Carbon source-responsive element gene transcriptions

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

"Deletion analysis of the ICL1 promoter led to the identification of an upstream activating sequence element, UASICL1 (5' CATTCATCCG 3'), necessary and sufficient for conferring carbon source-dependent regulation on a heterologous reporter gene. Similar sequence motifs were also found in the upstream regions of coregulated genes involved in gluconeogenesis. This carbon source-responsive element (CSRE) interacts with a protein factor, designated Ang1 (activator of nonfermentative growth), detectable only in extracts derived from derepressed cells."[1]

"Carbon source-responsive element (CSRE) are bound by the transcriptional activators Sip4 and Cat8 to induce the expression of gluconeogenesis genes in S. cerevisiae (Hiesinger, Roth, Meissner, & Schuller, 2001)."[2]

CSRE samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CATTCATCCG and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CATTCATCCG (starting with SuccessablesCSRE.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 CATTCATCCG, 0.
  2. positive strand, negative direction, looking for CATTCATCCG, 0.
  3. positive strand, positive direction, looking for CATTCATCCG, 0.
  4. negative strand, positive direction, looking for CATTCATCCG, 0.
  5. complement, negative strand, negative direction, looking for GTAAGTAGGC, 0.
  6. complement, positive strand, negative direction, looking for GTAAGTAGGC, 0.
  7. complement, positive strand, positive direction, looking for GTAAGTAGGC, 0.
  8. complement, negative strand, positive direction, looking for GTAAGTAGGC, 0.
  9. inverse complement, negative strand, negative direction, looking for CGGATGAATG, 0.
  10. inverse complement, positive strand, negative direction, looking for CGGATGAATG, 0.
  11. inverse complement, positive strand, positive direction, looking for CGGATGAATG, 0.
  12. inverse complement, negative strand, positive direction, looking for CGGATGAATG, 0.
  13. inverse negative strand, negative direction, looking for GCCTACTTAC, 0.
  14. inverse positive strand, negative direction, looking for GCCTACTTAC, 0.
  15. inverse positive strand, positive direction, looking for GCCTACTTAC, 0.
  16. inverse negative strand, positive direction, looking for GCCTACTTAC, 0.

TCCG samplings

For the Basic programs testing consensus sequence TCCG (starting with SuccessablesTCCG.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: 64, TCCG at 4279, TCCG at 4273, TCCG at 4254, TCCG at 4166, TCCG at 4142, TCCG at 4103, TCCG at 3997, TCCG at 3991, TCCG at 3927, TCCG at 3896, TCCG at 3872, TCCG at 3716, TCCG at 3612, TCCG at 3586, TCCG at 3574, TCCG at 3475, TCCG at 3448, TCCG at 3442, TCCG at 3397, TCCG at 3227, TCCG at 3221, TCCG at 3088, TCCG at 3082, TCCG at 2693, TCCG at 2565, TCCG at 2559, TCCG at 2520, TCCG at 2515, TCCG at 2390, TCCG at 2364, TCCG at 2358, TCCG at 2229, TCCG at 2223, TCCG at 2106, TCCG at 2073, TCCG at 1964, TCCG at 1938, TCCG at 1797, TCCG at 1750, TCCG at 1557, TCCG at 1461, TCCG at 1311, TCCG at 1285, TCCG at 1279, TCCG at 1108, TCCG at 1020, TCCG at 994, TCCG at 988, TCCG at 949, TCCG at 854, TCCG at 828, TCCG at 822, TCCG at 698, TCCG at 694, TCCG at 688, TCCG at 649, TCCG at 562, TCCG at 552, TCCG at 451, TCCG at 425, TCCG at 415, TCCG at 371, TCCG at 263, TCCG at 120.
  2. Positive strand, negative direction: 2, TCCG at 2353, TCCG at 1501.
  3. Positive strand, positive direction, looking for TCCG, 45, TCCG at 4402, TCCG at 4189, TCCG at 3754, TCCG at 3695, TCCG at 3688, TCCG at 3675, TCCG at 3659, TCCG at 3637, TCCG at 3585, TCCG at 3523, TCCG at 3485, TCCG at 3035, TCCG at 2877, TCCG at 2807, TCCG at 2694, TCCG at 2551, TCCG at 2483, TCCG at 2367, TCCG at 2317, TCCG at 2116, TCCG at 1906, TCCG at 1856, TCCG at 1568, TCCG at 1512, TCCG at 1484, TCCG at 1428, TCCG at 1384, TCCG at 1328, TCCG at 1260, TCCG at 1176, TCCG at 1092, TCCG at 1008, TCCG at 924, TCCG at 824, TCCG at 672, TCCG at 588, TCCG at 553, TCCG at 504, TCCG at 370, TCCG at 315, TCCG at 274, TCCG at 211, TCCG at 158, TCCG at 91, TCCG at 9.
  4. Negative strand, positive direction, looking for TCCG, 11, TCCG at 4243, TCCG at 3798, TCCG at 1961, TCCG at 1445, TCCG at 1434, TCCG at 1345, TCCG at 1334, TCCG at 1098, TCCG at 735, TCCG at 678, TCCG at 307.
  5. inverse complement, negative strand, negative direction: 28, CGGA at 4522, CGGA at 4347, CGGA at 4298, CGGA at 4119, CGGA at 4035, CGGA at 3840, CGGA at 3568, CGGA at 3296, CGGA at 3198, CGGA at 3126, CGGA at 2768, CGGA at 2670, CGGA at 2536, CGGA at 2433, CGGA at 2335, CGGA at 2266, CGGA at 2007, CGGA at 1621, CGGA at 1504, CGGA at 1256, CGGA at 1196, CGGA at 1063, CGGA at 965, CGGA at 897, CGGA at 730, CGGA at 665, CGGA at 506, CGGA at 457.
  6. inverse complement, positive strand, negative direction: 8, CGGA at 4325, CGGA at 2728, CGGA at 2393, CGGA at 2355, CGGA at 1810, CGGA at 857, CGGA at 701, CGGA at 428.
  7. inverse complement, positive strand, positive direction: 49, CGGA at 4404, CGGA at 4305, CGGA at 4239, CGGA at 4191, CGGA at 3756, CGGA at 3682, CGGA at 3677, CGGA at 3432, CGGA at 3360, CGGA at 3286, CGGA at 3102, CGGA at 3037, CGGA at 2986, CGGA at 2898, CGGA at 2889, CGGA at 2879, CGGA at 2528, CGGA at 2522, CGGA at 2479, CGGA at 2392, CGGA at 1858, CGGA at 1796, CGGA at 1597, CGGA at 1514, CGGA at 1467, CGGA at 1430, CGGA at 1409, CGGA at 1367, CGGA at 1330, CGGA at 1309, CGGA at 1303, CGGA at 1262, CGGA at 1234, CGGA at 1010, CGGA at 989, CGGA at 926, CGGA at 905, CGGA at 889, CGGA at 826, CGGA at 805, CGGA at 723, CGGA at 674, CGGA at 596, CGGA at 590, CGGA at 460, CGGA at 433, CGGA at 284, CGGA at 249, CGGA at 132.
  8. inverse complement, negative strand, positive direction: 9, CGGA at 4346, CGGA at 3516, CGGA at 1691, CGGA at 1530, CGGA at 1203, CGGA at 1087, CGGA at 744, CGGA at 357, CGGA at 300.

