N box gene transcriptions: Difference between revisions

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For the Basic programs testing consensus sequence CACNAG (starting with SuccessablesLeal.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 CACNAG (starting with SuccessablesLeal.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 CACNAG, 3, CACGAG at 4403, CACCAG at 3812, CACTAG at 1481.
# negative strand, negative direction, looking for CACNAG, 3, CACGAG at 4403, CACCAG at 3812, CACTAG at 1481.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for CACNAG, 10, CACGAG at 4472, CACAAG at 3634, CACTAG at 3493, CACTAG at 3369, CACGAG at 3232, CACAAG at 2244, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for CACNAG, 7, CACCAG at 4379, CACGAG at 3152, CACCAG at 2940, CACTAG at 2513, CACTAG at 2377, CACGAG at 2090, CACAAG at 107.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for CACNAG, 11, CACCAG at 3719, CACCAG at 2995, CACTAG at 2638, CACCAG at 2604, CACCAG at 1630, CACCAG at 1462, CACCAG at 1362, CACCAG at 1126, CACCAG at 706, CACCAG at 622, CACGAG at 243.
# complement, negative strand, negative direction, looking for GTGNTC, 0.
# complement, negative strand, negative direction, looking for GTGNTC, 10, GTGCTC at 4472, GTGTTC at 3634, GTGATC at 3493, GTGATC at 3369, GTGCTC at 3232, GTGTTC at 2244, GTGCTC at 1182, GTGCTC at 708, GTGCTC at 572, GTGCTC  at 435.
# complement, positive strand, negative direction, looking for GTGNTC, 3, GTGCTC at 4403, GTGGTC at 3812, GTGATC at 1481.
# complement, positive strand, negative direction, looking for GTGNTC, 3, GTGCTC at 4403, GTGGTC at 3812, GTGATC at 1481.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for GTGNTC, 11, GTGGTC at 3719, GTGGTC at 2995, GTGATC at 2638, GTGGTC at 2604, GTGGTC at 1630, GTGGTC at 1462, GTGGTC at 1362, GTGGTC at 1126, GTGGTC at 706, GTGGTC at 622, GTGCTC at 243.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for GTGNTC, 7, GTGGTC at 4379, GTGCTC at 3152, GTGGTC at 2940, GTGATC at 2513, GTGATC at 2377, GTGCTC at 2090, GTGTTC at 107.
# inverse complement, negative strand, negative direction, looking for CTNGTG, 0.
# inverse complement, negative strand, negative direction, looking for CTNGTG, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.

Revision as of 22:42, 22 March 2021

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

"Human pColQ1a carries consensus sequences for transcriptional factors E-protein (E-box, CANNTG), NFAT (GGAAA), c-Ets transcription factor [c-Ets, (C/A)GGA(A/T)], Elk-1, N-box (CCGGAA), and MEF2 (CTAAAAATAA), which play essential roles in muscle-specific and NMJ-specific transcriptional activities (Lee et al., 2004)."[1]

Human genes

Gene expressions

Interactions

Consensus sequences

CCGGAA[1]

Binding site for

"The [basic helix–loop–helix] bHLH proteins from group E were usually bound to the CACGCG [Coupling element] or CACGAG (N-box) motif."[2]

"Group E comprises two families in which the proteins have a conserved Pro or Gly residue within the basic region that mediates preferential binding to the N-box sequences CACGGC or CACGAC."[3]

"The HEY1 gene binds E-box (CANGTG) and N-box (CACNAG) sites (31,32)."[4]

The "putative consensus binding sites of Notch target genes in human IDE promoter" included the N-box from "the first translation start site (ATG)" -3711/-3715 position in a forward (+) orientation with a consensus sequence of CACNAG of the bHLH protein HES-1 with a strong DNA binding activity.[5] For the closer binding position -310/-305 in a reverse (-) orientation of the bHLH protein Hey-1 CACNAG had a weak DNA binding activity.[5] The "Class C" DNA binding site at position -379/-374 in a reverse (-) orientation with a consensus sequence of CACGNG of the bHLH Hey-1 protein had a strong DNA binding activity.[5]

