Nuclear factor Y gene transcriptions: Difference between revisions

Jump to navigation Jump to search
VisualWikitext
mNo edit summary
 
Line 1: Line 1:
{{AE}} Henry A. Hoff
{{AE}} Henry A. Hoff


The protein encoded by this gene is one subunit of a trimeric complex NF-Y, forming a highly conserved transcription factor that binds to CCAAT motifs in the promoter regions in a variety of genes.<ref name=Oldfield25132174>{{ cite journal
The protein encoded by this gene is one subunit of a trimeric complex NF-Y, forming a highly conserved transcription factor that binds to CCAAT motifs in the promoter regions in a variety of genes.<ref name=Oldfield>{{ cite journal
| vauthors = Oldfield AJ, Yang P, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jothi R
| vauthors = Oldfield AJ, Yang P, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jothi R
| title = Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors
| title = Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors
Line 10: Line 10:
| date = September 2014
| date = September 2014
| pmid = 25132174
| pmid = 25132174
| pmc = 4157648
| doi = 10.1016/j.molcel.2014.07.005 }}</ref>
| doi = 10.1016/j.molcel.2014.07.005 }}</ref>


Line 22: Line 21:
| accessdate = }}</ref>
| accessdate = }}</ref>


Nuclear transcription factor Y subunit beta is a [[protein]] that in humans is encoded by the ''NFYB'' [[gene]].<ref name=Li1774067>{{ cite journal
Nuclear transcription factor Y subunit beta is a [[protein]] that in humans is encoded by the ''NFYB'' [[gene]].<ref name=Li>{{ cite journal
| vauthors = Li XY, Mattei MG, Zaleska-Rutczynska Z, Hooft van Huijsduijnen R, Figueroa F, Nadeau J, Benoist C, Mathis D
| vauthors = Li XY, Mattei MG, Zaleska-Rutczynska Z, Hooft van Huijsduijnen R, Figueroa F, Nadeau J, Benoist C, Mathis D
| title = One subunit of the transcription factor NF-Y maps close to the major histocompatibility complex in murine and human chromosomes
| title = One subunit of the transcription factor NF-Y maps close to the major histocompatibility complex in murine and human chromosomes
Line 31: Line 30:
| date = March 1992
| date = March 1992
|pmid = 1774067
|pmid = 1774067
|pmc =
| doi = 10.1016/0888-7543(91)90070-U }}</ref><ref name=Maity>{{ cite journal
| doi = 10.1016/0888-7543(91)90070-U }}</ref><ref name=Maity9612081>{{ cite journal
| vauthors = Maity SN, de Crombrugghe B
| vauthors = Maity SN, de Crombrugghe B
| title = Role of the CCAAT-binding protein CBF/NF-Y in transcription
| title = Role of the CCAAT-binding protein CBF/NF-Y in transcription
| journal = Trends Biochem Sci
| journal = Trends Biochemical Sciences
| volume = 23
| volume = 23
| issue = 5
| issue = 5
Line 41: Line 39:
| date = June 1998
| date = June 1998
| pmid = 9612081
| pmid = 9612081
| pmc =
| doi = 10.1016/S0968-0004(98)01201-8 }}</ref>
| doi = 10.1016/S0968-0004(98)01201-8 }}</ref>


