Hypoxia response element gene transcriptions: Difference between revisions

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# RDr8ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.
# RDr9ci: 0.
==Hypoxia response element Samplings==
{{main|Model samplings}}
Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (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:
# negative strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
===HRE UTRs===
{{main|UTR promoter gene transcriptions}}
===HRE core promoters===
{{main|Core promoter gene transcriptions}}
===HRE proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===HRE distal promoters===
{{main|Distal promoter gene transcriptions}}
===Random dataset samplings===
# HREr0: 0.
# HREr1: 0.
# HREr2: 0.
# HREr3: 0.
# HREr4: 0.
# HREr5: 0.
# HREr6: 0.
# HREr7: 0.
# HREr8: 0.
# HREr9: 0.
# HREr0ci: 0.
# HREr1ci: 0.
# RHREr2ci: 0.
# HREr3ci: 0.
# HREr4ci: 0.
# HREr5ci: 0.
# HREr6ci: 0.
# HREr7ci: 0.
# HREr8ci: 0.
# HREr9ci: 0.


==Acknowledgements==
==Acknowledgements==

Revision as of 05:22, 7 May 2021

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

"We recently discovered a strongly conserved distal 5' [hypoxia response element] HRE and suggested that it might contribute to oxygen-regulated [Erythropoietin] EPO expression.18 This 5' HRE resides within a DNaseI hypersensitive site - 9.2 kb upstream of the EPO transcriptional start site, [WT CATACGTGCAGGGAGACACA], contains both the 5'-ACGTG-3' core [hypoxia-inducible factor] HIF DNA binding site as well as the ancillary 5'-CACA-3' element,11 and confers hypoxia-inducible exogenous reporter gene expression in Epo expressing and non-expressing cell lines.18"[1]

Human genes

Gene expressions

"We have previously shown for PAG1, another HIF-2 target gene, that a single distal - 82 kb 5' HRE resides in an isolated DNA region, bound by many additional transcription factors, and forms multiple chromatin loops both locally and over a long distance with the promoter region.21 While in this case HIF-2α did interact with the HRE, neither hypoxia nor the presence of HIF was needed for the long-range chromatin interaction with the promoter region. Only the presence of the core 5'-ACGTG-3' HIF binding DNA sequence was required to maintain this interaction, suggesting that preformed chromatin loops enable oxygen-regulated conditional gene regulation. This model has subsequently been confirmed for many other HIF target genes by genomewide approaches.38,39 Therefore, the EPO 5' HRE might well be functionally required for hypoxia-inducible gene expression by maintaining a constitutive chromatin architecture that supports promoter activity in a cell type-specific manner. The finding that only additional large but not small 5' HRE deletions fully abrogated endogenous Epo induction and HIF:promoter interaction in 3' HRE mutant Kelly cells suggests that, like in the case of the PAG1 gene, additional transcription factors bind close to the consensus HRE sequence and are involved in chromatin looping and trans-activation of the EPO promoter. We still have no explanation why a small 5' HRE deletion alone inhibited HIF-promoter interaction, but in combination with a 3' HRE mutation partially rescued the inhibitory effect of the 3' HRE mutation. Nonetheless, it is without precedent that the extended 5' HRE strongly cis-enhanced HIF binding to the promoter and 3' HRE."[1]

Interactions

Consensus sequences

"Putative EPO promoter HREs. Location of two conserved potential promoter HREs (pHRE1 and pHRE2; [CACGC]) close to the GATA ([GATA]) and [Wilms tumor gene] WT1 ([GCCTCTCCCCCACCCCCACCCGCGCACGCAC]) sites in the EPO proximal 5' region. [For human and other vertebrates] is a UCSC Genome Browser output (version hg19), including 161 transcription factor ChIP-sequencing (ChIP-seq) tracks derived from the ENCODE database (version 3), clusters of DNaseI hypersensitivity sites (HSS) from 125 cell types, and the transcriptional start site (TSS), with a closer view of the region in 50 vertebrates extracted using the 100-MULTIZ whole-genome multiple sequence alignment algorithm."[1]

Binding site for

Enhancer activity

Promoter occurrences

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.