Promoter occurrences

"Transcriptional upregulation of pColQ1a at the [neuromuscular junction] NMJ is mediated by the N-box (CCGGAA; Lee et al., 2004). The N-box (CGGAA) is also the neuregulin-response element in mouse Chrnd encoding the δ subunit of acetylcholine receptor (AChR; Fromm and Burden, 1998) and in rat Chrne encoding the AChR ε subunit (Sapru et al., 1998). Similar involvement of the neuregulin-responsive N-box in the NMJ-specific transcription of ColQ in mouse have also been reported (Lee et al., 2004; Ting et al., 2005). Also, specific activation of pColQ1 and pColQ1a in slow- and fast-twitch muscles, respectively, is mediated by a slow upstream regulatory element (SURE) in pColQ1 and a fast intronic regulatory element (FIRE) in pColQ1a (Lee et al., 2004; Ting et al., 2005)."[1]

Hypotheses

  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

N-box (Lee) samplings

Copying a responsive elements consensus sequence CCGGAA 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 CCGGAA (starting with SuccessablesN-box.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 CCGGAA, 1, CCGGAA at 3569.
  2. positive strand, negative direction, looking for CCGGAA, 0.
  3. positive strand, positive direction, looking for CCGGAA, 10, CCGGAA at 1797, CCGGAA at 1515, CCGGAA at 1431, CCGGAA at 1331, CCGGAA at 1263, CCGGAA at 1011, CCGGAA at 927, CCGGAA at 827, CCGGAA at 675, CCGGAA at 591.
  4. negative strand, positive direction, looking for CCGGAA, 0.
  5. complement, negative strand, negative direction, looking for GGCCTT, 0.
  6. complement, positive strand, negative direction, looking for GGCCTT, 1, GGCCTT at 3569.
  7. complement, positive strand, positive direction, looking for GGCCTT, 0.
  8. complement, negative strand, positive direction, looking for GGCCTT, 10, GGCCTT at 1797, GGCCTT at 1515, GGCCTT at 1431, GGCCTT at 1331, GGCCTT at 1263, GGCCTT at 1011, GGCCTT at 927, GGCCTT at 827, GGCCTT at 675, GGCCTT at 591.
  9. inverse complement, negative strand, negative direction, looking for TTCCGG, 1, TTCCGG at 4167.
  10. inverse complement, positive strand, negative direction, looking for TTCCGG, 0.
  11. inverse complement, positive strand, positive direction, looking for TTCCGG, 10, TTCCGG at 1513, TTCCGG at 1429, TTCCGG at 1329, TTCCGG at 1261, TTCCGG at 1009, TTCCGG at 925, TTCCGG at 825, TTCCGG at 673, TTCCGG at 589, TTCCGG at 212.
  12. inverse complement, negative strand, positive direction, looking for TTCCGG, 1, TTCCGG at 4244.
  13. inverse negative strand, negative direction, looking for AAGGCC, 0.
  14. inverse positive strand, negative direction, looking for AAGGCC, 1, AAGGCC at 4167.
  15. inverse positive strand, positive direction, looking for AAGGCC, 1, AAGGCC at 4244.
  16. inverse negative strand, positive direction, looking for AAGGCC, 10, AAGGCC at 1513, AAGGCC at 1429, AAGGCC at 1329, AAGGCC at 1261, AAGGCC at 1009, AAGGCC at 925, AAGGCC at 825, AAGGCC at 673, AAGGCC at 589, AAGGCC at 212.

N-box (Lee) UTRs

Negative strand, negative direction: TTCCGG at 4167, CCGGAA at 3569.

N-box (Lee) proximal promoters

Negative strand, positive direction: TTCCGG at 4244.

N-box (Lee) distal promoters

Positive strand, positive direction: CCGGAA at 1797, CCGGAA at 1515, TTCCGG at 1513, CCGGAA at 1431, TTCCGG at 1429, CCGGAA at 1331, TTCCGG at 1329, CCGGAA at 1263, TTCCGG at 1261, CCGGAA at 1011, TTCCGG at 1009, CCGGAA at 927, TTCCGG at 925, CCGGAA at 827, TTCCGG at 825, CCGGAA at 675, TTCCGG at 673, CCGGAA at 591, TTCCGG at 589, TTCCGG at 212.

