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C-EBP box gene transcriptions

Introduction

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

“ATF4 regulates transcription of its target genes through the formation of homodimers or heterooligomers with the transcription factors Jun, AP-1 and C/EBP38,39 that bind to CARE (C/EBP-ATF) responsive elements having the consensus sequence XTTXCATCA (where X = G, A or T).39 In the region from -625 to -618 bp relative to the SESN2 translation start codon (from -228 to -221 bp relative to the transcription start site) we found a candidate sequence for the ATF4 binding site TTTTCATCA.”[1]

Consensus sequences

Consensus sequences

The consensus sequence for the CCAAT-enhancer-binding site (C/EBP) is TAGCATT (Yao).[2]

“TTAGGACAT [Misra] is the C/EBP box”.[3]

Hypotheses

Hypotheses

Main article: Hypotheses
  1. A1BG has no A boxes in either promoter.
  2. A1BG is not transcribed by an ATA box.
  3. AGCE1 does not participate in the transcription of A1BG.
C/EBP boxes samplings

C/EBP boxes samplings

Main article: Model samplings

C/EBP boxes samplings

TTAGGACAT (Misra) is a C/EBP box that does not occur in either promoter of A1BG using “⌘F”.

For the Basic programs testing consensus sequence 5′-TTAGGACAT-3′ (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 5′-TTAGGACAT-3′, 0.
  2. negative strand, positive direction, looking for 5′-TTAGGACAT-3′, 0.
  3. positive strand, negative direction, looking for 5′-TTAGGACAT-3′, 0.
  4. positive strand, positive direction, looking for 5′-TTAGGACAT-3′, 0.
  5. complement, negative strand, negative direction, looking for 5′-AATCCTGTA-3′, 0.
  6. complement, negative strand, positive direction, looking for 5′-AATCCTGTA-3′, 0.
  7. complement, positive strand, negative direction, looking for 5′-AATCCTGTA-3′, 0.
  8. complement, positive strand, positive direction, looking for 5′-AATCCTGTA-3′, 0.
  9. inverse complement, negative strand, negative direction, looking for 5′-ATGTCCTAA-3′, 0.
  10. inverse complement, negative strand, positive direction, looking for 5′-ATGTCCTAA-3′, 0.
  11. inverse complement, positive strand, negative direction, looking for 5′-ATGTCCTAA-3′, 0.
  12. inverse complement, positive strand, positive direction, looking for 5′-ATGTCCTAA-3′, 0.
  13. inverse negative strand, negative direction, looking for 5′-TACAGGATT-3′, 0.
  14. inverse negative strand, positive direction, looking for 5′-TACAGGATT-3′, 0.
  15. inverse positive strand, negative direction, looking for 5′-TACAGGATT-3′, 0.
  16. inverse positive strand, positive direction, looking for 5′-TACAGGATT-3′, 0.

TAGCATT (Yao) is a C/EBP box that does not occur in either promoter of A1BG using “⌘F”.

For the Basic programs testing consensus sequence 5′-TAGCATT-3′ (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 5′-TAGCATT-3′, 0.
  2. negative strand, positive direction, looking for 5′-TAGCATT-3′, 0.
  3. positive strand, negative direction, looking for 5′-TAGCATT-3′, 0.
  4. positive strand, positive direction, looking for 5′-TAGCATT-3′, 0.
  5. complement, negative strand, negative direction, looking for 5′-ATCGTAA-3′, 0.
  6. complement, negative strand, positive direction, looking for 5′-ATCGTAA-3′, 0.
  7. complement, positive strand, negative direction, looking for 5′-ATCGTAA-3′, 0.
  8. complement, positive strand, positive direction, looking for 5′-ATCGTAA-3′, 0.
  9. inverse complement, negative strand, negative direction, looking for 5′-AATGCTA-3′, 0.
  10. inverse complement, negative strand, positive direction, looking for 5′-AATGCTA-3′, 0.
  11. inverse complement, positive strand, negative direction, looking for 5′-AATGCTA-3′, 0.
  12. inverse complement, positive strand, positive direction, looking for 5′-AATGCTA-3′, 0.
  13. inverse negative strand, negative direction, looking for 5′-TTACGAT-3′, 0.
  14. inverse negative strand, positive direction, looking for 5′-TTACGAT-3′, 0.
  15. inverse positive strand, negative direction, looking for 5′-TTACGAT-3′, 0.
  16. inverse positive strand, positive direction, looking for 5′-TTACGAT-3′, 0.
Acknowledgements

Acknowledgements

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

See also

See also

References

References

  1. ↑ Alisa A. Garaeva, Irina E. Kovaleva, Peter M. Chumakov & Alexandra G. Evstafieva (15 January 2016). “Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4″. Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.
  2. ↑ Yao EF, Denison MS (June 1992). “DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer”. Biochemistry. 31 (21): 5060–7. doi:10.1021/bi00136a019. PMID 1318077.
  3. ↑ Ravi P. Misra, Azad Bonni, Cindy K. Miranti, Victor M. Rivera, Morgan Sheng, and Michael E.Greenberg (14 October 1994). “L-type Voltage-sensitive Calcium Channel Activation Stimulates Gene Expression by a Serum Response Factor-dependent Pathway” (PDF). The Journal of Biological Chemistry. 269 (41): 25483–25493. PMID 7929249. Retrieved 7 December 2019.
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