Cytoplasmic polyadenylation element gene transcriptions: Difference between revisions

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# CPEr3: 0.
# CPEr3: 0.
# CPEr4: 3, TTTTTAT at 3536, TTTTTAT at 1407, TTTTTAT at 1348.
# CPEr4: 3, TTTTTAT at 3536, TTTTTAT at 1407, TTTTTAT at 1348.
# RDr5: 0.
# CPEr5: 1, TTTTTAT at 2708.
# RDr6: 0.
# CPEr6: 0.
# RDr7: 0.
# CPEr7: 0.
# RDr8: 0.
# CPEr8: 2, TTTTTAT at 2293, TTTTTAT at 77.
# RDr9: 0.
# CPEr9: 0.
# RDr0ci: 0.
# CPEr0ci: 1, ATAAAAA at 200.
# RDr1ci: 0.
# CPEr1ci: 0.
# RDr2ci: 0.
# CPEr2ci: 0.
# RDr3ci: 0.
# CPEr3ci: 0.
# RDr4ci: 0.
# CPEr4ci: 0.
# RDr5ci: 0.
# CPEr5ci: 0.
# RDr6ci: 0.
# CPEr6ci: 0.
# RDr7ci: 0.
# CPEr7ci: 0.
# RDr8ci: 0.
# CPEr8ci: 3, ATAAAAA at 1033, ATAAAAA at 927, ATAAAAA at 708.
# RDr9ci: 0.
# CPEr9ci: 0.


===CPEr UTRs===
===CPEr arbitrary (evens) (4560-2846) UTRs===


# CPEr4: TTTTTAT at 3536.
# CPEr4: TTTTTAT at 3536.


===CPEr core promoters===
===CPEr alternate (odds) (4560-2846) UTRs===


# CPEr1: TTTTTAT at 4495.
# CPEr1: TTTTTAT at 4495.


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


# CPEr5: TTTTTAT at 2708.


===CPEr distal promoters===
===CPEr arbitrary negative direction (evens) (2596-1) distal promoters===


# CPEr0: TTTTTAT at 226.
# CPEr0: TTTTTAT at 226.
# CPEr4: TTTTTAT at 1407, TTTTTAT at 1348.
# CPEr4: TTTTTAT at 1407, TTTTTAT at 1348.
# CPEr8: TTTTTAT at 2293, TTTTTAT at 77.
# CPEr0ci: ATAAAAA at 200.
# CPEr8ci: ATAAAAA at 1033, ATAAAAA at 927, ATAAAAA at 708.


==Response element analysis and results==
===CPEr arbitrary positive direction (odds) (4050-1) distal promoters===
 
# CPEr5: TTTTTAT at 2708.
 
===CPEr alternate positive direction (evens) (4050-1) distal promoters===
 
# CPEr0: TTTTTAT at 226.
# CPEr4: TTTTTAT at 3536, TTTTTAT at 1407, TTTTTAT at 1348.
# CPEr8: TTTTTAT at 2293, TTTTTAT at 77.
# CPEr0ci: ATAAAAA at 200.
# CPEr8ci: ATAAAAA at 1033, ATAAAAA at 927, ATAAAAA at 708.
 
==Cytoplasmic polyadenylation elements analysis and results==
{{main|Complex locus A1BG and ZNF497#Cytoplasmic polyadenylation elements}}
{{main|Complex locus A1BG and ZNF497#Cytoplasmic polyadenylation elements}}
Response element (AAAAAA).<Author reference>
"Cytoplasmic polyadenylation is determined by the cytoplasmic polyadenylation element (CPE; consensus sequence UUUUUAU) that resides in mRNA 3′ untranslated regions (UTRs)."<ref name=Ivshina/>


