H and ACA box gene transcriptions: Difference between revisions

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"The box H/ACA snoRNAs were most recently recognized as a small RNA family by virtue of an ACA trinucleotide located 3 nt upstream of the mature snoRNA 3' end (41). In addition to this ACA box, they have the consensus H box sequence (5'-ANANNA-3') but have no other primary sequence identity. Despite this lack of primary sequence conservation, the H and ACA boxes are embedded in an evolutionarily conserved hairpin-hinge-hairpin-tail core secondary structure with the H box in the single-stranded hinge region and the ACA box in the single-stranded tail (5, 16)."<ref name=Mitchell>{{ cite journal
"The box H/ACA snoRNAs were most recently recognized as a small RNA family by virtue of an ACA trinucleotide located 3 nt upstream of the mature snoRNA 3' end (41). In addition to this ACA box, they have the consensus H box sequence (5'-ANANNA-3') but have no other primary sequence identity. Despite this lack of primary sequence conservation, the H and ACA boxes are embedded in an evolutionarily conserved hairpin-hinge-hairpin-tail core secondary structure with the H box in the single-stranded hinge region and the ACA box in the single-stranded tail (5, 16)."<ref name=Mitchell>{{ cite journal
|author=James R. Mitchell, Jeffrey Cheng, ang Kathleen Collins
|author=James R. Mitchell, Jeffrey Cheng, and Kathleen Collins
|title=A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3' End
|title=A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3' End
|journal=Molecular and Cellular Biology
|journal=Molecular and Cellular Biology
Line 44: Line 44:
For the Basic programs (starting with SuccessablesHACA.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 (starting with SuccessablesHACA.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  is SuccessablesHACA--.bas, looking for 5'-ACAGGA-3', 0.
# negative strand, negative direction  is SuccessablesHACA--.bas, looking for 5'-ACAGGA-3', 0.
# positive strand, negative direction is SuccessablesHACA+-.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 2690.
# negative strand, positive direction is SuccessablesHACA-+.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3572.
# negative strand, positive direction is SuccessablesHACA-+.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3572.
# positive strand, negative direction is SuccessablesHACA+-.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 2690.
# positive strand, positive direction is SuccessablesHACA++.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3620.
# positive strand, positive direction is SuccessablesHACA++.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3620.
# complement, negative strand, negative direction is SuccessablesHACAc--.bas, looking for 5'-TGTCCT-3', 1, 5'-TGTCCT-3' at 2690.
# complement, negative strand, positive direction is SuccessablesHACAc-+.bas, looking for 5'-TGTCCT-3', 1, 5'-TGTCCT-3' at 3620.
# complement, positive strand, negative direction is SuccessablesHACAc+-.bas, looking for 5'-TGTCCT-3', 0.
# complement, positive strand, positive direction is SuccessablesHACAc++.bas, looking for 5'-TGTCCT-3', 1, 5'-TGTCCT-3' at 3572.
# inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 3389, 5'-TCCTGT-3' at 3756, 5'-TCCTGT-3' at 4468.
# inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 3389, 5'-TCCTGT-3' at 3756, 5'-TCCTGT-3' at 4468.
# inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 5'-TCCTGT-3', 2, 5'-TCCTGT-3' at 144, 5'-TCCTGT-3' at 3622.
# inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 5'-TCCTGT-3', 2, 5'-TCCTGT-3' at 144, 5'-TCCTGT-3' at 3622.
# inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 5'-TCCTGT-3', 1, 5'-TCCTGT-3' at 1911.
# inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 5'-TCCTGT-3', 1, 5'-TCCTGT-3' at 1911.
# inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 2460, 5'-TCCTGT-3' at 3131, 5'-TCCTGT-3' at 4252.
# inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 2460, 5'-TCCTGT-3' at 3131, 5'-TCCTGT-3' at 4252.
# inverse, negative strand, negative direction, is SuccessablesHACAi--.bas, looking for 5'-AGGACA-3', 1, 5'-AGGACA-3' at 1911.
# inverse, negative strand, positive direction, is SuccessablesHACAi-+.bas, looking for 5'-AGGACA-3', 3, 3'-AGGACA-3' at 2460, 3'-AGGACA-3' at 3131, 3'-AGGACA-3' at 4252.
# inverse, positive strand, negative direction, is SuccessablesHACAi+-.bas, looking for 5'-AGGACA-3', 3, 5'-AGGACA-3' at 3389, 5'-AGGACA-3' at 3756, 5'-AGGACA-3' at 4468.
# inverse, positive strand, positive direction, is SuccessablesHACAi++.bas, looking for 5'-AGGACA-3', 2, 5'-AGGACA-3' at 144, 5'-AGGACA-3' at 3622.


