Inositol, choline-responsive element gene transcriptions

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

"When fused to the DNA-binding domain of [𝛃-galactosidase (Gal)] Gal4p, Ino2p but not Ino4p was able to activate a [upstream activation site] UASGAL-containing reporter gene even in the absence of the heterologous Fbfl subunit. By deletion studies, two separate transcriptional activation domains were identified in the N-terminal part of Ino2p. Thus, the [basic helix-loop-helix] bHLH domains of Ino2p and Ino4p constitute the dimerization/DNA-binding module of Fbfl mediating its interaction with the [inositol, choline-responsive element] ICRE, while transcriptional activation is effected exclusively by Ino2p."[1]

Human genes

Interactions

Consensus sequences

"This ICRE (consensus sequence TYTTCACATGY) contains the core sequence CANNTG, which is also known as an E box and which serves as a recognition site for DNA-binding proteins of the basic helix-loop-helix (bHLH) family (3). Members of the bHLH family comprise determinants of cellular differentiation and proliferation in mammalian and invertebrate systems such as the myogenic transcription factors MyoD, MRF4, myogenin and Myf-5(4) as well as factors not restricted to specialized tisues (E12, E47, daughterless, c-Myc and Mad; 5-7). Proteins of the bHLH group may form either homodimers or heterodimers or both, dependent on the individual structure of the respective interaction surface provided by the HLH domain(8)."[1]

  1. negative strand in the negative direction is SuccessablesE--.bas, looking for CANNTG: 2, CACATG at 797, CACATG at 324, and complements.
  2. negative strand in the positive direction is SuccessablesE-+.bas, looking for CANNTG: 4, CACATG at 3956, CACATG at 3742, CACATG at 3707, CACATG at 2031, and complements.
  3. positive strand in the negative direction is SuccessablesE+-.bas, looking for CANNTG: 1, CACATG at 2667, and complements.

"The UAS INO is thus also referred to as the inositol/choline-responsive element (ICRE). The UAS INO contains the consensus sequence CATGTGAAAT, which includes the canonical basic helix-loop-helix (bHLH) binding site CANNTG (Lopes et al. 1991)."[2]

"All IN01 fusion constructs that retained regulation in response to the phospholipid precursors inositol and choline, contained at least one copy of a nine bp repeated element (consensus, 5'-ATGTGAAAT-3')."[3]

CANNTG samplings

For the Basic programs (starting with SuccessablesE.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 looking for, and found:

  1. negative strand in the negative direction is SuccessablesE--.bas, looking for CANNTG: 10, CAGATG at 4212, CATTTG at 3482, CAGATG at 2988, CACCTG at 2116, CAGTTG at 1513, CAGATG at 1224, CAAGTG at 1179, CACATG at 797, CAGATG at 481, CACATG at 324, and complements.
  2. negative strand in the positive direction is SuccessablesE-+.bas, looking for CANNTG: 26, CACTTG at 4015, CATGTG at 3958, CACATG at 3956, CATGTG at 3902, CAGCTG at 3777, CACATG at 3742, CACATG at 3707, CAGATG at 3475, CATCTG at 3404, CAGCTG at 3241, CAGGTG at 3149, CACCTG at 3046, CACCTG at 2568, CAAGTG at 2510, CACCTG at 2432, CAGCTG at 2404, CAGGTG at 2374, CACCTG at 2249, CAGGTG at 2127, CAGCTG at 2054, CACATG at 2031, CAGGTG at 1968, CACCTG at 958, CACCTG at 858, CACGTG at 570, CAGGTG at 196, and complements.
  3. positive strand in the negative direction is SuccessablesE+-.bas, looking for CANNTG: 21, CACTTG at 4011, CACCTG at 3969, CAGGTG at 3953, CAGATG at 3919, CAACTG at 3850, CAGATG at 3627, CAGATG at 3620, CACTTG at 3241, CACTTG at 3102, CACTTG at 2920, CACATG at 2667, CACTTG at 2579, CAGGTG at 2570, CACTTG at 2126, CAGGTG at 2079, CAAATG at 1579, CACCTG at 1172, CACCTG at 1130, CACCTG at 393, CATTTG at 364, CATATG at 41, and complements.
  4. positive strand in the positive direction is SuccessablesE++.bas, looking for CANNTG: 11, CAAGTG at 4202, CACTTG at 3936, CACGTG at 3884, CAGGTG at 3086, CACGTG at 2961, CAGGTG at 2028, CAGGTG at 1843, CACGTG at 1219, CATGTG at 567, CACGTG at 547, CACCTG at 186, and complements.

