Z box gene transcriptions

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Editor-In-Chief: Henry A. Hoff

This female specimen is a zebrafish (Danio rerio) breed with fantails. Credit: Azul.{{free media}}

"Both miRNAs [miR‐141 and miR‐200c] map closely on human chromosome 12p13.31 and the stem–loop sequences are separated by only a 338‐base‐pair spacer sequence [...]. This spacer and the putative promoter 600 bp upstream from the hsa‐miR‐200c stem–loop contain six putative binding sequences for [zinc‐finger E‐box binding homeobox 1] ZEB1, two of which were restricted to ZEB factors (Z‐box 1 and 2, CAGGTA)."[1]

The "overall miRNA gene structure and the two Z‐boxes, as well as E‐box 2, are highly conserved in evolution from zebrafish to human [...]."[1]

"Mutation of the two highly conserved Z‐boxes showed that Z‐box 2 confers the strongest repressive function by ZEB1 [...] and also made the promoter activity insensitive to stable knockdown of ZEB1 [...]. A direct binding of ZEB1 to the two conserved ZEB1 sites (Z‐boxes) was shown by electromobility shift assay by using recombinant DNA‐binding domain of ZEB1 and nuclear extracts from SW480 colorectal cancer cells [...]. By applying chromatin immunoprecipitation (ChIP) with chromatin from SW480 or HCT116 colorectal cancer cells, we could show that endogenous ZEB1 binds to the native promoter region [...]. These data indicate that the transcriptional repressor ZEB1 can directly suppress expression of both miR‐141 and miR‐200c by binding to their putative common promoter."[1]

"The absolute transcriptional activity of the promoter was 55‐fold higher than the activity of the spacer sequence. [Mutations] (mut) of the Z‐boxes render the promoter less sensitive to suppression by ZEB1."[1]

"Mutation of the two conserved Z‐boxes (Z1, Z2) strongly reduced the specific binding complex [...]."[1]

HY5 proteins

"The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of RbcS1A (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002)."[2]

Consensus sequences

"Snail-related and E2A factors bind to a consensus E-box promoter element (CANNTG), whereas ZEB factors bind to a related, but not necessarily identical sequence (CAGGTG/A), termed Z-Box. We detected 2 potential binding sites for Snail-related and E2A factors (E-box 1 and 2) and 3 for ZEB factors (E-box 2 and Z-box 1 and 2) in the human lama3a promoter [...]. Furthermore, sequence comparison of 1000 nucleotides upstream of the translation start site of the human and mouse lama3 gene showed that these sites are located in a highly conserved region of approximately 210 nucleotides, whereas further upstream sequences were not conserved [...]. Three of the 4 potential repressive elements were conserved between mouse and human, indicating their functional relevance."[3]

"HY5 binds to the promoter of light-responsive genes featuring "ACGT-containing elements" such as the G-box (CACGTG), C-box (GACGTC), Z-box (ATACGGT), and A-box (TACGTA) (4, 6)."[4]

"Snail-related and E2A factors bind to [...] (CAGGTG/A), termed Z-Box."[3]

"HY5 binds to [...], Z-box (ATACGGT), [...]."[4]

"The HY5 protein interacts with [...] Z- (ATACGTGT) boxes [...]."[2]

The more general Z-box consensus sequence accommodating these variations appears to be A(C/T)A(C/G)GT(A/G)T:

  1. Negative strand, positive direction: ACAGGTGT at 1969, contains CAGGTG[3].
  2. Positive strand, positive direction: ACACGTGT at 2962.
  3. ci, positive strand, negative direction: ACACCTGT at 1131, ATACCTAT at 2996, ACACCTGT at 3970.

But neither ones found contain Z-box (ATACGGT, ACCGTAT)[4] or (ATACGTGT, ACACGTAT)[2]. It may be better to sample the three Z-boxes separately:

  1. CAGGT(A/G), (C/T)ACCTG,[3] ZboxSp, Z-boxes 1-3 contain: AGGTG or CACCT.[5],
  2. ATACGGT[4] ZboxN, and
  3. ATACGTGT[2] ZboxSo.

