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. 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

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 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 5 2 2.5 2.5 ± 2.5 (--0,+-5)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 1 2 0.5 0.5
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real PREs are greater 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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