N-box (Bai) samplings

Copying a responsive elements consensus sequence CACGAG and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CACGAG (starting with SuccessablesN-boxB.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 CACGAG, 1, CACGAG at 4403.
  2. positive strand, negative direction, looking for CACGAG, 6, CACGAG at 4472, CACGAG at 3232, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.
  3. positive strand, positive direction, looking for CACGAG, 2, CACGAG at 3152, CACGAG at 2090.
  4. negative strand, positive direction, looking for CACGAG, 1, CACGAG at 243.
  5. complement, negative strand, negative direction, looking for GTGCTC, 6, GTGCTC at 4472, GTGCTC at 3232, GTGCTC at 1182, GTGCTC at 708, GTGCTC at 572, GTGCTC at 435.
  6. complement, positive strand, negative direction, looking for GTGCTC, 1, GTGCTC at 4403.
  7. complement, positive strand, positive direction, looking for GTGCTC, 1, GTGCTC at 243.
  8. complement, negative strand, positive direction, looking for GTGCTC, 2, GTGCTC at 3152, GTGCTC at 2090.
  9. inverse complement, negative strand, negative direction, looking for CTCGTG, 1, CTCGTG at 3914.
  10. inverse complement, positive strand, negative direction, looking for CTCGTG, 0.
  11. inverse complement, positive strand, positive direction, looking for CTCGTG, 5, CTCGTG at 3739, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855.
  12. inverse complement, negative strand, positive direction, looking for CTCGTG, 1, CTCGTG at 4376.
  13. inverse negative strand, negative direction, looking for GAGCAC, 0.
  14. inverse positive strand, negative direction, looking for GAGCAC, 1, GAGCAC at 3914.
  15. inverse positive strand, positive direction, looking for GAGCAC, 1, GAGCAC at 4376.
  16. inverse negative strand, positive direction, looking for GAGCAC, 5, GAGCAC at 3739, GAGCAC at 1627, GAGCAC at 1207, GAGCAC at 955, GAGCAC at 855.

N-box (Bai) UTRs

Negative strand, negative direction: CACGAG at 4403, CTCGTG at 3914.

Positive strand, negative direction: CACGAG at 4472, CACGAG at 3232.

N-box (Bai) core promoters

Negative strand, positive direction: CTCGTG at 4376.

N-box (Bai) distal promoters

Positive strand, negative direction: CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.

Negative strand, positive direction: CACGAG at 243.

Positive strand, positive direction: CTCGTG at 3739, CACGAG at 3152, CACGAG at 2090, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855.

