Activating transcription factor gene transcriptions: Difference between revisions

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{{AE}} Henry A. Hoff
{{AE}} Henry A. Hoff


Activating transcription factor (ATF) is a group of [[bZIP domain|bZIP]] [[transcription factor]]s, which act as homodimers or heterodimers with a range of other bZIP factors.<ref name="van Dam">{{ cite journal |author=van Dam H, Castellazzi M |title=Distinct roles of Jun : Fos and Jun : ATF dimers in oncogenesis |journal= Oncogene |volume=20 |issue=19 |pages=2453–64 |year=2001 |pmid= 11402340 |doi=10.1038/sj.onc.1204239 }}</ref> First, they have been described as members of the [[ATF/CREB|CREB/ATF]] family,<ref name="Karin">{{cite journal |author=Karin M1, Smeal T |title=Control of transcription factors by signal transduction pathways: the beginning of the end |journal= Trends Biochem Sci|volume=17 |issue=10 |pages=418–22 |year=1992 |pmid= 1455510 |doi=10.1016/0968-0004(92)90012-x}}</ref> whereas it turned out later that some of them might be more similar to [[AP-1 transcription factor|AP-1]]-like factors such as [[c-Jun]] or [[c-Fos]].<ref name="TFClass">{{ cite web | title = Classification of Human Transcription Factors (TFClass)| url = https://web.archive.org/web/20140407072323/http://tfclass.bioinf.med.uni-goettingen.de/tfclass }}</ref> In general, ATFs are known to respond to extracellular signals and this suggests an important role that they have in maintaining homeostasis. Some of these ATFs, such as ATF3, ATF4, and ATF6 are known to play a role in stress responses.<ref>{{ cite journal|date=2001-07-25|title=The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis
Activating transcription factor (ATF) is a group of [[bZIP domain|bZIP]] [[transcription factor]]s, which act as homodimers or heterodimers with a range of other bZIP factors.<ref name="van Dam">{{ cite journal |author=van Dam H, Castellazzi M |title=Distinct roles of Jun : Fos and Jun : ATF dimers in oncogenesis |journal= Oncogene |volume=20 |issue=19 |pages=2453–64 |year=2001 |pmid= 11402340 |doi=10.1038/sj.onc.1204239 }}</ref> First, they have been described as members of the [[ATF/CREB|CREB/ATF]] family,<ref name="Karin">{{cite journal |author=Karin M1, Smeal T |title=Control of transcription factors by signal transduction pathways: the beginning of the end
|journal= Trends Biochem Sci
|volume=17
|issue=10
|pages=418–22
|year=1992
|pmid= 1455510
|doi=10.1016/0968-0004(92)90012-x}}</ref> whereas it turned out later that some of them might be more similar to [[AP-1 transcription factor|AP-1]]-like factors such as [[c-Jun]] or [[c-Fos]].<ref name="TFClass">{{ cite web
| title = Classification of Human Transcription Factors (TFClass)
| url = https://web.archive.org/web/20140407072323/http://tfclass.bioinf.med.uni-goettingen.de/tfclass }}</ref> Some of these ATFs, such as ATF3, ATF4, and ATF6 are known to play a role in stress responses.<ref name=Hai>{{ cite journal
|date=2001-07-25
|title=The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis
|url=
|url=
|journal=Gene
|journal=Gene
Line 10: Line 21:
|pmid=11483355
|pmid=11483355
|issn=0378-1119
|issn=0378-1119
|last1=Hai|first1=Tsonwin|last2=Hartman|first2=Matthew G.}}</ref> Another example of ATF function would be ATFx that can suppress apoptosis.<ref>{{ cite journal
|last1=Hai|first1=Tsonwin|last2=Hartman|first2=Matthew G.}}</ref> Another example of ATF function would be ATFx that can suppress apoptosis.<ref name=Green>{{ cite journal
|last1=Green|first1=M. R.|last2=Persengiev|first2=S. P.
|last1=Green|first1=M. R.|last2=Persengiev|first2=S. P.
|date=2003-06-01
|date=2003-06-01
Line 33: Line 44:
|url=https://www.ncbi.nlm.nih.gov/gene/2623
|url=https://www.ncbi.nlm.nih.gov/gene/2623
|accessdate=24 October 2020 }}</ref>
|accessdate=24 October 2020 }}</ref>
==Gene expressions==
{{main|Gene expressions}}
==Interactions==
{{main|Interaction gene transcriptions}}


