Hac1p gene transcriptions: Difference between revisions

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| Reals || UTR || negative || 0 || 2 || 0 || 0  
| Reals || UTR || negative || 0 || 2 || 0 || 0  
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|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.05
|-
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0  
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0.05
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
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| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5  
| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5  
|-
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
| Randoms || Distal || arbitrary negative || 1 || 10 || 0.1 || 0
|-
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate negative || 1 || 10 || 0.1 || 0  
|-
|-
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5  
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5  
|-
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0  
| Randoms || Distal || arbitrary positive || 1 || 10 || 0.1 || 0.15
|-
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate positive || 2 || 10 || 0.2 || 0.15
|}
|}


Comparison:
Comparison:


The occurrences of real KAR2s are larger than the randoms. This suggests that the real unfolded protein response elements are likely active or activable.
The occurrences of real KAR2 distals are greater than the randoms. This suggests that the real KAR2s are likely active or activable.


==UPRE-1 samplings==
==UPRE-1 samplings==

Revision as of 05:27, 8 January 2023

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

"The [unfolded protein response] UPR has been shown to play important roles in overexpression and secretion of some recombinant proteins [9]. Manipulating the level of transcription factors and [endoplasmic reticulum] ER chaperones in the UPR pathway improved secretion of recombinant proteins [10, 11]. An important characteristic of the UPR is that it is directly linked to transcription activation processes governed by ER stress conditions. In Sachcharomyces cerevisiae this process is mediated by a unique mechanism involving cooperative action of Hac1 transcription factor (TF) and a short conserved DNA sequence referred to as unfolded protein response element (UPRE) in the promoter of UPR target genes [12]. The UPRE regulatory cis acting element lies within 22-bp upstream of the promoter of UPR responsive genes, which is crucial for transcriptional induction under ER stress [13]. The best characterized UPRE core sequence was UPRE-1 (CANCNTG) from S. cerevisiae (for examples from KAR2, CAGCGTG and PDI1, CACCGTG) [13, 14]. The similar UPRE-1 is also found in the promoter region of the P. pastoris KAR2 (CAGCGTG), INO1 (CAACTTG) and HAC1 (CAACTTG) genes [15]. The presence of an HAC1 UPRE implies that Hac1p can up-regulate its own transcription. Unconventional splicing of HAC1 mRNA after ER stress signaling generates the active form of basic leucine zipper (bZIP) transcription factor Hac1p, which binds to the UPRE [16]."[1]

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for Hac1p is 5'-CAGCGTG-3'.[2]

KAR2 samplings

Main article: Model samplings

Copying 5'-CAGCGTG-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CAGCGTG (starting with SuccessablesHac.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 CAGCGTG, 0.
  2. negative strand, positive direction, looking for CAGCGTG, 0.
  3. positive strand, negative direction, looking for CAGCGTG, 1, CAGCGTG at 740.
  4. positive strand, positive direction, looking for CAGCGTG, 0.
  5. inverse complement, negative strand, negative direction, looking for CACGCTG, 0.
  6. inverse complement, negative strand, positive direction, looking for CACGCTG, 1, CACGCTG at 778.
  7. inverse complement, positive strand, negative direction, looking for CACGCTG, 0.
  8. inverse complement, positive strand, positive direction, looking for CACGCTG, 0.

KAR2 negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: CAGCGTG at 740.

KAR2 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CACGCTG at 778.

KAR2 random dataset samplings

  1. KAR2r0: 1, CAGCGTG at 3076.
  2. KAR2r1: 0.
  3. KAR2r2: 0.
  4. KAR2r3: 0.
  5. KAR2r4: 1, CAGCGTG at 1562.
  6. KAR2r5: 1, CAGCGTG at 370.
  7. KAR2r6: 0.
  8. KAR2r7: 0.
  9. KAR2r8: 0.
  10. KAR2r9: 0.
  11. KAR2r0ci: 0.
  12. KAR2r1ci: 0.
  13. KAR2r2ci: 0.
  14. KAR2r3ci: 0.
  15. KAR2r4ci: 0.
  16. KAR2r5ci: 0.
  17. KAR2r6ci: 0.
  18. KAR2r7ci: 0.
  19. KAR2r8ci: 0.
  20. KAR2r9ci: 0.

