UTR promoter gene transcriptions

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

"The 3′ UTR of eEF1A contains a putative [Nanos/Pumilio response element (PRE)] PRE sequence (TGTAAAT), suggesting that it is a Nanos/Pumilio target."[1]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

3' UTR binding sites

"Wilms’ tumor 1 (WT1) is essential for the development and homeostasis of multiple mesodermal tissues. Despite evidence for post-transcriptional roles, no endogenous WT1 target RNAs exist. Using RNA immunoprecipitation and UV cross-linking, we show that WT1 binds preferentially to 3′ untranslated regions (UTRs) of developmental targets."[2]

Recurrent "kmers occurring in 3′ UTRs were identified in the single-read FLASH data. The polyadenylation signal [ ATA box ] AATAAA had the highest Z-score, and three similar sequences were also found in the top 10 kmers. However, on correlation with down-regulation, the TGTAAAT motif was found by MEME (Bailey and Elkan 1994) at 294 sites (E-value 2.7 × 10−562), which is different from the motif identified by RIP-seq [...]."[2]

5' UTR binding sites

"We identified high-confidence transcription factor binding sites specific for AP-1, proximal to our putative TSSs within the 5′ UTR, consistent with published reports of its role in Gja1 expression (data not shown; Echetebu et al., 1999, Geimonen et al., 1998, Geimonen et al., 1996, Hernandez et al., 2006, Tacheau et al., 2008)."[3]

Complement copies

Main article: Complement copy gene transcriptions

Inverse copies

Main article: Inverse copy gene transcriptions

Complement-inverse copies

Main article: Complement-inverse copy gene transcriptions

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.

TGTAAAT samplings

Main article: Model samplings

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

For the Basic programs testing consensus sequence TGTAAAT (starting with SuccessablesTGT.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 TGTAAAT, 1, TGTAAAT at 4535.
  2. positive strand, negative direction, looking for TGTAAAT, 0.
  3. positive strand, positive direction, looking for TGTAAAT, 0.
  4. negative strand, positive direction, looking for TGTAAAT, 0.
  5. complement, negative strand, negative direction, looking for ACATTTA, 0.
  6. complement, positive strand, negative direction, looking for ACATTTA, 1, ACATTTA at 4535.
  7. complement, positive strand, positive direction, looking for ACATTTA, 0.
  8. complement, negative strand, positive direction, looking for ACATTTA, 0.
  9. inverse complement, negative strand, negative direction, looking for ATTTACA, 0.
  10. inverse complement, positive strand, negative direction, looking for ATTTACA, 0.
  11. inverse complement, positive strand, positive direction, looking for ATTTACA, 0.
  12. inverse complement, negative strand, positive direction, looking for ATTTACA, 0.
  13. inverse negative strand, negative direction, looking for TAAATGT, 0.
  14. inverse positive strand, negative direction, looking for TAAATGT, 0.
  15. inverse positive strand, positive direction, looking for TAAATGT, 0.
  16. inverse negative strand, positive direction, looking for TAAATGT, 0.

TGT UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction, looking for TGTAAAT, 1, TGTAAAT at 4535.

TGT random dataset samplings

  1. TGTr0: 0.
  2. TGTr1: 0.
  3. TGTr2: 0.
  4. TGTr3: 0.
  5. TGTr4: 1, TGTAAAT at 4184.
  6. TGTr5: 1, TGTAAAT at 3715.
  7. TGTr6: 0.
  8. TGTr7: 0.
  9. TGTr8: 2, TGTAAAT at 2947, TGTAAAT at 2502.
  10. TGTr9: 0.
  11. TGTr0ci: 0.
  12. TGTr1ci: 0.
  13. TGTr2ci: 1, ATTTACA at 3619.
  14. TGTr3ci: 0.
  15. TGTr4ci: 0.
  16. TGTr5ci: 0.
  17. TGTr6ci: 1, ATTTACA at 4374.
  18. TGTr7ci: 0.
  19. TGTr8ci: 1, ATTTACA at 197.
  20. TGTr9ci: 0.

TGTr arbitrary (evens) (4560-2846) UTRs

  1. TGTr4: TGTAAAT at 4184.
  2. TGTr8: TGTAAAT at 2947.
  3. TGTr2ci: ATTTACA at 3619.
  4. TGTr6ci: ATTTACA at 4374.

TGTr alternate (odds) (4560-2846) UTRs

  1. TGTr5: TGTAAAT at 3715.

TGTr alternate positive direction (evens) (4445-4265) core promoters

  1. TGTr6ci: ATTTACA at 4374.

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

  1. TGTr4: TGTAAAT at 4184.

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

  1. TGTr8: TGTAAAT at 2502.
  2. TGTr8ci: ATTTACA at 197.

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

  1. TGTr5: TGTAAAT at 3715.

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

  1. TGTr8: TGTAAAT at 2947, TGTAAAT at 2502.
  2. TGTr2ci: ATTTACA at 3619.
  3. TGTr8ci: ATTTACA at 197.

TGT analysis and results

Main article: Complex locus A1BG and ZNF497 § TGTs

"The 3′ UTR of eEF1A contains a putative [Nanos/Pumilio response element (PRE)] PRE sequence (TGTAAAT), suggesting that it is a Nanos/Pumilio target."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 4 10 0.4 0.25
Randoms UTR alternate negative 1 10 0.1 0.25
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 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0.05
Randoms Proximal alternate positive 1 10 0.1 0.05
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 2 10 0.2 0.1
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 1 10 0.1 0.25
Randoms Distal alternate positive 4 10 0.4 0.25

Comparison:

The occurrences of a real TGT UTR is greater than the randoms. This suggests that the real TGT is 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 Nathalie Oulhen, S. Zachary Swartz, Jessica Laird, Alexandra Mascaro, Gary M. Wessel (1 February 2017). "Transient translational quiescence in primordial germ cells". Development. 144 (7): 1201. doi:10.1242/dev.144170. Retrieved 6 March 2021.
  2. ↑ 2.0 2.1 Ruthrothaselvi Bharathavikru, Tatiana Dudnakova, Stuart Aitken, Joan Slight, Mara Artibani, Peter Hohenstein, David Tollervey and Nick Hastie (13 March 2017). "Transcription factor Wilms' tumor 1 regulates developmental RNAs through 3′ UTR interaction". Genes & Development. 31 (4): 347–352. doi:10.1101/gad.291500.116. Retrieved 6 March 2021.
  3. ↑ Michael J. Zeitz, Patrick J. Calhoun, Carissa C. James, Thomas Taetzsch, Kijana K. George, Stefanie Robel, Gregorio Valdez, James W. Smyth (May 2019). "Dynamic UTR Usage Regulates Alternative Translation to Modulate Gap Junction Formation during Stress and Aging". Cell Reports. 27 (9): 2737–2747.e5. doi:10.1016/j.celrep.2019.04.114. Retrieved 6 March 2021.

External links


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