Mig1p gene transcriptions

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

"The MIG1 gene was isolated as a multicopy inhibitor of the GAL1 promoter."[1]

"MIGI is a DNA binding protein involved in glucose repression, and binds to two sites in the SUC2 upstream region."[1]

"For one of the Egr proteins, Zif268, several binding sites have been identified by DNase I footprinting (Christy and Nathans, 1989). Identical high affinity Zif268 sites, GCGGGGGCG, were found in the promoters of the zif268, jun-D and 475 genes. These genes also contain several low affinity sites, which differ in one or two positions from the high affinity nonamer. The second Egr protein, Krox-20, also binds to this motif (Chavrier et al., 1990). The two MIG1 sites are very similar to the nonamer. The GC motif at MIG1 site B, CCGGGGGCG [...], differs from it in only one position. Site B is thus more conserved than the low affinity Zif268 sites in the 475 and zif268 genes, which differ in two positions (Christy and Nathans, 1989). It is therefore possible that the Egr proteins and MIG1 recognize the same sequence, of which site B is an acceptable variant."[1]

"This is supported by the fact that the G to C substitution in site B is also found in the low affinity Zif268 site of gene 475. The GC motif at MIG1 site A, GCGGGG, is identical to the first two-thirds of the nonamer. It is conceivable that this motif is sufficient for binding, when flanked by acceptable nucleotides. This would be similar to Sp1, which binds with high affinity to a GGGGCGGGGC motif, but also with lower affinity to the core site GGGCGG (Kadonaga et al., 1986)."[1]

"The MIG1 gene, an important element in glucose repression, was identified in a search for genes which would turn off the GAL1 promoter of S. cerevisiae[[1]]. Mutations called cat4 or ssn1, which turned out to be allelic to MIG1, were also isolated as extragenic suppressors of snf1 and snf4 mutations (311, 356). Mig1 is a C2H2 zinc finger protein that is able to bind to the promoters of a variety of genes repressed by glucose. Binding requires a GC box with the consensus sequence (G/C)(C/T)GGGG, but it also requires an AT-rich region 5′ to the GC box (200)."[2]

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for the Mig1p transcription factor is 5'-SYGGGG-3' or 5'-(C/G)(C/T)GGGG-3'.[3]

With HAS1 ending at zero and TDA1 beginning at above 1000 bp, 569 - 574 Mig1 (C/T)(C/T)CC(A/G)G.[4] This occurrence corresponds to the inverse complement of (Tang 2020).

Mig samplings

For the Basic programs testing consensus sequence (C/G)(C/T)GGGG (starting with SuccessablesMig.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: 4, GTGGGG at 4445, GTGGGG at 3058, GTGGGG at 2763, GTGGGG at 750.
  2. Positive strand, negative direction: 1, CTGGGG at 3037.
  3. Negative strand, positive direction: 14, CTGGGG at 4426, CTGGGG at 4411, GTGGGG at 4396, GTGGGG at 4042, GTGGGG at 3542, GTGGGG at 3451, CTGGGG at 1955, CTGGGG at 1866, GCGGGG at 1708, GCGGGG at 1027, GCGGGG at 491, CTGGGG at 349, CTGGGG at 279, GTGGGG at 55.
  4. Positive strand, positive direction: 8, GTGGGG at 4327, GTGGGG at 4285, CTGGGG at 4218, GTGGGG at 3614, GTGGGG at 2019, CCGGGG at 391, CCGGGG at 373, CCGGGG at 201.
  5. inverse complement, negative strand, negative direction, looking for CCCC(A/G)(C/G), 1, CCCCAG at 205.
  6. inverse complement, positive strand, negative direction, looking for CCCC(A/G)(C/G), 2, CCCCAG at 4447, CCCCAG at 2765.
  7. inverse complement, negative strand, positive direction, looking for CCCC(A/G)(C/G), 10, CCCCAG at 4329, CCCCAC at 4287, CCCCGG at 4002, CCCCAC at 3941, CCCCGG at 3557, CCCCAG at 3015, CCCCAG at 1892, CCCCGC at 393, CCCCGG at 375, CCCCAG at 203.
  8. inverse complement, positive strand, positive direction, looking for CCCC(A/G)(C/G), 8, CCCCGC at 4428, CCCCAG at 4413, CCCCAC at 4398, CCCCGG at 4304, CCCCAG at 1957, CCCCGC at 1792, CCCCAG at 1710, CCCCGG at 248.

