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Transcription factor 3 gene transcriptions

From Wikidoc - Reading time: 11 min

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

Transcription factor 3 (E2A immunoglobulin enhancer-binding factors E12/E47) (TCF3), is a protein that in humans is encoded by the TCF3 gene.[1][2] TCF3 has been shown to directly enhance Hes1 (a well-known target of Notch signaling) expression.[3]

This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. The 9aaTAD transactivation domains of E proteins and MLL are very similar and both bind to the KIX domain of general transcriptional mediator CBP.[4][5]

Human genes

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Main article: Human genes

Gene ID: 6929 is TCF3 transcription factor 3 on 19p13.3: "This gene encodes a member of the E protein (class I) family of helix-loop-helix transcription factors. E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development. Deletion of this gene or diminished activity of the encoded protein may play a role in lymphoid malignancies. This gene is also involved in several chromosomal translocations that are associated with lymphoid malignancies including pre-B-cell acute lymphoblastic leukemia (t(1;19), with PBX1), childhood leukemia (t(19;19), with TFPT) and acute leukemia (t(12;19), with ZNF384). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9."[6]

Gene expressions

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Main article: Gene expressions

Interactions

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Main article: Interaction gene transcriptions

Consensus sequences

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Main article: Consensus sequence gene transcriptions

Consensus sequence found in the promoter of TUG1 is GTCTGGT.[7]

Binding site for

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Enhancer activity

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Main article: Enhancer activity copy gene transcriptions

E proteins activate transcription by binding to regulatory E-box sequences on target genes as heterodimers or homodimers, and are inhibited by heterodimerization with inhibitor of DNA-binding (class IV) helix-loop-helix proteins. E proteins play a critical role in lymphopoiesis, and the encoded protein is required for B and T lymphocyte development.[6]

Promoter occurrences

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Main article: Promoter occurrence gene transcriptions

Hypotheses

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Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

TCF3 samplings

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Copying a responsive elements consensus sequence GTCTGGT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GTCTGGT (starting with SuccessablesTCF.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 GTCTGGT, 1, GTCTGGT at 2122.
  2. positive strand, negative direction, looking for GTCTGGT, 0.
  3. positive strand, positive direction, looking for GTCTGGT, 0.
  4. negative strand, positive direction, looking for GTCTGGT, 2, GTCTGGT at 3022, GTCTGGT at 103.
  5. complement, negative strand, negative direction, looking for CAGACCA, 0.
  6. complement, positive strand, negative direction, looking for CAGACCA, 1, CAGACCA at 2122.
  7. complement, positive strand, positive direction, looking for CAGACCA, 2, CAGACCA at 3022, CAGACCA at 103.
  8. complement, negative strand, positive direction, looking for CAGACCA, 0.
  9. inverse complement, negative strand, negative direction, looking for ACCAGAC, 0.
  10. inverse complement, positive strand, negative direction, looking for ACCAGAC, 0.
  11. inverse complement, positive strand, positive direction, looking for ACCAGAC, 1, ACCAGAC at 2942.
  12. inverse complement, negative strand, positive direction, looking for ACCAGAC, 1, ACCAGAC at 3549.
  13. inverse negative strand, negative direction, looking for TGGTCTG, 0.
  14. inverse positive strand, negative direction, looking for TGGTCTG, 0.
  15. inverse positive strand, positive direction, looking for TGGTCTG, 1, TGGTCTG at 3549.
  16. inverse negative strand, positive direction, looking for TGGTCTG, 1, TGGTCTG at 2942.

TCF negative direction (2596-1) distal promoters

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  1. Negative strand, negative direction: GTCTGGT at 2122.

TCF positive direction (4050-1) distal promoters

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  1. Negative strand, positive direction: GTCTGGT at 3022, GTCTGGT at 103.
  2. Negative strand, positive direction: ACCAGAC at 3549.
  3. Positive strand, positive direction: ACCAGAC at 2942.

TCF random dataset samplings

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  1. TCFr0: 0.
  2. TCFr1: 0.
  3. TCFr2: 0.
  4. TCFr3: 0.
  5. TCFr4: 0.
  6. TCFr5: 0.
  7. TCFr6: 0.
  8. TCFr7: 0.
  9. TCFr8: 0.
  10. TCFr9: 0.
  11. TCFr0ci: 0.
  12. TCFr1ci: 0.
  13. TCFr2ci: 0.
  14. TCFr3ci: 0.
  15. TCFr4ci: 0.
  16. TCFr5ci: 0.
  17. TCFr6ci: 0.
  18. TCFr7ci: 1, ACCAGAC at 1604.
  19. TCFr8ci: 1, ACCAGAC at 4291.
  20. TCFr9ci: 0.

TCFr arbitrary (evens) (4560-2846) UTRs

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  1. TCFr8ci: ACCAGAC at 4291.

TCFr alternate positive direction (evens) (4445-4265) core promoters

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  1. TCFr8ci: ACCAGAC at 4291.

TCFr alternate negative direction (odds) (2596-1) distal promoters

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  1. TCFr7ci: ACCAGAC at 1604.

TCFr arbitrary positive direction (odds) (4050-1) distal promoters

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  1. TCFr7ci: ACCAGAC at 1604.

TCF analysis and results

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Main article: Complex locus A1BG and ZNF497 § TCFs

Consensus sequence found in the promoter of TUG1 is GTCTGGT.[7]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.05
Randoms UTR alternate negative 0 10 0 0.05
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms Distal arbitrary negative 0 10 0 0.05
Randoms Distal alternate negative 1 10 0.1 0.05
Reals Distal positive 4 2 2 2 ± 1 (-+3,++1)
Randoms Distal arbitrary positive 1 10 0.1 0.05
Randoms Distal alternate positive 0 10 0 0.05

Comparison:

The occurrences of real TCFs are greater than the randoms. This suggests that the real TCFs are likely active or activable.

Acknowledgements

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

See also

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References

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  1. ↑ Henthorn P, McCarrick-Walmsley R, Kadesch T (February 1990). "Sequence of the cDNA encoding ITF-1, a positive-acting transcription factor". Nucleic Acids Research. 18 (3): 677. doi:10.1093/nar/18.3.677. PMID 2308859.
  2. ↑ Kamps MP, Murre C, Sun XH, Baltimore D (February 1990). "A new homeobox gene contributes the DNA binding domain of the t(1;19) translocation protein in pre-B ALL". Cell. 60 (4): 547–55. doi:10.1016/0092-8674(90)90658-2. PMID 1967983.
  3. ↑ E proteins and Notch signaling cooperate to promote T cell lineage specification and commitment
  4. ↑ Piskacek S (2007). "Nine-amino-acid transactivation domain: Establishment and prediction utilities". Genomics. 89 (6): 756–768. doi:10.1016/j.ygeno.2007.02.003. PMID 17467953.
  5. ↑ Piskacek, Martin; Vasku, A; Hajek, R; Knight, A (2015). "Shared structural features of the 9aaTAD family in complex with CBP". Mol. Biosyst. 11 (3): 844–851. doi:10.1039/c4mb00672k. PMID 25564305.
  6. ↑ 6.0 6.1 RefSeq (September 2011). "TCF3 transcription factor 3 [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 22 November 2020.
  7. ↑ 7.0 7.1 Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.
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