===HACA UTRs===
===HACA (4560-2846) UTRs===


# Negative strand, negative direction: TCCTGT at 4468, TCCTGT at 3756, TCCTGT at 3389.
# Negative strand, negative direction: TCCTGT at 4468, TCCTGT at 3756, TCCTGT at 3389.


===HACA proximal promoters===
===HACA negative direction (2811-2596) proximal promoters===
 
# Positive strand, negative direction: ACAGGA at 2690.
 
===HACA positive direction (4265-4050) proximal promoters===


# Positive strand, positive direction: TCCTGT at 4252.
# Positive strand, positive direction: TCCTGT at 4252.


===HACA distal promoters===
===HACA negative direction (2596-1) distal promoters===


# Positive strand, negative direction: ACAGGA at 2690, TCCTGT at 1911.
# Positive strand, negative direction: TCCTGT at 1911.


===HACA positive direction (4050-1) distal promoters===


# Negative strand, positive direction: TCCTGT at 3622, ACAGGA at 3572, TCCTGT at 144.
# Negative strand, positive direction: TCCTGT at 3622, ACAGGA at 3572, TCCTGT at 144.
# Positive strand, positive direction: TCCTGT at 4252, ACAGGA at 3620, TCCTGT at 3131, TCCTGT at 2460.
# Positive strand, positive direction: ACAGGA at 3620, TCCTGT at 3131, TCCTGT at 2460.


==H and ACA box random dataset samplings==
==H and ACA box random dataset samplings==
Line 99: Line 96:
# HACAr9ci: 0.
# HACAr9ci: 0.


===HACAr UTRs===
===HACAr arbitrary (evens) (4560-2846) UTRs===


# HACAr2ci: TCCTGT at 2879.
# HACAr2ci: TCCTGT at 2879.
# HACAr8ci: TCCTGT at 3449.
# HACAr8ci: TCCTGT at 3449.


===HACAr proximal promoters===
===HACAr alternate (odds) (4560-2846) UTRs===


# HACAr1: ACAGGA at 3275.
# HACAr7ci: TCCTGT at 4129.
# HACAr7ci: TCCTGT at 4129.


===HACAr distal promoters===
===HACAr alternate negative direction (odds) (2811-2596) proximal promoters===
 
# HACAr7: ACAGGA at 2793.
 
===HACAr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
# HACAr7ci: TCCTGT at 4129.
 
===HACAr arbitrary negative direction (evens) (2596-1) distal promoters===


# HACAr6: ACAGGA at 2593.
# HACAr6: ACAGGA at 2593.
Line 115: Line 121:
# HACAr4ci: TCCTGT at 801.
# HACAr4ci: TCCTGT at 801.


===HACAr alternate negative direction (odds) (2596-1) distal promoters===
# HACAr3: ACAGGA at 1344.
# HACAr1ci: TCCTGT at 1802.
# HACAr3ci: TCCTGT at 350.
===HACAr arbitrary positive direction (odds) (4050-1) distal promoters===


# HACAr1: ACAGGA at 3275.
# HACAr1: ACAGGA at 3275.
Line 122: Line 135:
# HACAr3ci: TCCTGT at 350.
# HACAr3ci: TCCTGT at 350.


==Response element analysis and results==
===HACAr alternate positive direction (evens) (4050-1) distal promoters===
 
# HACAr6: ACAGGA at 2593.
# HACAr0ci: TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
# HACAr2ci: TCCTGT at 2879, TCCTGT at 1204, TCCTGT at 725.
# HACAr4ci: TCCTGT at 801.
# HACAr8ci: TCCTGT at 3449.
 
==H and ACA boxes analysis and results==
{{main|Complex locus A1BG and ZNF497#H and ACA boxes}}
{{main|Complex locus A1BG and ZNF497#H and ACA boxes}}
The combined consensus sequence is 5'-ACAGGA-3'.<ref name=Mitchell/>
The combined consensus sequence is ACAGGA.<ref name=Mitchell/>