Hypoxia-inducible factor samplings

Copying ACGTG in "⌘F" yields eight between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence ACGTG (starting with SuccessablesHxRE.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 ACGTG, 8, ACGTG at 4339, ACGTG at 3288, ACGTG at 2760, ACGTG at 2425, ACGTG at 1999, ACGTG at 1718, ACGTG at 1346, ACGTG at 1338.
  2. negative strand, positive direction, looking for ACGTG, 1, ACGTG at 570.
  3. positive strand, negative direction, looking for ACGTG, 1, ACGTG at 4237.
  4. positive strand, positive direction, looking for ACGTG, 10, ACGTG at 4342, ACGTG at 3884, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, ACGTG at 1821, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, ACGTG at 547.
  5. complement, negative strand, negative direction, looking for TGCAC, 1, TGCAC at 4237.
  6. complement, negative strand, positive direction, looking for TGCAC, 10, TGCAC at 4342, TGCAC at 3884, TGCAC at 3342, TGCAC at 3321, TGCAC at 2961, TGCAC at 1821, TGCAC at 1471, TGCAC at 1371, TGCAC at 1219, TGCAC at 547.
  7. complement, positive strand, negative direction, looking for TGCAC, 8, TGCAC at 4339, TGCAC at 3288, TGCAC at 2760, TGCAC at 2425, TGCAC at 1999, TGCAC at 1718, TGCAC at 1346, TGCAC at 1338.
  8. complement, positive strand, positive direction, looking for TGCAC, 1, TGCAC at 570.
  9. inverse complement, negative strand, negative direction, looking for CACGT, 5, CACGT at 3429, CACGT at 2863, CACGT at 2081, CACGT at 1535, CACGT at 1470.
  10. inverse complement, negative strand, positive direction, looking for CACGT, 2, CACGT at 3254, CACGT at 569.
  11. inverse complement, positive strand, negative direction, looking for CACGT, 3, CACGT at 1772, CACGT at 531, CACGT at 342.
  12. inverse complement, positive strand, positive direction, looking for CACGT, 13, CACGT at 3960, CACGT at 3883, CACGT at 3464, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, CACGT at 1786, CACGT at 1218, CACGT at 783, CACGT at 546.
  13. inverse negative strand, negative direction, looking for GTGCA, 3, GTGCA at 1772, GTGCA at 531, GTGCA at 342.
  14. inverse negative strand, positive direction, looking for GTGCA, 13, GTGCA at 3960, GTGCA at 3883, GTGCA at 3464, GTGCA at 2960, GTGCA at 2800, GTGCA at 2681, GTGCA at 2334, GTGCA at 2326, GTGCA at 2063, GTGCA at 1786, GTGCA at 1218, GTGCA at 783, GTGCA at 546.
  15. inverse positive strand, negative direction, looking for GTGCA, 5, GTGCA at 3429, GTGCA at 2863, GTGCA at 2081, GTGCA at 1535, GTGCA at 1470.
  16. inverse positive strand, positive direction, looking for GTGCA, 2, GTGCA at 3254, GTGCA at 569.

HIF UTRs

Negative strand, negative direction: ACGTG at 4339, CACGT at 3429, ACGTG at 3288, CACGT at 2863.

Positive strand, negative direction: ACGTG at 4237.

HIF core promoters

Positive strand, positive direction: ACGTG at 4342.

HIF proximal promoters

Negative strand, negative direction: ACGTG at 2760.

HIF distal promoters

Negative strand, negative direction: ACGTG at 2425, CACGT at 2081, ACGTG at 1999, ACGTG at 1718, CACGT at 1535, CACGT at 1470, ACGTG at 1346, ACGTG at 1338, and complements.

Positive strand, negative direction: CACGT at 1772, CACGT at 531, CACGT at 342.

Negative strand, positive direction: CACGT at 3254, ACGTG at 570, CACGT at 569.

Positive strand, positive direction: CACGT at 3960, ACGTG at 3884, CACGT at 3883, CACGT at 3464, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, ACGTG at 1821, CACGT at 1786, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, CACGT at 1218, CACGT at 783, ACGTG at 547, CACGT at 546.

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

Hypoxia response element Samplings

Copying a responsive elements consensus sequence AAAAAAAA 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 AAAAAAAA (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 AAAAAAAA, 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 TTTTTTTT, 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 TTTTTTTT, 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 AAAAAAAA, 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.

HRE UTRs

HRE core promoters

HRE proximal promoters

HRE distal promoters

Random dataset samplings

  1. HREr0: 0.
  2. HREr1: 0.
  3. HREr2: 0.
  4. HREr3: 0.
  5. HREr4: 0.
  6. HREr5: 0.
  7. HREr6: 0.
  8. HREr7: 0.
  9. HREr8: 0.
  10. HREr9: 0.
  11. HREr0ci: 0.
  12. HREr1ci: 0.
  13. RHREr2ci: 0.
  14. HREr3ci: 0.
  15. HREr4ci: 0.
  16. HREr5ci: 0.
  17. HREr6ci: 0.
  18. HREr7ci: 0.
  19. HREr8ci: 0.
  20. HREr9ci: 0.

Acknowledgements

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

See also

References

  1. 1.0 1.1 1.2 Ilaria M. C. Orlando, Véronique N. Lafleur, Federica Storti, Patrick Spielmann, Lisa Crowther, Sara Santambrogio, Johannes Schödel, David Hoogewijs, David R. Mole, and Roland H. Wenger (19 December 2019). "Distal and proximal hypoxia response elements co-operate to regulate organ-specific erythropoietin gene expression". Haematologica. 105 (12): 2774–2784. doi:10.3324/haematol.2019.236406. PMID 33256376 Check |pmid= value (help). Retrieved 6 May 2021.

External links