TCCG (4560-2846) UTRs

  1. Negative strand, negative direction: CGGA at 4522, CGGA at 4347, CGGA at 4298, TCCG at 4279, TCCG at 4273, TCCG at 4254, TCCG at 4166, TCCG at 4142, CGGA at 4119, TCCG at 4103, CGGA at 4035, TCCG at 3997, TCCG at 3991, TCCG at 3927, TCCG at 3896, TCCG at 3872, CGGA at 3840, TCCG at 3716, TCCG at 3612, TCCG at 3586, TCCG at 3574, CGGA at 3568, TCCG at 3475, TCCG at 3448, TCCG at 3442, TCCG at 3397, CGGA at 3296, TCCG at 3227, TCCG at 3221, CGGA at 3198, CGGA at 3126, TCCG at 3088, TCCG at 3082.
  2. Positive strand, negative direction: CGGA at 4325.

TCCG positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: CGGA at 4346.
  2. Positive strand, positive direction: CGGA at 4404, TCCG at 4402, CGGA at 4305.

TCCG negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: CGGA at 2768, TCCG at 2693, CGGA at 2670.
  2. Positive strand, negative direction: CGGA at 2728.

TCCG positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: TCCG at 4243.
  2. Positive strand, positive direction: CGGA at 4239, CGGA at 4191, TCCG at 4189.

TCCG negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TCCG at 2565, TCCG at 2559, CGGA at 2536, TCCG at 2520, TCCG at 2515, CGGA at 2433, TCCG at 2390, TCCG at 2364, TCCG at 2358, CGGA at 2335, CGGA at 2266, TCCG at 2229, TCCG at 2223, TCCG at 2106, TCCG at 2073, CGGA at 2007, TCCG at 1964, TCCG at 1938, TCCG at 1797, TCCG at 1750, CGGA at 1621, TCCG at 1557, CGGA at 1504, TCCG at 1461, TCCG at 1311, TCCG at 1285, TCCG at 1279, CGGA at 1256, CGGA at 1196, TCCG at 1108, CGGA at 1063, TCCG at 1020, TCCG at 994, TCCG at 988, CGGA at 965, TCCG at 949, CGGA at 897, TCCG at 854, TCCG at 828, TCCG at 822, CGGA at 730, TCCG at 698, TCCG at 694, TCCG at 688, CGGA at 665, TCCG at 649, TCCG at 562, TCCG at 552, CGGA at 506, CGGA at 457, TCCG at 451, TCCG at 425, TCCG at 415, TCCG at 371, TCCG at 263, TCCG at 120.
  2. Positive strand, negative direction: CGGA at 2393, CGGA at 2355, TCCG at 2353, CGGA at 1810, TCCG at 1501, CGGA at 857, CGGA at 701, CGGA at 428.

TCCG positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TCCG at 3798, CGGA at 3516, TCCG at 1961, CGGA at 1691, CGGA at 1530, TCCG at 1445, TCCG at 1434, TCCG at 1345, TCCG at 1334, CGGA at 1203, TCCG at 1098, CGGA at 1087, CGGA at 744, TCCG at 735, TCCG at 678, CGGA at 357, TCCG at 307, CGGA at 300.
  2. Positive strand, positive direction: CGGA at 3756, TCCG at 3754, TCCG at 3695, TCCG at 3688, CGGA at 3682, CGGA at 3677, TCCG at 3675, TCCG at 3659, TCCG at 3637, TCCG at 3585, TCCG at 3523, TCCG at 3485, CGGA at 3432, CGGA at 3360, CGGA at 3286, CGGA at 3102, CGGA at 3037, TCCG at 3035, CGGA at 2986, CGGA at 2898, CGGA at 2889, CGGA at 2879, TCCG at 2877, TCCG at 2807, TCCG at 2694, CGGA at 2528, CGGA at 2522, TCCG at 2551, TCCG at 2483, CGGA at 2479, CGGA at 2392, TCCG at 2367, TCCG at 2317, TCCG at 2116, TCCG at 1906, CGGA at 1858, TCCG at 1856, CGGA at 1796, CGGA at 1597, TCCG at 1568, CGGA at 1514, TCCG at 1512, TCCG at 1484, CGGA at 1467, CGGA at 1430, TCCG at 1428, CGGA at 1409, TCCG at 1384, CGGA at 1367, CGGA at 1330, TCCG at 1328, CGGA at 1309, CGGA at 1303, CGGA at 1262, TCCG at 1260, CGGA at 1234, TCCG at 1176, TCCG at 1092, CGGA at 1010, TCCG at 1008, CGGA at 989, CGGA at 926, TCCG at 924, CGGA at 905, CGGA at 889, CGGA at 826, TCCG at 824, CGGA at 805, CGGA at 723, CGGA at 674, TCCG at 672, CGGA at 596, CGGA at 590, TCCG at 588, TCCG at 553, TCCG at 504, CGGA at 460, CGGA at 433, TCCG at 370, TCCG at 315, CGGA at 284, TCCG at 274, CGGA at 249, TCCG at 211, TCCG at 158, CGGA at 132, TCCG at 91, TCCG at 9.