Nuclear transcription factor Y subunit gamma is a [[protein]] that in humans is encoded by the ''NFYC'' [[gene]].<ref name=Sinha8921405>{{ cite journal
Nuclear transcription factor Y subunit gamma is a [[protein]] that in humans is encoded by the ''NFYC'' [[gene]].<ref name=Sinha>{{ cite journal
| vauthors = Sinha S, Maity SN, Seldin MF, de Crombrugghe B
| vauthors = Sinha S, Maity SN, Seldin MF, de Crombrugghe B
| title = Chromosomal assignment and tissue expression of CBF-C/NFY-C, the third subunit of the mammalian CCAAT-binding factor
| title = Chromosomal assignment and tissue expression of CBF-C/NFY-C, the third subunit of the mammalian CCAAT-binding factor
Line 53: Line 50:
|date = February 1997
|date = February 1997
| pmid = 8921405
| pmid = 8921405
| pmc =
| doi = 10.1006/geno.1996.0555 }}</ref><ref name=Bellorini>{{ cite journal
| doi = 10.1006/geno.1996.0555 }}</ref><ref name=Bellorini9249075>{{ cite journal
| vauthors = Bellorini M, Zemzoumi K, Farina A, Berthelsen J, Piaggio G, Mantovani R
| vauthors = Bellorini M, Zemzoumi K, Farina A, Berthelsen J, Piaggio G, Mantovani R
| title = Cloning and expression of human NF-YC
| title = Cloning and expression of human NF-YC
Line 63: Line 59:
| date = August 1997
| date = August 1997
| pmid = 9249075
| pmid = 9249075
| pmc =
| doi = 10.1016/S0378-1119(97)00109-1 }}</ref><ref name=entrez4802/>
| doi = 10.1016/S0378-1119(97)00109-1 }}</ref><ref name=entrez4802/>


NF-Y complex serves as a [[pioneer factor]] by promoting [[chromatin]] accessibility to facilitate other co-localizing cell type-specific transcription factors.<ref name=Oldfield25132174/>
NF-Y complex serves as a [[pioneer factor]] by promoting [[chromatin]] accessibility to facilitate other co-localizing cell type-specific transcription factors.<ref name=Oldfield/>


NF-Y has also been implicated as a central player in [[Transcription (biology)|transcription]] start site (TSS) selection in [[animals]].<ref name=Oldfield31296853>{{ cite journal
NF-Y has also been implicated as a central player in [[Transcription (biology)|transcription]] start site (TSS) selection in [[animals]].<ref name=Oldfield31296853>{{ cite journal
Line 113: Line 108:
| date = November 1991
| date = November 1991
| pmid = 1774067
| pmid = 1774067
| pmc =
| doi = 10.1016/0888-7543(91)90070-U }}</ref><ref name=Maity/>
| doi = 10.1016/0888-7543(91)90070-U }}</ref><ref name=Maity9612081>{{ cite journal
| vauthors = Maity SN, de Crombrugghe B
| title = Role of the CCAAT-binding protein CBF/NF-Y in transcription
| journal = Trends in Biochemical Sciences
| volume = 23
| issue = 5
| pages = 174–8
| date = May 1998
| pmid = 9612081
| pmc =
| doi = 10.1016/S0968-0004(98)01201-8 }}</ref>


Nuclear transcription factor Y subunit beta is a [[protein]] that in humans is encoded by the ''NFYB'' [[gene]].<ref name=Li1774067/><ref name=Maity9612081/>
Nuclear transcription factor Y subunit beta is a [[protein]] that in humans is encoded by the ''NFYB'' [[gene]].<ref name=Li1774067/><ref name=Maity/>


Nuclear transcription factor Y subunit gamma is a [[protein]] that in humans is encoded by the ''NFYC'' [[gene]].<ref name=Sinha8921405/><ref name=Bellorini9249075>{{ cite journal
Nuclear transcription factor Y subunit gamma is a [[protein]] that in humans is encoded by the ''NFYC'' [[gene]].<ref name=Sinha/><ref name=Bellorini/><ref name=entrez4802/>
| vauthors = Bellorini M, Zemzoumi K, Farina A, Berthelsen J, Piaggio G, Mantovani R
| title = Cloning and expression of human NF-YC
| journal = Gene
| volume = 193
| issue = 1
| pages = 119–25
| date = August 1997
| pmid = 9249075
| pmc =
| doi = 10.1016/S0378-1119(97)00109-1 }}</ref><ref name=entrez4802/>