ICRE (Schwank) samplings

Copying an apparent consensus sequence of T(C/T)TTCACATG(C/T), TCTTCACAT and putting it in "⌘F" finds none located 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 T(C/T)TTCANNTG(C/T) (starting with SuccessablesICRE.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 T(C/T)TTCANNTG(C/T), 0.
  2. negative strand, positive direction, looking for T(C/T)TTCANNTG(C/T), 0.
  3. positive strand, negative direction, looking for T(C/T)TTCANNTG(C/T), 0.
  4. positive strand, positive direction, looking for T(C/T)TTCANNTG(C/T), 0.
  5. complement, negative strand, negative direction, looking for A(A/G)AAGTNNAC(A/G), 0.
  6. complement, negative strand, positive direction, looking for A(A/G)AAGTNNAC(A/G), 0.
  7. complement, positive strand, negative direction, looking for A(A/G)AAGTNNAC(A/G), 0.
  8. complement, positive strand, positive direction, looking for A(A/G)AAGTNNAC(A/G), 0.
  9. inverse complement, negative strand, negative direction, looking for (A/G)CANNTGAA(A/G)A, 0.
  10. inverse complement, negative strand, positive direction, looking for (A/G)CANNTGAA(A/G)A, 2, GCACCTGAAGA at 962, GCACCTGAAGA at 862.
  11. inverse complement, positive strand, negative direction, looking for (A/G)CANNTGAA(A/G)A, 1, ACATTTGAAGA at 368.
  12. inverse complement, positive strand, positive direction, looking for (A/G)CANNTGAA(A/G)A, 0.
  13. inverse negative strand, negative direction, looking for (C/T)GTNNACTT(C/T)T, 1, TGTAAACTTCT at 368.
  14. inverse negative strand, positive direction, looking for (C/T)GTNNACTT(C/T)T, 0.
  15. inverse positive strand, negative direction, looking for (C/T)GTNNACTT(C/T)T, 0.
  16. inverse positive strand, positive direction, looking for (C/T)GTNNACTT(C/T)T, 2, CGTGGACTTCT at 962, CGTGGACTTCT at 862.

ICRE (Schwank) negative direction distal promoters

  1. Positive strand, negative direction: ACATTTGAAGA at 368.

ICRE (Schwank) positive direction distal promoters

  1. Negative strand, positive direction: GCACCTGAAGA at 962, GCACCTGAAGA at 862.

ICRE (Schwank) random dataset samplings

  1. ICRE(Schwank)r0: 0.
  2. ICRE(Schwank)r1: 0.
  3. ICRE(Schwank)r2: 0.
  4. ICRE(Schwank)r3: 0.
  5. ICRE(Schwank)r4: 0.
  6. ICRE(Schwank)r5: 0.
  7. ICRE(Schwank)r6: 0.
  8. ICRE(Schwank)r7: 0.
  9. ICRE(Schwank)r8: 0.
  10. ICRE(Schwank)r9: 0.
  11. ICRE(Schwank)r0ci: 0.
  12. ICRE(Schwank)r1ci: 0.
  13. ICRE(Schwank)r2ci: 0.
  14. ICRE(Schwank)r3ci: 0.
  15. ICRE(Schwank)r4ci: 0.
  16. ICRE(Schwank)r5ci: 0.
  17. ICRE(Schwank)r6ci: 0.
  18. ICRE(Schwank)r7ci: 0.
  19. ICRE(Schwank)r8ci: 0.
  20. ICRE(Schwank)r9ci: 0.

ICRE (Schwank) analysis and results

Main article: Complex locus A1BG and ZNF497 § ICRE (Schwank)

"This ICRE (consensus sequence TYTTCACATGY) contains the core sequence CANNTG, which is also known as an E box and which serves as a recognition site for DNA-binding proteins of the basic helix-loop-helix (bHLH) family (3)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
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 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 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 2 2 1 1 ± 1 (-+2,++0)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real ICREs (Schwank) are greater than the randoms which are all zeros. This suggests that the real ICREs (Schwank) are likely active or activable.

