GAAC element gene transcriptions: Difference between revisions

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==GAAC element analysis and results==
==GAAC element analysis and results==
{{main|Complex locus A1BG and ZNF497#GAAC elements}}
{{main|Complex locus A1BG and ZNF497#GAAC elements}}
The GAAC portion of the GAAC element is the inverse of the [[Homeobox gene transcriptions|Homeobox motif]].


==Acknowledgements==
==Acknowledgements==

Revision as of 23:33, 11 April 2022

Editor-In-Chief: Henry A. Hoff

This micrograph stained with chlorazol black, reveals an Entamoeba histolytica cyst. Credit: CDC/ Dr. George Healy.

The GAAC element is usually a core promoter element containing guanine (G), adenine (A), and cytosine (C), "able to direct a new transcription start site 2-7 bases downstream of itself, independent of TATA and Inr regions."[1]

Genetics

Main article: Genetics
File:Bob, the guinea pig.jpg
This is an image of Bob, the guinea pig. Credit: selbst.

Genetics involves the expression, transmission, and variation of inherited characteristics.

Def. a "branch of biology that deals with the transmission and variation of inherited characteristics, in particular chromosomes and DNA"[2] is called genetics.

Promoters

Main articles: Promoter gene transcriptions and Promoters
File:Preinitiation complex.png
The diagram shows the RNA polymerase II holoenzyme attached to the DNA template strand. Credit: ArneLH.

Although human DNA like most other life forms on Earth has two strands forming a double helix, only one of the strands, the template strand, is usually used to transcribe a gene product such as messenger ribonucleic acid (mRNA).

On the template strand is a nucleotide sequence (the gene promoter) that is usually interacted with by the transcription mechanism before any product of the gene is transcribed.

Consensus sequences

Main article: Consensus sequences

The consensus sequence in the direction of transcription on the template strand is 3'-GAACT-5'.[1] T is thymine.

Dispersed promoters

Main articles: Dispersed promoter gene transcriptions and Dispersed promoters

A dispersed promoter contains "several start sites over 50–100 nucleotides and [is] typically found in CpG islands in vertebrates".[3] "CpGs are ... relatively enriched around the TSS. In fact, the enrichment pattern peaks sharply close to the core promoter 15 bp upstream of the TSS".[4] Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the cytosines in such an arrangement tend to be methylated.

"[I]n vertebrates dispersed promoters are more common than focused promoters."[3]

General transcription factors II D

Main articles: General transcription factor II D gene transcriptions and General transcription factor II Ds

This element also controls the rate of transcription initiation and interacts in a sequence-specific manner with the transcription factor II D (TFIID) complex.[1]

Entamoeba histolytica

The GAAC element is present "in 31/37 protein-encoding E. histolytica genes ... It has a variable location between the TATA box and the Inr sequences".[1]

Human genes

Main article: Human genes

"The genes encoding the two type I collagen chains are selectively activated in ... fibroblasts and osteoblasts [within the promoter by] a sequence located between -3.2 and -2.3 kb".[5] "[T]wo short elements ... tendon-specific element (TSE) 1 and TSE2 [within this sequence are] necessary to direct reporter gene expression".[5] The binding sequence of TSE2 "corresponded to an E-box."[5] TSE1 and TSE2 need to cooperate with each other and "other cis-acting elements of the proximal promoter to activate gene expression in tendon fibroblasts."[5] "[A] short sequence [in TSE1 contains] a GAACT motif that [binds] a tendon-specific nuclear protein."[5]

Hypotheses

Main article: Hypotheses
  1. A1BG has no GAAC elements in either promoter.
  2. A1BG is not transcribed by a GAAC element.
  3. A GAAC element does not participate in the transcription of A1BG.

GAAC element samplings

The GAAC element is usually a core promoter element containing guanine (G), adenine (A), and cytosine (C), "able to direct a new transcription start site 2-7 bases downstream of itself, independent of TATA and Inr regions."[1]