{|class="wikitable"
{|class="wikitable"
Line 134: Line 150:
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)  
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)  
|-
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0  
| Reals || UTR || negative || 3 || 2 || 1.5 || 1.5 ± 0.5 (--2,+-1)
|-
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.1
|-
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0  
| Randoms || UTR || alternate negative || 1 || 10 || 0.1 || 0.1
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || negative || 0 || 10 || 0 || 0
| Randoms || Core || negative || 0 || 10 || 0 || 0
|-
| Randoms || Core || positive || 0 || 10 || 0 || 0
|-
|-
| Reals || Core || positive || 0 || 2 || 0 || 0  
| Reals || Core || positive || 0 || 2 || 0 || 0  
|-
| Randoms || Core || negative || 0 || 10 || 0 || 0
|-
|-
| Randoms || Core || positive || 0 || 10 || 0 || 0
| Randoms || Core || positive || 0 || 10 || 0 || 0
Line 151: Line 171:
|-
|-
| Randoms || Proximal || negative || 0 || 10 || 0 || 0  
| Randoms || Proximal || negative || 0 || 10 || 0 || 0  
|-
| Randoms || Proximal || positive || 0 || 10 || 0 || 0
|-
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
|-
| Randoms || Proximal || negative || 0 || 10 || 0 || 0
|-
|-
| Randoms || Proximal || positive || 0 || 10 || 0 || 0  
| Randoms || Proximal || positive || 0 || 10 || 0 || 0  
|-
|-
| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5
| Reals || Distal || negative || 6 || 2 || 3 || 3 ± 2 (--5,+-1)
|-
| Randoms || Distal || negative || 9 || 10 || 0.9 || 0.45 ± 0.45
|-
| Randoms || Distal || positive || 0 || 10 || 0 || 0.45 ± 0.45
|-
|-
| Randoms || Distal || negative || 1 || 10 || 0.1 || 0.05
| Reals || Distal || positive || 0 || 2 || 0 || 0  
|-
|-
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5
| Randoms || Distal || negative || 10 || 10 || 1 || 0.55 ± 0.45
|-
|-
| Randoms || Distal || positive || 0 || 10 || 0 || 0.05
| Randoms || Distal || positive || 1 || 10 || 0.1 || 0.55 ± 0.45
|}
|}


Comparison:
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.
The occurrences of real CPEs are greater than the randoms. This suggests that the real CPEs are likely active or activable.


==Acknowledgements==
==Acknowledgements==

Latest revision as of 19:08, 28 August 2023

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

"The most well-understood mechanism for controlling cytoplasmic polyadenylation is regulation of mRNAs containing the cytoplasmic polyadenylation element (CPE; consensus UUUUUAU) by CPE-binding protein (CPEB)1."[1]

Human genes

Main article: Human genes

CPEB1

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

"Cytoplasmic polyadenylation is determined by the cytoplasmic polyadenylation element (CPE; consensus sequence UUUUUAU) that resides in mRNA 3′ untranslated regions (UTRs)."[2]

"CPE: cytoplasmic polyadenylation element [consensus (U)4–5(A)1-2U]".[1]

Binding site for

Hypotheses

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

CPE samplings

Main article: Model samplings

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

For the Basic programs testing consensus sequence TTTTTAT (starting with SuccessablesCPE.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 TTTTTAT, 7, TTTTTAT at 4220, TTTTTAT at 4070, TTTTTAT at 2302, TTTTTAT at 1875, TTTTTAT at 766, TTTTTAT at 632, TTTTTAT at 489.
  2. positive strand, negative direction, looking for TTTTTAT, 1, TTTTTAT at 218.
  3. positive strand, positive direction, looking for TTTTTAT, 0.
  4. negative strand, positive direction, looking for TTTTTAT, 0.
  5. complement, negative strand, negative direction, looking for AAAAATA, 1, AAAAATA at 218.
  6. complement, positive strand, negative direction, looking for AAAAATA, 7, AAAAATA at 4220, AAAAATA at 4070, AAAAATA at 2302, AAAAATA at 1875, AAAAATA at 766, AAAAATA at 632, AAAAATA at 489.
  7. complement, positive strand, positive direction, looking for AAAAATA, 0.
  8. complement, negative strand, positive direction, looking for AAAAATA, 0.
  9. inverse complement, negative strand, negative direction, looking for ATAAAAA, 0.
  10. inverse complement, positive strand, negative direction, looking for ATAAAAA, 1, ATAAAAA at 3172.
  11. inverse complement, positive strand, positive direction, looking for ATAAAAA, 0.
  12. inverse complement, negative strand, positive direction, looking for ATAAAAA, 0.
  13. inverse negative strand, negative direction, looking for TATTTTT, 1, TATTTTT at 3172.
  14. inverse positive strand, negative direction, looking for TATTTTT, 0.
  15. inverse positive strand, positive direction, looking for TATTTTT, 0.
  16. inverse negative strand, positive direction, looking for TATTTTT, 0.

CPE UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TTTTTAT at 4220, TTTTTAT at 4070.

Positive strand, negative direction: ATAAAAA at 3172.

CPE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TTTTTAT at 2302, TTTTTAT at 1875, TTTTTAT at 766, TTTTTAT at 632, TTTTTAT at 489.