KAR2r arbitrary (evens) (4560-2846) UTRs

  1. KAR2r0: CAGCGTG at 3076.

KAR2r arbitrary negative direction (evens) (2596-1) distal promoters

  1. KAR2r4: CAGCGTG at 1562.

KAR2r alternate negative direction (odds) (2596-1) distal promoters

  1. KAR2r5: CAGCGTG at 370.

KAR2r arbitrary positive direction (odds) (4050-1) distal promoters

  1. KAR2r5: CAGCGTG at 370.

KAR2r alternate positive direction (evens) (4050-1) distal promoters

  1. KAR2r0: CAGCGTG at 3076.
  2. KAR2r4: CAGCGTG at 1562.

KAR2 analysis and results

Main article: Complex locus A1BG and ZNF497 § KAR2s

The upstream activating sequence (UAS) for Hac1p is CAGCGTG.[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.05
Randoms UTR alternate negative 0 10 0 0.05
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 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
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5
Randoms Distal arbitrary negative 1 10 0.1 0
Randoms Distal alternate negative 1 10 0.1 0
Reals Distal positive 1 2 0.5 0.5
Randoms Distal arbitrary positive 1 10 0.1 0.15
Randoms Distal alternate positive 2 10 0.2 0.15

Comparison:

The occurrences of real KAR2 distals are greater than the randoms. This suggests that the real KAR2s are likely active or activable.

UPRE-1 samplings

For the Basic programs testing consensus sequence CANCNTG (starting with SuccessablesUPRE.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 CANCNTG, 3, CACCGTG at 2664, CATCATG at 2342, CATCTTG at 286, and complements.
  2. negative strand, positive direction, looking for CANCNTG, 7, CATCATG at 4364, CATCCTG at 4185, CACCATG at 3827, CACCCTG at 2967, CACCATG at 2473, CAACCTG at 946, CAACCTG at 846.
  3. positive strand, negative direction, looking for CANCNTG, 21, CAGCCTG at 4348, CAGCCTG at 4036, CATCCTG at 3905, CACCCTG at 3743, CAGCCTG at 3297, CAGCCTG at 3127, CAGCCTG at 2769, CAACATG at 2613, CAGCCTG at 2434, CAGCATG at 2276, CAGCCTG at 2267, CAACATG at 2151, CAGCCTG at 2008, CATCCTG at 1840, CAACATG at 1206, CAGCCTG at 1197, CAGCCTG at 898, CAGCGTG at 740, CAGCCTG at 731, CATCCTG at 595, CAGCCTG at 507.
  4. positive strand, positive direction, looking for CANCNTG, 0.
  5. complement, negative strand, negative direction, looking for GTNGNAC, 21, GTCGGAC at 4348, GTCGGAC at 4036, GTAGGAC at 3905, GTGGGAC at 3743, GTCGGAC at 3297, GTCGGAC at 3127, GTCGGAC at 2769, GTTGTAC at 2613, GTCGGAC at 2434, GTCGTAC at 2276, GTCGGAC at 2267, GTTGTAC at 2151, GTCGGAC at 2008, GTAGGAC at 1840, GTTGTAC at 1206, GTCGGAC at 1197, GTCGGAC at 898, GTCGCAC at 740, GTCGGAC at 731, GTAGGAC at 595, GTCGGAC at 507.
  6. complement, negative strand, positive direction, looking for GTNGNAC, 7, GTAGTAC at 4364, GTAGGAC at 4185, GTGGTAC at 3827, GTGGGAC at 2967, GTGGTAC at 2473, GTTGGAC at 946, GTTGGAC at 846.
  7. complement, positive strand, negative direction, looking for GTNGNAC, 3, GTGGCAC at 2664, GTAGTAC at 2342, GTAGAAC at 286.
  8. complement, positive strand, positive direction, looking for GTNGNAC, 0.
  9. inverse complement, negative strand, negative direction, looking for CANGNTG, 0.
  10. inverse complement, negative strand, positive direction, looking for CANGNTG, 7, CAGGCTG at 3639, CAGGATG at 3574, CAGGGTG at 3539, CATGTTG at 2476, CAGGCTG at 2319, CATGATG at 2143, CACGCTG at 778.
  11. inverse complement, positive strand, negative direction, looking for CANGNTG, 10, CATGGTG at 4109, CAAGGTG at 3143, CATGGTG at 2616, CACGGTG at 2526, CATGCTG at 2325, CATGGTG at 2279, CATGTTG at 1852, CAGGCTG at 1463, CATGGTG at 1209, CACGGTG at 655.
  12. inverse complement, positive strand, positive direction, looking for CANGNTG, 2, CACGTTG at 2802, CATGGTG at 2599.
  13. inverse negative strand, negative direction, looking for GTNCNAC, 10, GTACCAC at 4109, GTTCCAC at 3143, GTACCAC at 2616, GTGCCAC at 2526, GTACGAC at 2325, GTACCAC at 2279, GTACAAC at 1852, GTCCGAC at 1463, GTACCAC at 1209, GTGCCAC at 655.
  14. inverse negative strand, positive direction, looking for GTNCNAC, 2, GTGCAAC at 2802, GTACCAC at 2599.
  15. inverse positive strand, negative direction, looking for GTNCNAC, 0.
  16. inverse positive strand, positive direction, looking for GTNCNAC, 7, GTCCGAC at 3639, GTCCTAC at 3574, GTCCCAC at 3539, GTACAAC at 2476, GTCCGAC at 2319, GTACTAC at 2143, GTGCGAC at 778.