{|class="wikitable"
{|class="wikitable"
Line 130: Line 151:
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)  
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)  
|-
|-
| Reals || UTR || negative || 0 || 2 || 0 || 0  
| Reals || UTR || negative || 3 || 2 || 1.5 || 1.5 ± 1.5 (--3,+-0)
|-
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || UTR || arbitrary negative || 2 || 10 || 0.2 || 0.2
|-
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0  
| Randoms || UTR || alternate negative || 2 || 10 || 0.2 || 0.2
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || negative || 0 || 10 || 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  
| Reals || Core || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Core || positive || 0 || 10 || 0 || 0
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0
|-
| Reals || Proximal || negative || 1 || 2 || 0.5 || 0.5 ± 0.5 (--0,+-1)
|-
| Randoms || Proximal || arbitrary negative || 0 || 10 || 0 || 0.05
|-
| Randoms || Proximal || alternate negative || 1 || 10 || 0.1 || 0.05
|-
| Reals || Proximal || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+0,++1)
|-
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
| Randoms || Proximal || arbitrary positive || 1 || 10 || 0.1 || 0.05
|-
|-
| Randoms || Proximal || negative || 0 || 10 || 0 || 0  
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0.05
|-
|-
| Reals || Proximal || positive || 0 || 2 || 0 || 0  
| Reals || Distal || negative || 1 || 2 || 0.5 || 0.5 ± 0.5 (--0,+-1)
|-
|-
| Randoms || Proximal || positive || 0 || 10 || 0 || 0  
| Randoms || Distal || arbitrary negative || 7 || 10 || 0.7 || 0.5
|-
|-
| Reals || Distal || negative || 0 || 2 || 0 || 0  
| Randoms || Distal || alternate negative || 3 || 10 || 0.3 || 0.5
|-
|-
| Randoms || Distal || negative || 0 || 10 || 0 || 0
| Reals || Distal || positive || 6 || 2 || 3 || 3 ± 0 (-+3,++3)
|-
|-
| Reals || Distal || positive || 0 || 2 || 0 || 0  
| Randoms || Distal || arbitrary positive || 5 || 10 || 0.5 || 0.7
|-
|-
| Randoms || Distal || positive || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate positive || 9 || 10 || 0.9 || 0.7
|}
|}


Comparison:
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.
The occurrences of real HACA UTRs, proximals and distals are greater than the randoms. This suggests that the real HACAs are likely active or activable.


==Acknowledgements==
==Acknowledgements==

Latest revision as of 22:07, 29 August 2023

Editor-In-Chief: Henry A. Hoff

Consensus sequences

"The box H/ACA snoRNAs were most recently recognized as a small RNA family by virtue of an ACA trinucleotide located 3 nt upstream of the mature snoRNA 3' end (41). In addition to this ACA box, they have the consensus H box sequence (5'-ANANNA-3') but have no other primary sequence identity. Despite this lack of primary sequence conservation, the H and ACA boxes are embedded in an evolutionarily conserved hairpin-hinge-hairpin-tail core secondary structure with the H box in the single-stranded hinge region and the ACA box in the single-stranded tail (5, 16)."[1]

The "3' end of mature hTR (45) has an ACA trinucleotide 3 nt upstream of its 3' end. In addition, the 3' region of hTR contains a single H box consensus sequence (5'-AGAGGA-3')."[1]

"Comparison with the murine telomerase RNA (mTR) (7) suggests that the snoRNA-like features of hTR are evolutionarily conserved. The mTR 3' end (nt 169 to 397 as numbered in reference 25) has ~76% sequence identity with the corresponding region of hTR (nt 211 to 451) and includes consensus H (5'-ACAGGA-3') and ACA box sequences."[1]

An H box has a consensus sequence of 3'-ACACCA-5'.[2]

The combined consensus sequence is 5'-ACAGGA-3'.[1]

H and ACA boxes in promoters of A1BG

For the Basic programs (starting with SuccessablesHACA.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 is SuccessablesHACA--.bas, looking for 5'-ACAGGA-3', 0.
  2. positive strand, negative direction is SuccessablesHACA+-.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 2690.
  3. negative strand, positive direction is SuccessablesHACA-+.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3572.
  4. positive strand, positive direction is SuccessablesHACA++.bas, looking for 5'-ACAGGA-3', 1, 5'-ACAGGA-3' at 3620.
  5. inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 3389, 5'-TCCTGT-3' at 3756, 5'-TCCTGT-3' at 4468.
  6. inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 5'-TCCTGT-3', 2, 5'-TCCTGT-3' at 144, 5'-TCCTGT-3' at 3622.
  7. inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 5'-TCCTGT-3', 1, 5'-TCCTGT-3' at 1911.
  8. inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 5'-TCCTGT-3', 3, 5'-TCCTGT-3' at 2460, 5'-TCCTGT-3' at 3131, 5'-TCCTGT-3' at 4252.