Positive strand, negative direction: TTTTTAT at 218.

Cytoplasmic polyadenylation element random dataset samplings

  1. CPEr0: 1, TTTTTAT at 226.
  2. CPEr1: 1, TTTTTAT at 4495.
  3. CPEr2: 0.
  4. CPEr3: 0.
  5. CPEr4: 3, TTTTTAT at 3536, TTTTTAT at 1407, TTTTTAT at 1348.
  6. CPEr5: 1, TTTTTAT at 2708.
  7. CPEr6: 0.
  8. CPEr7: 0.
  9. CPEr8: 2, TTTTTAT at 2293, TTTTTAT at 77.
  10. CPEr9: 0.
  11. CPEr0ci: 1, ATAAAAA at 200.
  12. CPEr1ci: 0.
  13. CPEr2ci: 0.
  14. CPEr3ci: 0.
  15. CPEr4ci: 0.
  16. CPEr5ci: 0.
  17. CPEr6ci: 0.
  18. CPEr7ci: 0.
  19. CPEr8ci: 3, ATAAAAA at 1033, ATAAAAA at 927, ATAAAAA at 708.
  20. CPEr9ci: 0.

CPEr arbitrary (evens) (4560-2846) UTRs

  1. CPEr4: TTTTTAT at 3536.

CPEr alternate (odds) (4560-2846) UTRs

  1. CPEr1: TTTTTAT at 4495.

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

  1. CPEr5: TTTTTAT at 2708.

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

  1. CPEr0: TTTTTAT at 226.
  2. CPEr4: TTTTTAT at 1407, TTTTTAT at 1348.
  3. CPEr8: TTTTTAT at 2293, TTTTTAT at 77.
  4. CPEr0ci: ATAAAAA at 200.
  5. CPEr8ci: ATAAAAA at 1033, ATAAAAA at 927, ATAAAAA at 708.

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

  1. CPEr5: TTTTTAT at 2708.

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

  1. CPEr0: TTTTTAT at 226.
  2. CPEr4: TTTTTAT at 3536, TTTTTAT at 1407, TTTTTAT at 1348.
  3. CPEr8: TTTTTAT at 2293, TTTTTAT at 77.
  4. CPEr0ci: ATAAAAA at 200.
  5. CPEr8ci: ATAAAAA at 1033, ATAAAAA at 927, ATAAAAA at 708.

Cytoplasmic polyadenylation elements analysis and results

Main article: Complex locus A1BG and ZNF497 § Cytoplasmic polyadenylation elements

"Cytoplasmic polyadenylation is determined by the cytoplasmic polyadenylation element (CPE; consensus sequence UUUUUAU) that resides in mRNA 3′ untranslated regions (UTRs)."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 0.5 (--2,+-1)
Randoms UTR arbitrary negative 1 10 0.1 0.1
Randoms UTR alternate negative 1 10 0.1 0.1
Reals Core negative 0 2 0 0
Randoms Core negative 0 10 0 0
Randoms Core positive 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core negative 0 10 0 0
Randoms Core positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal negative 0 10 0 0
Randoms Proximal positive 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal negative 0 10 0 0
Randoms Proximal positive 0 10 0 0
Reals Distal negative 6 2 3 3 ± 2 (--5,+-1)
Randoms Distal negative 9 10 0.9 0.45 ± 0.45
Randoms Distal positive 0 10 0 0.45 ± 0.45
Reals Distal positive 0 2 0 0
Randoms Distal negative 10 10 1 0.55 ± 0.45
Randoms Distal positive 1 10 0.1 0.55 ± 0.45

Comparison:

The occurrences of real CPEs are greater than the randoms. This suggests that the real CPEs are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 Andrew C Lin, Chin Lik Tan, Chien-Ling Lin, Laure Strochlic, Yi-Shuian Huang, Joel D Richter & Christine E Holt (2 March 2009). "Cytoplasmic polyadenylation and cytoplasmic polyadenylation element-dependent mRNA regulation are involved in Xenopus retinal axon development". Neural Development. 4: 8. doi:10.1186/1749-8104-4-8. |access-date= requires |url= (help)
  2. ↑ 2.0 2.1 Maria Ivshina, Paul Lasko, and Joel D. Richter (October 2014). "Cytoplasmic polyadenylation element binding proteins in development, health, and disease". Annual Review of Cell and Developmental Biology. 30: 393–415. doi:10.1146/annurev-cellbio-101011-155831. Retrieved 17 April 2021.

External links

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