Translational control sequence gene transcriptions

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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

Main article: Human genes

Gene expressions

Main article: 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

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

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

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

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.

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 SuccessablesTCS.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 (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.
  2. positive strand, negative direction, looking for (A/T)TT(A/G)TCT, 1, TTTATCT at 1731.
  3. positive strand, positive direction, looking for (A/T)TT(A/G)TCT, 3, TTTGTCT at 3179, TTTGTCT at 2652, TTTATCT at 2627.
  4. negative strand, positive direction, looking for (A/T)TT(A/G)TCT, 0.
  5. complement, negative strand, negative direction, looking for (A/T)AA(C/T)AGA, 1, AAATAGA at 1731.
  6. 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.
  7. complement, positive strand, positive direction, looking for (A/T)AA(C/T)AGA, 0.
  8. complement, negative strand, positive direction, looking for (A/T)AA(C/T)AGA, 3, AAACAGA at 3179, AAACAGA at 2652, AAATAGA at 2627.
  9. inverse complement, negative strand, negative direction, looking for AGA(C/T)AA(A/T), 1, AGATAAT at 236.
  10. inverse complement, positive strand, negative direction, looking for AGA(C/T)AA(A/T), 0.
  11. inverse complement, positive strand, positive direction, looking for AGA(C/T)AA(A/T), 1, AGACAAA at 2262.
  12. inverse complement, negative strand, positive direction, looking for AGA(C/T)AA(A/T), 0.
  13. inverse negative strand, negative direction, looking for TCT(A/G)TT(A/T), 0.
  14. inverse positive strand, negative direction, looking for TCT(A/G)TT(A/T), 1, TCTATTA at 236.
  15. inverse positive strand, positive direction, looking for TCT(A/G)TT(A/T), 0.
  16. inverse negative strand, positive direction, looking for TCT(A/G)TT(A/T), 1, TCTGTTT at 2262.

TCS (4560-2846) UTRs

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

TCS negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATTATCT at 1710, TTTGTCT at 168, ATTGTCT at 13.
  2. Negative strand, negative direction: AGATAAT at 236.
  3. Positive strand, negative direction: TTTATCT at 1731.

TCS positive direction (4050-1) distal promoters

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

TCS random dataset samplings

  1. TCSr0: 1, ATTATCT at 4102.
  2. TCSr1: 2, TTTATCT at 3099, TTTGTCT at 7.
  3. TCSr2: 2, TTTATCT at 3576, TTTGTCT at 3099.
  4. TCSr3: 1, TTTATCT at 771.
  5. TCSr4: 4, ATTGTCT at 3797, TTTATCT at 1679, ATTGTCT at 1353, ATTATCT at 167.
  6. TCSr5: 1, TTTGTCT at 2173.
  7. TCSr6: 1, ATTGTCT at 1985.
  8. TCSr7: 0.
  9. TCSr8: 1, ATTATCT at 1366.
  10. TCSr9: 1, TTTGTCT at 24.
  11. TCSr0ci: 2, AGACAAT at 4236, AGACAAA at 2332.
  12. TCSr1ci: 1, AGATAAA at 164.
  13. TCSr2ci: 1, AGATAAT at 3945.
  14. TCSr3ci: 3, AGACAAT at 3487, AGATAAT at 2775, AGACAAT at 2743.
  15. TCSr4ci: 0.
  16. TCSr5ci: 1, AGATAAT at 1144.
  17. TCSr6ci: 1, AGATAAT at 2001.
  18. TCSr7ci: 0.
  19. TCSr8ci: 1, AGATAAT at 3579.
  20. TCSr9ci: 1, AGATAAT at 4169.

TCSr arbitrary (evens) (4560-2846) UTRs

  1. TCSr0: ATTATCT at 4102.
  2. TCSr2: TTTATCT at 3576, TTTGTCT at 3099.
  3. TCSr4: ATTGTCT at 3797.
  4. TCSr0ci: AGACAAT at 4236.
  5. TCSr2ci: AGATAAT at 3945.
  6. TCSr8ci: AGATAAT at 3579.

TCSr alternate (odds) (4560-2846) UTRs

  1. TCSr1: TTTATCT at 3099.
  2. TCSr3ci: AGACAAT at 3487.
  3. TCSr9ci: AGATAAT at 4169.

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

  1. TCSr3ci: AGATAAT at 2775, AGACAAT at 2743.

TCSr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. TCSr9ci: AGATAAT at 4169.

TCSr alternate positive direction (evens) (4265-4050) proximal promoters

  1. TCSr0: ATTATCT at 4102.
  2. TCSr0ci: AGACAAT at 4236.

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

  1. TCSr4: TTTATCT at 1679, ATTGTCT at 1353, ATTATCT at 167.
  2. TCSr6: ATTGTCT at 1985.
  3. TCSr8: ATTATCT at 1366.
  4. TCSr0ci: AGACAAA at 2332.
  5. TCSr6ci: AGATAAT at 2001.

TCSr alternate negative direction (odds) (2596-1) distal promoters

  1. TCSr1: TTTGTCT at 7.
  2. TCSr3: TTTATCT at 771.
  3. TCSr5: TTTGTCT at 2173.
  4. TCSr1ci: AGATAAA at 164.
  5. TCSr5ci: AGATAAT at 1144.

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

  1. TCSr1: TTTATCT at 3099, TTTGTCT at 7.
  2. TCSr3: TTTATCT at 771.
  3. TCSr5: TTTGTCT at 2173.
  4. TCSr1ci: AGATAAA at 164.
  5. TCSr3ci: AGACAAT at 3487, AGATAAT at 2775, AGACAAT at 2743.
  6. TCSr5ci: AGATAAT at 1144.

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

  1. TCSr0: ATTATCT at 4102.
  2. TCSr2: TTTATCT at 3576, TTTGTCT at 3099.
  3. TCSr4: ATTGTCT at 3797, TTTATCT at 1679, ATTGTCT at 1353, ATTATCT at 167.
  4. TCSr6: ATTGTCT at 1985.
  5. TCSr8: ATTATCT at 1366.
  6. TCSr0ci: AGACAAA at 2332.
  7. TCSr2ci: AGATAAT at 3945.
  8. TCSr6ci: AGATAAT at 2001.
  9. TCSr8ci: AGATAAT at 3579.

TCS analysis and results

Main article: Complex locus A1BG and ZNF497 § TCSs

(A/T)TT(A/G)TCT, based on "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]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 1.5 (--3,+-0)
Randoms UTR arbitrary negative 7 10 0.7 0.5
Randoms UTR alternate negative 3 10 0.3 0.5
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 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.15
Randoms Proximal alternate positive 2 10 0.2 0.15
Reals Distal negative 5 2 2.5 2.5 ± 1.5 (+-1,--4)
Randoms Distal arbitrary negative 7 10 0.7 0.6
Randoms Distal alternate negative 5 10 0.5 0.6
Reals Distal positive 4 2 2 2 ± 2 (-+0,++4)
Randoms Distal arbitrary positive 9 10 0.9 1.1
Randoms Distal alternate positive 13 10 1.3 1.1

Comparison:

The occurrences of real TCS UTRs and distals are greater than the randoms. This suggests that the real TCSs 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 1.2 1.3 1.4 1.5 1.6 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

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