Acta Scientific Medical Sciences (ASMS)(ISSN: 2582-0931)

Research Article Volume 8 Issue 10

Correlation between Eukaryotic Noncoding QED Genetic Codes and Cis-Regulatory Elements

Rama Shankar Singh*

Gen-Med R&D, LLC, Orlando, FL 32817, USA

*Corresponding Author: Rama Shankar Singh, Gen-Med R&D, LLC, Orlando, FL 32817, USA. Email: gen-med@comcast.net

Received: July 25, 2024; Published: September 18, 2024

Abstract

The eukaryotic genome contains protein-encoding genes and cis-regulatory elements in the promoter regions of genes that control protein synthesis to maintain cellular homeostasis. Gene variants and protein synthesis errors produce dysfunctional proteins that cause disease. Thus, the genetic code and regulatory elements are closely linked to diseases. Eukaryotic nuclei contain the material responsible for heredity (DNA), but protein synthesis occurs elsewhere; genetic information is transmitted via transcription and splicing to the cytoplasm prior to protein synthesis. Cis-regulatory elements are found in eukaryotes but not in prokaryotes. The triplet genetic coding system proposed in 1963 was based on cells lacking introns, as introns were unknown until 1977, and lacking the control systems found in eukaryotes. The eukaryotic QED (quadruplet expanded DNA) genetic code model [1] is the first and only distinct genetic model for eukaryotes. The QED code has twenty independent encoding codons and thirty-five independent noncoding codons. Among the thirty-five noncoding QED codons are TATA, (CG) (CG), GC-rich, YCAY (Y-T or C), UAGG, GCAU, AT-rich, CG-rich, ATCG, START, and STOP. Here, we establish the applicable regulatory roles of noncoding QED codons like cis-regulatory elements by comparing their sequences. Some cis-regulatory elements, such as TATA and CAAT, located in the upstream promotor region are known to be involved in the initiation of transcription. These bases are identical to QED noncoding bases. More than twenty cis-regulatory elements and QED noncoding codon bases closely coincide and are listed in the text. Thus, it is reasonable to accept the application of the QED noncoding codon system to eukaryotic regulatory elements. Consequently, the noncoding QED code provides opportunities to correct dysfunctional proteins and identify cures for human diseases. A case in point is the tandem repeat (TR) neurodegenerative Huntington’s disease. The triplet codons CAA and CAG encode glutamine (Gln); however, only TR CAG causes Huntington's disease without forming polyglutamine. Huntington's disease is explained by the QED code, in which CAA encodes Gln, but CAG is noncoding and does not promote polyglutamine formation but causes the disease.

 Keywords: QED Code; Eukaryote; Prokaryote; Encoding; Noncoding; Cis-Elements; TATA; CAAT; CAG; Tandem Repeat; Human Diseases

References

  1. Rama Shankar Singh. “Quadruplet Expanded DNA (QED) Genetic Code for Eukaryotic Cells”. Acta Scientific Medical Sciences12 (2023): 70-82.
  2. Crick F H. “On the genetic code”. Science 139 (1963): 461-464.
  3. Berget SM., et al. “Spliced segments at the 5' terminus of adenovirus 2 late mRNA”. Proceedings of the National Academy of Sciences of the United States of America 74 (1977): 3171-3175.
  4. Roberts RJ and Sharp P A. "For their discoveries of split genes" The Nobel Prize in physiology or medicine 1993”. NobelPrize.org. Nobel Prize outreach AB 2022.
  5. Kornberg RD. “The Nobel Prize in chemistry 2006”. NobelPrize.org. Nobel Prize (2022).
  6. Wang Z and Burge C B. “Splicing regulation: From a parts list of regulatory elements to an integrated splicing code RNA”. 14 (2008): 802-813.
  7. Nilsion TW., et al. “Expansion of the eukaryotic proteome by alternative splicing”. Nature 463 (2010): 457-463.
  8. Jacob F and Monod J. “Genetic regulatory mechanisms in the synthesis of proteins”. Journal of Molecular Biology 3 (1961): 318-356.
  9. Jacob F., et al. “The Nobel Prize in physiology or medicine 1965”. NobelPrize.org. Nobel Prize outreach AB 2022 (1965).
  10. Horton CA., et al. “Short tandem repeats bind transcription factors to tune eukaryotic gene expression”. Science 381 (2023): 1304-1321.
  11. Maston GA., et al. “Transcriptional regulatory elements in the human genome”. Annual Review of Genomics and Human Genetics 7 (2006): 29-59.
  12. Novoyatleva T., et al. “Pre-mRNA missplicing as a cause of human disease”. Progress in Molecular and Subcellular Biology 44 (2006): 27-46.
  13. Ward A J and Cooper TA. “The pathobiology of splicing”. Journal of Pathology 220 (2010): 152-163.
  14. “Genetic Modifiers of Huntington’s disease (GeM -HD) Consortium, (lead contact -James F. Gusella), CAG Repeat Not Polyglutamine Length Determines Timing of Huntington’s Disease Onset”. Cell 178 (2019): 887-900.
  15. Hannan A J. “Tandem repeats mediating genetic plasticity in health and disease”. Nature Reviews 19 (2018): 287-298.
  16. Gall-Duncan T., et al. “Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences”. Cold Spring Harbor Laboratory Press 32 (2022): 1-27.
  17. Carl G., et al. “Hold out the genome: a roadmap to solving the cis-regulatory code”. Nature 625 (2024): 41-50.
  18. Wang J and Agarwal V. “How DNA encodes the start of transcription”. Science 384 (2024): 382-383.
  19. Dudnyk K., et al. “Sequence basis of transcription initiation in the human genome”. Science 384 (2024): 409-425.
  20. White MA. “Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed Sequences”. Genomics 106 (2015): 165-170.
  21. Gagniuc P and Ionescu-Tirgoviste C. “Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters”. BMC Genomics 13 (2012): 512.
  22. Liu X., et al. “TiGER: a database for tissue-specific gene expression and regulation”. BMC Bioinformation 9 (2008): 271.
  23. Holley RW., et al. “The Nobel Prize in physiology or medicine 1968”. NobelPrize.org. Nobel Prize outreach AB 2022 (2022).
  24. David Baltimore., et al. “The 1975 Nobel Prize in Physiology or Medicine "for their discoveries concerning the interaction between tumours viruses and the genetic material of the cell".
  25. Lewis M. “The lac repressor, C. R”. Biologies 328 (2005): 521-548.

Citation

Citation: Rama Shankar Singh. “Correlation between Eukaryotic Noncoding QED Genetic Codes and Cis-Regulatory Elements”.Acta Scientific Medical Sciences 8.10 (2024): 89-96.

Copyright

Copyright: © 2024 Rama Shankar Singh. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.




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