UTRs

  1. Positive strand, negative direction: CAGCCTG at 4348, CATGGTG at 4109, CAGCCTG at 4036, CATCCTG at 3905, CACCCTG at 3743, CAGCCTG at 3297, CAAGGTG at 3143, CAGCCTG at 3127.

Core promoters

  1. Negative strand, positive direction: CATCATG at 4364.

Proximal promoters

  1. Negative strand, negative direction: CACCGTG at 2664.
  2. Positive strand, negative direction: CAGCCTG at 2769, CATGGTG at 2616, CAACATG at 2613, CACGGTG at 2526, CATGCTG at 2325, CATGGTG at 2279, CATGTTG at 1852, CAGGCTG at 1463, CATGGTG at 1209, CACGGTG at 655.


  1. Negative strand, positive direction: CATCCTG at 4185.

Distal promoters

  1. Negative strand, negative direction: CATCATG at 2342, CATCTTG at 286.
  2. Positive strand, negative direction: CAGCCTG at 2434, CAGCATG at 2276, CAGCCTG at 2267, CAACATG at 2151, CAGCCTG at 2008, CATCCTG at 1840, CAACATG at 1206, CAGCCTG at 1197, CAGCCTG at 898, CAGCGTG at 740, CAGCCTG at 731, CATCCTG at 595, CAGCCTG at 507.


  1. Negative strand, positive direction: CACCATG at 3827, CAGGCTG at 3639, CAGGATG at 3574, CAGGGTG at 3539, CACCCTG at 2967, CATGTTG at 2476, CACCATG at 2473, CAGGCTG at 2319, CATGATG at 2143, CAACCTG at 946, CAACCTG at 846, CACGCTG at 778.
  2. Positive strand, positive direction: CACGTTG at 2802, CATGGTG at 2599.