TCCG random dataset samplings

  1. TCCGr0: 13, TCCG at 4417, TCCG at 4318, TCCG at 4117, TCCG at 3378, TCCG at 2897, TCCG at 2763, TCCG at 2748, TCCG at 2669, TCCG at 2508, TCCG at 948, TCCG at 928, TCCG at 876, TCCG at 366.
  2. TCCGr1: 20, TCCG at 4303, TCCG at 4076, TCCG at 4068, TCCG at 3925, TCCG at 3840, TCCG at 3776, TCCG at 3649, TCCG at 3035, TCCG at 2973, TCCG at 2814, TCCG at 2083, TCCG at 1836, TCCG at 1678, TCCG at 1643, TCCG at 956, TCCG at 816, TCCG at 801, TCCG at 657, TCCG at 572, TCCG at 325.
  3. TCCGr2: 19, TCCG at 4124, TCCG at 3971, TCCG at 3561, TCCG at 3548, TCCG at 3396, TCCG at 3367, TCCG at 2844, TCCG at 2614, TCCG at 1664, TCCG at 1576, TCCG at 1248, TCCG at 1101, TCCG at 796, TCCG at 647, TCCG at 637, TCCG at 569, TCCG at 522, TCCG at 415, TCCG at 411.
  4. TCCGr3: 15, TCCG at 3955, TCCG at 3657, TCCG at 3374, TCCG at 3133, TCCG at 2722, TCCG at 2473, TCCG at 2361, TCCG at 2307, TCCG at 1823, TCCG at 1581, TCCG at 1196, TCCG at 482, TCCG at 413, TCCG at 115, TCCG at 81.
  5. TCCGr4: 17, TCCG at 3873, TCCG at 3765, TCCG at 3490, TCCG at 2818, TCCG at 2740, TCCG at 2734, TCCG at 2172, TCCG at 2114, TCCG at 2092, TCCG at 1814, TCCG at 1269, TCCG at 893, TCCG at 778, TCCG at 677, TCCG at 396, TCCG at 381, TCCG at 12.
  6. TCCGr5: 22, TCCG at 4290, TCCG at 4253, TCCG at 4036, TCCG at 3462, TCCG at 3451, TCCG at 3381, TCCG at 3368, TCCG at 2822, TCCG at 2520, TCCG at 2470, TCCG at 2460, TCCG at 2358, TCCG at 1541, TCCG at 1222, TCCG at 1157, TCCG at 1022, TCCG at 779, TCCG at 397, TCCG at 296, TCCG at 282, TCCG at 51, TCCG at 5.
  7. TCCGr6: 14, TCCG at 4295, TCCG at 4210, TCCG at 3578, TCCG at 3338, TCCG at 2817, TCCG at 2787, TCCG at 2756, TCCG at 2642, TCCG at 1797, TCCG at 1188, TCCG at 1154, TCCG at 698, TCCG at 555, TCCG at 491.
  8. TCCGr7: 18, TCCG at 4465, TCCG at 4088, TCCG at 3838, TCCG at 3795, TCCG at 3554, TCCG at 3004, TCCG at 2740, TCCG at 2665, TCCG at 1905, TCCG at 1826, TCCG at 1739, TCCG at 1477, TCCG at 1384, TCCG at 1121, TCCG at 686, TCCG at 434, TCCG at 396, TCCG at 212.
  9. TCCGr8: 17, TCCG at 4470, TCCG at 4253, TCCG at 2552, TCCG at 2487, TCCG at 2442, TCCG at 2123, TCCG at 2076, TCCG at 2044, TCCG at 2010, TCCG at 1940, TCCG at 1460, TCCG at 1024, TCCG at 968, TCCG at 918, TCCG at 363, TCCG at 118, TCCG at 84.
  10. TCCGr9: 20, TCCG at 4502, TCCG at 4444, TCCG at 4289, TCCG at 4102, TCCG at 3661, TCCG at 3339, TCCG at 3010, TCCG at 2929, TCCG at 2807, TCCG at 2765, TCCG at 2721, TCCG at 2098, TCCG at 2025, TCCG at 1951, TCCG at 1566, TCCG at 1556, TCCG at 1345, TCCG at 1038, TCCG at 776, TCCG at 526.
  11. TCCGr0ci: 18, CGGA at 4320, CGGA at 3911, CGGA at 3361, CGGA at 3216, CGGA at 2750, CGGA at 2665, CGGA at 2632, CGGA at 2203, CGGA at 2033, CGGA at 2012, CGGA at 1894, CGGA at 1700, CGGA at 1431, CGGA at 1311, CGGA at 1144, CGGA at 950, CGGA at 730, CGGA at 673.
  12. TCCGr1ci: 15, CGGA at 3983, CGGA at 3560, CGGA at 3504, CGGA at 3214, CGGA at 2464, CGGA at 2315, CGGA at 1787, CGGA at 1508, CGGA at 1419, CGGA at 1300, CGGA at 1153, CGGA at 1121, CGGA at 937, CGGA at 173, CGGA at 120.
  13. TCCGr2ci: 13, CGGA at 4450, CGGA at 4266, CGGA at 4126, CGGA at 4083, CGGA at 3875, CGGA at 3865, CGGA at 3565, CGGA at 3434, CGGA at 3371, CGGA at 2886, CGGA at 2402, CGGA at 2226, CGGA at 1578.
  14. TCCGr3ci: 9, CGGA at 4203, CGGA at 3926, CGGA at 3147, CGGA at 2897, CGGA at 2564, CGGA at 1486, CGGA at 1326, CGGA at 955, CGGA at 759.
  15. TCCGr4ci: 23, CGGA at 4497, CGGA at 4382, CGGA at 4262, CGGA at 4233, CGGA at 4217, CGGA at 4019, CGGA at 3829, CGGA at 2922, CGGA at 2820, CGGA at 2794, CGGA at 2786, CGGA at 2552, CGGA at 2528, CGGA at 2524, CGGA at 2507, CGGA at 1276, CGGA at 1129, CGGA at 1014, CGGA at 879, CGGA at 614, CGGA at 573, CGGA at 556, CGGA at 505.
  16. TCCGr5ci: 11, CGGA at 4521, CGGA at 3540, CGGA at 3336, CGGA at 3182, CGGA at 3029, CGGA at 3023, CGGA at 2079, CGGA at 1380, CGGA at 1054, CGGA at 575, CGGA at 497.
  17. TCCGr6ci: 18, CGGA at 4244, CGGA at 4127, CGGA at 3607, CGGA at 3413, CGGA at 3389, CGGA at 3298, CGGA at 3223, CGGA at 2996, CGGA at 2819, CGGA at 2613, CGGA at 2577, CGGA at 2267, CGGA at 2120, CGGA at 1190, CGGA at 1156, CGGA at 516, CGGA at 441, CGGA at 406.
  18. TCCGr7ci: 24, CGGA at 4539, CGGA at 4111, CGGA at 4097, CGGA at 3902, CGGA at 3880, CGGA at 3864, CGGA at 3659, CGGA at 3421, CGGA at 3302, CGGA at 3217, CGGA at 3213, CGGA at 3195, CGGA at 2995, CGGA at 2205, CGGA at 2006, CGGA at 1386, CGGA at 1295, CGGA at 1283, CGGA at 1221, CGGA at 986, CGGA at 787, CGGA at 693, CGGA at 667, CGGA at 51.
  19. TCCGr8ci: 15, CGGA at 4408, CGGA at 3881, CGGA at 3614, CGGA at 3404, CGGA at 3029, CGGA at 3005, CGGA at 2936, CGGA at 2754, CGGA at 2489, CGGA at 2125, CGGA at 2078, CGGA at 1462, CGGA at 1055, CGGA at 794, CGGA at 683.
  20. TCCGr9ci: 25, CGGA at 4385, CGGA at 4232, CGGA at 4163, CGGA at 3919, CGGA at 3910, CGGA at 3631, CGGA at 3422, CGGA at 3396, CGGA at 3231, CGGA at 3061, CGGA at 2882, CGGA at 2831, CGGA at 2601, CGGA at 2470, CGGA at 2181, CGGA at 2151, CGGA at 2047, CGGA at 1843, CGGA at 1708, CGGA at 1143, CGGA at 1084, CGGA at 557, CGGA at 367, CGGA at 293, CGGA at 115.