HACA (4560-2846) UTRs

  1. Negative strand, negative direction: TCCTGT at 4468, TCCTGT at 3756, TCCTGT at 3389.

HACA negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: ACAGGA at 2690.

HACA positive direction (4265-4050) proximal promoters

  1. Positive strand, positive direction: TCCTGT at 4252.

HACA negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: TCCTGT at 1911.

HACA positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TCCTGT at 3622, ACAGGA at 3572, TCCTGT at 144.
  2. Positive strand, positive direction: ACAGGA at 3620, TCCTGT at 3131, TCCTGT at 2460.

H and ACA box random dataset samplings

  1. HACAr0: 0.
  2. HACAr1: 1, ACAGGA at 3275.
  3. HACAr2: 0.
  4. HACAr3: 1, ACAGGA at 1344.
  5. HACAr4: 0.
  6. HACAr5: 0.
  7. HACAr6: 1, ACAGGA at 2593.
  8. HACAr7: 1, ACAGGA at 2793.
  9. HACAr8: 0.
  10. HACAr9: 0.
  11. HACAr0ci: 3, TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
  12. HACAr1ci: 1, TCCTGT at 1802.
  13. HACAr2ci: 3, TCCTGT at 2879, TCCTGT at 1204, TCCTGT at 725.
  14. HACAr3ci: 1, TCCTGT at 350.
  15. HACAr4ci: 1, TCCTGT at 801.
  16. HACAr5ci: 0.
  17. HACAr6ci: 0.
  18. HACAr7ci: 1, TCCTGT at 4129.
  19. HACAr8ci: 1, TCCTGT at 3449.
  20. HACAr9ci: 0.

HACAr arbitrary (evens) (4560-2846) UTRs

  1. HACAr2ci: TCCTGT at 2879.
  2. HACAr8ci: TCCTGT at 3449.

HACAr alternate (odds) (4560-2846) UTRs

  1. HACAr1: ACAGGA at 3275.
  2. HACAr7ci: TCCTGT at 4129.

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

  1. HACAr7: ACAGGA at 2793.

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

  1. HACAr7ci: TCCTGT at 4129.

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

  1. HACAr6: ACAGGA at 2593.
  2. HACAr0ci: TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
  3. HACAr2ci: TCCTGT at 1204, TCCTGT at 725.
  4. HACAr4ci: TCCTGT at 801.

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

  1. HACAr3: ACAGGA at 1344.
  2. HACAr1ci: TCCTGT at 1802.
  3. HACAr3ci: TCCTGT at 350.

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

  1. HACAr1: ACAGGA at 3275.
  2. HACAr3: ACAGGA at 1344.
  3. HACAr7: ACAGGA at 2793.
  4. HACAr1ci: TCCTGT at 1802.
  5. HACAr3ci: TCCTGT at 350.

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

  1. HACAr6: ACAGGA at 2593.
  2. HACAr0ci: TCCTGT at 2253, TCCTGT at 1551, TCCTGT at 1009.
  3. HACAr2ci: TCCTGT at 2879, TCCTGT at 1204, TCCTGT at 725.
  4. HACAr4ci: TCCTGT at 801.
  5. HACAr8ci: TCCTGT at 3449.

H and ACA boxes analysis and results

Main article: Complex locus A1BG and ZNF497 § H and ACA boxes

The combined consensus sequence is ACAGGA.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 1.5 (--3,+-0)
Randoms UTR arbitrary negative 2 10 0.2 0.2
Randoms UTR alternate negative 2 10 0.2 0.2
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 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Proximal arbitrary positive 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 7 10 0.7 0.5
Randoms Distal alternate negative 3 10 0.3 0.5
Reals Distal positive 6 2 3 3 ± 0 (-+3,++3)
Randoms Distal arbitrary positive 5 10 0.5 0.7
Randoms Distal alternate positive 9 10 0.9 0.7

Comparison:

The occurrences of real HACA UTRs, proximals and distals are greater than the randoms. This suggests that the real HACAs 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 1.4 James R. Mitchell, Jeffrey Cheng, and Kathleen Collins (January 1999). "A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3' End" (PDF). Molecular and Cellular Biology. 19 (1): 567–576. Retrieved 5 November 2018.
  2. ↑ Timofey S. Rozhdestvensky, Thean Hock Tang, Inna V. Tchirkova, Jürgen Brosius, Jean‐Pierre Bachellerie and Alexander Hüttenhofer (2003). "Binding of L7Ae protein to the K‐turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea". Nucleic Acids Research. 31 (3): 869–77. doi:10.1093/nar/gkg175. Retrieved 2014-06-08.

External links

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