Leu3 gene transcriptions: Difference between revisions
Jump to navigation
Jump to search
m (→Leu samplings) |
|||
| Line 156: | Line 156: | ||
==Response element analysis and results== | ==Response element analysis and results== | ||
{{main|Complex locus A1BG and ZNF497# | {{main|Complex locus A1BG and ZNF497#Leu3s}} | ||
Leu3 is from 536 - 545 nts yielding consensus sequences (C/G)C(G/T)NNNN(A/C)G(C/G)".<ref name=Kim/> | Leu3 is from 536 - 545 nts yielding consensus sequences (C/G)C(G/T)NNNN(A/C)G(C/G)".<ref name=Kim/> | ||
| Line 163: | Line 163: | ||
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1) | ! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1) | ||
|- | |- | ||
| Reals || UTR || negative || | | Reals || UTR || negative || 11 || 2 || 5.5 || 5.5 ± 0.5 (--6,+-5) | ||
|- | |- | ||
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0 | | Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0 | ||
| Line 175: | Line 175: | ||
| Randoms || Core || alternate negative || 0 || 10 || 0 || 0 | | Randoms || Core || alternate negative || 0 || 10 || 0 || 0 | ||
|- | |- | ||
| Reals || Core || positive || | | Reals || Core || positive || 3 || 2 || 1.5 || 0 | ||
|- | |- | ||
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0 | | Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0 | ||
| Line 181: | Line 181: | ||
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0 | | Randoms || Core || alternate positive || 0 || 10 || 0 || 0 | ||
|- | |- | ||
| Reals || Proximal || negative || | | Reals || Proximal || negative || 2 || 2 || 1 || 1 | ||
|- | |- | ||
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0 | | Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0 | ||
| Line 193: | Line 193: | ||
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0 | | Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0 | ||
|- | |- | ||
| Reals || Distal || negative || | | Reals || Distal || negative || 21 || 2 || 10.5 || 10.5 ± 1.5 (--9,+-12) | ||
|- | |- | ||
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0 | | Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0 | ||
| Line 199: | Line 199: | ||
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0 | | Randoms || Distal || alternate negative || 0 || 10 || 0 || 0 | ||
|- | |- | ||
| Reals || Distal || positive || | | Reals || Distal || positive || 46 || 2 || 23 || (-+24,++22) | ||
|- | |- | ||
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0 | | Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0 | ||
Revision as of 19:43, 27 September 2022
Associate Editor(s)-in-Chief: Henry A. Hoff
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]
"Leu3, a well-known transcription factor of genes involved in the metabolism of branched amino acids [13], also has a negative effect on UGA4 and UGA1 expression but does not affect UGA2 expression [10, 11, 14]. Even though Leu3 could not be detected bound to the UGA4 promoter, it interferes in the interaction of Dal81 but not of Uga3 with the UGA4 promoter [11]. The transcription factors Uga3, Dal81 and Leu3 belong to the class III family (Zn(II)2Cys6 proteins), and they recognize highly related sequences rich in GGC triplets [15]."[2]
Human genes
Gene expressions
Interactions
"Although there is a putative consensus site for Leu3 within the UASGABA element of UGA4 and UGA1 genes, we were not able to detect any interaction between Leu3 and the UGA4 promoter [11]."[2]
Consensus sequences
Leu3 is from 536 - 545 nts yielding consensus sequences (C/G)C(G/T)NNNN(A/C)G(C/G).[1]
Binding site for
Complement copies
Inverse copies
Complement-inverse copies
Enhancer activity
Promoter occurrences
"The regulatory regions of the UGA4 and UGA1 genes contain a UASGABA element (5′-AAAAACCGCCGGCGGCAAT-3′) target of Uga3 and Dal81 factors. Within this element there is a consensus site [CCGCCGGCGG] for Leu3 [8, 10, 11, 35]."[2]
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.
Leu samplings
Copying a responsive elements consensus sequence (C/G)C(G/T)NNNN(A/C)G(C/G) 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 (C/G)C(G/T)NNNN(A/C)G(C/G) (starting with SuccessablesLeu.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 (C/G)C(G/T)NNNN(A/C)G(C/G), 16, GCGAACTCGG at 4297, CCGAGTACGG at 4118, CCGACTCCGC at 3998, CCGTCGTAGG at 3903, CCTGGTCCGG at 3873, CCGACTCCGC at 3089, CCGTGTACGG at 2669, CCGAGTACGG at 2535, CCGACTCCGC at 2230, CCGAGTGCGG at 2208, CCGCCCACGG at 1255, GCTCAAACGC at 1188, CCGTGTGCGG at 964, GCGAGGTCGG at 896, CCTCCAACGC at 864, CCGAGTGCGG at 664.
