Cytoplasmic polyadenylation element gene transcriptions

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

CPEB1

Gene expressions

Interactions

Consensus sequences

"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

A1BG has no regulatory elements in either promoter.
A1BG is not transcribed by a regulatory element.
No regulatory element participates in the transcription of A1BG.

CPE 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:

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.
positive strand, negative direction, looking for TTTTTAT, 1, TTTTTAT at 218.
positive strand, positive direction, looking for TTTTTAT, 0.
negative strand, positive direction, looking for TTTTTAT, 0.
complement, negative strand, negative direction, looking for AAAAATA, 1, AAAAATA at 218.
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.
complement, positive strand, positive direction, looking for AAAAATA, 0.
complement, negative strand, positive direction, looking for AAAAATA, 0.
inverse complement, negative strand, negative direction, looking for ATAAAAA, 0.
inverse complement, positive strand, negative direction, looking for ATAAAAA, 1, ATAAAAA at 3172.
inverse complement, positive strand, positive direction, looking for ATAAAAA, 0.
inverse complement, negative strand, positive direction, looking for ATAAAAA, 0.
inverse negative strand, negative direction, looking for TATTTTT, 1, TATTTTT at 3172.
inverse positive strand, negative direction, looking for TATTTTT, 0.
inverse positive strand, positive direction, looking for TATTTTT, 0.
inverse negative strand, positive direction, looking for TATTTTT, 0.

CPE UTRs

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

Positive strand, negative direction: ATAAAAA at 3172.

CPE distal promoters

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.

Random dataset samplings

RDr0: 0.
RDr1: 0.
RDr2: 0.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 0.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

Response element analysis and results

Response element (AAAAAA).<Author reference>

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	negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	negative	0	10	0	0
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	positive	0	10	0	0
Reals	Distal	negative	1	2	0.5	0.5
Randoms	Distal	negative	1	10	0.1	0.05
Reals	Distal	positive	1	2	0.5	0.5
Randoms	Distal	positive	0	10	0	0.05

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.

References

↑ ^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)
↑ 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

[Lin-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)

[Ivshina-2] 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.

[1]

[2]

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions