Rgt1p gene transcriptions

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

"Using MAP-C [Mutation Analysis in Pools by Chromosome conformation capture], we show that inducible interchromosomal pairing between HAS1pr-TDA1pr alleles in saturated cultures of Saccharomyces yeast is mediated by three transcription factors, Leu3, Sdd4 (Ypr022c), and Rgt1. The coincident, combined binding of all three factors is strongest at the HAS1pr-TDA1pr locus and is also specific to saturated conditions. We applied MAP-C to further explore the biochemical mechanism of these contacts, and find they require the structured regulatory domain of Rgt1, but no known interaction partners of Rgt1."[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

With HAS1 ending at zero and TDA1 beginning at above 1000 bp, Leu3 is from 536 - 545 nts yielding consensus sequences (C/G)C(G/T)NNNN(A/C)G(C/G), 569 - 574 Mig1 (C/T)(C/T)CC(A/G)G and Sdd4 (A/C/T)CCCAC, 585 - 592 Rgt1 (A/T)(A/T)N(A/T)(C/T)CCG, 610 - 617 Rgt1 (A/T)(A/T)N(A/T)(C/T)CCG, 630 - 637 Rgt CGG(A/G)(A/T)N(A/T)(A/T).[1]

Binding site for

Complement copies

Main article: Complement copy gene transcriptions

Inverse copies

Main article: Inverse copy gene transcriptions

With HAS1 ending at zero and TDA1 beginning at above 1000 bp, 585 - 592 Rgt1 (A/T)(A/T)N(A/T)(C/T)CCG, 610 - 617 Rgt1 (A/T)(A/T)N(A/T)(C/T)CCG, 630 - 637 Rgt CGG(A/G)(A/T)N(A/T)(A/T), the third Rgt1 is the inverse of the first two.[1]

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.

RGT samplings

Copying a responsive elements consensus sequence CGGAACTA or CGGGACTT 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 CGG(A/G)(A/T)N(A/T)(A/T) (starting with SuccessablesRGT.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 CGG(A/G)(A/T)N(A/T)(A/T), 0.
  2. positive strand, negative direction, looking for CGG(A/G)(A/T)N(A/T)(A/T), 2, CGGAAGTT at 2732, CGGGAAAA at 2459.
  3. positive strand, positive direction, looking for CGG(A/G)(A/T)N(A/T)(A/T), 1, CGGGTCAA at 3380.
  4. negative strand, positive direction, looking for CGG(A/G)(A/T)N(A/T)(A/T), 0.
  5. complement, negative strand, negative direction, looking for GCC(C/T)(A/T)N(A/T)(A/T), 2, GCCTTCAA at 2732, CGGCTTTT at 2459.
  6. complement, positive strand, negative direction, looking for GCC(C/T)(A/T)N(A/T)(A/T), 0.
  7. complement, positive strand, positive direction, looking for GCC(C/T)(A/T)N(A/T)(A/T), 0.
  8. complement, negative strand, positive direction, looking for GCC(C/T)(A/T)N(A/T)(A/T), 1, GCCCAGTT at 3380.
  9. inverse complement, negative strand, negative direction, looking for (A/T)(A/T)N(A/T)(C/T)CCG, 3, ATTTTCCG at 3442, TTTTTCCG at 1108, AACTCCCG at 89.
  10. inverse complement, positive strand, negative direction, looking for (A/T)(A/T)N(A/T)(C/T)CCG, 0.
  11. inverse complement, positive strand, positive direction, looking for (A/T)(A/T)N(A/T)(C/T)CCG, 2, TACTCCCG at 3480, AATATCCG at 2551.
  12. inverse complement, negative strand, positive direction, looking for (A/T)(A/T)N(A/T)(C/T)CCG, 0.
  13. inverse negative strand, negative direction, looking for (A/T)(A/T)N(A/T)(A/G)GGC, 0.
  14. inverse positive strand, negative direction, looking for (A/T)(A/T)N(A/T)(A/G)GGC, 3, TAAAAGGC at 3442, AAAAAGGC at 1108, TTGAGGGC at 89.
  15. inverse positive strand, positive direction, looking for (A/T)(A/T)N(A/T)(A/G)GGC, 0.
  16. inverse negative strand, positive direction, looking for (A/T)(A/T)N(A/T)(A/G)GGC, 2, ATGAGGGC at 3480, TTATAGGC at 2551.

Rgt (4560-2846) UTRs

  1. Negative strand, negative direction: ATTTTCCG at 3442.

Rgt negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: CGGAAGTT at 2732.

Rgt negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TTTTTCCG at 1108, AACTCCCG at 89.
  2. Positive strand, negative direction: CGGGAAAA at 2459.

Rgt positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: CGGGTCAA at 3380.
  2. Positive strand, positive direction: TACTCCCG at 3480, AATATCCG at 2551.

Rgt random dataset samplings

  1. Rgtr0: 4, CGGGAAAT at 4126, CGGGATTA at 3974, CGGGTGTT at 3707, CGGAATAA at 2016.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

Rgtr arbitrary (evens) (4560-2846) UTRs

  1. Rgtr0: CGGGAAAT at 4126, CGGGATTA at 3974, CGGGTGTT at 3707.

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

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

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

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

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

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

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

  1. Rgtr0: CGGAATAA at 2016.

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

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

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

  1. Rgtr0: CGGGATTA at 3974, CGGGTGTT at 3707, CGGAATAA at 2016.

Rgt analysis and results

Main article: Complex locus A1BG and ZNF497 § Rgts

630 - 637 Rgt CGG(A/G)(A/T)N(A/T)(A/T).[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
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 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 1 2 0.5 0.5
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
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 3 2 1.5 1.5 ± 0.5 (--2,+-1)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 3 2 1.5 1.5 ± 0.5 (-+0,++3)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real Rgts are greater than the randoms. This suggests that the real Rgts 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 Seungsoo Kim, Maitreya J Dunham, Jay Shendure (13 May 2019). "A combination of transcription factors mediates inducible interchromosomal contacts" (PDF). eLife. 8: e42499. doi:10.7554/eLife.42499.001. Retrieved 20 February 2021.

External links

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