SIP1-mediated Epithelial Mesenchymal Transition (EMT)

In vivo SIP1, or Zinc finger E-box-binding homeobox 2 (ZEB2), binds "to potential SIP1-binding sites (Z-boxes) located in the vicinity of the cyclin D1 transcription start site."[5]

Three "Z-boxes with coordinates -1014 to -1010 (Z-box 1); -857 to -853 (Z-box 2); and -300 to -290 (Z-box 3) are occupied by SIP1 in [doxorubicin (DOX)] DOX-stimulated cells. In contrast, neither sequences upstream of Z-box 1 [...], nor sequences containing Z-boxes 4 and 5 located at the first exon/intron boundary (-390 to -409) [...] were detected in association with SIP1."[5]

Z-boxes 1-3 contain AGGTG.[5]

The "mutation of Z-boxes 1–3 markedly activated reporter activity in SIP1-expressing cells [...]."[5]

"SIP1 represses cyclin D1 transcriptional activity via direct interaction with Z-boxes 1–3 in the cyclin D1 promoter."[5]

Hypotheses

  1. A1BG has no Z boxes in either promoter.

NSoSp form samplings

An overall general Z-box consensus sequence accommodating these variations: ATACGTGT[2], CAGGT(A/G)[3] and ATACGGT[4] appears to be ATACGTGT + CAGGT(A/G) = A(C/T)A(C/G)GT(A/G)T, here called the ZboxG, then A(C/T)A(C/G)GT(A/G)T + ATACGGT = A(C/T)A(C/G)G(G/T)(A/G/T)T or here called the NSoSp form.

Direct form A(C/T)A(C/G)G(G/T)(A/G/T)T has the complement inverse of A(A/C/T)(A/C)C(C/G)T(A/G)T, where A(C/T)ACGT(A/G)T produces ACACGTAT, ATACGTAT, ACACGTGT, ATACGTGT enantiomorphs.

Note: Positive strand, positive direction: ACACGTGT at 2962 equals inverse complement, positive strand, positive direction: ACACGTGT at 2962.

For the Basic programs testing consensus sequence A(C/T)A(C/G)G(G/T)(A/G/T)T (starting with SuccessablesZboxNSoSp.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: 1, ACACGTTT at 2865.
  2. Positive strand, negative direction: 0.
  3. Negative strand, positive direction: 1, ACAGGTGT at 1969.
  4. Positive strand, positive direction: 1, ACACGTGT at 2962.
  5. inverse complement, negative strand, negative direction: 2, ATCCGTAT at 3451, ACCCGTGT at 1116.
  6. inverse complement, positive strand, negative direction: 4, ACACCTGT at 3970, ACCCCTGT at 3061, ATACCTAT at 2996, ACACCTGT at 1131.
  7. inverse complement, negative strand, positive direction: 1, ACCCCTGT at 3617.
  8. inverse complement, positive strand, positive direction: 1, ACCCCTGT at 1869.

NSoSp (4560-2846) UTRs

  1. Negative strand, negative direction: ATCCGTAT at 3451, ACACGTTT at 2865.
  2. Positive strand, negative direction: ACACCTGT at 3970, ACCCCTGT at 3061, ATACCTAT at 2996.

NSoSp negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ACCCGTGT at 1116.
  2. Positive strand, negative direction: ACACCTGT at 1131.

NSoSp positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: ACCCCTGT at 3617, ACAGGTGT at 1969.
  2. Positive strand, positive direction: ACACGTGT at 2962, ACCCCTGT at 1869.

NSoSp random dataset samplings

Note: NSoSpr1: ACACGTAT at 3790 equals NSoSpr1ci: ACACGTAT at 3790.