TCCGr arbitrary (evens) (4560-2846) UTRs

  1. TCCGr0: TCCG at 4417, TCCG at 4318, TCCG at 4117, TCCG at 3378, TCCG at 2897.
  2. TCCGr2: TCCG at 4124, TCCG at 3971, TCCG at 3561, TCCG at 3548, TCCG at 3396, TCCG at 3367.
  3. TCCGr4: TCCG at 3873, TCCG at 3765, TCCG at 3490.
  4. TCCGr6: TCCG at 4295, TCCG at 4210, TCCG at 3578, TCCG at 3338.
  5. TCCGr8: TCCG at 4470, TCCG at 4253.
  6. TCCGr0ci: CGGA at 4320, CGGA at 3911, CGGA at 3361, CGGA at 3216.
  7. TCCGr2ci: CGGA at 4450, CGGA at 4266, CGGA at 4126, CGGA at 4083, CGGA at 3875, CGGA at 3865, CGGA at 3565, CGGA at 3434, CGGA at 3371, CGGA at 2886.
  8. TCCGr4ci: CGGA at 4497, CGGA at 4382, CGGA at 4262, CGGA at 4233, CGGA at 4217, CGGA at 4019, CGGA at 3829, CGGA at 2922.
  9. TCCGr6ci: CGGA at 4244, CGGA at 4127, CGGA at 3607, CGGA at 3413, CGGA at 3389, CGGA at 3298, CGGA at 3223, CGGA at 2996.
  10. TCCGr8ci: CGGA at 4408, CGGA at 3881, CGGA at 3614, CGGA at 3404, CGGA at 3029, CGGA at 3005, CGGA at 2936.

