DAF-16 binding element gene transcriptions: Difference between revisions

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(Created page with "{{AE}} Henry A. Hoff "DAF-16 binding element (DBE), GTAAACA or TGTTTAC, and DAF-16-associated element (DAE), TGATAAG or CTTATCA, enriched in DAF-16 regulated genes [2, 4, 13,...")
 
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|pmid=2702736
|pmid=2702736
|accessdate=27 August 2020 }}</ref> Note: GTAAACA is the inverse complement (ic) of TGTTTAC and TGATAAG is the ic of CTTATCA.
|accessdate=27 August 2020 }}</ref> Note: GTAAACA is the inverse complement (ic) of TGTTTAC and TGATAAG is the ic of CTTATCA.
==Human genes==
{{main|Forkhead box gene transcriptions}}
Gene ID: 2308 is FOXO1 forkhead box O1 on 13q14.11: "This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in myogenic growth and differentiation. Translocation of this gene with PAX3 has been associated with alveolar rhabdomyosarcoma."<ref name=RefSeq2308>{{ cite web
|author=RefSeq
|title=FOXO1 forkhead box O1 [ Homo sapiens (human) ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=July 2008
|url=https://www.ncbi.nlm.nih.gov/gene/2308
|accessdate=3 December 2020 }}</ref>


==Consensus sequences==
==Consensus sequences==
{{main|Consensus sequence gene transcriptions}}
5'-GTAAACA-3'.<ref name=Li/>


5'-GTAAACA-3'.<ref name=Li/>
"Most paralogous FOX proteins bind to the canonical DNA response element 5′-RYAAAYA-3′ (R = A or G, Y = C or T)<sup>11–13</sup>."<ref name=Li2017>{{ cite journal
|author=Jun Li, Ana Carolina Dantas Machado, Ming Guo, Jared M. Sagendorf, Zhan Zhou, Longying Jiang, Xiaojuan Chen, Daichao Wu, Lingzhi Qu, Zhuchu Chen, Lin Chen, Remo Rohs, and Yongheng Chen
|title=Structure of the forkhead domain of FOXA2 bound to a complete DNA consensus site
|journal=Biochemistry
|date=25 July 2017
|volume=56
|issue=29
|pages=3745-3753
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5614898/
|arxiv=
|bibcode=
|doi=10.1021/acs.biochem.7b00211
|pmid=28644006
|accessdate=28 August 2020 }}</ref>
 
"Forkhead box protein O1 (FOXO1), a master transcriptional factor for gluconeogenesis in the liver, directly regulates TXNIP expression through the binding of the promoter region of TXNIP which contains a conserved consensus sequence, ′GTAAACAA′, of the FOXO binding site [100,101]."<ref name=Yoshihara>{{ cite journal
|author=Eiji Yoshihara
|title=TXNIP/TBP-2: A Master Regulator for Glucose Homeostasis
|journal=Antioxidants
|date=18 August 2020
|volume=9
|issue=8
|pages=765-84
|url=https://www.mdpi.com/2076-3921/9/8/765/pdf
|arxiv=
|bibcode=
|doi=10.3390/antiox9080765
|pmid=32824669
|accessdate=5 September 2020 }}</ref>
 
==Hypotheses==
{{main|Hypotheses}}
# A1BG has no DBEs in either promoter.
# A1BG is not transcribed by a DBE.
# DBE does not participate in the transcription of A1BG.


==Samplings==
==Samplings==
{{main|Model samplings}}
Copying an apparent consensus sequence of 5'-(A/G)(C/T)AAA(C/T)A-3' and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.


Copying the consensus element GTAAACA into ⌘F found no elements in either promoter of A1BG.
Copying the consensus element GTAAACA into ⌘F found no elements in either promoter of A1BG.
For the Basic programs testing consensus sequence 5'-(A/G)(C/T)AAA(C/T)A-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:
# negative strand, negative direction, looking for 5'-(A/G)(C/T)AAA(C/T)A-3', 0.
# negative strand, positive direction, looking for 5'-(A/G)(C/T)AAA(C/T)A-3', 0.
# positive strand, negative direction, looking for 5'-(A/G)(C/T)AAA(C/T)A-3', 0.
# positive strand, positive direction, looking for 5'-(A/G)(C/T)AAA(C/T)A-3', 0.
# complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
===AAA core promoters===
{{main|Core promoter gene transcriptions}}
===AAA proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===AAA distal promoters===
{{main|Distal promoter gene transcriptions}}