UPRE-1 random dataset samplings

  1. UPRE1r0: 5, CATCATG at 3097, CAGCGTG at 3076, CACCATG at 2602, CATCCTG at 1550, CAGCTTG at 717.
  2. UPRE1r1: 1, CAACTTG at 1138.
  3. UPRE1r2: 6, CACCGTG at 3354, CACCGTG at 1878, CAACGTG at 1697, CATCTTG at 1063, CACCCTG at 456, CATCTTG at 211.
  4. UPRE1r3: 1, CAGCTTG at 1501.
  5. UPRE1r4: 5, CATCGTG at 4271, CATCCTG at 3918, CAGCTTG at 1633, CAGCGTG at 1562, CACCCTG at 1152.
  6. UPRE1r5: 1, CAGCGTG at 370.
  7. UPRE1r6: 7, CACCATG at 3919, CACCTTG at 3633, CACCTTG at 3166, CAACTTG at 3066, CACCCTG at 941, CAACATG at 296, CAACATG at 43.
  8. UPRE1r7: 0.
  9. UPRE1r8: 4, CACCTTG at 2849, CACCGTG at 1405, CAGCCTG at 1184, CACCTTG at 498.
  10. UPRE1r9: 5, CAGCTTG at 4112, CATCTTG at 3410, CACCTTG at 2988, CAGCCTG at 2003, CAACATG at 1063.
  11. UPRE1r0ci: 5, CAGGCTG at 2840, CAAGCTG at 1297, CAGGCTG at 1249, CAAGATG at 1125, CATGCTG at 289.
  12. UPRE1r1ci: 3, CAGGCTG at 4143, CATGGTG at 2114, CAAGGTG at 566.
  13. UPRE1r2ci: 2, CAAGCTG at 3892, CAAGTTG at 2570.
  14. UPRE1r3ci: 4, CAGGATG at 2255, CAAGTTG at 1617, CAGGGTG at 1415, CACGATG at 1357.
  15. UPRE1r4ci: 3, CACGATG at 4033, CAAGGTG at 794, CAAGGTG at 332.
  16. UPRE1r5ci: 4, CAGGCTG at 1834, CACGGTG at 928, CATGCTG at 723, CAGGGTG at 334.
  17. UPRE1r6ci: 7, CAGGGTG at 3517, CAGGGTG at 3140, CAAGGTG at 3118, CAGGATG at 2707, CACGGTG at 2196, CATGTTG at 1548, CAGGTTG at 585.
  18. UPRE1r7ci: 2, CAGGGTG at 1724, CATGCTG at 875.
  19. UPRE1r8ci: 6, CATGGTG at 2900, CAGGTTG at 2481, CATGATG at 1792, CAAGTTG at 1729, CAGGGTG at 1593, CAGGTTG at 773.
  20. UPRE1r9ci: 6, CAGGATG at 3372, CAAGTTG at 1837, CAAGATG at 1423, CATGGTG at 1066, CAAGGTG at 953, CAGGCTG at 259.

UPRE1r UTRs

  1. UPRE1r0: CATCATG at 3097, CAGCGTG at 3076.
  2. UPRE1r2: CACCGTG at 3354.
  3. UPRE1r4: CATCGTG at 4271, CATCCTG at 3918.
  4. UPRE1r6: CACCATG at 3919, CACCTTG at 3633, CACCTTG at 3166, CAACTTG at 3066.
  5. UPRE1r8: CACCTTG at 2849.
  6. UPRE1r2ci: CAAGCTG at 3892.
  7. UPRE1r4ci: CACGATG at 4033.
  8. UPRE1r6ci: CAGGGTG at 3517, CAGGGTG at 3140, CAAGGTG at 3118.
  9. UPRE1r8ci: CATGGTG at 2900.