  1. NSoSpr0: 3, ACACGGGT at 3704, ATAGGGGT at 3015, ATACGGGT at 2046.
  2. NSoSpr1: 2, ACACGTAT at 3790, ATAGGGTT at 277.
  3. NSoSpr2: 3, ATACGTGT at 1595, ATAGGGGT at 1283, ATAGGTTT at 407.
  4. NSoSpr3: 0.
  5. NSoSpr4: 1 ACAGGTAT at 698.
  6. NSoSpr5: 0.
  7. NSoSpr6: 2, ATACGTTT at 3446, ACAGGGTT at 1946.
  8. NSoSpr7: 1, ACACGGAT at 4098.
  9. NSoSpr8: 1, ATACGTTT at 3569.
  10. NSoSpr9: 0.
  11. NSoSpr0ci: 0.
  12. NSoSpr1ci: 1, ACACGTAT at 3790.
  13. NSoSpr2ci: 2, ATACGTGT at 1595, ACCCCTGT at 1051.
  14. NSoSpr3ci: 3, AACCCTAT at 3678, ACCCCTAT at 3353, ATACCTAT at 1082.
  15. NSoSpr4ci: 2, ACACCTGT at 1959, AACCGTGT at 425.
  16. NSoSpr5ci: 1, ACACCTAT at 1484.
  17. NSoSpr6ci: 1, AACCGTAT at 1719.
  18. NSoSpr7ci: 2, ACCCGTGT at 3666, ATCCGTGT at 1742.
  19. NSoSpr8ci: 2, AAACCTAT at 4004, ATCCCTGT at 450.
  20. NSoSpr9ci: 0.

NSoSpr arbitrary (evens) (4560-2846) UTRs

  1. NSoSpr0: ACACGGGT at 3704, ATAGGGGT at 3015.
  2. NSoSpr6: ATACGTTT at 3446.
  3. NSoSpr8ci: AAACCTAT at 4004.

NSoSpr alternate (odds) (4560-2846) UTRs

  1. NSoSpr1: ACACGTAT at 3790.
  2. NSoSpr7: ACACGGAT at 4098.
  3. NSoSpr1ci: ACACGTAT at 3790.
  4. NSoSpr3ci: AACCCTAT at 3678, ACCCCTAT at 3353.
  5. NSoSpr7ci: ACCCGTGT at 3666.

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

  1. NSoSpr7: ACACGGAT at 4098.

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

  1. NSoSpr0: ATACGGGT at 2046.
  2. NSoSpr2: ATACGTGT at 1595, ATAGGGGT at 1283, ATAGGTTT at 407.
  3. NSoSpr4: ACAGGTAT at 698.
  4. NSoSpr6: ACAGGGTT at 1946.
  5. NSoSpr2ci: ATACGTGT at 1595, ACCCCTGT at 1051.
  6. NSoSpr4ci: ACACCTGT at 1959, AACCGTGT at 425.
  7. NSoSpr8ci: ATCCCTGT at 450.

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

  1. NSoSpr1: ATAGGGTT at 277.
  2. NSoSpr3ci: ATACCTAT at 1082.
  3. NSoSpr5ci: ACACCTAT at 1484.
  4. NSoSpr7ci: ATCCGTGT at 1742.

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

  1. NSoSpr1: ACACGTAT at 3790, ATAGGGTT at 277.
  2. NSoSpr1ci: ACACGTAT at 3790.
  3. NSoSpr3ci: AACCCTAT at 3678, ACCCCTAT at 3353, ATACCTAT at 1082.
  4. NSoSpr5ci: ACACCTAT at 1484.
  5. NSoSpr7ci: ACCCGTGT at 3666, ATCCGTGT at 1742.

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

  1. NSoSpr0: ACACGGGT at 3704, ATAGGGGT at 3015, ATACGGGT at 2046.
  2. NSoSpr2: ATACGTGT at 1595, ATAGGGGT at 1283, ATAGGTTT at 407.
  3. NSoSpr4: ACAGGTAT at 698.
  4. NSoSpr6: ATACGTTT at 3446, ACAGGGTT at 1946.
  5. NSoSpr2ci: ATACGTGT at 1595, ACCCCTGT at 1051.
  6. NSoSpr4ci: ACACCTGT at 1959, AACCGTGT at 425.
  7. NSoSpr8ci: AAACCTAT at 4004, ATCCCTGT at 450.

