HY box gene transcriptions: Difference between revisions

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Positive strand, positive direction: TGTGGG at 3533, CCCTCA at 3185, TGTGGG at 2965, CCCACA at 1803, CCCTCA at 1783, CCCTCA at 662, CCCTCA at 494.
Positive strand, positive direction: TGTGGG at 3533, CCCTCA at 3185, TGTGGG at 2965, CCCACA at 1803, CCCTCA at 1783, CCCTCA at 662, CCCTCA at 494.
==HY boxes random dataset samplings==
# RDr0: 0.
# RDr1: 0.
# RDr2: 0.
# RDr3: 0.
# RDr4: 0.
# RDr5: 0.
# RDr6: 0.
# RDr7: 0.
# RDr8: 0.
# RDr9: 0.
# RDr0ci: 0.
# RDr1ci: 0.
# RDr2ci: 0.
# RDr3ci: 0.
# RDr4ci: 0.
# RDr5ci: 0.
# RDr6ci: 0.
# RDr7ci: 0.
# RDr8ci: 0.
# RDr9ci: 0.
===RDr arbitrary UTRs===
===RDr alternate UTRs===
===RDr arbitrary negative direction core promoters===
===RDr alternate negative direction core promoters===
===RDr arbitrary positive direction core promoters===
===RDr alternate positive direction core promoters===
===RDr arbitrary negative direction proximal promoters===
===RDr alternate negative direction proximal promoters===
===RDr arbitrary positive direction proximal promoters===
===RDr alternate positive direction proximal promoters===
===RDr arbitrary negative direction distal promoters===
===RDr alternate negative direction distal promoters===
===RDr arbitrary positive direction distal promoters===
===RDr alternate positive direction distal promoters===
==HY boxes analysis and results==
{{main|Complex locus A1BG and ZNF497#HY boxes}}
The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."<ref name=Kalousova/>
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0
|-
| 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 || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0
|}
Comparison:
The occurrences of real responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.


==Acknowledgements==
==Acknowledgements==

Revision as of 07:43, 24 May 2022

Editor-In-Chief: Henry A. Hoff

"Deletion, mutagenesis, and tandem repeat analyses identified the core responsive element as the region between −89 and −60 bp (termed the hypertrophy box [HY box]), which showed specific binding to RUNX‐2."[1]

The "HY box is the core element responsive to RUNX‐2 in human COL10A1 promoter."[1]

Boxes

Main articles: Box gene transcriptions and Boxes

A repeating sequence of nucleotides that forms a transcription or a regulatory signal is a box.

Consensus sequences

Main article: Consensus sequences

"Deletion analysis by a series of 5′-deletion constructs identified the responsive region to RUNX-2 as being between −81 bp and −76 bp, containing a putative RUNX-2 binding sequence (TGAGGG), which is similar to that identified in the promoter region of human interleukin-3 (TGTGGG) (33)."[1] This suggests a consensus sequence of 3'-TG(A/T)GGG-5' on the template strand in the direction of transcription.

RUNX2

The gene RUNX2 "is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex."[2]

COL10A1

The gene COL10A1 "encodes the alpha chain of type X collagen, a short chain collagen expressed by hypertrophic chondrocytes during endochondral ossification. Unlike type VIII collagen, the other short chain collagen, type X collagen is a homotrimer."[3]

Human COL10A1, GeneID: 1300, has an HY box as the core responsive element.[1]

Hypotheses

Main article: Hypotheses
  1. A1BG is not transcribed by an HY box.