UPRE1r core promoters

  1. UPRE1r0ci: CAGGCTG at 2840.

UPRE1r proximal promoters

  1. UPRE1r0: CACCATG at 2602.
  2. UPRE1r6ci: CAGGATG at 2707.


  1. UPRE1r9: CAGCTTG at 4112.
  2. UPRE1r1ci: CAGGCTG at 4143.

UPRE1r distal promoters

  1. UPRE1r0: CATCCTG at 1550, CAGCTTG at 717.
  2. UPRE1r2: CACCGTG at 1878, CAACGTG at 1697, CATCTTG at 1063, CACCCTG at 456, CATCTTG at 211.
  3. UPRE1r4: CAGCTTG at 1633, CAGCGTG at 1562, CACCCTG at 1152.
  4. UPRE1r6: CACCCTG at 941, CAACATG at 296, CAACATG at 43.
  5. UPRE1r8: CACCGTG at 1405, CAGCCTG at 1184, CACCTTG at 498.
  6. UPRE1r0ci: CAAGCTG at 1297, CAGGCTG at 1249, CAAGATG at 1125, CATGCTG at 289.
  7. UPRE1r2ci: CAAGTTG at 2570.
  8. UPRE1r4ci: CAAGGTG at 794, CAAGGTG at 332.
  9. UPRE1r6ci: CACGGTG at 2196, CATGTTG at 1548, CAGGTTG at 585.
  10. UPRE1r8ci: CAGGTTG at 2481, CATGATG at 1792, CAAGTTG at 1729, CAGGGTG at 1593, CAGGTTG at 773.


  1. UPRE1r1: CAACTTG at 1138.
  2. UPRE1r3: CAGCTTG at 1501.
  3. UPRE1r5: CAGCGTG at 370.
  4. UPRE1r9: CATCTTG at 3410, CACCTTG at 2988, CAGCCTG at 2003, CAACATG at 1063.
  5. UPRE1r1ci: CATGGTG at 2114, CAAGGTG at 566.
  6. UPRE1r3ci: CAGGATG at 2255, CAAGTTG at 1617, CAGGGTG at 1415, CACGATG at 1357.
  7. UPRE1r5ci: CAGGCTG at 1834, CACGGTG at 928, CATGCTG at 723, CAGGGTG at 334.
  8. UPRE1r7ci: CAGGGTG at 1724, CATGCTG at 875.
  9. UPRE1r9ci: CAGGATG at 3372, CAAGTTG at 1837, CAAGATG at 1423, CATGGTG at 1066, CAAGGTG at 953, CAGGCTG at 259.

UPRE-1 analysis and results

Main article: Complex locus A1BG and ZNF497 § UPRE-1s

"The best characterized UPRE core sequence was UPRE-1 (CANCNTG) from S. cerevisiae".[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 8 2 4.0 4.0
Randoms UTR arbitrary negative 16 10 1.6 1.05
Randoms UTR alternate negative 5 10 0.5 1.05
Reals Core negative 0 2 0 0.25
Randoms Core negative 1 10 0.1 0.05
Reals Core positive 1 2 0.5 0.25
Randoms Core positive 0 10 0 0.05
Reals Proximal negative 11 2 5.5 3.0
Randoms Proximal negative 2 10 0.2 0.2
Reals Proximal positive 1 2 0.5 3.0
Randoms Proximal positive 2 10 0.2 0.2
Reals Distal negative 15 2 7.5 7.25
Randoms Distal negative 31 10 3.1 2.8
Reals Distal positive 14 2 7.0 7.25
Randoms Distal positive 25 10 2.5 2.8

Comparison:

The occurrences of real UPRE-1s are larger than the randoms. This suggests that the real UPRE-1s are likely active or activable.

See also

References

  1. ↑ 1.0 1.1 Niwed Kullawong, Sutipa Tanapongpipat, Lily Eurwilaichitr and Witoon Tirasophon (2018). "Unfolded Protein Response (UPR) Induced Hybrid Promoters for Heterologous Gene Expression in Pichia pastoris" (PDF). Chiang Mai Journal of Science. 45 (7): 2554–2565. Retrieved 11 January 2021.
  2. ↑ 2.0 2.1 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.

External links


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