Translational control sequence gene transcriptions: Difference between revisions

Revision as of 15:23, 20 April 2021

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

"Maternal mRNAs are translationally regulated during early development. Zar1 and its closely related homolog, Zar2, are both crucial in early development. Xenopus laevis Zygote arrest 2 (Zar2) binds to the Translational Control Sequence (TCS) in maternal mRNAs and regulates translation."^[1]

Human genes

Gene expressions

"The 3′ UTR of Wee1 mRNA contains two cytoplasmic polyadenylation elements (CPEs) and two Translational Control Sequences (TCSs) that regulate translation [17, 20]. The TCSs repress translation in immature oocytes and during maturation they confer cytoplasmic polyadenylation to the mRNA and stimulate translation. The function of the TCS is mediated by its trans-acting factor Zar2. Like the TCS, Zar2 represses translation in immature oocytes and this repression is relieved in maturing oocytes [9]. Mos is another developmentally important protein that is encoded by a maternal mRNA. The Mos protein is absent in immature oocytes and starts to be synthesized shortly after re-entry into the meiotic cell cycle. Appropriate translational control of the Mos mRNA is crucial for timely oocyte maturation and prevention of premature mitotic cell cycles [21–23]. The Mos 3′ UTR contains a CPE, a Musashi binding element (MBE), and also a TCS [9, 12, 24–26]."^[1]

Interactions

Consensus sequences

Wee1 UTR probe found TCS1 AUUAUCU and TCS2 AUUGUCU.^[1]

Mos probe found TCS UUUGUCU.^[1] These suggest a consensus sequence of (A/U)UU(A/G)UCU, apparently excluding UUUAUCU.^[1] "Putative TCSs have been identified in Wee1, PCM-1 and Mos 3′ UTRs. The TCSs are slightly different: AUUAUCU (Wee1 TCS1), AUUGUCU (Wee1 TCS2) and UUUGUCU (Mos and PCM-1 TCS) [20]".^[1]

Binding site for

Enhancer activity

Promoter occurrences

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.

TCS samplings

Copying a responsive elements consensus sequence (A/T)TT(A/G)TCT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or four between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/T)TT(A/G)TCT (starting with SuccessablesAAA.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 (A/T)TT(A/G)TCT, 6, TTTGTCT at 4518, ATTATCT at 4079, TTTGTCT at 2878, ATTATCT at 1710, TTTGTCT at 168, ATTGTCT at 13.
positive strand, negative direction, looking for (A/T)TT(A/G)TCT, 1, TTTATCT at 1731.
positive strand, positive direction, looking for (A/T)TT(A/G)TCT, 3, TTTGTCT at 3179, TTTGTCT at 2652, TTTATCT at 2627.
negative strand, positive direction, looking for (A/T)TT(A/G)TCT, 0.
complement, negative strand, negative direction, looking for (A/T)AA(C/T)AGA, 1, AAATAGA at 1731.
complement, positive strand, negative direction, looking for (A/T)AA(C/T)AGA, 6, AAACAGA at 4518, TAATAGA at 4079, AAACAGA at 2878, TAATAGA at 1710, AAACAGA at 168, TAACAGA at 13.
complement, positive strand, positive direction, looking for (A/T)AA(C/T)AGA, 0.
complement, negative strand, positive direction, looking for (A/T)AA(C/T)AGA, 3, AAACAGA at 3179, AAACAGA at 2652, AAATAGA at 2627.
inverse complement, negative strand, negative direction, looking for AGA(C/T)AA(A/T), 1, AGATAAT at 236.
inverse complement, positive strand, negative direction, looking for AGA(C/T)AA(A/T), 0.
inverse complement, positive strand, positive direction, looking for AGA(C/T)AA(A/T), 1, AGACAAA at 2262.
inverse complement, negative strand, positive direction, looking for AGA(C/T)AA(A/T), 0.
inverse negative strand, negative direction, looking for TCT(A/G)TT(A/T), 0.
inverse positive strand, negative direction, looking for TCT(A/G)TT(A/T), 1, TCTATTA at 236.
inverse positive strand, positive direction, looking for TCT(A/G)TT(A/T), 0.
inverse negative strand, positive direction, looking for TCT(A/G)TT(A/T), 1, TCTGTTT at 2262.

TCS UTRs

Negative strand, negative direction: TTTGTCT at 4518, ATTATCT at 4079, TTTGTCT at 2878.

TCS distal promoters

Negative strand, negative direction: ATTATCT at 1710, AGATAAT at 236, TTTGTCT at 168, ATTGTCT at 13.

Positive strand, negative direction: TTTATCT at 1731.

Positive strand, positive direction: TTTGTCT at 3179, TTTGTCT at 2652, TTTATCT at 2627, AGACAAA at 2262.

