Mig1p gene transcriptions: Difference between revisions

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==Mig random dataset samplings==
==Mig random dataset samplings==


# RDr0: 0.
# Migr0: 3, CCGGGG at 2766, CTGGGG at 2318, GTGGGG at 532.
# RDr1: 0.
# Migr1: 5, CTGGGG at 3919, CTGGGG at 3681, CCGGGG at 819, GTGGGG at 662, CTGGGG at 63.
# RDr2: 0.
# RDr2: 0.
# RDr3: 0.
# RDr3: 0.
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===RDr arbitrary (evens) (4560-2846) UTRs===
===RDr arbitrary (evens) (4560-2846) UTRs===


===RDr alternate (odds) (4560-2846) UTRs===
===Migr alternate (odds) (4560-2846) UTRs===
 
# Migr1: CTGGGG at 3919, CTGGGG at 3681.


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
Line 148: Line 150:
===RDr alternate positive direction (evens) (4445-4265) core promoters===
===RDr alternate positive direction (evens) (4445-4265) core promoters===


===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
===Migr arbitrary negative direction (evens) (2811-2596) proximal promoters===
 
# Migr0: CCGGGG at 2766.


===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
Line 156: Line 160:
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===


===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
===Migr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# Migr0: CTGGGG at 2318, GTGGGG at 532.
 
===Migr alternate negative direction (odds) (2596-1) distal promoters===
 
# Migr1: CCGGGG at 819, GTGGGG at 662, CTGGGG at 63.
 
===Migr arbitrary positive direction (odds) (4050-1) distal promoters===


===RDr alternate negative direction (odds) (2596-1) distal promoters===
# Migr1: CTGGGG at 3919, CTGGGG at 3681, CCGGGG at 819, GTGGGG at 662, CTGGGG at 63.


===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
===Migr alternate positive direction (evens) (4050-1) distal promoters===


===RDr alternate positive direction (evens) (4050-1) distal promoters===
# Migr0: CCGGGG at 2766, CTGGGG at 2318, GTGGGG at 532.


==Mig analysis and results==
==Mig analysis and results==

Revision as of 20:32, 4 July 2022

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. 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.

RDr arbitrary (evens) (4560-2846) UTRs

Migr alternate (odds) (4560-2846) UTRs

  1. Migr1: CTGGGG at 3919, CTGGGG at 3681.

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

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

  1. Migr0: CCGGGG at 2766.

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

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

  1. Migr0: CTGGGG at 2318, GTGGGG at 532.

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

  1. Migr1: CCGGGG at 819, GTGGGG at 662, CTGGGG at 63.

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.

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

  1. Migr0: CCGGGG at 2766, CTGGGG at 2318, GTGGGG at 532.

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
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 50 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 11 2 5.5 5.5
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 1 2 0.5 0.5
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 2 2 1 1
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 28 2 14 14 ± 5 (-+19,++9)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

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.

External links

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