- positive strand, negative direction, looking for (C/G)C(G/T)NNNN(A/C)G(C/G), 18, CCTCAGGAGC at 4439, GCTACTCAGG at 4138, GCTGAGGCGG at 3999, GCTACTCAGG at 3217, GCTGAGGCGG at 3090, GCTACACAGG at 2689, GCTACTCCGG at 2354, CCTGGACAGC at 2273, GCTGAGGCGG at 2231, CCGGGTGCGG at 2197, GCGACAGAGC at 2019, GCTACTCAGG at 1275, GCTAATCAGG at 984, GCGCTCCAGC at 895, GCTACTAAGG at 818, CCTGACCAGC at 737, CCTGGGCCGG at 513, CCGGGTGCGG at 380.
- positive strand, positive direction, looking for (C/G)C(G/T)NNNN(A/C)G(C/G), 24, CCTCCCCCGC at 4438, CCTCACTCGC at 4353, CCGTGAGAGG at 4010, CCGAAGTCGG at 3998, CCGATATCGG at 3702, CCGCCAACGG at 3492, CCTTACGAGG at 3370, CCGCACTCGG at 2558, CCGTCCGAGG at 1909, CCGCGGGAGG at 1773, GCGGCCACGC at 1763, CCTCCAGCGC at 1689, GCTCCTGCGG at 1672, CCGCTCACGC at 1589, GCGGAAGCGG at 1308, CCGCGTGCGG at 1302, GCTCACGCGG at 1162, GCTCTCGAGC at 1108, GCGTGTGCGG at 804, GCGCGTGAGC at 688, CCGGAAGCGG at 595, CCTCGCTCGG at 432, CCTTTTGAGG at 295, CCGGTCCAGG at 218.
- negative strand, positive direction, looking for (C/G)C(G/T)NNNN(A/C)G(C/G), 25, CCTGGGGCGG at 4429, CCTCAGCAGC at 4026, CCTGGGAAGC at 3763, CCTGGGCAGC at 2896, CCTGGCCAGG at 2574, CCTCCCAAGC at 2399, CCTGTGTAGG at 2255, CCGAGGACGC at 1671, GCGAGTGCGG at 1590, GCTCTTAAGC at 1540, CCGCGGCAGC at 1441, CCTTCCGCGG at 1437, CCGCGGCAGC at 1341, CCTTCCGCGG at 1337, CCTACTGAGC at 1288, CCGAGTGCGG at 1170, CCGCGAGAGC at 1105, CCGAGTGCGG at 1086, CCGACTGCGG at 1002, GCGCACTCGC at 689, CCTTCCGCGC at 681, CCGAGTGCGG at 582, CCGCAGACGG at 399, CCGAGGGAGG at 314, GCTCCAGAGG at 17.
Leu3 (4560-2846) UTRs
- Negative strand, negative direction: GCGAACTCGG at 4297, CCGAGTACGG at 4118, CCGACTCCGC at 3998, CCGTCGTAGG at 3903, CCTGGTCCGG at 3873, CCGACTCCGC at 3089.
- Positive strand, negative direction: CCTCAGGAGC at 4439, GCTACTCAGG at 4138, GCTGAGGCGG at 3999, GCTACTCAGG at 3217, GCTGAGGCGG at 3090.
Leu3 positive direction (4445-4265) core promoters
- Negative strand, positive direction: CCTGGGGCGG at 4429.
- Positive strand, positive direction: CCTCCCCCGC at 4438, CCTCACTCGC at 4353.
Leu3 negative direction (2811-2596) proximal promoters
- Negative strand, negative direction: CCGTGTACGG at 2669.
- Positive strand, negative direction: GCTACACAGG at 2689.
Leu3 negative direction (2596-1) distal promoters
- Negative strand, negative direction:CCGAGTACGG at 2535, CCGACTCCGC at 2230, CCGAGTGCGG at 2208, CCGCCCACGG at 1255, GCTCAAACGC at 1188, CCGTGTGCGG at 964, GCGAGGTCGG at 896, CCTCCAACGC at 864, CCGAGTGCGG at 664.