NSoSp analysis and results

Main article: Complex locus A1BG and ZNF497 § NSoSps

An overall general Z-box consensus sequence accommodating these variations: ATACGTGT[2], CAGGT(A/G)[3] and ATACGGT[4] appears to be ATACGTGT + CAGGT(A/G) = A(C/T)A(C/G)GT(A/G)T, here called the ZboxG, then A(C/T)A(C/G)GT(A/G)T + ATACGGT = A(C/T)A(C/G)G(G/T)(A/G/T)T or here called the NSoSp form.

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5 ± 0.5 (--2,+-3)
Randoms UTR arbitrary negative 4 10 0.4 0.5
Randoms UTR alternate negative 6 10 0.6 0.5
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 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 2 2 1 1 ± 0 (--1,+-1)
Randoms Distal arbitrary negative 11 10 1.1 0.75
Randoms Distal alternate negative 4 10 0.4 0.75
Reals Distal positive 4 2 2 2 ± 0 (-+2,++2)
Randoms Distal arbitrary positive 9 10 0.9 1.2
Randoms Distal alternate positive 15 10 1.5 1.2

Comparison:

The occurrences of real NSoSp UTRs and positive distals are greater than the randoms, the negative distals are within the randoms. This suggests that the real NSoSps are likely active or activable.

General Z-box (ZboxG) samplings

Using the two versions of the consensus sequence and "⌘F" to locate these sequences in the nucleotides for A1BG listed in A1BG gene transcriptions revealed no occurrence of either.

For the Basic programs testing consensus sequence A(C/T)A(C/G)GT(A/G)T (starting with SuccessablesZbox.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. Negative strand, positive direction: 1, ACAGGTGT at 1969.
  3. Positive strand, negative direction: 0.
  4. Positive strand, positive direction: 1, ACACGTGT at 2962.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, negative strand, positive direction: 0.
  7. inverse complement, positive strand, negative direction: 3, ACACCTGT at 3970, ATACCTAT at 2996, ACACCTGT at 1131.
  8. inverse complement, positive strand, positive direction: 0.

ZboxG (4560-2846) UTRs

  1. Positive strand, negative direction: ACACCTGT at 3970, ATACCTAT at 2996.

ZboxG negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: ACACCTGT at 1131.

ZboxG positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: ACAGGTGT at 1969.
  2. Positive strand, positive direction: ACACGTGT at 2962.

ZboxG random dataset samplings

  1. ZboxGr0: 0.
  2. ZboxGr1: 1, ACACGTAT at 3790.
  3. ZboxGr2: 1 ATACGTGT at 1595.
  4. ZboxGr3: 0.
  5. ZboxGr4: 1, ACAGGTAT at 698.
  6. ZboxGr5: 0.
  7. ZboxGr6: 0.
  8. ZboxGr7: 0.
  9. ZboxGr8: 0.
  10. ZboxGr9: 0.
  11. ZboxGr0ci: 0.
  12. ZboxGr1ci: 1, ACACGTAT at 3790.
  13. ZboxGr2ci: 1, ATACGTGT at 1595.
  14. ZboxGr3ci: 1, ATACCTAT at 1082.
  15. ZboxGr4ci: 1, ACACCTGT at 1959.
  16. ZboxGr5ci: 1, ACACCTAT at 1484.
  17. ZboxGr6ci: 0.
  18. ZboxGr7ci: 0.
  19. ZboxGr8ci: 0.
  20. ZboxGr9ci: 0.

ZboxGr alternate (odds) (4560-2846) UTRs

  1. ZboxGr1: ACACGTAT at 3790.

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

  1. ZboxGr2: ATACGTGT at 1595.
  2. ZboxGr4: ACAGGTAT at 698.
  3. ZboxGr2ci: ATACGTGT at 1595.
  4. ZboxGr4ci: ACACCTGT at 1959.

