Hac1p gene transcriptions: Difference between revisions

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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:
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:
# negative strand, negative direction, looking for CANCNTG, 3, CACCGTG at 2664, CATCATG at 2342, CATCTTG at 286, and complements.
# negative strand, negative direction, looking for CANCNTG, 3, CACCGTG at 2664, CATCATG at 2342, CATCTTG at 286, and complements.
# negative strand, positive direction, looking for CANCNTG, 0.
# 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.
# positive strand, negative direction, looking for CANCNTG, 0.
# 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.
# positive strand, positive direction, looking for CANCNTG, 0.
# positive strand, positive direction, looking for CANCNTG, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for GTNGNAC, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for GTNGNAC, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for GTNGNAC, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for GTNGNAC, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for CANGNTG, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for CANGNTG, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for CANGNTG, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for CANGNTG, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.

Revision as of 12:55, 12 January 2021

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

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. complement, negative strand, negative direction, looking for GTCGCAC, 1, GTCGCAC at 740.
  6. complement, negative strand, positive direction, looking for GTCGCAC, 0.
  7. complement, positive strand, negative direction, looking for GTCGCAC, 0.
  8. complement, positive strand, positive direction, looking for GTCGCAC, 0.
  9. inverse complement, negative strand, negative direction, looking for CACGCTG, 0.
  10. inverse complement, negative strand, positive direction, looking for CACGCTG, 1, CACGCTG at 778.
  11. inverse complement, positive strand, negative direction, looking for CACGCTG, 0.
  12. inverse complement, positive strand, positive direction, looking for CACGCTG, 0.
  13. inverse negative strand, negative direction, looking for GTGCGAC, 0.
  14. inverse negative strand, positive direction, looking for GTGCGAC, 0.
  15. inverse positive strand, negative direction, looking for GTGCGAC, 0.
  16. inverse positive strand, positive direction, looking for GTGCGAC, 1, GTGCGAC at 778.

KAR2 distal promoters

Positive strand: CAGCGTG at 740, and complement.

Negative strand: CACGCTG at 778, and complement.

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, 0.
  6. complement, negative strand, positive direction, looking for GTNGNAC, 0.
  7. complement, positive strand, negative direction, looking for GTNGNAC, 0.
  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, 0.
  11. inverse complement, positive strand, negative direction, looking for CANGNTG, 0.
  12. inverse complement, positive strand, positive direction, looking for CANGNTG, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse negative strand, positive direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  16. inverse positive strand, positive direction, looking for AAAAAAAA, 0.

See also

References

  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. 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