TCCGr alternate (odds) (4560-2846) UTRs

  1. TCCGr1: TCCG at 4303, TCCG at 4076, TCCG at 4068, TCCG at 3925, TCCG at 3840, TCCG at 3776, TCCG at 3649, TCCG at 3035, TCCG at 2973.
  2. TCCGr3: TCCG at 3955, TCCG at 3657, TCCG at 3374, TCCG at 3133.
  3. TCCGr5: TCCG at 4290, TCCG at 4253, TCCG at 4036, TCCG at 3462, TCCG at 3451, TCCG at 3381, TCCG at 3368.
  4. TCCGr7: TCCG at 4465, TCCG at 4088, TCCG at 3838, TCCG at 3795, TCCG at 3554, TCCG at 3004.
  5. TCCGr9: TCCG at 4502, TCCG at 4444, TCCG at 4289, TCCG at 4102, TCCG at 3661, TCCG at 3339, TCCG at 3010, TCCG at 2929.
  6. TCCGr1ci: CGGA at 3983, CGGA at 3560, CGGA at 3504, CGGA at 3214.
  7. TCCGr3ci: 9, CGGA at 4203, CGGA at 3926, CGGA at 3147, CGGA at 2897.
  8. TCCGr5ci: CGGA at 4521, CGGA at 3540, CGGA at 3336, CGGA at 3182, CGGA at 3029, CGGA at 3023.
  9. TCCGr7ci: CGGA at 4539, CGGA at 4111, CGGA at 4097, CGGA at 3902, CGGA at 3880, CGGA at 3864, CGGA at 3659, CGGA at 3421, CGGA at 3302, CGGA at 3217, CGGA at 3213, CGGA at 3195, CGGA at 2995.
  10. TCCGr9ci: CGGA at 4385, CGGA at 4232, CGGA at 4163, CGGA at 3919, CGGA at 3910, CGGA at 3631, CGGA at 3422, CGGA at 3396, CGGA at 3231, CGGA at 3061, CGGA at 2882.

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

  1. TCCGr2: TCCG at 2844.
  2. TCCGr4: TCCG at 2818.
  3. TCCGr6: TCCG at 2817.
  4. TCCGr4ci: CGGA at 2820.
  5. TCCGr6ci: CGGA at 2819.

TCCGr alternate negative direction (odds) (2846-2811) core promoters

  1. TCCGr1: TCCG at 2814.
  2. TCCGr5: TCCG at 2822.
  3. TCCGr5ci: CGGA at 2079, CGGA at 1380, CGGA at 1054, CGGA at 575, CGGA at 497.
  4. TCCGr9ci: CGGA at 2831.

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

  1. TCCGr1: TCCG at 4303.
  2. TCCGr5: TCCG at 4290.
  3. TCCGr9: TCCG at 4444, TCCG at 4289.
  4. TCCGr9ci: CGGA at 4385.

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

  1. TCCGr0: TCCG at 4417, TCCG at 4318.
  2. TCCGr6: 1TCCG at 4295.
  3. TCCGr0ci: CGGA at 4320.
  4. TCCGr2ci: CGGA at 4266.
  5. TCCGr4ci: CGGA at 4382.
  6. TCCGr8ci: CGGA at 4408.

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

  1. TCCGr0: TCCG at 2763, TCCG at 2748, TCCG at 2669.
  2. TCCGr2: TCCG at 2614.
  3. TCCGr4: TCCG at 2740, TCCG at 2734.
  4. TCCGr6: TCCG at 2817, TCCG at 2787, TCCG at 2756, TCCG at 2642.
  5. TCCGr0ci: CGGA at 2750, CGGA at 2665, CGGA at 2632.
  6. TCCGr4ci: CGGA at 2794, CGGA at 2786.
  7. TCCGr6ci: CGGA at 2613.
  8. TCCGr8ci: CGGA at 2754.

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

  1. TCCGr3: TCCG at 2722.
  2. TCCGr7: TCCG at 2740, TCCG at 2665.
  3. TCCGr9: TCCG at 2807, TCCG at 2765, TCCG at 2721.
  4. TCCGr9ci: CGGA at 2601.

TCCGr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. TCCGr1: TCCG at 4076, TCCG at 4068.
  2. TCCGr5: TCCG at 4253.
  3. TCCGr7: TCCG at 4088.
  4. TCCGr9: TCCG at 4102.
  5. TCCGr3ci: CGGA at 4203.
  6. TCCGr7ci: CGGA at 4111, CGGA at 4097.
  7. TCCGr9ci: CGGA at 4232, CGGA at 4163.

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

  1. TCCGr0: TCCG at 4117.
  2. TCCGr2: TCCG at 4124.
  3. TCCGr6: TCCG at 4210.
  4. TCCGr8: TCCG at 4253.
  5. TCCGr2ci: CGGA at 4126, CGGA at 4083.
  6. TCCGr4ci: CGGA at 4262, CGGA at 4233, CGGA at 4217.

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

  1. TCCGr0: TCCG at 2508, TCCG at 948, TCCG at 928, TCCG at 876, TCCG at 366.
  2. TCCGr2: TCCG at 1664, TCCG at 1576, TCCG at 1248, TCCG at 1101, TCCG at 796, TCCG at 647, TCCG at 637, TCCG at 569, TCCG at 522, TCCG at 415, TCCG at 411.
  3. TCCGr4: TCCG at 2172, TCCG at 2114, TCCG at 2092, TCCG at 1814, TCCG at 1269, TCCG at 893, TCCG at 778, TCCG at 677, TCCG at 396, TCCG at 381, TCCG at 12.
  4. TCCGr6: TCCG at 1797, TCCG at 1188, TCCG at 1154, TCCG at 698, TCCG at 555, TCCG at 491.
  5. TCCGr8: TCCG at 2552, TCCG at 2487, TCCG at 2442, TCCG at 2123, TCCG at 2076, TCCG at 2044, TCCG at 2010, TCCG at 1940, TCCG at 1460, TCCG at 1024, TCCG at 968, TCCG at 918, TCCG at 363, TCCG at 118, TCCG at 84.
  6. TCCGr0ci: CGGA at 2203, CGGA at 2033, CGGA at 2012, CGGA at 1894, CGGA at 1700, CGGA at 1431, CGGA at 1311, CGGA at 1144, CGGA at 950, CGGA at 730, CGGA at 673.
  7. TCCGr2ci: CGGA at 2402, CGGA at 2226, CGGA at 1578.
  8. TCCGr4ci: CGGA at 2552, CGGA at 2528, CGGA at 2524, CGGA at 2507, CGGA at 1276, CGGA at 1129, CGGA at 1014, CGGA at 879, CGGA at 614, CGGA at 573, CGGA at 556, CGGA at 505.
  9. TCCGr6ci: CGGA at 2577, CGGA at 2267, CGGA at 2120, CGGA at 1190, CGGA at 1156, CGGA at 516, CGGA at 441, CGGA at 406.
  10. TCCGr8ci: CGGA at 2489, CGGA at 2125, CGGA at 2078, CGGA at 1462, CGGA at 1055, CGGA at 794, CGGA at 683.