ICRE (Case) samplings

For the Basic programs testing consensus sequence CANNTGAAAT (starting with SuccessablesICREL.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 CANNTGAAAT, 0.
  2. negative strand, positive direction, looking for CANNTGAAAT, 0.
  3. positive strand, negative direction, looking for CANNTGAAAT, 0.
  4. positive strand, positive direction, looking for CANNTGAAAT, 0.
  5. complement, negative strand, negative direction, looking for GTNNACTTTA, 0.
  6. complement, negative strand, positive direction, looking for GTNNACTTTA, 0.
  7. complement, positive strand, negative direction, looking for GTNNACTTTA, 0.
  8. complement, positive strand, positive direction, looking for GTNNACTTTA, 0.
  9. inverse complement, negative strand, negative direction, looking for ATTTCANNTG, 0.
  10. inverse complement, negative strand, positive direction, looking for ATTTCANNTG, 0.
  11. inverse complement, positive strand, negative direction, looking for ATTTCANNTG, 0.
  12. inverse complement, positive strand, positive direction, looking for ATTTCANNTG, 0.
  13. inverse negative strand, negative direction, looking for TAAAGTNNAC, 0.
  14. inverse negative strand, positive direction, looking for TAAAGTNNAC, 0.
  15. inverse positive strand, negative direction, looking for TAAAGTNNAC, 0.
  16. inverse positive strand, positive direction, looking for TAAAGTNNAC, 0.

ICRE (Lopes) samplings

For the Basic programs testing consensus sequence ATGTGAAAT (starting with SuccessablesICREL2.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 ANNTGAAAT, 0.
  2. negative strand, positive direction, looking for ANNTGAAAT, 0.
  3. positive strand, negative direction, looking for ANNTGAAAT, 1, AGCTGAAAT at 2747.
  4. positive strand, positive direction, looking for ANNTGAAAT, 0.
  5. complement, negative strand, negative direction, looking for TNNACTTTA, 1, TCGACTTTA at 2747.
  6. complement, negative strand, positive direction, looking for TNNACTTTA, 0.
  7. complement, positive strand, negative direction, looking for TNNACTTTA, 0.
  8. complement, positive strand, positive direction, looking for TNNACTTTA, 0.
  9. inverse complement, negative strand, negative direction, looking for ATTTCANNT, 0.
  10. inverse complement, negative strand, positive direction, looking for ATTTCANNT, 0.
  11. inverse complement, positive strand, negative direction, looking for ATTTCANNT, 0.
  12. inverse complement, positive strand, positive direction, looking for ATTTCANNT, 0.
  13. inverse negative strand, negative direction, looking for TAAAGTNNA, 0.
  14. inverse negative strand, positive direction, looking for TAAAGTNNA, 0.
  15. inverse positive strand, negative direction, looking for TAAAGTNNA, 0.
  16. inverse positive strand, positive direction, looking for TAAAGTNNA, 0.

ICRE (Lopes) negative direction proximal promoters

  1. Positive strand, negative direction: AGCTGAAAT at 2747.

ICRE (Lopes) random dataset samplings

  1. ICRE(Lopes)r0: 0.
  2. ICRE(Lopes)r1: 0.
  3. ICRE(Lopes)r2: 1, ACCTGAAAT at 2128.
  4. ICRE(Lopes)r3: 1, ATGTGAAAT at 97.
  5. ICRE(Lopes)r4: 0.
  6. ICRE(Lopes)r5: 0.
  7. ICRE(Lopes)r6: 0.
  8. ICRE(Lopes)r7: 0.
  9. ICRE(Lopes)r8: 0.
  10. ICRE(Lopes)r9: 0.
  11. ICRE(Lopes)r0ci: 0.
  12. ICRE(Lopes)r1ci: 0.
  13. ICRE(Lopes)r2ci: 1, ATTTCACGT at 3409.
  14. ICRE(Lopes)r3ci: 1, ATTTCATTT at 924.
  15. ICRE(Lopes)r4ci: 0.
  16. ICRE(Lopes)r5ci: 1, ATTTCAACT at 1179.
  17. ICRE(Lopes)r6ci: 0.
  18. ICRE(Lopes)r7ci: 0.
  19. ICRE(Lopes)r8ci: 1, ATTTCATAT at 876.
  20. ICRE(Lopes)r9ci: 0.