For the Basic programs (starting with SuccessablesGAAC.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGAAC--.bas, looking for GAACT, 13, GAACT at 4294, GAACT at 4012, GAACT at 3571, GAACT at 3401, GAACT at 3242, GAACT at 3103, GAACT at 2714, GAACT at 2580, GAACT at 2379, GAACT at 2127, GAACT at 1300, GAACT at 1009, GAACT at 843, and complements.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGAAC-+.bas, looking for GAACT, 2, GAACT at 4048, GAACT at 1951, and complements.
  3. positive strand in the negative direction is SuccessablesGAAC+-.bas, looking for GAACT, 2, GAACT at 3460, GAACT at 1685, and complements.
  4. positive strand in the positive direction is SuccessablesGAAC++.bas, looking for GAACT, 2, GAACT at 4131, GAACT at 4016, and complements.
  5. complement, negative strand, negative direction is SuccessablesGAACc--.bas, looking for CTTGA, 2, CTTGA at 3460, CTTGA at 1685.
  6. complement, negative strand, positive direction is SuccessablesGAACc-+.bas, looking for CTTGA, 2, CTTGA at 4016, CTTGA at 4131.
  7. complement, positive strand, negative direction is SuccessablesGAACc+-.bas, looking for CTTGA, 13, CTTGA at 4294, CTTGA at 4012, CTTGA at 3571, CTTGA at 3401, CTTGA at 3242, CTTGA at 3103, CTTGA at 2714, CTTGA at 2580, CTTGA at 2379, CTTGA at 2127, CTTGA at 1300, CTTGA at 1009, CTTGA at 843.
  8. complement, positive strand, positive direction is SuccessablesGAACc++.bas, looking for CTTGA, 2, CTTGA at 4048, CTTGA at 1951.
  9. inverse complement, negative strand, negative direction is SuccessablesGAACci--.bas, looking for AGTTC, 3, AGTTC at 4178, AGTTC at 4027, AGTTC at 3844, and complements.
  10. inverse complement, negative strand, positive direction is SuccessablesGAACci-+.bas, looking for AGTTC, 3, AGTTC at 4200, AGTTC at 2954, AGTTC at 1987, and complements.
  11. inverse complement, positive strand, negative direction is SuccessablesGAACci+-.bas, looking for AGTTC, 6, AGTTC at 4417, AGTTC at 4175, AGTTC at 4024, AGTTC at 1177, AGTTC at 719, AGTTC at 253, and complements.
  12. inverse complement, positive strand, positive direction is SuccessablesGAACci++.bas, looking for AGTTC, 2, AGTTC at 2615, AGTTC at 2508.
  13. inverse, negative strand, negative direction, is SuccessablesGAACi--.bas, looking for TCAAG, 6, TCAAG at 4417, TCAAG at 4175, TCAAG at 4024, TCAAG at 1177, TCAAG at 719, TCAAG at 253.
  14. inverse, negative strand, positive direction, is SuccessablesGAACi-+.bas, looking for TCAAG, 2, TCAAG at 2615, TCAAG at 2508.
  15. inverse, positive strand, negative direction, is SuccessablesGAACi+-.bas, looking for TCAAG, 3, TCAAG at 4178, TCAAG at 4027, TCAAG at 3844.
  16. inverse, positive strand, positive direction, is SuccessablesGAACi++.bas, looking for TCAAG, 3, TCAAG at 4200, TCAAG at 2954, TCAAG at 1987.

GAAC UTRs

  1. Negative strand, negative direction: GAACT at 4294, AGTTC at 4178, AGTTC at 4027, GAACT at 4012, AGTTC at 3844, GAACT at 3571, GAACT at 3401, GAACT at 3242, GAACT at 3103.
  2. Positive strand, negative direction: AGTTC at 4417, AGTTC at 4175, AGTTC at 4024, GAACT at 3460.

GAAC proximal promoters

  1. Negative strand, negative direction: GAACT at 2714.


  1. Negative strand, positive direction: AGTTC at 4200.
  2. Positive strand, positive direction: GAACT at 4131, GAACT at 4016.

GAAC distal promoters

  1. Negative strand, negative direction: GAACT at 2580, GAACT at 2379, GAACT at 2127, GAACT at 1300, GAACT at 1009, GAACT at 843.
  2. Positive strand, negative direction: GAACT at 1685, AGTTC at 1177, AGTTC at 719, AGTTC at 253.


  1. Negative strand, positive direction: GAACT at 4048, AGTTC at 2954, AGTTC at 1987, GAACT at 1951.
  2. Positive strand, positive direction: AGTTC at 2615, AGTTC at 2508.

GAAC element random dataset samplings

  1. GAACr0: 6, GAACT at 3494, GAACT at 3230, GAACT at 2501, GAACT at 1331, GAACT at 1302, GAACT at 897.
  2. GAACr1: 4, GAACT at 1035, GAACT at 940, GAACT at 471, GAACT at 95.
  3. GAACr2: 3, GAACT at 4058, GAACT at 3023, GAACT at 2237.
  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.

GAACr UTRs

  1. GAACr0: GAACT at 3494, GAACT at 3230.

RDr core promoters

RDr proximal promoters

GAACr distal promoters

  1. GAACr0: GAACT at 2501, GAACT at 1331, GAACT at 1302, GAACT at 897.


  1. GAACr1: GAACT at 1035, GAACT at 940, GAACT at 471, GAACT at 95.

GAAC element analysis and results

Main article: Complex locus A1BG and ZNF497 § GAAC elements

The GAAC portion of the GAAC element is the inverse of the Homeobox motif.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Upinder Singh, Joshua B. Rogers (August 21, 1998). "The Novel Core Promoter Element GAAC in the hgl5 Gene of Entamoeba histolytica Is Able to Direct a Transcription Start Site Independent of TATA or Initiator Regions". The Journal of Biological Chemistry. 273 (34): 21663–8. doi:10.1074/jbc.273.34.21663. Retrieved 2013-02-13.
  2. ↑ "genetics". San Francisco, California: Wikimedia Foundation, Inc. April 16, 2014. Retrieved 2014-05-07.
  3. ↑ 3.0 3.1 Tamar Juven-Gershon, Jer-Yuan Hsu, Joshua W. M. Theisen, and James T. Kadonaga (June 2008). "The RNA Polymerase II Core Promoter – the Gateway to Transcription". Current Opinion in Cell Biology. 20 (3): 253–9. doi:10.1016/j.ceb.2008.03.003. Retrieved 2013-02-13.
  4. ↑ Serge Saxonov, Paul Berg, and Douglas L. Brutlag (January 31, 2006). "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proceedings of the National Academy of Sciences USA. 103 (5): 1412–7. doi:10.1073/pnas.0510310103. Retrieved 2013-02-13.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 Catherine Terraz, Gaelle Brideau, Pierre Ronco and Jérôme Rossert (May 24, 2002). "A Combination of cis-Acting Elements Is Required to Activate the Pro-α1(I) Collagen Promoter in Tendon Fibroblasts of Transgenic Mice". The Journal of Biological Chemistry. 277 (21): 19019–26. doi:10.1074/jbc.M200125200. Retrieved 2013-02-13.

Further reading

External links

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