Mig (4560-2846) UTRs

  1. Negative strand, negative direction: GTGGGG at 4445, GTGGGG at 3058.
  2. Positive strand, negative direction: CCCCAG at 4447, CTGGGG at 3037.

Mig positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: CTGGGG at 4426, CTGGGG at 4411, GTGGGG at 4396, CCCCAG at 4329, CCCCAC at 4287.
  2. Positive strand, positive direction: CCCCGC at 4428, CCCCAG at 4413, CCCCAC at 4398, GTGGGG at 4327, CCCCGG at 4304, GTGGGG at 4285.

Mig negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: GTGGGG at 2763.
  2. Positive strand, negative direction: CCCCAG at 2765.

Mig positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: CTGGGG at 4218.

Mig negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GTGGGG at 750, CCCCAG at 205.

Mig positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: GTGGGG at 4042, CCCCGG at 4002, CCCCAC at 3941, CCCCGG at 3557, GTGGGG at 3542, GTGGGG at 3451, CCCCAG at 3015, CTGGGG at 1955, CCCCAG at 1892, CTGGGG at 1866, GCGGGG at 1708, GCGGGG at 1027, GCGGGG at 491, CCCCGC at 393, CCCCGG at 375, CTGGGG at 349, CTGGGG at 279, CCCCAG at 203, GTGGGG at 55.
  2. Positive strand, positive direction: GTGGGG at 3614, GTGGGG at 2019, CCCCAG at 1957, CCCCGC at 1792, CCCCAG at 1710, CCGGGG at 391, CCGGGG at 373, CCCCGG at 248, CCGGGG at 201.

Mig random dataset samplings

  1. Migr0: 3, CCGGGG at 2766, CTGGGG at 2318, GTGGGG at 532.
  2. Migr1: 5, CTGGGG at 3919, CTGGGG at 3681, CCGGGG at 819, GTGGGG at 662, CTGGGG at 63.
  3. Migr2: 10, CTGGGG at 4005, GCGGGG at 3911, CCGGGG at 3294, CCGGGG at 2815, GTGGGG at 2607, CCGGGG at 2156, GTGGGG at 2142, CTGGGG at 840, CCGGGG at 803, GCGGGG at 464.
  4. Migr3: 5, CCGGGG at 3751, CCGGGG at 3402, GCGGGG at 1315, GTGGGG at 514, GCGGGG at 10.
  5. Migr4: 11, GCGGGG at 4088, GTGGGG at 2763, CTGGGG at 2392, GCGGGG at 1754, GCGGGG at 1650, CCGGGG at 1466, CTGGGG at 1170, CCGGGG at 809, GCGGGG at 567, CCGGGG at 350, CTGGGG at 86.
  6. Migr5: 10, CCGGGG at 4448, CCGGGG at 4427, GTGGGG at 4317, GCGGGG at 4278, CCGGGG at 2692, CTGGGG at 2492, GCGGGG at 2232, CCGGGG at 2030, CTGGGG at 867, GCGGGG at 736.
  7. Migr6: 3, GTGGGG at 3741, GCGGGG at 2286, GTGGGG at 338.
  8. Migr7: 14, CCGGGG at 3944, CTGGGG at 3569, CTGGGG at 3336, GTGGGG at 3077, GCGGGG at 2749, CCGGGG at 2104, CCGGGG at 1375, GTGGGG at 1255, CCGGGG at 1095, GCGGGG at 1066, GCGGGG at 1046, CTGGGG at 969, GTGGGG at 238, GTGGGG at 134.
  9. Migr8: 11, CCGGGG at 4379, CCGGGG at 3867, GTGGGG at 3667, CCGGGG at 3458, CCGGGG at 3317, GTGGGG at 2588, CCGGGG at 1310, CCGGGG at 1246, GCGGGG at 1192, GCGGGG at 243, GTGGGG at 100.
  10. Migr9: 6, GCGGGG at 3963, GCGGGG at 2856, CTGGGG at 1714, CTGGGG at 1700, CCGGGG at 1369, GTGGGG at 800.
  11. Migr0ci: 2, CCCCAG at 1207, CCCCAG at 31.
  12. Migr1ci: 6, CCCCGG at 4470, CCCCGG at 4295, CCCCGC at 4280, CCCCAC at 1920, CCCCGC at 1353, CCCCGC at 232.
  13. Migr2ci: 8, CCCCAG at 3940, CCCCAC at 3835, CCCCAC at 3350, CCCCAC at 3314, CCCCGG at 3292, CCCCAG at 983, CCCCGG at 961, CCCCAG at 604.
  14. Migr3ci: 6, CCCCGC at 1865, CCCCGG at 1607, CCCCGG at 851, CCCCAG at 295, CCCCAG at 54, CCCCAC at 33.
  15. Migr4ci: 8, CCCCGG at 4209, CCCCAG at 3331, CCCCAG at 2747, CCCCGC at 875, CCCCGG at 754, CCCCGC at 501, CCCCGG at 348, CCCCAC at 235.
  16. Migr5ci: 5, CCCCGG at 3335, CCCCGG at 3015, CCCCGG at 2028, CCCCGC at 986, CCCCGC at 348.
  17. Migr6ci: 7, CCCCGG at 3735, CCCCGC at 3588, CCCCAG at 3513, CCCCGG at 3388, CCCCAG at 1005, CCCCAG at 683, CCCCGC at 290.
  18. Migr7ci: 3, CCCCGG at 2732, CCCCGG at 1842, CCCCAC at 175.
  19. Migr8ci: 4, CCCCGG at 4117, CCCCAG at 2477, CCCCGC at 1262, CCCCGG at 1093.
  20. Migr9ci: 3, CCCCGG at 3918, CCCCGC at 2760, CCCCGG at 2550.

