606, GAAC at 1299, GAAC at 1008, GAAC at 842, GAAC at 327, GAAC at 280.
  14. inverse negative strand, positive direction, looking for GAAC, 13, GAAC at 4443, GAAC at 4067, GAAC at 4047, GAAC at 3936, GAAC at 3855, GAAC at 3837, GAAC at 3093, GAAC at 2775, GAAC at 2578, GAAC at 2224, GAAC at 1950, GAAC at 1810, GAAC at 362.
  15. inverse positive strand, negative direction, looking for GAAC, 15, GAAC at 4450, GAAC at 3783, GAAC at 3723, GAAC at 3667, GAAC at 3459, GAAC at 3244, GAAC at 2716, GAAC at 2381, GAAC at 1955, GAAC at 1684, GAAC at 1551, GAAC at 1302, GAAC at 1011, GAAC at 845, GAAC at 286.
  16. inverse positive strand, positive direction, looking for GAAC, 13, GAAC at 4388, GAAC at 4299, GAAC at 4130, GAAC at 4015, GAAC at 3373, GAAC at 3001, GAAC at 2741, GAAC at 2418, GAAC at 1798, GAAC at 1578, GAAC at 654, GAAC at 526, GAAC at 129.

Homeobox UTRs

  1. Negative strand, negative direction: CTTG at 4450, CAAG at 4417, CAAG at 4175, CAAG at 4024, CTTG at 3783, CTTG at 3723, CTTG at 3667, CTTG at 3459, CTTG at 3244.
  2. Positive strand, negative direction: CTTG at 4293, CTTG at 4267, CTTG at 4187, CAAG at 4183, CAAG at 4178, CAAG at 4027, CAAG at 4019, CTTG at 4011, CAAG at 3844, CTTG at 3792, CAAG at 3758, CAAG at 3634, CTTG at 3570, CTTG at 3400, CAAG at 3373, CAAG at 3339, CAAG at 3306, CAAG at 3273, CTTG at 3241, CAAG at 3140, CTTG at 3102, CAAG at 2963, CTTG at 2920.

Homeobox core promoters

  1. Negative strand, positive direction: CTTG at 4388, CTTG at 4299.
  2. Positive strand, positive direction: CTTG at 4443.

Home proximal promoters

  1. Negative strand, negative direction: CTTG at 2716.
  2. Positive strand, negative direction: CTTG at 2713.


  1. Negative strand, positive direction: CTTG at 4130.
  2. Positive strand, positive direction: CAAG at 4200, CAAG at 4073, CTTG at 4067.

Home distal promoters

  1. Negative strand, negative direction: CTTG at 2381, CTTG at 1955, CTTG at 1684, CTTG at 1551, CTTG at 1302, CAAG at 1177, CTTG at 1011, CTTG at 845, CAAG at 719, CAAG at 344, CTTG at 286, CAAG at 253, CAAG at 44.
  2. Positive strand, negative direction: CTTG at 2579, CTTG at 2378, CAAG at 2244, CTTG at 2126, CAAG at 2022, CTTG at 1972, CTTG at 1926, CAAG at 1817, CTTG at 1648, CTTG at 1618, CTTG at 1606, CAAG at 1496, CTTG at 1299, CTTG at 1008, CAAG at 874, CTTG at 842, CAAG at 692, CAAG at 556, CAAG at 454, CAAG at 419, CTTG at 327, CTTG at 280, CAAG at 114, CAAG at 70.


  1. Negative strand, positive direction: CTTG at 4015, CTTG at 3373, CTTG at 3001, CTTG at 2741, CAAG at 2692, CAAG at 2615, CAAG at 2593, CAAG at 2508, CTTG at 2418, CAAG at 2398, CAAG at 2189, CAAG at 1947, CTTG at 1798, CTTG at 1578, CAAG at 1525, CAAG at 1510, CAAG at 1426, CAAG at 1326, CAAG at 1258, CAAG at 1006, CAAG at 922, CAAG at 822, CAAG at 754, CAAG at 670, CTTG at 654, CAAG at 586, CTTG at 526, CAAG at 502, CAAG at 338, CAAG at 177, CTTG at 129.
  2. Positive strand, positive direction: CTTG at 4047, CTTG at 3936, CTTG at 3855, CTTG at 3837, CAAG at 3624, CAAG at 3351, CTTG at 3093, CAAG at 2954, CAAG at 2933, CAAG at 2922, CTTG at 2775, CTTG at 2578, CTTG at 2224, CTTG at 1950, CAAG at 1987, CAAG at 1926, CTTG at 1810, CAAG at 1489, CAAG at 1389, CAAG at 508, CTTG at 362, CAAG at 305, CAAG at 107.

Homeoboxes 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 UTRs

RDr alternate UTRs

RDr arbitrary negative direction core promoters

RDr alternate negative direction core promoters

RDr arbitrary positive direction core promoters

RDr alternate positive direction core promoters

RDr arbitrary negative direction proximal promoters

RDr alternate negative direction proximal promoters

RDr arbitrary positive direction proximal promoters

RDr alternate positive direction proximal promoters

RDr arbitrary negative direction distal promoters

RDr alternate negative direction distal promoters

RDr arbitrary positive direction distal promoters

RDr alternate positive direction distal promoters

Response element analysis and results

Main article: Complex locus A1BG and ZNF497 § Homeoboxes

The "binding of wild type and mutants TTF-1 HD to oligonucleotides containing either 5'-TAAT-3' or 5'-CAAG-3' indicate that only in the presence of the latter motif the Gln50 in TTF-1 HD is utilized for DNA recognition."[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 larger 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.

See also

References

  1. ↑ Anna Kalousová, Vladimı́r Beneš, Jan Pačes, Václav Pačes and Zbyněk Kozmik (June 1999). "DNA Binding and Transactivating Properties of the Paired and Homeobox Protein Pax4". Biochemical and Biophysical Research Communications. 259 (3): 510–518. PMID 10364449. Retrieved 6 May 2020.
  2. ↑ 2.0 2.1 2.2 G. Damante, D. Fabbro, L. Pelizari, D. Civitareale, S. Guazzi, M. Polycarpou-Schwartz, S. Cauci, F. Quadrifoglio, S. Formisano and R. Di Lauro (20 June 1994). "Sequence-specific DNA recognition by the thyroid transcription factor-1 homeodomain" (PDF). Nucleic Acids Research. 22 (15): 3075–83. doi:10.1093/nar/22.15.3075. PMID 7915030. Retrieved 6 May 2020.

External links

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