MYB recognition element gene transcriptions: Difference between revisions
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==Human genes== | |||
{{main|Human genes}} | |||
Gene ID: 4602 is MYB [myeloblastosis] MYB proto-oncogene, transcription factor on 6q23.3: "This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants."<ref name=RefSeq4602>{{ cite web | |||
|author=RefSeq | |||
|title=MYB MYB proto-oncogene, transcription factor [ Homo sapiens (human) ] | |||
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine | |||
|location=8600 Rockville Pike, Bethesda MD, 20894 USA | |||
|date=January 2016 | |||
|url=https://www.ncbi.nlm.nih.gov/gene/4602 | |||
|accessdate=7 February 2021 }}</ref> | |||
==Gene expressions== | |||
{{main|Gene expressions}} | |||
"Chalcone synthase (CHS), chalcone flavanone isomerase (CFI), flavanone 3-hydroxylase (F3H) and flavonol synthase (FLS) catalyze successive steps in the biosynthetic pathway leading to the production of flavonols."<ref name=Hartmann/> | |||
In "''Arabidopsis thaliana'' all four corresponding genes are coordinately expressed in response to light, and are spatially coexpressed in siliques, flowers and leaves."<ref name=Hartmann/> | |||
"Light regulatory units (LRUs) sufficient for light responsiveness were identified in all four promoters."<ref name=Hartmann/> | |||
A "R response element (RRE) was identified in the CHS promoter."<ref name=Hartmann/> | |||
"Only the ACE from the CFI promoter shows flanking sequences giving rise to a symmetrical G-box (Foster et al., 1994; Menkens et al., 1995) that also fits the consensus of the R motif (CANNTG; Blackwell and Weintraub, 1990; Bodeau and Walbot, 1996) which is recognized by [basic helix-loop-helix] BHLH factors."<ref name=Hartmann/> | |||
The gain-of-function for the ''FLS'' gene (MRE, ACE) lies between -97 and -42.<ref name=Hartmann/> | |||
For the ''F3H'' gene the ACE lies between -463 and -382 and the MRE lies between -99 and -63.<ref name=Hartmann/> | |||
For the ''CFI'' gene the ACE, MRE lie between -99 and -39.<ref name=Hartmann/> | |||
For the ''CHS'' gene the ACE, RRE, MRE lie between -106 and -69.<ref name=Hartmann/> | |||
==Consensus sequences== | ==Consensus sequences== | ||
{{main|Consensus sequence gene transcriptions}} | |||
"These elements fit the type II MYB consensus sequence A(A/C)C(A/T)A(A/C)C, suggesting that they are MYB recognition elements (MREs)."<ref name=Rushton>{{ cite journal | "These elements fit the type II MYB consensus sequence A(A/C)C(A/T)A(A/C)C, suggesting that they are MYB recognition elements (MREs)."<ref name=Rushton>{{ cite journal | ||
|author=Paul J Rushton and Imre E Somssich | |author=Paul J Rushton and Imre E Somssich | ||
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The consensus sequence for the ACE is 5'-CACGT-3'.<ref name=Hartmann/> | The consensus sequence for the ACE is 5'-CACGT-3'.<ref name=Hartmann/> | ||
== | ==Hypotheses== | ||
{{main|Hypotheses}} | |||
# A1BG has no MYB recognition elements (MRE) in either promoter. | |||
# A1BG is not transcribed by a MRE. | |||
# No MRE participates in the transcription of A1BG. | |||
" | ==MRE samplings== | ||
{{main|Model samplings}} | |||
Copying an apparent core consensus sequence for the MYBRE of AACAAAC or TAACTG and putting it in "⌘F" finds none located between ZSCAN22 and none or one between ZNF497 and A1BG as can be found by the computer programs. | |||
For the Basic programs testing consensus sequence A(A/C)C(A/T)A(A/C)C (starting with SuccessablesMYB.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 A(A/C)C(A/T)A(A/C)C, 2, ACCAACC at 3946, ACCAACC at 3606. | |||
# positive strand, negative direction, looking for A(A/C)C(A/T)A(A/C)C, 5, AACAACC at 2844, AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390. | |||
# positive strand, positive direction, looking for A(A/C)C(A/T)A(A/C)C, 0. | |||
# negative strand, positive direction, looking for A(A/C)C(A/T)A(A/C)C, 1, ACCAAAC at 3176. | |||
# complement, negative strand, negative direction, looking for T(G/T)G(A/T)T(G/T)G, 5, TTGTTGG at 2844, TTGTTTG at 2511, TTGTTTG at 2486, TTGTTTG at 1587, TTGTTTG at 1390. | |||
# complement, positive strand, negative direction, looking for T(G/T)G(A/T)T(G/T)G, 2, TGGTTGG at 3946, TGGTTGG at 3606. | |||
# complement, positive strand, positive direction, looking for T(G/T)G(A/T)T(G/T)G, 1, TGGTTTG at 3176. | |||
# complement, negative strand, positive direction, looking for T(G/T)G(A/T)T(G/T)G, 0. | |||
# inverse complement, negative strand, negative direction, looking for G(G/T)T(A/T)G(G/T)T, 5, GGTAGGT at 4457, GGTTGTT at 3139, GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392. | |||
# inverse complement, positive strand, negative direction, looking for G(G/T)T(A/T)G(G/T)T, 0. | |||
# inverse complement, positive strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 1, GGTAGGT at 3109. | |||
# inverse complement, negative strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 0. | |||
# inverse negative strand, negative direction, looking for C(A/C)A(A/T)C(A/C)A, 0. | |||
# inverse positive strand, negative direction, looking for C(A/C)A(A/T)C(A/C)A, 5, CCATCCA at 4457, CCAACAA at 3139, CAAACAA at 2488, CAAACAA at 2484, CAAACAA at 1392. | |||
# inverse positive strand, positive direction, looking for C(A/C)A(A/T)C(A/C)A, 0. | |||
# inverse negative strand, positive direction, looking for C(A/C)A(A/T)C(A/C)A, 1, CCATCCA at 3109. | |||
===MRE UTR gene transcriptions=== | |||
