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Gene transcriptions/Elements/GAACs

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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]

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

Genetics

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Main resource: Genetics
 
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

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Main resources: Gene transcriptions/Promoters and Promoters
 
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

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Main resource: Consensus sequences

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

Dispersed promoters

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Main resources: Gene transcriptions/Promoters/Dispersed 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

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Main resources: Gene transcriptions/General factors/II Ds 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

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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

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Main resources: Genes/Human and 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

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Main resource: Hypotheses
  1. A1BG is not transcribed by a GAAC element.

Samplings

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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 3'-G-A-A-C-T-5', 13, 3'-GAACT-5', 843, 3'-GAACT-5', 1009, 3'-GAACT-5', 1300, 3'-GAACT-5', 2127, 3'-GAACT-5', 2379, 3'-GAACT-5', 2580, 3'-GAACT-5', 2714, 3'-GAACT-5', 3103, 3'-GAACT-5', 3242, 3'-GAACT-5', 3401, 3'-GAACT-5', 3571, 3'-GAACT-5', 4012, 3'-GAACT-5', 4294,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGAAC-+.bas, looking for 3'-G-A-A-C-T-5', 1, 3'-GAACT-5', 609,
  3. positive strand in the negative direction is SuccessablesGAAC+-.bas, looking for 3'-G-A-A-C-T-5', 2, 3'-GAACT-5', 1685, 3'-GAACT-5', 3460,
  4. positive strand in the positive direction is SuccessablesGAAC++.bas, looking for 3'-G-A-A-C-T-5', 2, 3'-GAACT-5', 577, 3'-GAACT-5', 692,
  5. complement, negative strand, negative direction is SuccessablesGAACc--.bas, looking for 3'-C-T-T-G-A-5', 2, 3'-CTTGA-5', 1685, 3'-CTTGA-5', 3460,
  6. complement, negative strand, positive direction is SuccessablesGAACc-+.bas, looking for 3'-C-T-T-G-A-5', 2, 3'-CTTGA-5', 577, 3'-CTTGA-5', 692,
  7. complement, positive strand, negative direction is SuccessablesGAACc+-.bas, looking for 3'-C-T-T-G-A-5', 13, 3'-CTTGA-5', 843, 3'-CTTGA-5', 1009, 3'-CTTGA-5', 1300, 3'-CTTGA-5', 2127, 3'-CTTGA-5', 2379, 3'-CTTGA-5', 2580, 3'-CTTGA-5', 2714, 3'-CTTGA-5', 3103, 3'-CTTGA-5', 3242, 3'-CTTGA-5', 3401, 3'-CTTGA-5', 3571, 3'-CTTGA-5', 4012, 3'-CTTGA-5', 4294,
  8. complement, positive strand, positive direction is SuccessablesGAACc++.bas, looking for 3'-C-T-T-G-A-5', 1, 3'-CTTGA-5', 609,
  9. inverse complement, negative strand, negative direction is SuccessablesGAACci--.bas, looking for 3'-A-G-T-T-C-5', 3, 3'-AGTTC-5', 3844, 3'-AGTTC-5', 4027, 3'-AGTTC-5', 4178,
  10. inverse complement, negative strand, positive direction is SuccessablesGAACci-+.bas, looking for 3'-A-G-T-T-C-5', 1, 3'-AGTTC-5', 761,
  11. inverse complement, positive strand, negative direction is SuccessablesGAACci+-.bas, looking for 3'-A-G-T-T-C-5', 6, 3'-AGTTC-5', 253, 3'-AGTTC-5', 719, 3'-AGTTC-5', 1177, 3'-AGTTC-5', 4024, 3'-AGTTC-5', 4175, 3'-AGTTC-5', 4417,
  12. inverse complement, positive strand, positive direction is SuccessablesGAACci++.bas, looking for 3'-A-G-T-T-C-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesGAACi--.bas, looking for 3'-T-C-A-A-G-5', 6, 3'-TCAAG-5', 253, 3'-TCAAG-5', 719, 3'-TCAAG-5', 1177, 3'-TCAAG-5', 4024, 3'-TCAAG-5', 4175, 3'-TCAAG-5', 4417,
  14. inverse, negative strand, positive direction, is SuccessablesGAACi-+.bas, looking for 3'-T-C-A-A-G-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesGAACi+-.bas, looking for 3'-T-C-A-A-G-5', 3, 3'-TCAAG-5', 3844, 3'-TCAAG-5', 4027, 3'-TCAAG-5', 4178,
  16. inverse, positive strand, positive direction, is SuccessablesGAACi++.bas, looking for 3'-T-C-A-A-G-5', 1, 3'-TCAAG-5', 761.

See also

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References

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  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. http://www.jbc.org/content/273/34/21663.full. 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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586601/. 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. http://www.pnas.org/content/103/5/1412.full. 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. http://www.jbc.org/content/277/21/19019.long. Retrieved 2013-02-13. 

Further reading

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