Migr arbitrary (evens) (4560-2846) UTRs

  1. Migr2: CTGGGG at 4005, GCGGGG at 3911, CCGGGG at 3294.
  2. Migr4: GCGGGG at 4088.
  3. Migr6: GTGGGG at 3741.
  4. Migr8: CCGGGG at 4379, CCGGGG at 3867, GTGGGG at 3667, CCGGGG at 3458, CCGGGG at 3317.
  5. Migr2ci: CCCCAG at 3940, CCCCAC at 3835, CCCCAC at 3350, CCCCAC at 3314, CCCCGG at 3292.
  6. Migr4ci: CCCCGG at 4209, CCCCAG at 3331.
  7. Migr6ci: CCCCGG at 3735, CCCCGC at 3588, CCCCAG at 3513, CCCCGG at 3388.
  8. Migr8ci: CCCCGG at 4117.

Migr alternate (odds) (4560-2846) UTRs

  1. Migr1: CTGGGG at 3919, CTGGGG at 3681.
  2. Migr3: CCGGGG at 3751, CCGGGG at 3402.
  3. Migr5: CCGGGG at 4448, CCGGGG at 4427, GTGGGG at 4317, GCGGGG at 4278.
  4. Migr7: CCGGGG at 3944, CTGGGG at 3569, CTGGGG at 3336, GTGGGG at 3077.
  5. Migr9: GCGGGG at 3963, GCGGGG at 2856.
  6. Migr1ci: CCCCGG at 4470, CCCCGG at 4295, CCCCGC at 4280.
  7. Migr5ci: CCCCGG at 3335, CCCCGG at 3015.
  8. Migr9ci: CCCCGG at 3918.

