Ndt80p gene transcriptions: Difference between revisions

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(Created page with "{{AE}} Henry A. Hoff ==Human genes== ==Interactions== ==Consensus sequences== The upstream activating sequence (UAS) for the Ndt80p is 5'-DNCRCAAAW-3'.<ref name=Tang>{{ ci...")
 
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{{AE}} Henry A. Hoff
{{AE}} Henry A. Hoff
Ndt80 is a meiosis-specific transcription factor required for successful completion of meiosis and spore formation.<ref name=Xu>{{ cite journal
| vauthors = Xu L, Ajimura M, Padmore R, Klein C, Kleckner N
| title = NDT80, a meiosis-specific gene required for exit from pachytene in ''Saccharomyces cerevisiae''
| journal = Molecular and Cellular Biology
| volume = 15
| issue = 12
| pages = 6572–81
|date = December 1995
|pmid = 8524222
| pmc = 230910
| doi = 10.1128/MCB.15.12.6572 }}</ref> The DNA-binding domain of Ndt80 has been isolated, and the structure reveals that this protein is a member of the Ig-fold family of transcription factors.<ref name=Lamoureux>{{ cite journal
| vauthors = Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN
| title = Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
| journal = The EMBO Journal
| volume = 21
| issue = 21
| pages = 5721–32
| date = November 2002
| pmid = 12411490
| pmc = 131069
| doi = 10.1093/emboj/cdf572 }}</ref> Ndt80 also competes with the repressor SUM1 for binding to promoters containing MSEs.<ref name=Hendrickson>{{ cite journal
| vauthors = Hendrickson WA, Ward KB
| title = Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin
| journal = Biochemical and Biophysical Research Communications
| volume = 66
| issue = 4
| pages = 1349–56
| date = October 1975
| pmid = 5
| doi = 10.1016/0006-291x(75)90508-2 }}</ref>
Direct "binding of Ndt80 to the [mid sporulation element CRCAAAA/T (Ozsarac et al. 1997)] MSE is necessary for activating transcription of the middle sporulation genes."<ref name=Chu>{{ cite journal
| author = Shelley Chu and Ira Herskowitz
| title = Gametogenesis in Yeast Is Regulated by a Transcriptional Cascade Dependent on Ndt80
| journal = Molecular Cell
| volume = 1
| issue = 5
| pages = 685–96
| date = April 1, 1998
| pmid = 9660952
| doi = 10.1016/S1097-2765(00)80068-4 }}</ref>
"These genomic sequences were analysed for the presence of [...] middle sporulation elements (MSE) motif (5'-ACACAAA-3') using the NCBI BLAST tool."<ref name=Branco>{{ cite journal
|author=J. Branco, M. Ola, R. M. Silva, E. Fonseca, N. C. Gomes, C. Martins-Cruz, A. P. Silva, A. Silva-Dias, C. Pina-Vaz, C. Erraught, L. Brennan, A. G. Rodrigues, G. Butler and I. M. Miranda
|title=Impact of ''ERG3'' mutations and expression of ergosterol genes controlled by ''UPC2'' and NDT80 in ''Candida parapsilosis'' azole resistance
|journal=Clinical Microbiology and Infection
|date=August 2017
|volume=23
|issue=8
|pages=575.e1-575.e8
|url=https://www.sciencedirect.com/science/article/pii/S1198743X17300903
|arxiv=
|bibcode=
|doi=10.1016/j.cmi.2017.02.002
|pmid=28196695
|accessdate=5 September 2020 }}</ref>


==Human genes==
==Human genes==
Line 22: Line 79:
|accessdate=18 September 2020 }}</ref>
|accessdate=18 September 2020 }}</ref>


==Samplings==
==Ndt80 samplings==
 
Copying DNCRCAAAW, (A/G/T)(A/C/G/T)C(A/G)CAAA(A/T), or TCCGCA in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
 
For the Basic programs testing consensus sequence (A/G/T)(A/C/G/T)C(A/G)CAAA(A/T) (starting with SuccessablesNDT.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.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
 