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

  1. ZboxGr3ci: ATACCTAT at 1082.
  2. ZboxGr5ci: ACACCTAT at 1484.

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

  1. ZboxGr1: ACACGTAT at 3790.
  2. ZboxGr3ci: ATACCTAT at 1082.
  3. ZboxGr5ci: ACACCTAT at 1484.

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

  1. ZboxGr2: ATACGTGT at 1595.
  2. ZboxGr4: ACAGGTAT at 698.
  3. ZboxGr2ci: ATACGTGT at 1595.
  4. ZboxGr4ci: ACACCTGT at 1959.

ZboxG analysis and results

Main article: Complex locus A1BG and ZNF497 § ZboxGs

The more general Z-box consensus sequence accommodating two variations appears to be A(C/T)A(C/G)GT(A/G)T, where using ATACGTGT[2] and CAGGT(A/G)[3] produces ATACGTGT + CAGGT(A/G) = A(C/T)A(C/G)GT(A/G)T.

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1 ± 1 (--0,+-2)
Randoms UTR arbitrary negative 0 10 0 0.05
Randoms UTR alternate negative 1 10 0.1 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 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 4 10 0.4 0.3
Randoms Distal alternate negative 2 10 0.2 0.3
Reals Distal positive 2 2 1 1 ± 0 (-+1,++1)
Randoms Distal arbitrary positive 3 10 0.3 0.35
Randoms Distal alternate positive 4 10 0.4 0.35

Comparison:

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

Z-box (ZboxSp) samplings

CAGGT(A/G), (C/T)ACCTG,[3] ZboxSp, Z-boxes 1-3 contain: AGGTG or CACCT.[5]

For the Basic programs testing consensus sequence CAGGT(A/G) (starting with SuccessablesZboxSp.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: 3, CAGGTG at 3953, CAGGTG at 2570, CAGGTG at 2079.
  3. Negative strand, positive direction: 8, CAGGTA at 4034, CAGGTA at 3730, CAGGTG at 3149, CAGGTA at 3113, CAGGTG at 2374, CAGGTG at 2127, CAGGTG at 1968, CAGGTG at 196.
  4. Positive strand, positive direction: 6, CAGGTA at 4369, CAGGTA at 3579, CAGGTG at 3086, CAGGTG at 2028, CAGGTA at 1932, CAGGTG at 1843.
  5. inverse complement, negative strand, negative direction: 1, CACCTG at 2116.
  6. inverse complement, positive strand, negative direction: 6, CACCTG at 3969, TACCTG at 3860, CACCTG at 1172, CACCTG at 1130, TACCTG at 800, CACCTG at 393.
  7. inverse complement, negative strand, positive direction: 7, CACCTG at 3046, CACCTG at 2568, CACCTG at 2432, CACCTG at 2249, TACCTG at 1198, CACCTG at 958, CACCTG at 858.
  8. inverse complement, positive strand, positive direction: 1, CACCTG at 186.

ZboxSp (4560-2846) UTRs

  1. Positive strand, negative direction: CACCTG at 3969, CAGGTG at 3953, TACCTG at 3860.

ZboxSp positive direction (4445-4265) core promoters

  1. Positive strand, positive direction: CAGGTA at 4369.

ZboxSp negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CACCTG at 2116.
  2. Positive strand, negative direction: CAGGTG at 2570, CAGGTG at 2079, CACCTG at 1172, CACCTG at 1130, TACCTG at 800, CACCTG at 393.

ZboxSp positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CAGGTA at 4034, CAGGTA at 3730, CAGGTG at 3149, CAGGTA at 3113, CAGGTG at 2374, CAGGTG at 2127, CAGGTG at 1968, CAGGTG at 196.
  2. Positive strand, positive direction: CAGGTA at 3579, CAGGTG at 3086, CACCTG at 3046, CACCTG at 2568, CACCTG at 2432, CACCTG at 2249, CAGGTG at 2028, CAGGTA at 1932, CAGGTG at 1843, TACCTG at 1198, CACCTG at 958, CACCTG at 858, CACCTG at 186.