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

  1. TCCGr1: TCCG at 2083, TCCG at 1836, TCCG at 1678, TCCG at 1643, TCCG at 956, TCCG at 816, TCCG at 801, TCCG at 657, TCCG at 572, TCCG at 325.
  2. TCCGr3: TCCG at 2473, TCCG at 2361, TCCG at 2307, TCCG at 1823, TCCG at 1581, TCCG at 1196, TCCG at 482, TCCG at 413, TCCG at 115, TCCG at 81.
  3. TCCGr7: TCCG at 1905, TCCG at 1826, TCCG at 1739, TCCG at 1477, TCCG at 1384, TCCG at 1121, TCCG at 686, TCCG at 434, TCCG at 396, TCCG at 212.
  4. TCCGr9: TCCG at 2098, TCCG at 2025, TCCG at 1951, TCCG at 1566, TCCG at 1556, TCCG at 1345, TCCG at 1038, TCCG at 776, TCCG at 526.
  5. TCCGr1ci: CGGA at 2464, CGGA at 2315, CGGA at 1787, CGGA at 1508, CGGA at 1419, CGGA at 1300, CGGA at 1153, CGGA at 1121, CGGA at 937, CGGA at 173, CGGA at 120.
  6. TCCGr3ci: CGGA at 2564, CGGA at 1486, CGGA at 1326, CGGA at 955, CGGA at 759.
  7. TCCGr5ci: CGGA at 2079, CGGA at 1380, CGGA at 1054, CGGA at 575, CGGA at 497.
  8. TCCGr7ci: CGGA at 2205, CGGA at 2006, CGGA at 1386, CGGA at 1295, CGGA at 1283, CGGA at 1221, CGGA at 986, CGGA at 787, CGGA at 693, CGGA at 667, CGGA at 51.
  9. TCCGr9ci: CGGA at 2470, CGGA at 2181, CGGA at 2151, CGGA at 2047, CGGA at 1843, CGGA at 1708, CGGA at 1143, CGGA at 1084, CGGA at 557, CGGA at 367, CGGA at 293, CGGA at 115.

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

  1. TCCGr1: TCCG at 3925, TCCG at 3840, TCCG at 3776, TCCG at 3649, TCCG at 3035, TCCG at 2973, TCCG at 2814, TCCG at 2083, TCCG at 1836, TCCG at 1678, TCCG at 1643, TCCG at 956, TCCG at 816, TCCG at 801, TCCG at 657, TCCG at 572, TCCG at 325.
  2. TCCGr3: TCCG at 3955, TCCG at 3657, TCCG at 3374, TCCG at 3133, TCCG at 2722, TCCG at 2473, TCCG at 2361, TCCG at 2307, TCCG at 1823, TCCG at 1581, TCCG at 1196, TCCG at 482, TCCG at 413, TCCG at 115, TCCG at 81.
  3. TCCGr5: TCCG at 4036, TCCG at 3462, TCCG at 3451, TCCG at 3381, TCCG at 3368, TCCG at 2822, TCCG at 2520, TCCG at 2470, TCCG at 2460, TCCG at 2358, TCCG at 1541, TCCG at 1222, TCCG at 1157, TCCG at 1022, TCCG at 779, TCCG at 397, TCCG at 296, TCCG at 282, TCCG at 51, TCCG at 5.
  4. TCCGr7: TCCG at 3838, TCCG at 3795, TCCG at 3554, TCCG at 3004, TCCG at 2740, TCCG at 2665, TCCG at 1905, TCCG at 1826, TCCG at 1739, TCCG at 1477, TCCG at 1384, TCCG at 1121, TCCG at 686, TCCG at 434, TCCG at 396, TCCG at 212.
  5. TCCGr9: TCCG at 3661, TCCG at 3339, TCCG at 3010, TCCG at 2929, TCCG at 2807, TCCG at 2765, TCCG at 2721, TCCG at 2098, TCCG at 2025, TCCG at 1951, TCCG at 1566, TCCG at 1556, TCCG at 1345, TCCG at 1038, TCCG at 776, TCCG at 526.
  6. TCCGr1ci: CGGA at 3983, CGGA at 3560, CGGA at 3504, CGGA at 3214, CGGA at 2464, CGGA at 2315, CGGA at 1787, CGGA at 1508, CGGA at 1419, CGGA at 1300, CGGA at 1153, CGGA at 1121, CGGA at 937, CGGA at 173, CGGA at 120.
  7. TCCGr3ci: CGGA at 3926, CGGA at 3147, CGGA at 2897, CGGA at 2564, CGGA at 1486, CGGA at 1326, CGGA at 955, CGGA at 759.
  8. TCCGr5ci: CGGA at 3540, CGGA at 3336, CGGA at 3182, CGGA at 3029, CGGA at 3023, CGGA at 2079, CGGA at 1380, CGGA at 1054, CGGA at 575, CGGA at 497.
  9. TCCGr7ci: CGGA at 3902, CGGA at 3880, CGGA at 3864, CGGA at 3659, CGGA at 3421, CGGA at 3302, CGGA at 3217, CGGA at 3213, CGGA at 3195, CGGA at 2995, CGGA at 2205, CGGA at 2006, CGGA at 1386, CGGA at 1295, CGGA at 1283, CGGA at 1221, CGGA at 986, CGGA at 787, CGGA at 693, CGGA at 667, CGGA at 51.
  10. TCCGr9ci: CGGA at 3919, CGGA at 3910, CGGA at 3631, CGGA at 3422, CGGA at 3396, CGGA at 3231, CGGA at 3061, CGGA at 2882, CGGA at 2831, CGGA at 2601, CGGA at 2470, CGGA at 2181, CGGA at 2151, CGGA at 2047, CGGA at 1843, CGGA at 1708, CGGA at 1143, CGGA at 1084, CGGA at 557, CGGA at 367, CGGA at 293, CGGA at 115.