== Interactions ==
== Interactions ==


NFYA has been shown to [[Protein-protein interaction|interact]] with:
NFYA has been shown to [[Protein-protein interaction|interact]] with:
* [[Serum response factor]]<ref name=Yamada10571058>{{ cite journal
* [[Serum response factor]]<ref name=Yamada>{{ cite journal
| vauthors = Yamada K, Osawa H, Granner DK
| vauthors = Yamada K, Osawa H, Granner DK
| title = Identification of proteins that interact with NF-YA
| title = Identification of proteins that interact with NF-YA
Line 153: Line 127:
| pmid = 10571058
| pmid = 10571058
| doi = 10.1016/S0014-5793(99)01311-3 }}</ref> and
| doi = 10.1016/S0014-5793(99)01311-3 }}</ref> and
* [[ZHX1]].<ref name=Yamada10571058/><ref name=Yamada10441475>{{ cite journal
* [[ZHX1]].<ref name=Yamada/><ref name=Yamada10441475>{{ cite journal
| vauthors = Yamada K, Printz RL, Osawa H, Granner DK
| vauthors = Yamada K, Printz RL, Osawa H, Granner DK
| title = Human ZHX1: cloning, chromosomal location, and interaction with transcription factor NF-Y
| title = Human ZHX1: cloning, chromosomal location, and interaction with transcription factor NF-Y
Line 220: Line 194:
| doi = 10.1074/jbc.274.34.24270 }}</ref>
| doi = 10.1074/jbc.274.34.24270 }}</ref>


NFYA, NFYB and NFYC form the NFY complex and it has been shown that the NFY complex serves as a pioneer factor by promoting chromatin accessibility to facilitate other co-localizing cell type-specific transcription factors.<ref name=Oldfield25132174/>
NFYA, NFYB and NFYC form the NFY complex and it has been shown that the NFY complex serves as a pioneer factor by promoting chromatin accessibility to facilitate other co-localizing cell type-specific transcription factors.<ref name=Oldfield/>


==Consensus sequences==
==Consensus sequences==
Line 279: Line 253:


==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 -->
Line 284: Line 263:


<!-- footer categories -->
<!-- footer categories -->
[[Category:Resources last modified in September 2020]]
[[Category:Resources last modified in February 2021]]

Latest revision as of 05:13, 9 February 2021

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

The protein encoded by this gene is one subunit of a trimeric complex NF-Y, forming a highly conserved transcription factor that binds to CCAAT motifs in the promoter regions in a variety of genes.[1]

Subunit NFYA associates with a tight dimer composed of the NFYB and NFYC subunits, resulting in a trimer that binds to DNA with high specificity and affinity. The sequence specific interactions of the complex are made by the NFYA subunit, suggesting a role as the regulatory subunit.

There is evidence of post-transcriptional regulation in this gene product, either by protein degradation or control of translation.

Regulation is represented by alternative splicing in the glutamine-rich activation domain, with clear tissue-specific preferences for the two isoforms.[2]

Nuclear transcription factor Y subunit beta is a protein that in humans is encoded by the NFYB gene.[3][4]

Nuclear transcription factor Y subunit gamma is a protein that in humans is encoded by the NFYC gene.[5][6][7]

NF-Y complex serves as a pioneer factor by promoting chromatin accessibility to facilitate other co-localizing cell type-specific transcription factors.[1]

NF-Y has also been implicated as a central player in transcription start site (TSS) selection in animals.[8]

It safeguards the integrity of the nucleosome-depleted region and PIC localization at protein-coding gene promoters. Observation of the histone nature of these subunits is supported by two types of evidence; protein sequence alignments and experiments with mutants.[9]

Additional regulation, preliminarily supported by the EST database, may be represented by alternative splicing in this subunit C.[7]

Two microRNAs; miR-30c and miR-30e are located within introns of the nfyc gene. These microRNAs are actively transcribed in human insulin-producing beta cells in the Islets of Langerhans that also show high expression of nfyc and CDH1 genes. The expression of these intronic microRNAs is essential for maintaining the differentiated phenotype of human islet beta cells. Inhibition of miR-30 family microRNAs induces epithelial-mesenchymal transition of human pancreatic islet cells.[10]

Human genes

Nuclear transcription factor Y subunit alpha is a protein that in humans is encoded by the NFYA gene.[11][4]

Nuclear transcription factor Y subunit beta is a protein that in humans is encoded by the NFYB gene.[11][4]

Nuclear transcription factor Y subunit gamma is a protein that in humans is encoded by the NFYC gene.[5][6][7]

Interactions

NFYA has been shown to interact with:

NFYB has been shown to interact with:

NFYC has been shown to interact with:

NFYA, NFYB and NFYC form the NFY complex and it has been shown that the NFY complex serves as a pioneer factor by promoting chromatin accessibility to facilitate other co-localizing cell type-specific transcription factors.[1]

Consensus sequences

Consensus sequences for the nuclear factor Y are CAATGGCG, CCAATGGAA and CCAATGGCA.[19]

NFY samplings

Copying an apparent consensus sequence for the NFY CCAATGG(A/C)(A/G) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCAATGG(A/C)(A/G) (starting with SuccessablesNFY.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 CCAATGG(A/C)(A/G), 0.
  2. positive strand, negative direction, looking for CCAATGG(A/C)(A/G), 0.
  3. positive strand, positive direction, looking for CCAATGG(A/C)(A/G), 0.
  4. negative strand, positive direction, looking for CCAATGG(A/C)(A/G), 0.
  5. complement, negative strand, negative direction, looking for GGTTACC(G/T)(C/T), 0.
  6. complement, positive strand, negative direction, looking for GGTTACC(G/T)(C/T), 0.
  7. complement, positive strand, positive direction, looking for GGTTACC(G/T)(C/T), 0.
  8. complement, negative strand, positive direction, looking for GGTTACC(G/T)(C/T), 0.
  9. inverse complement, negative strand, negative direction, looking for (C/T)(G/T)CCATTGG, 0.
  10. inverse complement, positive strand, negative direction, looking for (C/T)(G/T)CCATTGG, 0.
  11. inverse complement, positive strand, positive direction, looking for (C/T)(G/T)CCATTGG, 0.
  12. inverse complement, negative strand, positive direction, looking for (C/T)(G/T)CCATTGG, 0.
  13. inverse negative strand, negative direction, looking for (A/G)(A/C)GGTAACC, 0.
  14. inverse positive strand, negative direction, looking for (A/G)(A/C)GGTAACC, 0.
  15. inverse positive strand, positive direction, looking for (A/G)(A/C)GGTAACC, 0.
  16. inverse negative strand, positive direction, looking for (A/G)(A/C)GGTAACC, 0.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Oldfield AJ, Yang P, Conway AE, Cinghu S, Freudenberg JM, Yellaboina S, Jothi R (September 2014). "Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors". Molecular Cell. 55 (5): 708–22. doi:10.1016/j.molcel.2014.07.005. PMID 25132174.
  2. ↑ "Entrez Gene: NFYA nuclear transcription factor Y, alpha".
  3. ↑ Li XY, Mattei MG, Zaleska-Rutczynska Z, Hooft van Huijsduijnen R, Figueroa F, Nadeau J, Benoist C, Mathis D (March 1992). "One subunit of the transcription factor NF-Y maps close to the major histocompatibility complex in murine and human chromosomes". Genomics. 11 (3): 630–4. doi:10.1016/0888-7543(91)90070-U. PMID 1774067.
  4. ↑ 4.0 4.1 4.2 Maity SN, de Crombrugghe B (June 1998). "Role of the CCAAT-binding protein CBF/NF-Y in transcription". Trends Biochemical Sciences. 23 (5): 174–8. doi:10.1016/S0968-0004(98)01201-8. PMID 9612081.
  5. ↑ 5.0 5.1 Sinha S, Maity SN, Seldin MF, de Crombrugghe B (February 1997). "Chromosomal assignment and tissue expression of CBF-C/NFY-C, the third subunit of the mammalian CCAAT-binding factor". Genomics. 37 (2): 260–3. doi:10.1006/geno.1996.0555. PMID 8921405.
  6. ↑ 6.0 6.1 Bellorini M, Zemzoumi K, Farina A, Berthelsen J, Piaggio G, Mantovani R (August 1997). "Cloning and expression of human NF-YC". Gene. 193 (1): 119–25. doi:10.1016/S0378-1119(97)00109-1. PMID 9249075.