ICRE(Lopes)r arbitrary UTRs

  1. ICRE(Lopes)r2ci: ATTTCACGT at 3409.

ICRE(Lopes)r arbitrary negative direction distal promoters

  1. ICRE(Lopes)r2: ACCTGAAAT at 2128.

ICRE(Lopes)r alternate negative direction distal promoters

  1. ICRE(Lopes)r3: ATGTGAAAT at 97.
  2. ICRE(Lopes)r3ci: ATTTCATTT at 924.
  3. ICRE(Lopes)r5ci: ATTTCAACT at 1179.

ICRE(Lopes)r arbitrary positive direction distal promoters

  1. ICRE(Lopes)r3: ATGTGAAAT at 97.
  2. ICRE(Lopes)r3ci: ATTTCATTT at 924.
  3. ICRE(Lopes)r5ci: ATTTCAACT at 1179.

ICRE(Lopes)r alternate positive direction distal promoters

  1. ICRE(Lopes)r2: ACCTGAAAT at 2128.
  2. ICRE(Lopes)r2ci: ATTTCACGT at 3409.

ICRE (Lopes) analysis and results

Main article: Complex locus A1BG and ZNF497 § ICRE (Lopes)

"The UAS INO is thus also referred to as the inositol/choline-responsive element (ICRE). The UAS INO contains the consensus sequence CATGTGAAAT, which includes the canonical basic helix-loop-helix (bHLH) binding site CANNTG (Lopes et al. 1991)."[2]

"All IN01 fusion constructs that retained regulation in response to the phospholipid precursors inositol and choline, contained at least one copy of a nine bp repeated element (consensus, 5'-ATGTGAAAT-3')."[3]

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 1 2 0.5 0.5 ± 0.5 (+-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 0 2 0 0
Randoms Distal arbitrary negative 1 10 0.1 0.2
Randoms Distal alternate negative 3 10 0.3 0.2
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 3 10 0.3 0.25
Randoms Distal alternate positive 2 10 0.2 0.25

Comparison:

The occurrence of real ICRE (Lopes) is greater than the randoms. This suggests that the real ICRE (Lopes) is likely active or activable.

See also

References

  1. ↑ 1.0 1.1 1.2 Sabine Schwank, Ronald Ebbert, Karin Rautenstrau𝛃, Eckhart Schweizer and Hans-Joachim Schüller (25 January 1995). "Yeast transcriptional activator IN02 interacts as an Ino2p/Ino4p basic helix-loop-helix heteromeric complex with the inositol/choline responsive element necessary for expression of phospholipid biosynthetic genes in Saccharomyces cerevisiae" (PDF). Nucleic Acids Research. 23 (2): 230–37. doi:10.1093/nar/23.2.230. Retrieved 10 August 2020.
  2. ↑ 2.0 2.1 Kendall C. Case, Michael Salsaa, Wenxi Yu and Miriam L. Greenberg (28 December 2018). Gomez-Cambronero J., Frohman M., ed. Regulation of Inositol Biosynthesis: Balancing Health and Pathophysiology, In: Lipid Signaling in Human Diseases. Handbook of Experimental Pharmacology, vol 259. Cham: Springer. pp. 221–260. doi:10.1007/164_2018_181. ISBN 978-3-030-33667-7. Retrieved 29 January 2021.
  3. ↑ 3.0 3.1 John M. Lopes, Jeanne P. Hirsch, Patricia A. Chorgo, Karen L. Schulze and Susan A. Henry (April 11, 1991). "Analysis of sequences in the INOl promoter that are involved in its regulation by phospholipid precursors" (PDF). Nucleic Acids Research. 19 (7): 1687–1693. doi:10.1093/nar/19.7.1687. PMID 2027776. Retrieved 29 January 2021.

External links


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