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

  1. Migr2: CCGGGG at 2815.

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

  1. Migr5: CCGGGG at 4427, GTGGGG at 4317, GCGGGG at 4278.
  2. Migr1ci: CCCCGG at 4295, CCCCGC at 4280.

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

  1. Migr8: CCGGGG at 4379.

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

  1. Migr0: CCGGGG at 2766.
  2. Migr2: GTGGGG at 2607.
  3. Migr4: GTGGGG at 2763.
  4. Migr4ci: CCCCAG at 2747.

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

  1. Migr5: CCGGGG at 2692.
  2. Migr7: GCGGGG at 2749.
  3. Migr7ci: CCCCGG at 2732.
  4. Migr9ci: CCCCGC at 2760.

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

  1. Migr4: GCGGGG at 4088.
  2. Migr4ci: CCCCGG at 4209.
  3. Migr8ci: CCCCGG at 4117.

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

  1. Migr0: CTGGGG at 2318, GTGGGG at 532.
  2. Migr2: CCGGGG at 2156, GTGGGG at 2142, CTGGGG at 840, CCGGGG at 803, GCGGGG at 464.
  3. Migr4: CTGGGG at 2392, GCGGGG at 1754, GCGGGG at 1650, CCGGGG at 1466, CTGGGG at 1170, CCGGGG at 809, GCGGGG at 567, CCGGGG at 350, CTGGGG at 86.
  4. Migr6: GCGGGG at 2286, GTGGGG at 338.
  5. Migr8: GTGGGG at 2588, CCGGGG at 1310, CCGGGG at 1246, GCGGGG at 1192, GCGGGG at 243, GTGGGG at 100.
  6. Migr0ci: CCCCAG at 1207, CCCCAG at 31.
  7. Migr2ci: CCCCAG at 983, CCCCGG at 961, CCCCAG at 604.
  8. Migr4ci: CCCCGC at 875, CCCCGG at 754, CCCCGC at 501, CCCCGG at 348, CCCCAC at 235.
  9. Migr6ci: CCCCAG at 1005, CCCCAG at 683, CCCCGC at 290.
  10. Migr8ci: CCCCAG at 2477, CCCCGC at 1262, CCCCGG at 1093.

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

  1. Migr1: CCGGGG at 819, GTGGGG at 662, CTGGGG at 63.
  2. Migr3: GCGGGG at 1315, GTGGGG at 514, GCGGGG at 10.
  3. Migr5: CTGGGG at 2492, GCGGGG at 2232, CCGGGG at 2030, CTGGGG at 867, GCGGGG at 736.
  4. Migr7: CCGGGG at 2104, CCGGGG at 1375, GTGGGG at 1255, CCGGGG at 1095, GCGGGG at 1066, GCGGGG at 1046, CTGGGG at 969, GTGGGG at 238, GTGGGG at 134.
  5. Migr9: CTGGGG at 1714, CTGGGG at 1700, CCGGGG at 1369, GTGGGG at 800.
  6. Migr1ci: CCCCAC at 1920, CCCCGC at 1353, CCCCGC at 232.
  7. Migr3ci: CCCCGC at 1865, CCCCGG at 1607, CCCCGG at 851, CCCCAG at 295, CCCCAG at 54, CCCCAC at 33.
  8. Migr5ci:CCCCGG at 2028, CCCCGC at 986, CCCCGC at 348.
  9. Migr7ci: CCCCGG at 1842, CCCCAC at 175.
  10. Migr9ci: CCCCGG at 2550.

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

  1. Migr1: CTGGGG at 3919, CTGGGG at 3681, CCGGGG at 819, GTGGGG at 662, CTGGGG at 63.
  2. Migr3: CCGGGG at 3751, CCGGGG at 3402, GCGGGG at 1315, GTGGGG at 514, GCGGGG at 10.
  3. Migr5: CCGGGG at 2692, CTGGGG at 2492, GCGGGG at 2232, CCGGGG at 2030, CTGGGG at 867, GCGGGG at 736.
  4. Migr7: CCGGGG at 3944, CTGGGG at 3569, CTGGGG at 3336, GTGGGG at 3077, GCGGGG at 2749, CCGGGG at 2104, CCGGGG at 1375, GTGGGG at 1255, CCGGGG at 1095, GCGGGG at 1066, GCGGGG at 1046, CTGGGG at 969, GTGGGG at 238, GTGGGG at 134.
  5. Migr9: GCGGGG at 3963, GCGGGG at 2856, CTGGGG at 1714, CTGGGG at 1700, CCGGGG at 1369, GTGGGG at 800.
  6. Migr1ci: CCCCAC at 1920, CCCCGC at 1353, CCCCGC at 232.
  7. Migr3ci: CCCCGC at 1865, CCCCGG at 1607, CCCCGG at 851, CCCCAG at 295, CCCCAG at 54, CCCCAC at 33.
  8. Migr5ci: CCCCGG at 3335, CCCCGG at 3015, CCCCGG at 2028, CCCCGC at 986, CCCCGC at 348.
  9. Migr7ci: CCCCGG at 2732, CCCCGG at 1842, CCCCAC at 175.
  10. Migr9ci: CCCCGG at 3918, CCCCGC at 2760, CCCCGG at 2550.

