CARE gene transcriptions: Difference between revisions

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The occurrences of real CAREs are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.
The occurrences of real CAREs are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.
==CARE (Garaeva) 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.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
===CARE (Garaeva) UTRs===
===CARE (Garaeva) negative direction core promoters===
===CARE (Garaeva) positive direction core promoters===
===CARE (Garaeva) negative direction proximal promoters===
===CARE (Garaeva) positive direction proximal promoters===
===CARE (Garaeva) negative direction distal promoters===
===CARE (Garaeva) positive direction distal promoters===
==CARE (Garaeva) 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.
===CARE (Garaeva)r arbitrary UTRs===
===CARE (Garaeva)r alternate UTRs===
===CARE (Garaeva)r arbitrary negative direction core promoters===
===CARE (Garaeva)r alternate negative direction core promoters===
===CARE (Garaeva)r arbitrary positive direction core promoters===
===CARE (Garaeva)r alternate positive direction core promoters===
===CARE (Garaeva)r arbitrary negative direction proximal promoters===
===CARE (Garaeva)r alternate negative direction proximal promoters===
===CARE (Garaeva)r arbitrary positive direction proximal promoters===
===CARE (Garaeva)r alternate positive direction proximal promoters===
===CARE (Garaeva)r arbitrary negative direction distal promoters===
===CARE (Garaeva)r alternate negative direction distal promoters===
===CARE (Garaeva)r arbitrary positive direction distal promoters===
===CARE (Garaeva)r alternate  positive direction distal promoters===
==CARE (Garaeva) analysis and results==
{{main|Complex locus A1BG and ZNF497#Name of response elements}}
"ATF4 regulates transcription of its target genes through the formation of homodimers or heterooligomers with the transcription factors Jun, AP-1 and C/EBP<sup>38,39</sup> that bind to CARE (C/EBP-ATF) responsive elements having the consensus sequence XTTXCATCA (where X = G, A or T).<sup>39</sup>"<ref name=Garaeva/>
{|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 18:05, 7 May 2022

Editor-In-Chief: Henry A. Hoff

"Some other cis-acting elements, such as pyrimidine boxes (GGTTTT) and TAT boxes (TATCCAT), are usually present in the vicinity of the GARE sequence of genes regulated by GA in cereal aleurone cells (Gubler and Jacobsen 1992; Cercos et al. 1999; Tsuji et al. 2006). For example, GARE and a novel CARE (CAACTC regulatory elements) elements are present in the promoter of rice RAmy1A (Ueguchi-Tanaka et al. 2000; Sutoh and Yamauchi 2003). Cis-element analyses have shown that the OsGAMYB protein activates RAmy1A expression through interaction with GARE in the promoter (Washio 2003). In addition, GARE and CARE are also present in a cysteine proteinase gene REP-1, which is expressed in rice aleurone and is induced by GAs and repressed by ABA. These two elements have been identified as necessary and sufficient for conferring GA inducibility of the REP-1 promoter. Mutations of CARE in the promoters of RAmy1A and REP-1 result in loss of GA inducibility and GAMYB transactivation, suggesting that CARE is a regulatory element for the GA-inducible expression of hydrolase genes in germinating seeds (Sutoh and Yamauchi 2003)."[1]

"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."[2]

CARE (Fan) sampling of A1BG promoters

Main articles: Gene transcriptions/CAREs and CAREs

For the Basic programs (starting with SuccessablesCARE.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. Negative strand, negative direction: 1, CAACTC at 86.
  2. Negative strand, positive direction: 1, CAACTC at 3292.
  3. Positive strand, negative direction: 0.
  4. Positive strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 1, GAGTTG at 1406.
  6. inverse complement, negative strand, positive direction: 0.
  7. inverse complement, positive strand, negative direction: 4, GAGTTG at 4096, GAGTTG at 3115, GAGTTG at 2704, GAGTTG at 2592.
  8. inverse complement, positive strand, positive direction: 2, GAGTTG at 3290, GAGTTG at 1621.

CARE (Fan) UTR promoters

  1. Positive strand, negative direction: GAGTTG at 4096, GAGTTG at 3115.

CARE (Fan) Proximal promoters

  1. Positive strand, negative direction: GAGTTG at 2704.

CARE (Fan) distal promoters

Main article: Distal promoter gene transcriptions
  1. Negative strand, negative direction: GAGTTG at 1406, CAACTC at 86.
  2. Positive strand, negative direction: GAGTTG at 2592.
  1. Negative strand, positive direction: CAACTC at 3292.
  2. Positive strand, positive direction: GAGTTG at 3290, GAGTTG at 1621.

