Polycomb response element gene transcriptions

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

"Recruitment of Drosophila melanogaster [Polycomb-group] PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs)."[1]

Only "Pleiohomeotic (Pho) is present at all strong PREs."[1]

"The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2."[1]

"PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites".[1]

Human genes

Consensus sequences

"Two predicted [Pleiohomeotic] Pho-Phol binding sites, CGCCATTT, that closely resemble the extended Pho-Phol consensus sequence, CGCCAT(T/A)TT (Kahn et al. 2014), are located within PRE1.1 [...]."[1]

"Only one additional site resembling the Pho-Phol core consensus sequence (GCCAT) is near region 4, 137-bp downstream from the TSS. The nearest upstream GCCAT sequences are ∼1 kb from the TSS (−968 and −1049)."[1]

Core samplings

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

For the Basic programs testing consensus sequence GCCAT (starting with SuccessablesPRE1.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 GCCAT, 0.
  2. positive strand, negative direction, looking for GCCAT, 3, GCCAT at 3685, GCCAT at 3283, GCCAT at 38.
  3. positive strand, positive direction, looking for GCCAT, 0.
  4. negative strand, positive direction, looking for GCCAT, 0.
  5. complement, negative strand, negative direction, looking for CGGTA, 3, CGGTA at 3685, CGGTA at 3283, CGGTA at 38.
  6. complement, positive strand, negative direction, looking for CGGTA, 0.
  7. complement, positive strand, positive direction, looking for CGGTA, 0.
  8. complement, negative strand, positive direction, looking for CGGTA, 0.
  9. inverse complement, negative strand, negative direction, looking for ATGGC, 0.
  10. inverse complement, positive strand, negative direction, looking for ATGGC, 7, ATGGC at 3629, ATGGC at 3005, ATGGC at 2907, ATGGC at 2153, ATGGC at 1949, ATGGC at 1743, ATGGC at 954.
  11. inverse complement, positive strand, positive direction, looking for ATGGC, 0.
  12. inverse complement, negative strand, positive direction, looking for ATGGC, 1, ATGGC at 2160.
  13. inverse negative strand, negative direction, looking for TACCG, 7, TACCG at 3629, TACCG at 3005, TACCG at 2907, TACCG at 2153, TACCG at 1949, TACCG at 1743, TACCG at 954.
  14. inverse positive strand, negative direction, looking for TACCG, 0.
  15. inverse positive strand, positive direction, looking for TACCG, 1, TACCG at 2160.
  16. inverse negative strand, positive direction, looking for TACCG, 0.

PRE (4560-2846) UTRs

  1. Positive strand, negative direction: GCCAT at 3685, GCCAT at 3283.
  2. Positive strand, negative direction: ATGGC at 3629, ATGGC at 3005, ATGGC at 2907.

PRE negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: GCCAT at 38.
  2. Positive strand, negative direction: ATGGC at 2153, ATGGC at 1949, ATGGC at 1743, ATGGC at 954.

PRE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: ATGGC at 2160.

PRE random dataset samplings

  1. PREr0: 6, GCCAT at 4000, GCCAT at 3795, GCCAT at 3302, GCCAT at 2388, GCCAT at 1183, GCCAT at 775.
  2. PREr1: 5, GCCAT at 3406, GCCAT at 1907, GCCAT at 1675, GCCAT at 1557, GCCAT at 257.
  3. PREr2: 5, GCCAT at 4541, GCCAT at 2580, GCCAT at 1470, GCCAT at 790, GCCAT at 207.
  4. PREr3: 4, GCCAT at 3452, GCCAT at 1767, GCCAT at 1458, GCCAT at 400.
  5. PREr4: 10, GCCAT at 3657, GCCAT at 3573, GCCAT at 3024, GCCAT at 2221, GCCAT at 2143, GCCAT at 2049, GCCAT at 1549, GCCAT at 1094, GCCAT at 867, GCCAT at 462.
  6. PREr5: 4, GCCAT at 2802, GCCAT at 1201, GCCAT at 291, GCCAT at 85.
  7. PREr6: 5, GCCAT at 3996, GCCAT at 3725, GCCAT at 2291, GCCAT at 2202, GCCAT at 459.
  8. PREr7: 4, GCCAT at 3064, GCCAT at 2443, GCCAT at 2269, GCCAT at 410.
  9. PREr8: 2, GCCAT at 4020, GCCAT at 2460.
  10. PREr9: 4, GCCAT at 3345, GCCAT at 1560, GCCAT at 363, GCCAT at 77.
  11. PREr0ci: 3, ATGGC at 4239, ATGGC at 1219, ATGGC at 486.
  12. PREr1ci: 4, ATGGC at 3940, ATGGC at 2103, ATGGC at 2001, ATGGC at 1283.
  13. PREr2ci: 3, ATGGC at 3639, ATGGC at 772, ATGGC at 429.
  14. PREr3ci: 4, ATGGC at 3950, ATGGC at 3370, ATGGC at 2875, ATGGC at 2694.
  15. PREr4ci: 9, ATGGC at 4204, ATGGC at 3744, ATGGC at 3265, ATGGC at 1904, ATGGC at 1365, ATGGC at 1076, ATGGC at 870, ATGGC at 637, ATGGC at 524.
  16. PREr5ci: 4, ATGGC at 3787, ATGGC at 3062, ATGGC at 3053, ATGGC at 243.
  17. PREr6ci: 7, ATGGC at 3544, ATGGC at 2558, ATGGC at 1958, ATGGC at 1894, ATGGC at 1854, ATGGC at 251, ATGGC at 74.
  18. PREr7ci: 1, ATGGC at 3389.
  19. PREr8ci: 6, ATGGC at 3257, ATGGC at 3107, ATGGC at 2423, ATGGC at 1781, ATGGC at 640, ATGGC at 159.
  20. PREr9ci: 5, ATGGC at 4343, ATGGC at 3788, ATGGC at 1724, ATGGC at 443, ATGGC at 333.