  7. ↑ 7.0 7.1 7.2 "Entrez Gene: NFYC nuclear transcription factor Y, gamma".
  8. ↑ Oldfield AJ, Henriques T, Burkholder AB, Paulet D, Cinghu S, Yang P, Scruggs BS, Lavender CA, Kumar D, Bennett B, Rivals E (2019-07-11). "NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region". Nature Communications. 10 (1): 3072. doi:10.1038/s41467-019-10905-7. PMC 6624317 Check |pmc= value (help). PMID 31296853.
  9. ↑ "Entrez Gene: NFYB nuclear transcription factor Y, beta".
  10. ↑ Joglekar MV, Patil D, Joglekar VM, Rao GV, Reddy DN, Mitnala S, Shouche Y, Hardikar AA (September–October 2009). "The miR-30 family microRNAs confer epithelial phenotype to human pancreatic cells". Islets. 1 (2): 137–147. doi:10.4161/isl.1.2.9578. PMID 21099261.
  11. ↑ 11.0 11.1 Li XY, Mattei MG, Zaleska-Rutczynska Z, Hooft van Huijsduijnen R, Figueroa F, Nadeau J, Benoist C, Mathis D (November 1991). "One subunit of the transcription factor NF-Y maps close to the major histocompatibility complex in murine and human chromosomes". Genomics. 11 (3): 630–4. doi:10.1016/0888-7543(91)90070-U. PMID 1774067.
  12. ↑ 12.0 12.1 Yamada K, Osawa H, Granner DK (October 1999). "Identification of proteins that interact with NF-YA". FEBS Letters. 460 (1): 41–5. doi:10.1016/S0014-5793(99)01311-3. PMID 10571058.
  13. ↑ Yamada K, Printz RL, Osawa H, Granner DK (August 1999). "Human ZHX1: cloning, chromosomal location, and interaction with transcription factor NF-Y". Biochemical and Biophysical Research Communications. 261 (3): 614–21. doi:10.1006/bbrc.1999.1087. PMID 10441475.
  14. ↑ Imbriano C, Bolognese F, Gurtner A, Piaggio G, Mantovani R (July 2001). "HSP-CBF is an NF-Y-dependent coactivator of the heat shock promoters CCAAT boxes". J. Biol. Chem. 276 (28): 26332–9. doi:10.1074/jbc.M101553200. PMID 11306579.
  15. ↑ Pise-Masison CA, Dittmer J, Clemens KE, Brady JN (March 1997). "Physical and functional interaction between the human T-cell lymphotropic virus type 1 Tax1 protein and the CCAAT binding protein NF-Y". Mol. Cell. Biol. 17 (3): 1236–43. doi:10.1128/mcb.17.3.1236. PMC 231848. PMID 9032250.
  16. ↑ Izumi H, Molander C, Penn LZ, Ishisaki A, Kohno K, Funa K (April 2001). "Mechanism for the transcriptional repression by c-Myc on PDGF beta-receptor". J. Cell Sci. 114 (Pt 8): 1533–44. PMID 11282029.
  17. ↑ Bellorini M, Lee DK, Dantonel JC, Zemzoumi K, Roeder RG, Tora L, Mantovani R (June 1997). "CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues". Nucleic Acids Research. 25 (11): 2174–81. doi:10.1093/nar/25.11.2174. PMC 146709. PMID 9153318.
  18. ↑ Taira T, Sawai M, Ikeda M, Tamai K, Iguchi-Ariga SM, Ariga H (August 1999). "Cell cycle-dependent switch of up-and down-regulation of human hsp70 gene expression by interaction between c-Myc and CBF/NF-Y". Journal Biol. Chem. 274 (34): 24270–9. doi:10.1074/jbc.274.34.24270. PMID 10446203.
  19. ↑ D. W. Yao, J. Luo, Q. Y. He, J. Li, H. Wang, H. B. Shi, H. F. Xu, M. Wang and J. J. Loor (May 2016). "Characterization of the liver X receptor-dependent regulatory mechanism of goat stearoyl-coenzyme A desaturase 1 gene by linoleic acid". Journal of Dairy Science. 99 (5): 3945–3957. doi:10.3168/jds.2015-10601. PMID 26947306. Retrieved 5 September 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Nuclear_factor_Y_gene_transcriptions&oldid=1689258"