===NDT UTR gene transcriptions===
{{main|UTR promoter gene transcriptions}}
 
===NDT core promoters===
{{main|Core promoter gene transcriptions}}
 
===NDT proximal promoters===
{{main|Proximal promoter gene transcriptions}}


Copying 5'-DNCRCAAAW-3', 5'-(A/G/T)(A/C/G/T)C(A/G)CAAA(A/T)-3', or 5'-TCCGCA-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
===NDT distal promoters===
{{main|Distal promoter gene transcriptions}}


==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]]
* [[Complex locus A1BG and ZNF497]]
* [[Transcription factor]]
{{Div col end}}
{{Div col end}}


Line 36: Line 127:


==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]


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[[Category:Resources last modified in September 2020]]
[[Category:Resources last modified in February 2021]]

Revision as of 14:24, 8 February 2021

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

Ndt80 is a meiosis-specific transcription factor required for successful completion of meiosis and spore formation.[1] The DNA-binding domain of Ndt80 has been isolated, and the structure reveals that this protein is a member of the Ig-fold family of transcription factors.[2] Ndt80 also competes with the repressor SUM1 for binding to promoters containing MSEs.[3]

Direct "binding of Ndt80 to the [mid sporulation element CRCAAAA/T (Ozsarac et al. 1997)] MSE is necessary for activating transcription of the middle sporulation genes."[4]

"These genomic sequences were analysed for the presence of [...] middle sporulation elements (MSE) motif (5'-ACACAAA-3') using the NCBI BLAST tool."[5]

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for the Ndt80p is 5'-DNCRCAAAW-3'.[6]

Ndt80 samplings

Copying DNCRCAAAW, (A/G/T)(A/C/G/T)C(A/G)CAAA(A/T), or TCCGCA in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G/T)(A/C/G/T)C(A/G)CAAA(A/T) (starting with SuccessablesNDT.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. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, positive direction, looking for AAAAAAAA, 0.
  16. inverse negative strand, positive direction, looking for AAAAAAAA, 0.

NDT UTR gene transcriptions

Main article: UTR promoter gene transcriptions

NDT core promoters

Main article: Core promoter gene transcriptions

NDT proximal promoters

Main article: Proximal promoter gene transcriptions

NDT distal promoters

Main article: Distal promoter gene transcriptions

See also

References

  1. ↑ Xu L, Ajimura M, Padmore R, Klein C, Kleckner N (December 1995). "NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae". Molecular and Cellular Biology. 15 (12): 6572–81. doi:10.1128/MCB.15.12.6572. PMC 230910. PMID 8524222.
  2. ↑ Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN (November 2002). "Structure of the sporulation-specific transcription factor Ndt80 bound to DNA". The EMBO Journal. 21 (21): 5721–32. doi:10.1093/emboj/cdf572. PMC 131069. PMID 12411490.
  3. ↑ Hendrickson WA, Ward KB (October 1975). "Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin". Biochemical and Biophysical Research Communications. 66 (4): 1349–56. doi:10.1016/0006-291x(75)90508-2. PMID 5.
  4. ↑ Shelley Chu and Ira Herskowitz (April 1, 1998). "Gametogenesis in Yeast Is Regulated by a Transcriptional Cascade Dependent on Ndt80". Molecular Cell. 1 (5): 685–96. doi:10.1016/S1097-2765(00)80068-4. PMID 9660952.
  5. ↑ J. Branco, M. Ola, R. M. Silva, E. Fonseca, N. C. Gomes, C. Martins-Cruz, A. P. Silva, A. Silva-Dias, C. Pina-Vaz, C. Erraught, L. Brennan, A. G. Rodrigues, G. Butler and I. M. Miranda (August 2017). "Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance". Clinical Microbiology and Infection. 23 (8): 575.e1–575.e8. doi:10.1016/j.cmi.2017.02.002. PMID 28196695. Retrieved 5 September 2020.
  6. ↑ Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Ndt80p_gene_transcriptions&oldid=1689114"