HY box samplings

For the Basic programs (starting with SuccessablesHY.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 in the negative direction is SuccessablesHY--.bas, looking for TG(A/T)GGG, 1, TGTGGG at 749,
  2. negative strand in the positive direction is SuccessablesHY-+.bas, looking for TG(A/T)GGG, 4, TGAGGG at 258, TGAGGG at 3479, TGAGGG at 3879, TGTGGG at 4395,
  3. positive strand in the negative direction is SuccessablesHY+-.bas, looking for TG(A/T)GGG, 5, TGAGGG at 88, TGAGGG at 2699, TGAGGG at 3652, TGTGGG at 3712, TGAGGG at 4558,
  4. positive strand in the positive direction is SuccessablesHY++.bas, looking for TG(A/T)GGG, 2, TGTGGG at 2965, TGTGGG at 3533,
  5. complement, negative strand, negative direction is SuccessablesHYc--.bas, looking for AC(A/T)CCC, 0,
  6. complement, negative strand, positive direction is SuccessablesHYc-+.bas, looking for AC(A/T)CCC, 2, ACACCC at 2965, ACACCC at 3533,
  7. complement, positive strand, negative direction is SuccessablesHYc+-.bas, looking for AC(A/T)CCC, 1 , ACACCC at 749,
  8. complement, positive strand, positive direction is SuccessablesHYc++.bas, looking for AC(A/T)CCC, 4, ACTCCC at 258, ACTCCC at 3479, ACTCCC at 3879, ACACCC at 4395,
  9. inverse complement, negative strand, negative direction is SuccessablesHYci--.bas, looking for CCC(A/T)CA, 4, CCCTCA at 2702, CCCACA at 3184, CCCTCA at 3889, CCCTCA at 4498,
  10. inverse complement, negative strand, positive direction is SuccessablesHYci-+.bas, looking for CCC(A/T)CA, 3, CCCTCA at 88, CCCTCA at 3207, CCCTCA at 3503,
  11. inverse complement, positive strand, negative direction is SuccessablesHYci+-.bas, looking for CCC(A/T)CA, 0,
  12. inverse complement, positive strand, positive direction is SuccessablesHYci++.bas, looking for CCC(A/T)CA, 5, CCCTCA at 494, CCCTCA at 662, CCCTCA at 1783, CCCACA at 1803, CCCTCA at 3185,
  13. inverse, negative strand, negative direction, is SuccessablesHYi--.bas, looking for GGG(A/T)GT, 0,
  14. inverse, negative strand, positive direction, is SuccessablesHYi-+.bas, looking for GGG(A/T)GT, 5, GGGAGT at 494, GGGAGT at 662, GGGAGT at 1783, GGGTGT at 1803, GGGAGT at 3185,
  15. inverse, positive strand, negative direction, is SuccessablesHYi+-.bas, looking for GGG(A/T)GT, 4, GGGAGT at 2702, GGGTGT at 3184, GGGAGT at 3889, GGGAGT at 4498,
  16. inverse, positive strand, positive direction, is SuccessablesHYi++.bas, looking for GGG(A/T)GT, 3, GGGAGT at 88, GGGAGT at 3207, GGGAGT at 3503.

HY box UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: CCCTCA at 4498, CCCTCA at 3889, CCCACA at 3184.

Positive strand, negative direction: TGAGGG at 4558, TGTGGG at 3712, TGAGGG at 3652.

HY box core promoters

Main article: Core promoter gene transcriptions

Negative strand, positive direction: TGTGGG at 4395.

HY box proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: CCCTCA at 2702.

Positive strand, negative direction: TGAGGG at 2699.

HY box distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TGTGGG at 749.

Positive strand, negative direction: TGAGGG at 88.

Negative strand, positive direction: TGAGGG at 3879, CCCTCA at 3503, TGAGGG at 3479, CCCTCA at 3207, TGAGGG at 258, CCCTCA at 88.

Positive strand, positive direction: TGTGGG at 3533, CCCTCA at 3185, TGTGGG at 2965, CCCACA at 1803, CCCTCA at 1783, CCCTCA at 662, CCCTCA at 494.

HY boxes 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.

RDr arbitrary UTRs

RDr alternate UTRs

RDr arbitrary negative direction core promoters

RDr alternate negative direction core promoters

RDr arbitrary positive direction core promoters

RDr alternate positive direction core promoters

RDr arbitrary negative direction proximal promoters

RDr alternate negative direction proximal promoters

RDr arbitrary positive direction proximal promoters

RDr alternate positive direction proximal promoters

RDr arbitrary negative direction distal promoters

RDr alternate negative direction distal promoters

RDr arbitrary positive direction distal promoters

RDr alternate positive direction distal promoters

HY boxes analysis and results

Main article: Complex locus A1BG and ZNF497 § HY boxes

The Pax-4 homeodomain [HD] was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."[4]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

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 Akiro Higashikawa, Taku Saito, Toshiyuki Ikeda, Satoru Kamekura, Naohiro Kawamura, Akinori Kan, Yasushi Oshima, Shinsuke Ohba, Naoshi Ogata, Katsushi Takeshita, Kozo Nakamura, Ung-Il Chung, Hiroshi Kawaguchi (2009). "Identification of the core element responsive to runt-related transcription factor 2 in the promoter of human type x collagen gene". Arthritis & Rheumatism. 60 (1): 166–78. doi:10.1002/art.24243. PMID 19116917. Retrieved 2013-06-18. Unknown parameter |month= ignored (help)
  2. ↑ "RUNX2 runt-related transcription factor 2 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. 2013. Retrieved 2013-06-18. Unknown parameter |month= ignored (help)
  3. ↑ HGNC (June 9, 2013). "COL10A1 collagen, type X, alpha 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-06-18.
  4. ↑

External links

Retrieved from "https://www.wikidoc.org/index.php?title=HY_box_gene_transcriptions&oldid=1724602"