TEA consensus sequence gene transcriptions

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

"The TEA/ATTS transcription factor family consists of mammalian, avian, nematode, insect and fungal members that share a conserved TEA domain. The TEA domain (Bürglin, 1991) represents a DNA‐binding region that is composed of 66–76 conserved amino acids (aa) in the N‐terminal section of the proteins."[1]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Transcriptional enhancer factor TEF-3 is a protein that in humans is encoded by the TEAD4 gene.[2][3][4]

This gene product is a member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain.[5] Members of the family in mammals are TEAD1, TEAD2, TEAD3, TEAD4. TEAD4 is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression. Alternatively spliced transcripts encoding distinct isoforms, some of which are translated through the use of a non-AUG (UUG) initiation codon, have been described for this gene.[4] Gene ablation experiments in mice (i.e. knockout mice) showed that TEAD4 is essential for the formation of blastocysts during preimplantation embryo development.[6][7] Although it was originally hypothesized to be essential for specification of trophectoderm lineage, it was later shown that functional trophectoderm can be produced leading to formation of blastocysts under in vitro conditions that suppress oxidative stress.[8] Transcriptional coregulators, such as WWTR1 (TAZ) bind to members in this transcription factor family.

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The TEA consensus sequence (TCS) in a fungal TEA/ATTS transcription factor target promoter has been defined as 5′‐CATTCY‐3′ (Andrianopoulos and Timberlake, 1994)."[1]

Binding site for

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

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.

TEA samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CATTC(C/T) and putting the sequence in "⌘F" finds three between ZNF497 and A1BG or 2 between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CATTC(C/T) (starting with SuccessablesTEA.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 CATTC(C/T), 2, CATTCT at 3893, CATTCT at 2503.
  2. positive strand, negative direction, looking for CATTC(C/T), 0.
  3. positive strand, positive direction, looking for CATTC(C/T), 1, CATTCC at 2457.
  4. negative strand, positive direction, looking for CATTC(C/T), 2, CATTCT at 3074, CATTCC at 2208.
  1. inverse complement, negative strand, negative direction, looking for (A/G)GAATG, 0.
  2. inverse complement, positive strand, negative direction, looking for (A/G)GAATG, 3, GGAATG at 4554, AGAATG at 3003, AGAATG at 1947.
  3. inverse complement, positive strand, positive direction, looking for (A/G)GAATG, 2, AGAATG at 1887, AGAATG at 523.
  4. inverse complement, negative strand, positive direction, looking for (A/G)GAATG, 8, AGAATG at 3834, GGAATG at 3566, GGAATG at 3440, GGAATG at 3366, AGAATG at 3068, AGAATG at 2840, AGAATG at 1419, AGAATG at 1319.

TEA (4560-2846) UTRs

  1. Negative strand, negative direction: CATTCT at 3893.
  2. Positive strand, negative direction: GGAATG at 4554, AGAATG at 3003.

TEA negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CATTCT at 2503.
  2. Positive strand, negative direction: AGAATG at 1947.

TEA positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CATTCT at 3074, CATTCC at 2208.
  2. Negative strand, positive direction: AGAATG at 3834, GGAATG at 3566, GGAATG at 3440, GGAATG at 3366, AGAATG at 3068, AGAATG at 2840, AGAATG at 1419, AGAATG at 1319.
  3. Positive strand, positive direction: CATTCC at 2457.
  4. Positive strand, positive direction: AGAATG at 1887, AGAATG at 523.

TEA random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

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

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

RDr arbitrary negative direction (evens) (2596-1) distal promoters

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

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

RDr alternate positive direction (evens) (4050-1) distal promoters

TEA analysis and results

Main article: Complex locus A1BG and ZNF497 § TEAs

"The TEA consensus sequence (TCS) in a fungal TEA/ATTS transcription factor target promoter has been defined as 5′‐CATTCY‐3′ (Andrianopoulos and Timberlake, 1994)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 0.5 (--1,+-2)
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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
Randoms Core alternate positive 0 10 0 0
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 2 2 1 1 (--1,+-1)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 13 2 6.5 6.5 ± 3.5 (-+10,++3)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

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

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Anja Schweizer, Steffen Rupp, Brad N. Taylor, Martin Röllinghoff, Klaus Schröppel (November 2000). "The TEA/ATTS transcription factor CaTec1p regulates hyphal development and virulence in Candida albicans". Molecular Microbiology. 38 (3): 435–445. doi:10.1046/j.1365-2958.2000.02132.x. Retrieved 21 April 2021.
  2. ↑ Jacquemin P, Depetris D, Mattei MG, Martial JA, Davidson I (January 1999). "Localization of human transcription factor TEF-4 and TEF-5 (TEAD2, TEAD3) genes to chromosomes 19q13.3 and 6p21.2 using fluorescence in situ hybridization and radiation hybrid analysis". Genomics. 55 (1): 127–9. doi:10.1006/geno.1998.5628. hdl:2268/13836. PMID 9889009.
  3. ↑ Stewart AF, Richard CW, Suzow J, Stephan D, Weremowicz S, Morton CC, Adra CN (October 1996). "Cloning of human RTEF-1, a transcriptional enhancer factor-1-related gene preferentially expressed in skeletal muscle: evidence for an ancient multigene family". Genomics. 37 (1): 68–76. doi:10.1006/geno.1996.0522. PMID 8921372.
  4. ↑ 4.0 4.1 "Entrez Gene: TEAD4 TEA domain family member 4".
  5. ↑ Bürglin TR (July 1991). "The TEA domain: a novel, highly conserved DNA-binding motif". Cell. 66 (1): 11–2. doi:10.1016/0092-8674(91)90132-I. PMID 2070413. Unknown parameter |s2cid= ignored (help)
  6. ↑ Yagi R, Kohn MJ, Karavanova I, Kaneko KJ, Vullhorst D, DePamphilis ML, Buonanno A (November 2007). "Transcription factor TEAD4 specifies the trophectoderm lineage at the beginning of mammalian development". Development. 134 (21): 3827–36. doi:10.1242/dev.010223. PMID 17913785.
  7. ↑ Nishioka N, Yamamoto S, Kiyonari H, Sato H, Sawada A, Ota M, Nakao K, Sasaki H (2008). "Tead4 is required for specification of trophectoderm in pre-implantation mouse embryos". Mechanisms of Development. 125 (3–4): 270–83. doi:10.1016/j.mod.2007.11.002. PMID 18083014. Unknown parameter |s2cid= ignored (help)
  8. ↑ Kaneko KJ, DePamphilis ML (September 2013). "TEAD4 establishes the energy homeostasis essential for blastocoel formation". Development. 140 (17): 3680–90. doi:10.1242/dev.093799. PMC 3742148. PMID 23903192.

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