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

  1. TCCGr0: TCCG at 3378, TCCG at 2897, TCCG at 2763, TCCG at 2748, TCCG at 2669, TCCG at 2508, TCCG at 948, TCCG at 928, TCCG at 876, TCCG at 366.
  2. TCCGr2: TCCG at 3971, TCCG at 3561, TCCG at 3548, TCCG at 3396, TCCG at 3367, TCCG at 2844, TCCG at 2614, TCCG at 1664, TCCG at 1576, TCCG at 1248, TCCG at 1101, TCCG at 796, TCCG at 647, TCCG at 637, TCCG at 569, TCCG at 522, TCCG at 415, TCCG at 411.
  3. TCCGr4: TCCG at 3873, TCCG at 3765, TCCG at 3490, TCCG at 2818, TCCG at 2740, TCCG at 2734, TCCG at 2172, TCCG at 2114, TCCG at 2092, TCCG at 1814, TCCG at 1269, TCCG at 893, TCCG at 778, TCCG at 677, TCCG at 396, TCCG at 381, TCCG at 12.
  4. TCCGr8: TCCG at 2552, TCCG at 2487, TCCG at 2442, TCCG at 2123, TCCG at 2076, TCCG at 2044, TCCG at 2010, TCCG at 1940, TCCG at 1460, TCCG at 1024, TCCG at 968, TCCG at 918, TCCG at 363, TCCG at 118, TCCG at 84.
  5. TCCGr0ci: CGGA at 3911, CGGA at 3361, CGGA at 3216, CGGA at 2750, CGGA at 2665, CGGA at 2632, CGGA at 2203, CGGA at 2033, CGGA at 2012, CGGA at 1894, CGGA at 1700, CGGA at 1431, CGGA at 1311, CGGA at 1144, CGGA at 950, CGGA at 730, CGGA at 673.
  6. TCCGr2ci: CGGA at 3875, CGGA at 3865, CGGA at 3565, CGGA at 3434, CGGA at 3371, CGGA at 2886, CGGA at 2402, CGGA at 2226, CGGA at 1578.
  7. TCCGr4ci: CGGA at 4019, CGGA at 3829, CGGA at 2922, CGGA at 2820, CGGA at 2794, CGGA at 2786, CGGA at 2552, CGGA at 2528, CGGA at 2524, CGGA at 2507, CGGA at 1276, CGGA at 1129, CGGA at 1014, CGGA at 879, CGGA at 614, CGGA at 573, CGGA at 556, CGGA at 505.
  8. TCCGr6ci: CGGA at 3607, CGGA at 3413, CGGA at 3389, CGGA at 3298, CGGA at 3223, CGGA at 2996, CGGA at 2819, CGGA at 2613, CGGA at 2577, CGGA at 2267, CGGA at 2120, CGGA at 1190, CGGA at 1156, CGGA at 516, CGGA at 441, CGGA at 406.
  9. TCCGr8ci: CGGA at 3881, CGGA at 3614, CGGA at 3404, CGGA at 3029, CGGA at 3005, CGGA at 2936, CGGA at 2754, CGGA at 2489, CGGA at 2125, CGGA at 2078, CGGA at 1462, CGGA at 1055, CGGA at 794, CGGA at 683.

TCCG analysis and results

Main article: Complex locus A1BG and ZNF497 § TCCGs

"Deletion analysis of the ICL1 promoter led to the identification of an upstream activating sequence element, UASICL1 (5' CATTCATCCG 3'), necessary and sufficient for conferring carbon source-dependent regulation on a heterologous reporter gene."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 34 2 17 17 ± 16 (--33,+-1)
Randoms UTR arbitrary negative 57 10 5.7 6.45 ± 0.75
Randoms UTR alternate negative 72 10 7.2 6.45 ± 0.75
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 5 10 0.5 0.65 ± 0.15
Randoms Core alternate negative 8 10 0.8 0.65 ± 0.15
Reals Core positive 12 2 6 6 ± 3 (-+9,++3)
Randoms Core arbitrary positive 5 10 0.5 0.6
Randoms Core alternate positive 7 10 0.7 0.6
Reals Proximal negative 4 2 2 2 (--3,+-1)
Randoms Proximal arbitrary negative 17 10 1.7 1.2
Randoms Proximal alternate negative 7 10 0.7 1.2
Reals Proximal positive 4 2 2 2 ± 1 (-+1,++3)
Randoms Proximal arbitrary positive 10 10 1.0 0.95
Randoms Proximal alternate positive 9 10 0.9 0.95
Reals Distal negative 64 2 32 32 ± (--56,+-8)
Randoms Distal arbitrary negative 89 10 8.9 8.6
Randoms Distal alternate negative 83 10 8.3 8.6
Reals Distal positive 106 2 53 53 ± 35 (++18,-+88)
Randoms Distal arbitrary positive 160 10 16.0 14.7 ± 1.3
Randoms Distal alternate positive 134 10 13.4 14.7 ± 1.3

Comparison:

The occurrences of real TCCG UTRs are outside the randoms, the cores are greater than the randoms, the lower proximals overlap the randoms, the negative direction distals are outside the randoms, the positive direction distals are greater than the randoms. This suggests that the real TCCGs are generally likely active or activable.

Using TCCG and its inverse complement (CGGA) to probe the promoters on either side of A1BG is likely to have a large number of occurrences because of the limited number of nucleotides (4).

The real core promoters are only in the positive direction, whereas in the randoms in both directions.