ZboxSp random dataset samplings

  1. ZboxSpr0: 1, CAGGTG at 3398.
  2. ZboxSpr1: 0.
  3. ZboxSpr2: 1, CAGGTG at 2198.
  4. ZboxSpr3: 3, CAGGTA at 4523, CAGGTG at 3527, CAGGTG at 2880.
  5. ZboxSpr4: 1, CAGGTA at 697.
  6. ZboxSpr5: 2, CAGGTG at 2213, CAGGTG at 697.
  7. ZboxSpr6: 1, CAGGTG at 3800.
  8. ZboxSpr7: 0.
  9. ZboxSpr8: 5, CAGGTA at 4549, CAGGTA at 3761, CAGGTA at 3308, CAGGTA at 2737, CAGGTG at 292.
  10. ZboxSpr9: 0.
  11. ZboxSpr0ci: 1, CACCTG at 999.
  12. ZboxSpr1ci: 0.
  13. ZboxSpr2ci: 1, CACCTG at 2124.
  14. ZboxSpr3ci: 2, TACCTG at 2667, TACCTG at 419.
  15. ZboxSpr4ci: 3, CACCTG at 1958, CACCTG at 1913, CACCTG at 1123.
  16. ZboxSpr5ci: 2, CACCTG at 3116, TACCTG at 1230.
  17. ZboxSpr6ci: 1, CACCTG at 4358.
  18. ZboxSpr7ci: 2, TACCTG at 1668, CACCTG at 1452.
  19. ZboxSpr8ci: 2, TACCTG at 2782, TACCTG at 2372.
  20. ZboxSpr9ci: 3, TACCTG at 2481, CACCTG at 1898, CACCTG at 922.

ZboxSpr arbitrary (evens) (4560-2846) UTRs

  1. ZboxSpr0: CAGGTG at 3398.
  2. ZboxSpr6: CAGGTG at 3800.
  3. ZboxSpr8: CAGGTA at 4549, CAGGTA at 3761, CAGGTA at 3308.
  4. ZboxSpr6ci: CACCTG at 4358.

ZboxSpr alternate (odds) (4560-2846) UTRs

  1. ZboxSpr3: CAGGTA at 4523, CAGGTG at 3527, CAGGTG at 2880.

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

  1. ZboxSpr6ci: CACCTG at 4358.

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

  1. ZboxSpr8: CAGGTA at 2737.
  2. ZboxSpr8ci: TACCTG at 2782.

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

  1. ZboxSpr3ci: TACCTG at 2667.

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

  1. ZboxSpr3: CAGGTA at 4523, CAGGTG at 3527, CAGGTG at 2880.

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

  1. ZboxSpr2: CAGGTG at 2198.
  2. ZboxSpr4: CAGGTA at 697.
  3. ZboxSpr8: CAGGTG at 292.
  4. ZboxSpr0ci: CACCTG at 999.
  5. ZboxSpr2ci: CACCTG at 2124.
  6. ZboxSpr4ci: CACCTG at 1958, CACCTG at 1913, CACCTG at 1123.
  7. ZboxSpr8ci: TACCTG at 2372.

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

  1. ZboxSpr5: CAGGTG at 2213, CAGGTG at 697.
  2. ZboxSpr3ci: TACCTG at 419.
  3. ZboxSpr7ci: TACCTG at 1668, CACCTG at 1452.
  4. ZboxSpr9ci: TACCTG at 2481, CACCTG at 1898, CACCTG at 922.

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

  1. ZboxSpr3: CAGGTG at 3527, CAGGTG at 2880.
  2. ZboxSpr5: CAGGTG at 2213, CAGGTG at 697.
  3. ZboxSpr3ci: TACCTG at 2667, TACCTG at 419.
  4. ZboxSpr7ci: TACCTG at 1668, CACCTG at 1452.
  5. ZboxSpr9ci: TACCTG at 2481, CACCTG at 1898, CACCTG at 922.