==Consensus sequences==
==Consensus sequences==
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Combined consensus sequences are XTTXCATCA (where X = G, A or T), TTTTCATCA, and (G/A/C)TT(G/A/T)C(G/A)TCA to produce 5'-NTT(A/G/T)C(A/G)TCA-3'.
Combined consensus sequences are XTTXCATCA (where X = G, A or T), TTTTCATCA, and (G/A/C)TT(G/A/T)C(G/A)TCA to produce 5'-NTT(A/G/T)C(A/G)TCA-3'.
==Binding site for==
==Inverse copies==
==Enhancer activity==
==Promoter occurrences==


==Hypotheses==
==Hypotheses==
Line 95: Line 92:
# inverse positive strand, positive direction is SuccessablesAAAi++.bas, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, positive direction is SuccessablesAAAi++.bas, looking for 5'-AAAAAAAA-3', 0.


===AAA core promoters===
===Activating transcription factor core promoters===
{{main|Core promoter gene transcriptions}}
{{main|Core promoter gene transcriptions}}


===AAA proximal promoters===
===Activating transcription factor proximal promoters===
{{main|Proximal promoter gene transcriptions}}
{{main|Proximal promoter gene transcriptions}}


===AAA distal promoters===
===Activating transcription factor distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Positive strand, negative direction: 5'-ATTTCATCA-3' at 2888 and complement.
Negative strand, positive direction: 5'-CTTGCGTCA-3' at 2423, 5'-CTTTCGTCA-3' at 1184 and complements.


==Acknowledgements==
==Acknowledgements==

Revision as of 18:17, 28 October 2020

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

Activating transcription factor (ATF) is a group of bZIP transcription factors, which act as homodimers or heterodimers with a range of other bZIP factors.[1] First, they have been described as members of the CREB/ATF family,[2] whereas it turned out later that some of them might be more similar to AP-1-like factors such as c-Jun or c-Fos.[3] Some of these ATFs, such as ATF3, ATF4, and ATF6 are known to play a role in stress responses.[4] Another example of ATF function would be ATFx that can suppress apoptosis.[5]

Genes include ATF1, ATF2, ATF3, ATF4, ATF5, ATF6, ATF7, ATFx.

Human genes

Main article: Human genes

Gene ID: 466 is ATF1 activating transcription factor 1 on 12q13.12: "This gene encodes an activating transcription factor, which belongs to the ATF subfamily and bZIP (basic-region leucine zipper) family. It influences cellular physiologic processes by regulating the expression of downstream target genes, which are related to growth, survival, and other cellular activities. This protein is phosphorylated at serine 63 in its kinase-inducible domain by serine/threonine kinases, cAMP-dependent protein kinase A, calmodulin-dependent protein kinase I/II, mitogen- and stress-activated protein kinase and cyclin-dependent kinase 3 (cdk-3). Its phosphorylation enhances its transactivation and transcriptional activities, and enhances cell transformation. Fusion of this gene and FUS on chromosome 16 or EWSR1 on chromosome 22 induced by translocation generates chimeric proteins in angiomatoid fibrous histiocytoma and clear cell sarcoma. This gene has a pseudogene on chromosome 6."[6]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The ATF4 binding consensus sequence has been reported as (G/A/C)TT(G/A/T)C(G/A)TCA (38), which matches the ChIP-seq data."[7]

Combined consensus sequences are XTTXCATCA (where X = G, A or T), TTTTCATCA, and (G/A/C)TT(G/A/T)C(G/A)TCA to produce 5'-NTT(A/G/T)C(A/G)TCA-3'.

Hypotheses

Main article: Hypotheses
  1. A1BG has no Activating transcription factor in either promoter.
  2. A1BG is not transcribed by an Activating transcription factor.
  3. Activating transcription factors do not participate in the transcription of A1BG.