==Acknowledgements==
==Acknowledgements==
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* [[A1BG gene transcriptions]]
* [[A1BG gene transcriptions]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Forkhead box gene transcriptions]]
{{Div col end}}
{{Div col end}}


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[[Category:Resources last modified in October 2020]]
[[Category:Resources last modified in December 2020]]

Revision as of 02:33, 4 December 2020

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

"DAF-16 binding element (DBE), GTAAACA or TGTTTAC, and DAF-16-associated element (DAE), TGATAAG or CTTATCA, enriched in DAF-16 regulated genes [2, 4, 13, 14]. The DBE was recognized by DAF-16, and the DAE by transcription factor PQM-1 [13]."[1] Note: GTAAACA is the inverse complement (ic) of TGTTTAC and TGATAAG is the ic of CTTATCA.

Human genes

Main article: Forkhead box gene transcriptions

Gene ID: 2308 is FOXO1 forkhead box O1 on 13q14.11: "This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. The specific function of this gene has not yet been determined; however, it may play a role in myogenic growth and differentiation. Translocation of this gene with PAX3 has been associated with alveolar rhabdomyosarcoma."[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

5'-GTAAACA-3'.[1]

"Most paralogous FOX proteins bind to the canonical DNA response element 5′-RYAAAYA-3′ (R = A or G, Y = C or T)11–13."[3]

"Forkhead box protein O1 (FOXO1), a master transcriptional factor for gluconeogenesis in the liver, directly regulates TXNIP expression through the binding of the promoter region of TXNIP which contains a conserved consensus sequence, ′GTAAACAA′, of the FOXO binding site [100,101]."[4]

Hypotheses

Main article: Hypotheses
  1. A1BG has no DBEs in either promoter.
  2. A1BG is not transcribed by a DBE.
  3. DBE does not participate in the transcription of A1BG.

Samplings

Main article: Model samplings

Copying an apparent consensus sequence of 5'-(A/G)(C/T)AAA(C/T)A-3' and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying the consensus element GTAAACA into ⌘F found no elements in either promoter of A1BG.

For the Basic programs testing consensus sequence 5'-(A/G)(C/T)AAA(C/T)A-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'-(A/G)(C/T)AAA(C/T)A-3', 0.
  2. negative strand, positive direction, looking for 5'-(A/G)(C/T)AAA(C/T)A-3', 0.
  3. positive strand, negative direction, looking for 5'-(A/G)(C/T)AAA(C/T)A-3', 0.
  4. positive strand, positive direction, looking for 5'-(A/G)(C/T)AAA(C/T)A-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

AAA core promoters

Main article: Core promoter gene transcriptions

AAA proximal promoters

Main article: Proximal promoter gene transcriptions

AAA distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Yan-Hui Li and Gai-Gai Zhang (12 April 2016). "Towards understanding the lifespan extension by reduced insulin signaling: bioinformatics analysis of DAF-16/FOXO direct targets in Caenorhabditis elegans". Oncotarget. 7 (15): 19185–19192. doi:10.18632/oncotarget.8313. PMID 2702736. Retrieved 27 August 2020.
  2. ↑ RefSeq (July 2008). "FOXO1 forkhead box O1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 3 December 2020.
  3. ↑ Jun Li, Ana Carolina Dantas Machado, Ming Guo, Jared M. Sagendorf, Zhan Zhou, Longying Jiang, Xiaojuan Chen, Daichao Wu, Lingzhi Qu, Zhuchu Chen, Lin Chen, Remo Rohs, and Yongheng Chen (25 July 2017). "Structure of the forkhead domain of FOXA2 bound to a complete DNA consensus site". Biochemistry. 56 (29): 3745–3753. doi:10.1021/acs.biochem.7b00211. PMID 28644006. Retrieved 28 August 2020.
  4. ↑ Eiji Yoshihara (18 August 2020). "TXNIP/TBP-2: A Master Regulator for Glucose Homeostasis". Antioxidants. 9 (8): 765–84. doi:10.3390/antiox9080765. PMID 32824669 Check |pmid= value (help). Retrieved 5 September 2020.

External links

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