Cytoplasmic polyadenylation element gene transcriptions: Difference between revisions

Revision as of 07:49, 16 April 2022

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.

Cytoplasmic polyadenylation element random dataset samplings

CPEr0: 1, TTTTTAT at 226.
CPEr1: 1, TTTTTAT at 4495.
CPEr2: 0.
CPEr3: 0.
CPEr4: 3, TTTTTAT at 3536, TTTTTAT at 1407, TTTTTAT at 1348.
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.

CPEr UTRs

CPEr4: TTTTTAT at 3536.

CPEr core promoters

CPEr1: TTTTTAT at 4495.

RDr proximal promoters

CPEr distal promoters

CPEr0: TTTTTAT at 226.
CPEr4: TTTTTAT at 1407, TTTTTAT at 1348.

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]

@@ Line 87: / Line 87: @@
 Positive strand, negative direction: TTTTTAT at 218.
-==Random dataset samplings==
+==Cytoplasmic polyadenylation element random dataset samplings==
-# RDr0: 0.
+# CPEr0: 1, TTTTTAT at 226.
-# RDr1: 0.
+# CPEr1: 1, TTTTTAT at 4495.
-# RDr2: 0.
+# CPEr2: 0.
-# RDr3: 0.
+# CPEr3: 0.
-# RDr4: 0.
+# CPEr4: 3, TTTTTAT at 3536, TTTTTAT at 1407, TTTTTAT at 1348.
 # RDr5: 0.
 # RDr6: 0.
@@ Line 110: / Line 110: @@
 # RDr9ci: 0.
-===RDr UTRs===
+===CPEr UTRs===
-{{main|UTR promoter gene transcriptions}}
-===RDr core promoters===
+# CPEr4: TTTTTAT at 3536.
-{{main|Core promoter gene transcriptions}}
+===CPEr core promoters===
+# CPEr1: TTTTTAT at 4495.
 ===RDr proximal promoters===
-{{main|Proximal promoter gene transcriptions}}
-===RDr distal promoters===
-{{main|Distal promoter gene transcriptions}}
+===CPEr distal promoters===
+# CPEr0: TTTTTAT at 226.
+# CPEr4: TTTTTAT at 1407, TTTTTAT at 1348.
 ==Response element analysis and results==

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transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions M-CAT boxes Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Nanos/Pumilio response element 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 Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Shue boxes Sip4p gene transcriptions Smp1p gene transcriptions Sp1 (Berberich) elements Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene 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 actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family 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 Tryptophan residue 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