PREr arbitrary (evens) (4560-2846) UTRs

  1. PREr0: GCCAT at 4000, GCCAT at 3795, GCCAT at 3302.
  2. PREr2: GCCAT at 4541.
  3. PREr4: GCCAT at 3657, GCCAT at 3573, GCCAT at 3024.
  4. PREr6: GCCAT at 3996, GCCAT at 3725.
  5. PREr8: GCCAT at 4020.
  6. PREr0ci: ATGGC at 4239.
  7. PREr2ci: ATGGC at 3639.
  8. PREr4ci: ATGGC at 4204, ATGGC at 3744, ATGGC at 3265, ATGGC at 1904, ATGGC at 1365, ATGGC at 1076, ATGGC at 870, ATGGC at 637, ATGGC at 524.
  9. PREr6ci: ATGGC at 3544.
  10. PREr8ci: ATGGC at 3257, ATGGC at 3107.

PREr alternate (odds) (4560-2846) UTRs

  1. PREr1: GCCAT at 3406.
  2. PREr3: GCCAT at 3452.
  3. PREr7: GCCAT at 3064.
  4. PREr9: GCCAT at 3345.
  5. PREr1ci: ATGGC at 3940.
  6. PREr3ci: ATGGC at 3950, ATGGC at 3370, ATGGC at 2875.
  7. PREr5ci: ATGGC at 3787, ATGGC at 3062, ATGGC at 3053.
  8. PREr7ci: ATGGC at 3389.
  9. PREr9ci: ATGGC at 4343, ATGGC at 3788.

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

  1. PREr9ci: ATGGC at 4343.

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

  1. PREr5: GCCAT at 2802.
  2. PREr3ci: ATGGC at 2694.

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

  1. PREr0ci: ATGGC at 4239.
  2. PREr4ci: ATGGC at 4204.

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

  1. PREr0: GCCAT at 2388, GCCAT at 1183, GCCAT at 775.
  2. PREr2: GCCAT at 2580, GCCAT at 1470, GCCAT at 790, GCCAT at 207.
  3. PREr4: GCCAT at 2221, GCCAT at 2143, GCCAT at 2049, GCCAT at 1549, GCCAT at 1094, GCCAT at 867, GCCAT at 462.
  4. PREr6: GCCAT at 2291, GCCAT at 2202, GCCAT at 459.
  5. PREr0ci: ATGGC at 1219, ATGGC at 486.
  6. PREr2ci: ATGGC at 772, ATGGC at 429.
  7. PREr4ci: ATGGC at 1904, ATGGC at 1365, ATGGC at 1076, ATGGC at 870, ATGGC at 637, ATGGC at 524.
  8. PREr6ci: ATGGC at 2558, ATGGC at 1958, ATGGC at 1894, ATGGC at 1854, ATGGC at 251, ATGGC at 74.
  9. PREr8ci: ATGGC at 2423, ATGGC at 1781, ATGGC at 640, ATGGC at 159.

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

  1. PREr1: GCCAT at 1907, GCCAT at 1675, GCCAT at 1557, GCCAT at 257.
  2. PREr3: GCCAT at 1767, GCCAT at 1458, GCCAT at 400.
  3. PREr5: GCCAT at 1201, GCCAT at 291, GCCAT at 85.
  4. PREr7: GCCAT at 2443, GCCAT at 2269, GCCAT at 410.
  5. PREr9: GCCAT at 1560, GCCAT at 363, GCCAT at 77.
  6. PREr1ci: ATGGC at 2103, ATGGC at 2001, ATGGC at 1283.
  7. PREr5ci: ATGGC at 243.
  8. PREr9ci: ATGGC at 1724, ATGGC at 443, ATGGC at 333.