- Positive strand, negative direction: GCTACTCCGG at 2354, CCTGGACAGC at 2273, GCTGAGGCGG at 2231, CCGGGTGCGG at 2197, GCGACAGAGC at 2019, GCTACTCAGG at 1275, GCTAATCAGG at 984, GCGCTCCAGC at 895, GCTACTAAGG at 818, CCTGACCAGC at 737, CCTGGGCCGG at 513, CCGGGTGCGG at 380.
Leu3 positive direction (4050-1) distal promoters
- Negative strand, positive direction: CCTCAGCAGC at 4026, CCTGGGAAGC at 3763, CCTGGGCAGC at 2896, CCTGGCCAGG at 2574, CCTCCCAAGC at 2399, CCTGTGTAGG at 2255, CCGAGGACGC at 1671, GCGAGTGCGG at 1590, GCTCTTAAGC at 1540, CCGCGGCAGC at 1441, CCTTCCGCGG at 1437, CCGCGGCAGC at 1341, CCTTCCGCGG at 1337, CCTACTGAGC at 1288, CCGAGTGCGG at 1170, CCGCGAGAGC at 1105, CCGAGTGCGG at 1086, CCGACTGCGG at 1002, GCGCACTCGC at 689, CCTTCCGCGC at 681, CCGAGTGCGG at 582, CCGCAGACGG at 399, CCGAGGGAGG at 314, GCTCCAGAGG at 17.
- Positive strand, positive direction: CCGTGAGAGG at 4010, CCGAAGTCGG at 3998, CCGATATCGG at 3702, CCGCCAACGG at 3492, CCTTACGAGG at 3370, CCGCACTCGG at 2558, CCGTCCGAGG at 1909, CCGCGGGAGG at 1773, GCGGCCACGC at 1763, CCTCCAGCGC at 1689, GCTCCTGCGG at 1672, CCGCTCACGC at 1589, GCGGAAGCGG at 1308, CCGCGTGCGG at 1302, GCTCACGCGG at 1162, GCTCTCGAGC at 1108, GCGTGTGCGG at 804, GCGCGTGAGC at 688, CCGGAAGCGG at 595, CCTCGCTCGG at 432, CCTTTTGAGG at 295, CCGGTCCAGG at 218.
Response element random dataset samplings
- RDr0: 0.
- RDr1: 0.
- RDr2: 0.
- RDr3: 0.
- RDr4: 0.
- 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.
RDr arbitrary (evens) (4560-2846) UTRs
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
RDr arbitrary negative direction (evens) (2596-1) distal promoters
RDr alternate negative direction (odds) (2596-1) distal promoters
RDr arbitrary positive direction (odds) (4050-1) distal promoters
RDr alternate positive direction (evens) (4050-1) distal promoters
Response element analysis and results
Leu3 is from 536 - 545 nts yielding consensus sequences (C/G)C(G/T)NNNN(A/C)G(C/G)".[1]
| Reals or randoms | Promoters | direction | Numbers | Strands | Occurrences | Averages (± 0.1) |
|---|---|---|---|---|---|---|
| Reals | UTR | negative | 11 | 2 | 5.5 | 5.5 ± 0.5 (--6,+-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 | 3 | 2 | 1.5 | 0 |
| Randoms | Core | arbitrary positive | 0 | 10 | 0 | 0 |
| Randoms | Core | alternate positive | 0 | 10 | 0 | 0 |
| Reals | Proximal | negative | 2 | 2 | 1 | 1 |
| 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 | 21 | 2 | 10.5 | 10.5 ± 1.5 (--9,+-12) |
| Randoms | Distal | arbitrary negative | 0 | 10 | 0 | 0 |
| Randoms | Distal | alternate negative | 0 | 10 | 0 | 0 |
| Reals | Distal | positive | 46 | 2 | 23 | (-+24,++22) |
| Randoms | Distal | arbitrary positive | 0 | 10 | 0 | 0 |
| Randoms | Distal | alternate positive | 0 | 10 | 0 | 0 |
Comparison:
The occurrences of real Leu3s are greater than the randoms. This suggests that the real Leu3s are likely active or activable.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 1.0 1.1 1.2 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.
- ↑ 2.0 2.1 2.2 Marcos Palavecino-Ruiz, Mariana Bermudez-Moretti, Susana Correa-Garcia (1 November 2017). "Unravelling the transcriptional regulation of Saccharomyces cerevisiae UGA genes: the dual role of transcription factor LEU3" (PDF). Microbiology. doi:10.1099/mic.0.000560. Retrieved 21 February 2021.