CATTCA samplings

Copying a responsive elements consensus sequence CATTCA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CATTCA (starting with SuccessablesCATT.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: 0.
  2. positive strand, negative direction: 0.
  3. negative strand, positive direction: 0.
  4. positive strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, positive strand, negative direction: 0.
  7. inverse complement, negative strand, positive direction: 2, TGAATG at 3781, TGAATG at 3444.
  8. inverse complement, positive strand, positive direction: 0.

CATT positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: 2, TGAATG at 3781, TGAATG at 3444.

CATTCA random dataset samplings

  1. CATTr0: 0.
  2. CATTr1: 0.
  3. CATTr2: 2, CATTCA at 4048, CATTCA at 1723.
  4. CATTr3: 2, CATTCA at 1829, CATTCA at 1337.
  5. CATTr4: 1, CATTCA at 1530.
  6. CATTr5: 0.
  7. CATTr6: 0.
  8. CATTr7: 0.
  9. CATTr8: 0.
  10. CATTr9: 2, CATTCA at 3713, CATTCA at 3642.
  11. CATTr0ci: 0.
  12. CATTr1ci: 1, TGAATG at 455.
  13. CATTr2ci: 2, TGAATG at 1293, TGAATG at 282.
  14. CATTr3ci: 1, TGAATG at 542.
  15. CATTr4ci: 1, TGAATG at 995.
  16. CATTr5ci: 1, TGAATG at 2408.
  17. CATTr6ci: 5, TGAATG at 4112, TGAATG at 2942, TGAATG at 2684, TGAATG at 2066, TGAATG at 249.
  18. CATTr7ci: 0.
  19. CATTr8ci: 1, TGAATG at 2466.
  20. CATTr9ci: 4, TGAATG at 4535, TGAATG at 4341, TGAATG at 4243, TGAATG at 1402.

CATTr arbitrary (evens) (4560-2846) UTRs

  1. CATTr2: CATTCA at 4048.
  2. CATTr6ci: TGAATG at 4112, TGAATG at 2942.

CATTr alternate (odds) (4560-2846) UTRs

  1. CATTr9: CATTCA at 3713, CATTCA at 3642.
  2. CATTr9ci: TGAATG at 4535, TGAATG at 4341, TGAATG at 4243.

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

  1. CATTr9ci: TGAATG at 4341, TGAATG at 4243.

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

  1. CATTr6ci: TGAATG at 2684.

CATTr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. CATTr9ci: TGAATG at 4243.

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

  1. CATTr6ci: 5, TGAATG at 4112.

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

  1. CATTr2: CATTCA at 1723.
  2. CATTr4: CATTCA at 1530.
  3. CATTr2ci: TGAATG at 1293, TGAATG at 282.
  4. CATTr4ci: TGAATG at 995.
  5. CATTr6ci: TGAATG at 2066, TGAATG at 249.
  6. CATTr8ci: TGAATG at 2466.

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

  1. CATTr3: CATTCA at 1829, CATTCA at 1337.
  2. CATTr1ci: TGAATG at 455.
  3. CATTr3ci: TGAATG at 542.
  4. CATTr5ci: TGAATG at 2408.
  5. CATTr9ci: TGAATG at 1402.

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

  1. CATTr3: CATTCA at 1829, CATTCA at 1337.
  2. CATTr9: CATTCA at 3713, CATTCA at 3642.
  3. CATTr1ci: TGAATG at 455.
  4. CATTr3ci: TGAATG at 542.
  5. CATTr5ci: TGAATG at 2408.
  6. CATTr9ci: TGAATG at 1402.

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

  1. CATTr2: CATTCA at 4048, CATTCA at 1723.
  2. CATTr4: CATTCA at 1530.
  3. CATTr2ci: TGAATG at 1293, TGAATG at 282.
  4. CATTr4ci: TGAATG at 995.
  5. CATTr6ci: TGAATG at 2942, TGAATG at 2684, TGAATG at 2066, TGAATG at 249.
  6. CATTr8ci: TGAATG at 2466.

CATTCA analysis and results

Main article: Complex locus A1BG and ZNF497 § CATTCAs

"Deletion analysis of the ICL1 promoter led to the identification of an upstream activating sequence element, UASICL1 (5' CATTCATCCG 3'), necessary and sufficient for conferring carbon source-dependent regulation on a heterologous reporter gene."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 3 10 0.3 0.4
Randoms UTR alternate negative 5 10 0.5 0.4
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 2 10 0.2 0.1
Randoms Core alternate positive 0 10 0 0.1
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 1 10 0.1 0.05
Randoms Proximal alternate negative 0 10 0 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0.05
Randoms Proximal alternate positive 1 10 0.1 0.05
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 8 10 0.8 0.7
Randoms Distal alternate negative 6 10 0.6 0.7
Reals Distal positive 2 2 1 1 ± 1 (-+2,++0)
Randoms Distal arbitrary positive 8 10 0.8 0.9
Randoms Distal alternate positive 10 10 1 0.9

Comparison:

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

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 1.2 A Schöler and H J Schüller (June 1994). "A carbon source-responsive promoter element necessary for activation of the isocitrate lyase gene ICL1 is common to genes of the gluconeogenic pathway in the yeast Saccharomyces cerevisiae" (PDF). Molecular and Cellular Biology. 14 (6): 3613–3622. Retrieved 9 February 2021.
  2. ↑ Roland Prielhofer, Michaela Reichinger, Nina Wagner, Katrien Claes, Christoph Kiziak, Brigitte Gasser, Diethard Mattanovich (17 July 2018). "Superior protein titers in half the fermentation time: Promoter and process engineering for the glucose‐regulated GTH1 promoter of Pichia pastoris". Biotechnology and Bioengineering. 115 (10): 2479–2488. doi:10.1002/bit.26800. Retrieved 29 December 2021.

External links


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