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

  1. PREr1: GCCAT at 3406, GCCAT at 1907, GCCAT at 1675, GCCAT at 1557, GCCAT at 257.
  2. PREr3: GCCAT at 3452, GCCAT at 1767, GCCAT at 1458, GCCAT at 400.
  3. PREr5: GCCAT at 2802, GCCAT at 1201, GCCAT at 291, GCCAT at 85.
  4. PREr7: GCCAT at 3064, GCCAT at 2443, GCCAT at 2269, GCCAT at 410.
  5. PREr9: GCCAT at 3345, GCCAT at 1560, GCCAT at 363, GCCAT at 77.
  6. PREr1ci: ATGGC at 3940, ATGGC at 2103, ATGGC at 2001, ATGGC at 1283.
  7. PREr3ci: ATGGC at 3950, ATGGC at 3370, ATGGC at 2875, ATGGC at 2694.
  8. PREr5ci: ATGGC at 3787, ATGGC at 3062, ATGGC at 3053, ATGGC at 243.
  9. PREr7ci: ATGGC at 3389.
  10. PREr9ci: ATGGC at 3788, ATGGC at 1724, ATGGC at 443, ATGGC at 333.

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

  1. PREr0: GCCAT at 4000, GCCAT at 3795, GCCAT at 3302, GCCAT at 2388, GCCAT at 1183, GCCAT at 775.
  2. PREr2: GCCAT at 2580, GCCAT at 1470, GCCAT at 790, GCCAT at 207.
  3. PREr4: GCCAT at 3657, GCCAT at 3573, GCCAT at 3024, GCCAT at 2221, GCCAT at 2143, GCCAT at 2049, GCCAT at 1549, GCCAT at 1094, GCCAT at 867, GCCAT at 462.
  4. PREr6: GCCAT at 3996, GCCAT at 3725, GCCAT at 2291, GCCAT at 2202, GCCAT at 459.
  5. PREr0ci: ATGGC at 1219, ATGGC at 486.
  6. PREr2ci: ATGGC at 3639, ATGGC at 772, ATGGC at 429.
  7. PREr4ci: ATGGC at 3744, ATGGC at 3265, ATGGC at 1904, ATGGC at 1365, ATGGC at 1076, ATGGC at 870, ATGGC at 637, ATGGC at 524.
  8. PREr6ci: ATGGC at 3544, ATGGC at 2558, ATGGC at 1958, ATGGC at 1894, ATGGC at 1854, ATGGC at 251, ATGGC at 74.
  9. PREr8ci: ATGGC at 3257, ATGGC at 3107, ATGGC at 2423, ATGGC at 1781, ATGGC at 640, ATGGC at 159.

PRE analysis and results

Main article: Complex locus A1BG and ZNF497 § PREs

"Only one additional site resembling the Pho-Phol core consensus sequence (GCCAT) is near region 4, 137-bp downstream from the TSS. The nearest upstream GCCAT sequences are ∼1 kb from the TSS (−968 and −1049)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5 ± 2.5 (--0,+-5)
Randoms UTR arbitrary negative 26 10 2.6 2.0
Randoms UTR alternate negative 14 10 1.4 2.0
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 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
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 0.1
Randoms Proximal alternate positive 2 10 0.2 0.1
Reals Distal negative 5 2 2.5 2.5 ± 2.5 (--0,+-5)
Randoms Distal arbitrary negative 37 10 3.7 3.0
Randoms Distal alternate negative 23 10 2.3 3.0
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Distal arbitrary positive 38 10 3.8 4.45
Randoms Distal alternate positive 51 10 5.1 4.45

Comparison:

The occurrences of real PRE UTRs and negative distals are greater than the randoms, the positive distals are less than the randoms. This suggests that the real PREs are likely active or activable.

Extended Pho-Phol samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CGCCAT(A/T)TT 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 CGCCAT(A/T)TT (starting with SuccessablesPhol.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 CGCCAT(A/T)TT, 0.
  2. positive strand, negative direction, looking for CGCCAT(A/T)TT, 0.
  3. positive strand, positive direction, looking for CGCCAT(A/T)TT, 0.
  4. negative strand, positive direction, looking for CGCCAT(A/T)TT, 0.
  5. complement, negative strand, negative direction, looking for GCGGTA(A/T)AA, 0.
  6. complement, positive strand, negative direction, looking for GCGGTA(A/T)AA, 0.
  7. complement, positive strand, positive direction, looking for GCGGTA(A/T)AA, 0.
  8. complement, negative strand, positive direction, looking for GCGGTA(A/T)AA, 0.
  9. inverse complement, negative strand, negative direction, looking for AA(A/T)ATGGCG, 0.
  10. inverse complement, positive strand, negative direction, looking for AA(A/T)ATGGCG, 0.
  11. inverse complement, positive strand, positive direction, looking for AA(A/T)ATGGCG, 0.
  12. inverse complement, negative strand, positive direction, looking for AA(A/T)ATGGCG, 0.
  13. inverse negative strand, negative direction, looking for TT(A/T)TACCGC, 0.
  14. inverse positive strand, negative direction, looking for TT(A/T)TACCGC, 0.
  15. inverse positive strand, positive direction, looking for TT(A/T)TACCGC, 0.
  16. inverse negative strand, positive direction, looking for TT(A/T)TACCGC, 0.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Elnaz Ghotbi, Kristina Lackey, Vicki Wong, Katie T. Thompson, Evan G. Caston, Minna Haddadi, Judith Benes and Richard S. Jones (1 March 2020). "Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene" (PDF). Genetics. 214 (3): 623–634. doi:10.1534/genetics.119.302981. PMID 31919108. Retrieved 7 September 2020.

External links


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