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

  1. Migr0: CCGGGG at 2766, CTGGGG at 2318, GTGGGG at 532.
  2. Migr2: CTGGGG at 4005, GCGGGG at 3911, CCGGGG at 3294, CCGGGG at 2815, GTGGGG at 2607, CCGGGG at 2156, GTGGGG at 2142, CTGGGG at 840, CCGGGG at 803, GCGGGG at 464.
  3. Migr4: GTGGGG at 2763, CTGGGG at 2392, GCGGGG at 1754, GCGGGG at 1650, CCGGGG at 1466, CTGGGG at 1170, CCGGGG at 809, GCGGGG at 567, CCGGGG at 350, CTGGGG at 86.
  4. Migr6: GTGGGG at 3741, GCGGGG at 2286, GTGGGG at 338.
  5. Migr8: CCGGGG at 3867, GTGGGG at 3667, CCGGGG at 3458, CCGGGG at 3317, GTGGGG at 2588, CCGGGG at 1310, CCGGGG at 1246, GCGGGG at 1192, GCGGGG at 243, GTGGGG at 100.
  6. Migr0ci: CCCCAG at 1207, CCCCAG at 31.
  7. Migr2ci: CCCCAG at 3940, CCCCAC at 3835, CCCCAC at 3350, CCCCAC at 3314, CCCCGG at 3292, CCCCAG at 983, CCCCGG at 961, CCCCAG at 604.
  8. Migr4ci: CCCCAG at 3331, CCCCAG at 2747, CCCCGC at 875, CCCCGG at 754, CCCCGC at 501, CCCCGG at 348, CCCCAC at 235.
  9. Migr6ci: CCCCGG at 3735, CCCCGC at 3588, CCCCAG at 3513, CCCCGG at 3388, CCCCAG at 1005, CCCCAG at 683, CCCCGC at 290.
  10. Migr8ci: CCCCAG at 2477, CCCCGC at 1262, CCCCGG at 1093.

Mig analysis and results

Main article: Complex locus A1BG and ZNF497 § Migs

Binding requires a GC box with the consensus sequence (G/C)(C/T)GGGG, but it also requires an AT-rich region 5′ to the GC box (200)."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 4 2 2 2 ± 0 (+-2,--2)
Randoms UTR arbitrary negative 22 10 2.2 2.1
Randoms UTR alternate negative 20 10 2.0 2.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.05
Randoms Core alternate negative 0 10 0 0.05
Reals Core positive 11 2 5.5 5.5 ± 0.5 (-+5,++6)
Randoms Core arbitrary positive 5 10 0.5 0.3
Randoms Core alternate positive 1 10 0.1 0.3
Reals Proximal negative 2 2 1 1 ± 0 (--1,+-1)
Randoms Proximal arbitrary negative 4 10 0.4 0.4
Randoms Proximal alternate negative 4 10 0.4 0.4
Reals Proximal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Proximal arbitrary positive 0 10 0 0.15
Randoms Proximal alternate positive 3 10 0.3 0.15
Reals Distal negative 2 2 1 1 ± 1 (+-0,--2)
Randoms Distal arbitrary negative 40 10 4.0 3.95
Randoms Distal alternate negative 39 10 3.9 3.95
Reals Distal positive 28 2 14 14 ± 5 (-+19,++9)
Randoms Distal arbitrary positive 56 10 5.6 5.95 ± 0.35
Randoms Distal alternate positive 63 10 6.3 5.95 ± 0.35

Comparison:

The occurrences of real Mig UTRs are at the lower end of the range of the randoms, positive direction cores, proximals, and positive direction distals are greater than the randoms, negative direction distals are less than the randoms. This suggests that the real Migs are likely active or activable but the UTRs may be random.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Jan Olof Nehlin and Hans Ronne (September 1990). "Yeast MIG1 repressor is related to the mammalian early growth response and Wilms' tumour finger proteins" (PDF). The EMBO Journal. 9 (9): 2891–2898. doi:10.3390/metabo10080320. PMID 2167835. Retrieved 6 February 2021.
  2. ↑ 2.0 2.1 Juana M. Gancedo (June 1998). "Yeast Carbon Catabolite Repression". Microbiology and Molecular Biology Reviews. 62 (2): 334–361. PMID 9618445. Retrieved 6 February 2021.
  3. ↑ Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.
  4. ↑ 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.

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