Acknowledgements

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

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 Tomomi M. Yamamoto, Jonathan M. Cook, Cassandra V. Kotter, Terry Khat, Kevin D. Silva, Michael Ferreyros, Justin W. Holt, Jefferson D. Knight, and Amanda Charlesworth (October 2013). "Zar1 represses translation in Xenopus oocytes and binds to the TCS in maternal mRNAs with different characteristics than Zar2". Biochim Biophys Acta. 1829 (10): 1034–46. doi:10.1016/j.bbagrm.2013.06.001. PMID 23827238. Retrieved 19 April 2021.

External links

[Yamamoto-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 Tomomi M. Yamamoto, Jonathan M. Cook, Cassandra V. Kotter, Terry Khat, Kevin D. Silva, Michael Ferreyros, Justin W. Holt, Jefferson D. Knight, and Amanda Charlesworth (October 2013). "Zar1 represses translation in Xenopus oocytes and binds to the TCS in maternal mRNAs with different characteristics than Zar2". Biochim Biophys Acta. 1829 (10): 1034–46. doi:10.1016/j.bbagrm.2013.06.001. PMID 23827238. Retrieved 19 April 2021.

[1]

@@ Line 52: / Line 52: @@
 For the Basic programs testing consensus sequence (A/T)TT(A/G)TCT (starting with SuccessablesAAA.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 (A/T)TT(A/G)TCT, 6, TTTGTCT at 4518, ATTATCT at 4079, TTTGTCT at 2878, ATTATCT at 1710, TTTGTCT at 168, ATTGTCT at 13.
-# positive strand, negative direction, looking for AAAAAAAA, 0.
+# positive strand, negative direction, looking for (A/T)TT(A/G)TCT, 1, TTTATCT at 1731.
-# positive strand, positive direction, looking for AAAAAAAA, 0.
+# positive strand, positive direction, looking for (A/T)TT(A/G)TCT, 3, TTTGTCT at 3179, TTTGTCT at 2652, TTTATCT at 2627.
-# negative strand, positive direction, looking for AAAAAAAA, 0.
+# negative strand, positive direction, looking for (A/T)TT(A/G)TCT, 0.
-# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# complement, negative strand, negative direction, looking for (A/T)AA(C/T)AGA, 1, AAATAGA at 1731.
 # complement, positive strand, negative direction, looking for (A/T)AA(C/T)AGA, 6, AAACAGA at 4518, TAATAGA at 4079, AAACAGA at 2878, TAATAGA at 1710, AAACAGA at 168, TAACAGA at 13.
-# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# complement, positive strand, positive direction, looking for (A/T)AA(C/T)AGA, 0.
-# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# complement, negative strand, positive direction, looking for (A/T)AA(C/T)AGA, 3, AAACAGA at 3179, AAACAGA at 2652, AAATAGA at 2627.
-# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, negative direction, looking for AGA(C/T)AA(A/T), 1, AGATAAT at 236.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for AGA(C/T)AA(A/T), 0.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction, looking for AGA(C/T)AA(A/T), 1, AGACAAA at 2262.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction, looking for AGA(C/T)AA(A/T), 0.
-# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
+# inverse negative strand, negative direction, looking for TCT(A/G)TT(A/T), 0.
-# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
+# inverse positive strand, negative direction, looking for TCT(A/G)TT(A/T), 1, TCTATTA at 236.
-# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
+# inverse positive strand, positive direction, looking for TCT(A/G)TT(A/T), 0.
-# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
+# inverse negative strand, positive direction, looking for TCT(A/G)TT(A/T), 1, TCTGTTT at 2262.
 ===TCS UTRs===
@@ Line 72: / Line 72: @@
 Negative strand, negative direction: TTTGTCT at 4518, ATTATCT at 4079, TTTGTCT at 2878.
-===TCS core promoters===
+===TCS distal promoters===
-{{main|Core promoter gene transcriptions}}
+{{main|Distal promoter gene transcriptions}}
+Negative strand, negative direction: ATTATCT at 1710, AGATAAT at 236, TTTGTCT at 168, ATTGTCT at 13.
-===TCS proximal promoters===
+Positive strand, negative direction: TTTATCT at 1731.
-{{main|Proximal promoter gene transcriptions}}
-===TCS distal promoters===
+Positive strand, positive direction: TTTGTCT at 3179, TTTGTCT at 2652, TTTATCT at 2627, AGACAAA at 2262.
-{{main|Distal promoter gene transcriptions}}
-Negative strand, negative direction: ATTATCT at 1710, TTTGTCT at 168, ATTGTCT at 13.
 ==Acknowledgements==

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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions 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 Mcm1 regulatory factor 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 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 Sip4p gene transcriptions Smp1p gene transcriptions 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 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