N-box (Gao) samplings

Copying a responsive elements consensus sequence CACG(A/G)C and putting the sequence in "⌘F" finds three 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 CACG(A/G)C (starting with SuccessablesAAA.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 CACG(A/G)C, 1, CACGAC at 3956.
  2. positive strand, negative direction, looking for CACG(A/G)C, 0.
  3. positive strand, positive direction, looking for CACG(A/G)C, 0.
  4. negative strand, positive direction, looking for CACG(A/G)C, 3, CACGGC at 1699, CACGGC at 980, CACGGC at 880.
  5. complement, negative strand, negative direction, looking for GTGC(C/T)G, 0.
  6. complement, positive strand, negative direction, looking for GTGC(C/T)G, 1, GTGCTG at 3956.
  7. complement, positive strand, positive direction, looking for GTGC(C/T)G, 3, GTGCCG at 1699, GTGCCG at 980, GTGCCG at 880.
  8. complement, negative strand, positive direction, looking for GTGC(C/T)G, 0.
  9. inverse complement, negative strand, negative direction, looking for G(C/T)CGTG, 8, GTCGTG at 3733, GTCGTG at 3072, GTCGTG at 1787, GTCGTG at 1142, GCCGTG at 959, GTCGTG at 678, GTCGTG at 542, GTCGTG at 405.
  10. inverse complement, positive strand, negative direction, looking for G(C/T)CGTG, 0.
  11. inverse complement, positive strand, positive direction, looking for G(C/T)CGTG, 11, GCCGTG at 4005, GTCGTG at 3043, GTCGTG at 2200, GTCGTG at 2104, GCCGTG at 1639, GTCGTG at 1459, GTCGTG at 1359, GTCGTG at 1123, GTCGTG at 1039, GTCGTG at 787, GTCGTG at 619.
  12. inverse complement, negative strand, positive direction, looking for G(C/T)CGTG, 2, GCCGTG at 3812, GTCGTG at 79.
  13. inverse negative strand, negative direction, looking for C(A/G)GCAC, 0.
  14. inverse positive strand, negative direction, looking for C(A/G)GCAC, 8, CAGCAC at 3733, CAGCAC at 3072, CAGCAC at 1787, CAGCAC at 1142, CGGCAC at 959, CAGCAC at 678, CAGCAC at 542, CAGCAC at 405.
  15. inverse positive strand, positive direction, looking for C(A/G)GCAC, 2, CGGCAC at 3812, CAGCAC at 79.
  16. inverse negative strand, positive direction, looking for C(A/G)GCAC, 11, CGGCAC at 4005, CAGCAC at 3043, CAGCAC at 2200, CAGCAC at 2104, CGGCAC at 1639, CAGCAC at 1459, CAGCAC at 1359, CAGCAC at 1123, CAGCAC at 1039, CAGCAC at 787, CAGCAC at 619.

N-box (Gao) UTRs

Negative strand, negative direction: CACGAC at 3956, GTCGTG at 3733, GTCGTG at 3072.

N-box (Gao) distal promoters

Negative strand, negative direction: GTCGTG at 1787, GTCGTG at 1142, GCCGTG at 959, GTCGTG at 678, GTCGTG at 542, GTCGTG at 405.

Negative strand, positive direction: GCCGTG at 3812, CACGGC at 1699, CACGGC at 980, CACGGC at 880, GTCGTG at 79.

Positive strand, positive direction: GCCGTG at 4005, GTCGTG at 3043, GTCGTG at 2200, GTCGTG at 2104, GCCGTG at 1639, GTCGTG at 1459, GTCGTG at 1359, GTCGTG at 1123, GTCGTG at 1039, GTCGTG at 787, GTCGTG at 619.

N-box (Leal) samplings

Copying a responsive elements consensus sequence CACNAG 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 CACNAG (starting with SuccessablesLeal.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 CACNAG, 3, CACGAG at 4403, CACCAG at 3812, CACTAG at 1481.
  2. positive strand, negative direction, looking for CACNAG, 10, CACGAG at 4472, CACAAG at 3634, CACTAG at 3493, CACTAG at 3369, CACGAG at 3232, CACAAG at 2244, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435.
  3. positive strand, positive direction, looking for CACNAG, 7, CACCAG at 4379, CACGAG at 3152, CACCAG at 2940, CACTAG at 2513, CACTAG at 2377, CACGAG at 2090, CACAAG at 107.
  4. negative strand, positive direction, looking for CACNAG, 11, CACCAG at 3719, CACCAG at 2995, CACTAG at 2638, CACCAG at 2604, CACCAG at 1630, CACCAG at 1462, CACCAG at 1362, CACCAG at 1126, CACCAG at 706, CACCAG at 622, CACGAG at 243.
  5. complement, negative strand, negative direction, looking for GTGNTC, 10, GTGCTC at 4472, GTGTTC at 3634, GTGATC at 3493, GTGATC at 3369, GTGCTC at 3232, GTGTTC at 2244, GTGCTC at 1182, GTGCTC at 708, GTGCTC at 572, GTGCTC at 435.
  6. complement, positive strand, negative direction, looking for GTGNTC, 3, GTGCTC at 4403, GTGGTC at 3812, GTGATC at 1481.
  7. complement, positive strand, positive direction, looking for GTGNTC, 11, GTGGTC at 3719, GTGGTC at 2995, GTGATC at 2638, GTGGTC at 2604, GTGGTC at 1630, GTGGTC at 1462, GTGGTC at 1362, GTGGTC at 1126, GTGGTC at 706, GTGGTC at 622, GTGCTC at 243.
  8. complement, negative strand, positive direction, looking for GTGNTC, 7, GTGGTC at 4379, GTGCTC at 3152, GTGGTC at 2940, GTGATC at 2513, GTGATC at 2377, GTGCTC at 2090, GTGTTC at 107.
  9. inverse complement, negative strand, negative direction, looking for CTNGTG, 0.
  10. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for GANCAC, 0.
  14. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, positive direction, looking for AAAAAAAA, 0.
  16. inverse negative strand, positive direction, looking for AAAAAAAA, 0.