CARE (Fan) random dataset samplings

  1. CAREr0: 0.
  2. CAREr1: 0.
  3. CAREr2: 2, CAACTC at 3285, CAACTC at 1310.
  4. CAREr3: 0.
  5. CAREr4: 0.
  6. CAREr5: 0.
  7. CAREr6: 0.
  8. CAREr7: 2, CAACTC at 3148, CAACTC at 69.
  9. CAREr8: 4, CAACTC at 3816, CAACTC at 2042, CAACTC at 1912, CAACTC at 1907.
  10. CAREr9: 1, CAACTC at 1315.
  11. CAREr0ci: 1, GAGTTG at 3165.
  12. CAREr1ci: 0.
  13. CAREr2ci: 3, GAGTTG at 1396, GAGTTG at 1035, GAGTTG at 299.
  14. CAREr3ci: 1, GAGTTG at 2263.
  15. CAREr4ci: 0.
  16. CAREr5ci: 0.
  17. CAREr6ci: 1, GAGTTG at 430.
  18. CAREr7ci: 2, GAGTTG at 2937, GAGTTG at 2872.
  19. CAREr8ci: 1, GAGTTG at 3150.
  20. CAREr9ci: 2, GAGTTG at 2739, GAGTTG at 538.

CARE (Fan) random UTRs

Main article: UTR promoter gene transcriptions
  1. CAREr2: CAACTC at 3285.
  2. CAREr8: CAACTC at 3816.
  3. CAREr0ci: GAGTTG at 3165.
  4. CAREr8ci: GAGTTG at 3150.

CARE (Fan) random distal promoters

Main article: Distal promoter gene transcriptions
  1. CAREr2: CAACTC at 1310.
  2. CAREr8: CAACTC at 2042, CAACTC at 1912, CAACTC at 1907.
  3. CAREr2ci: GAGTTG at 1396, GAGTTG at 1035, GAGTTG at 299.
  4. CAREr6ci: GAGTTG at 430.


  1. CAREr7: CAACTC at 3148, CAACTC at 69.
  2. CAREr9: CAACTC at 1315.
  3. CAREr3ci: GAGTTG at 2263.
  4. CAREr7ci: GAGTTG at 2937, GAGTTG at 2872.
  5. CAREr9ci: GAGTTG at 2739, GAGTTG at 538.

CARE analysis and results

Main article: Complex locus A1BG and ZNF497 § CAACTC regulatory elements (CAREs)

CAREs occur in the negative transcription direction in the UTR with an occurrence of 1.0, not in the core promoters on either side, in the proximal promoters in the negative direction for an occurrence of 0.5, and the distal promoters: negative direction occurrence of 1.5 and the positive direction occurrence of 1.5.

The random datasets had an occurrence in the UTR of 0.4, none in the core promoters, none in the proximal promoters, and an occurrence of 0.8 in the arbitrary negative direction and 0.8 in the positive direction.

The lack of closeness between the real and random datasets suggests that the real CAREs are likely active or activable.

"GARE and a novel CARE (CAACTC regulatory elements) elements are present in the promoter of rice RAmy1A (Ueguchi-Tanaka et al. 2000; Sutoh and Yamauchi 2003)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
Randoms UTR arbitrary negative 4 10 0.4 0.35
Randoms UTR alternate negative 3 10 0.3 0.35
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
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 1 10 0.1 0.1
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 3 2 1.5 1.5
Randoms Distal arbitrary negative 8 10 0.8 0.6
Randoms Distal alternate negative 4 10 0.4 0.6
Reals Distal positive 3 2 1.5 1.5
Randoms Distal arbitrary positive 8 10 0.8 0.8
Randoms Distal alternate positive 8 10 0.8 0.8

Comparison:

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

CARE (Garaeva) 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. negative strand, positive direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.

CARE (Garaeva) UTRs

CARE (Garaeva) negative direction core promoters

CARE (Garaeva) positive direction core promoters

CARE (Garaeva) negative direction proximal promoters

CARE (Garaeva) positive direction proximal promoters

CARE (Garaeva) negative direction distal promoters

CARE (Garaeva) positive direction distal promoters

CARE (Garaeva) 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.

CARE (Garaeva)r arbitrary UTRs

CARE (Garaeva)r alternate UTRs

CARE (Garaeva)r arbitrary negative direction core promoters

CARE (Garaeva)r alternate negative direction core promoters

CARE (Garaeva)r arbitrary positive direction core promoters

CARE (Garaeva)r alternate positive direction core promoters

CARE (Garaeva)r arbitrary negative direction proximal promoters

CARE (Garaeva)r alternate negative direction proximal promoters

CARE (Garaeva)r arbitrary positive direction proximal promoters

CARE (Garaeva)r alternate positive direction proximal promoters

CARE (Garaeva)r arbitrary negative direction distal promoters

CARE (Garaeva)r alternate negative direction distal promoters

CARE (Garaeva)r arbitrary positive direction distal promoters

CARE (Garaeva)r alternate positive direction distal promoters

CARE (Garaeva) analysis and results

Main article: Complex locus A1BG and ZNF497 § Name of response elements

"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"[2]

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 Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng (2007). "Gibberellin Signal Transduction in Rice". Journal of Integrative Plant Biology. 49 (6): 731−741. doi:10.1111/j.1744-7909.2007.00511.x. Retrieved 16 October 2018.
  2. ↑ 2.0 2.1 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.

External links


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