{{main|UTR promoter gene transcriptions}} | |||
Negative strand, negative direction: GGTAGGT at 4457, ACCAACC at 3946, ACCAACC at 3606, GGTTGTT at 3139. | |||
===MRE core promoters=== | |||
{{main|Core promoter gene transcriptions}} | |||
Positive strand, negative direction: AACAACC at 2844. | |||
===MRE distal promoters=== | |||
{{main|Distal promoter gene transcriptions}} | |||
Negative strand, negative direction: GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392. | |||
Positive strand, negative direction: AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390. | |||
Positive strand, positive direction: GGTAGGT at 3109. | |||
Negative strand, positive direction: ACCAAAC at 3176. | |||
==Acknowledgements== | ==Acknowledgements== | ||
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==See also== | ==See also== | ||
{{div col|colwidth=20em}} | {{div col|colwidth=20em}} | ||
* [[A1BG gene transcription core promoters]] | |||
* [[A1BG gene transcriptions]] | |||
* [[A1BG regulatory elements and regions]] | |||
* [[A1BG response element negative results]] | |||
* [[A1BG response element positive results]] | |||
* [[Complex locus A1BG and ZNF497]] | |||
* [[H box gene transcriptions]] | * [[H box gene transcriptions]] | ||
{{Div col end}} | {{Div col end}} | ||
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==External links== | ==External links== | ||
* [http://www.genome.jp/ GenomeNet KEGG database] | |||
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI] | |||
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search] | |||
* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search] | |||
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database] | |||
<!-- footer templates --> | <!-- footer templates --> | ||
{{Gene project | {{Gene project}} | ||
<!-- footer categories --> | <!-- footer categories --> | ||
[[Category:Resources last modified in February 2021]] | |||
[[Category:Resources last modified in | |||
Revision as of 02:15, 8 February 2021
Associate Editor(s)-in-Chief: Henry A. Hoff
{{free media}}"Another class of cis-acting elements is represented by Boxes P and L from the parsley phenylalanine ammonia-lyase (PAL) and 4-coumarate:CoA ligase (4CL) genes and the H-box from the bean chalcone synthase gene Chs15 [23,24]."[1]
"The combination of an [ACGT-containing element] ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."[2]
Human genes
Gene ID: 4602 is MYB [myeloblastosis] MYB proto-oncogene, transcription factor on 6q23.3: "This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants."[3]
Gene expressions
"Chalcone synthase (CHS), chalcone flavanone isomerase (CFI), flavanone 3-hydroxylase (F3H) and flavonol synthase (FLS) catalyze successive steps in the biosynthetic pathway leading to the production of flavonols."[2]
In "Arabidopsis thaliana all four corresponding genes are coordinately expressed in response to light, and are spatially coexpressed in siliques, flowers and leaves."[2]
"Light regulatory units (LRUs) sufficient for light responsiveness were identified in all four promoters."[2]
A "R response element (RRE) was identified in the CHS promoter."[2]
"Only the ACE from the CFI promoter shows flanking sequences giving rise to a symmetrical G-box (Foster et al., 1994; Menkens et al., 1995) that also fits the consensus of the R motif (CANNTG; Blackwell and Weintraub, 1990; Bodeau and Walbot, 1996) which is recognized by [basic helix-loop-helix] BHLH factors."[2]
The gain-of-function for the FLS gene (MRE, ACE) lies between -97 and -42.[2]
For the F3H gene the ACE lies between -463 and -382 and the MRE lies between -99 and -63.[2]
For the CFI gene the ACE, MRE lie between -99 and -39.[2]
For the CHS gene the ACE, RRE, MRE lie between -106 and -69.[2]
Consensus sequences
"These elements fit the type II MYB consensus sequence A(A/C)C(A/T)A(A/C)C, suggesting that they are MYB recognition elements (MREs)."[1]
The consensus sequence for the RRE is 5'-CATCTG-3'.[2]
The consensus sequence for the ACE is 5'-CACGT-3'.[2]
Hypotheses
- A1BG has no MYB recognition elements (MRE) in either promoter.