Leal UTRs

Leal core promoters

Leal proximal promoters

Leal distal promoters

"Class C" (Leal) samplings

Copying a responsive elements consensus sequence CACGNG 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 CACGNG (starting with SuccessablesClassC.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 CACGNG, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for GTGGNC, 0.
  6. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for CNGGTG, 0.
  10. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for GNGCAC, 0.
  14. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, positive direction, looking for AAAAAAAA, 0.
  16. inverse negative strand, positive direction, looking for AAAAAAAA, 0.

ClassC UTRs

ClassC core promoters

ClassC proximal promoters

ClassC distal promoters

Acknowledgements

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

See also

References

  1. 1.0 1.1 1.2 Kun Huang, Jin Li, Mikako Ito, Jun-Ichi Takeda, Bisei Ohkawara, Tomoo Ogi, Akio Masuda, and Kinji Ohno (8 September 2020). "Gene Expression Profile at the Motor Endplate of the Neuromuscular Junction of Fast-Twitch Muscle". Frontiers in Molecular Neuroscience. 13: 154–165. doi:10.3389/fnmol.2020.00154. PMID 33117128 Check |pmid= value (help). Retrieved 19 March 2021.
  2. Ge Bai, Da-Hai Yang, Peijian Chao, Heng Yao, MingLiang Fei, Yihan Zhang, Xuejun Chen, Bingguang Xiao, Feng Li, Zhen-Yu Wang, Jun Yang and He Xie (19 December 2020). "Genome-wide identification and expression analysis of NtbHLH gene family in tobacco (Nicotiana tabacum L.) and the role of NtbHLH86 in drought adaptation". Plant Diversity. 10: 4. doi:10.1016/j.pld.2020.10.004. Retrieved 19 March 2021.
  3. Min Gao, Yanxun Zhu, Jinhua Yang, Hongjing Zhang, Chenxia Cheng, Yucheng Zhang, Ran Wan, Zhangjun Fei & Xiping Wang (18 March 2019). "Identification of the grape basic helix–loop–helix transcription factor family and characterization of expression patterns in response to different stresses". Plant Growth Regulation. 88: 19–39. Retrieved 20 March 2021.
  4. Takahito Fukusumi, Theresa W. Guo, Shuling Ren, Sunny Haft, Chao Liu, Akihiro Sakai, Mizuo Ando, Yuki Saito, Sayed Sadat, and Joseph A. Califano (February 2021). "Reciprocal activation of HEY1 and NOTCH4 under SOX2 control promotes EMT in head and neck squamous cell carcinoma". International Journal of Oncology. 58 (2): 226–237. doi:10.3892/ijo.2020.5156. PMID 33491747 Check |pmid= value (help). Retrieved 21 March 2021.
  5. 5.0 5.1 5.2 María C. Leal, Ezequiel I. Surace, María P. Holgado, Carina C. Ferrari, Rodolfo Tarelli, Fernando Pitossi, Thomas Wisniewski, Eduardo M. Castaño, and Laura Morelli (19 October 2011). "Notch signaling proteins HES-1 and Hey-1 bind to insulin degrading enzyme (IDE) proximal promoter and repress its transcription and activity: Implications for cellular Aβ metabolism". Biochim Biophys Acta. 1823 (2): 227–235. doi:10.1016/j.bbamcr.2011.09.014. PMID 22036964. Retrieved 21 March 2021.

External links