Samplings

Main articles: Model samplings and Samplings

Copying the consensus for the ATF4: 5'-TTTTCA-3', 5'-CTTTCGTCA-3', or 5'-GTTTCA-3' 5'-GTTTCATC-3' 5'-ATTTCAT-3' (where X = G, A or T) and putting the sequence in "⌘F" finds no, no, no, no, no locations between ZSCAN22 and A1BG and no, one, no, no no, no locations between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3' (starting with SuccessablesATF.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/C/G)TT(A/G/T)C(A/G)TCA-3', 0.
  2. negative strand, positive direction, looking for 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3', 2, 5'-CTTGCGTCA-3' at 2423, 5'-CTTTCGTCA-3' at 1184.
  3. positive strand, negative direction, looking for 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3', 1, 5'-ATTTCATCA-3' at 2888.
  4. positive strand, positive direction, looking for 5'-(A/C/G)TT(A/G/T)C(A/G)TCA-3', 0.
  5. complement, negative strand, negative direction is SuccessablesATFc--.bas, looking for 5'-(C/G/T)AA(A/C/T)G(C/T)AGT-3', 1, 5'-TAAAGTAGT-3' at 2888.
  6. complement, negative strand, positive direction is SuccessablesATFc-+.bas, looking for 5'-(C/G/T)AA(A/C/T)G(C/T)AGT-3', 0.
  7. complement, positive strand, negative direction is SuccessablesATFc+-.bas, looking for 5'-(C/G/T)AA(A/C/T)G(C/T)AGT-3', 0.
  8. complement, positive strand, positive direction is SuccessablesATFc++.bas, looking for 5'-(C/G/T)AA(A/C/T)G(C/T)AGT-3', 2, 5'-GAACGCAGT-3' at 2423, 5'-GAAAGCAGT-3' at 1184.
  9. inverse complement, negative strand, negative direction is SuccessablesAAAci--.bas, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction is SuccessablesAAAci-+.bas, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction is SuccessablesAAAci+-.bas, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction is SuccessablesAAAci++.bas, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction is SuccessablesAAAi--.bas, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction is SuccessablesAAAi-+.bas, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction is SuccessablesAAAi+-.bas, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction is SuccessablesAAAi++.bas, looking for 5'-AAAAAAAA-3', 0.

Activating transcription factor core promoters

Main article: Core promoter gene transcriptions

Activating transcription factor proximal promoters

Main article: Proximal promoter gene transcriptions

Activating transcription factor distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, negative direction: 5'-ATTTCATCA-3' at 2888 and complement.

Negative strand, positive direction: 5'-CTTGCGTCA-3' at 2423, 5'-CTTTCGTCA-3' at 1184 and complements.

Acknowledgements

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

See also

References

  1. ↑ van Dam H, Castellazzi M (2001). "Distinct roles of Jun : Fos and Jun : ATF dimers in oncogenesis". Oncogene. 20 (19): 2453–64. doi:10.1038/sj.onc.1204239. PMID 11402340.
  2. ↑ Karin M1, Smeal T (1992). "Control of transcription factors by signal transduction pathways: the beginning of the end". Trends Biochem Sci. 17 (10): 418–22. doi:10.1016/0968-0004(92)90012-x. PMID 1455510.
  3. ↑ "Classification of Human Transcription Factors (TFClass)".
  4. ↑ Hai, Tsonwin; Hartman, Matthew G. (2001-07-25). "The molecular biology and nomenclature of the activating transcription factor/cAMP responsive element binding family of transcription factors: activating transcription factor proteins and homeostasis". Gene. 273 (1): 1–11. doi:10.1016/S0378-1119(01)00551-0. ISSN 0378-1119. PMID 11483355.
  5. ↑ Green, M. R.; Persengiev, S. P. (2003-06-01). "The role of ATF/CREB family members in cell growth, survival and apoptosis". Apoptosis. 8 (3): 225–228. doi:10.1023/A:1023633704132. PMID 12766482.
  6. ↑ RefSeq (August 2010). "ATF1 activating transcription factor 1 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 24 October 2020.
  7. ↑ Thomas D. Burton, Anthony O. Fedele, Jianling Xie, Lauren Sandeman and Christopher G. Proud (22 May 2020). "The gene for the lysosomal protein LAMP3 is a direct target of the transcription factor ATF4" (PDF). Journal of Biological Chemistry. 295 (21): 7418. doi:10.1074/jbc.RA119.011864. PMID 32312748 Check |pmid= value (help). Retrieved 5 September 2020.

External links

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