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

  1. ZboxSpr2: CAGGTG at 2198.
  2. ZboxSpr4: CAGGTA at 697.
  3. ZboxSpr6: CAGGTG at 3800.
  4. ZboxSpr8: CAGGTA at 3761, CAGGTA at 3308, CAGGTA at 2737, CAGGTG at 292.
  5. ZboxSpr0ci: CACCTG at 999.
  6. ZboxSpr2ci: CACCTG at 2124.
  7. ZboxSpr4ci: CACCTG at 1958, CACCTG at 1913, CACCTG at 1123.
  8. ZboxSpr8ci: TACCTG at 2782, TACCTG at 2372.

ZboxSp analysis and results

Main article: Complex locus A1BG and ZNF497 § ZboxSps

CAGGT(A/G).[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 1.5 (--0,+-3)
Randoms UTR arbitrary negative 6 10 0.6 0.45
Randoms UTR alternate negative 3 10 0.3 0.45
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 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Core arbitrary positive 0 10 0 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 2 10 0.2 0.15
Randoms Proximal alternate negative 1 10 0.1 0.15
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 3 10 0.3 0.15
Randoms Proximal alternate positive 0 10 0 0.15
Reals Distal negative 7 2 3.5 3.5 ± 2.5 (--1,+-6)
Randoms Distal arbitrary negative 9 10 0.9 0.85
Randoms Distal alternate negative 8 10 0.8 0.85
Reals Distal positive 21 2 10.5 10.5 ± 2.5 (-+8,++13)
Randoms Distal arbitrary positive 11 10 1.1 1.25
Randoms Distal alternate positive 14 10 1.4 1.25

Comparison:

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

Z-box (ZboxN) samplings

For the Basic programs testing consensus sequence ATACGGT (starting with SuccessablesZboxN.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: 0.
  8. inverse complement, positive strand, positive direction: 0.

ZboxN analysis and results

ATACGGT.[4]

No ZboxN occur on either side of A1BG.

Z-box (ZboxSo) samplings

For the Basic programs testing consensus sequence ATACGTGT (starting with SuccessablesZboxSo.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: 0.
  8. inverse complement, positive strand, positive direction: 0.

ZboxSo analysis and results

ATACGTGT.[2] None found.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Ulrike Burk, Jörg Schubert, Ulrich Wellner, Otto Schmalhofer, Elizabeth Vincan, Simone Spaderna, Thomas Brabletz (1 June 2008). "A reciprocal repression between ZEB1 and members of the miR‐200 family promotes EMT and invasion in cancer cells". EMBO Reports. 9 (6): 582–589. doi:10.1038/embor.2008.74. Retrieved 15 November 2018.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. Retrieved 26 March 2019.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 Simone Spaderna, Otto Schmalhofer, Falk Hlubek, Geert Berx, Andreas Eger, Susanne Merkel, Andreas Jung, Thomas Kirchner, Thomas Brabletz (September 2006). "A Transient, EMT-Linked Loss of Basement Membranes Indicates Metastasis and Poor Survival in Colorectal Cancer". Gastroenterology. 131 (3): 830–840. doi:10.1053/j.gastro.2006.06.016. Retrieved 15 November 2018.
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 Ganesh M. Nawkar, Chang Ho Kanga, Punyakishore Maibam, Joung Hun Park, Young Jun Jung, Ho Byoung Chae, Yong Hun Chi, In Jung Jung, Woe Yeon Kim, Dae-Jin Yun, and Sang Yeol Lee (21 February 2017). "HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis" (PDF). Proceedings of the National Academy of Sciences USA. 114 (8): 2084–89. doi:10.1073/pnas.1609844114. Retrieved 24 June 2021.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 Jakob Mejlvang, Marina Kriajevska, Cindy Vandewalle, Tatyana Chernova, A. Emre Sayan, Geert Berx, J. Kilian Mellon, and Eugene Tulchinsky (November 2007). "Direct Repression of Cyclin D1 by SIP1 Attenuates Cell Cycle Progression in Cells Undergoing an Epithelial Mesenchymal Transition". Molecular Biology of the Cell. 18 (11): 4615–4624. doi:10.1091/mbc.e07-05-0406. Retrieved 15 November 2018.

External links

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