- A1BG is not transcribed by a MRE.
- No MRE participates in the transcription of A1BG.
MRE samplings
Copying an apparent core consensus sequence for the MYBRE of AACAAAC or TAACTG and putting it in "⌘F" finds none located between ZSCAN22 and none or one between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence A(A/C)C(A/T)A(A/C)C (starting with SuccessablesMYB.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 A(A/C)C(A/T)A(A/C)C, 2, ACCAACC at 3946, ACCAACC at 3606.
- positive strand, negative direction, looking for A(A/C)C(A/T)A(A/C)C, 5, AACAACC at 2844, AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390.
- positive strand, positive direction, looking for A(A/C)C(A/T)A(A/C)C, 0.
- negative strand, positive direction, looking for A(A/C)C(A/T)A(A/C)C, 1, ACCAAAC at 3176.
- complement, negative strand, negative direction, looking for T(G/T)G(A/T)T(G/T)G, 5, TTGTTGG at 2844, TTGTTTG at 2511, TTGTTTG at 2486, TTGTTTG at 1587, TTGTTTG at 1390.
- complement, positive strand, negative direction, looking for T(G/T)G(A/T)T(G/T)G, 2, TGGTTGG at 3946, TGGTTGG at 3606.
- complement, positive strand, positive direction, looking for T(G/T)G(A/T)T(G/T)G, 1, TGGTTTG at 3176.
- complement, negative strand, positive direction, looking for T(G/T)G(A/T)T(G/T)G, 0.
- inverse complement, negative strand, negative direction, looking for G(G/T)T(A/T)G(G/T)T, 5, GGTAGGT at 4457, GGTTGTT at 3139, GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392.
- inverse complement, positive strand, negative direction, looking for G(G/T)T(A/T)G(G/T)T, 0.
- inverse complement, positive strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 1, GGTAGGT at 3109.
- inverse complement, negative strand, positive direction, looking for G(G/T)T(A/T)G(G/T)T, 0.
- inverse negative strand, negative direction, looking for C(A/C)A(A/T)C(A/C)A, 0.
- inverse positive strand, negative direction, looking for C(A/C)A(A/T)C(A/C)A, 5, CCATCCA at 4457, CCAACAA at 3139, CAAACAA at 2488, CAAACAA at 2484, CAAACAA at 1392.
- inverse positive strand, positive direction, looking for C(A/C)A(A/T)C(A/C)A, 0.
- inverse negative strand, positive direction, looking for C(A/C)A(A/T)C(A/C)A, 1, CCATCCA at 3109.
MRE UTR gene transcriptions
Negative strand, negative direction: GGTAGGT at 4457, ACCAACC at 3946, ACCAACC at 3606, GGTTGTT at 3139.
MRE core promoters
Positive strand, negative direction: AACAACC at 2844.
MRE distal promoters
Negative strand, negative direction: GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392.
Positive strand, negative direction: AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390.
Positive strand, positive direction: GGTAGGT at 3109.
Negative strand, positive direction: ACCAAAC at 3176.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Initial content for this page in some instances came from Wikiversity.
Initial content for this page in some instances incorporates text from the United States National Library of Medicine.
See also
References
- ↑ 1.0 1.1 Paul J Rushton and Imre E Somssich (August 1998). "Transcriptional control of plant genes responsive to pathogens" (PDF). Current Opinion in Plant Biology. 1 (4): 311–5. doi:10.1016/1369-5266(88)80052-9. Retrieved 5 November 2018.
- ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 Ulrike Hartmann, Martin Sagasser, Frank Mehrtens, Ralf Stracke and Bernd Weisshaar (January 2005). "Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes" (PDF). Plant Molecular Biology. 57 (2): 155–171. doi:10.1007/s11103-004-6910-0. Retrieved 10 November 2018.
- ↑ RefSeq (January 2016). "MYB MYB proto-oncogene, transcription factor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 7 February 2021.