John H. Frenster ^{1, @} and  Jeannette A. Hovsepian ^{2, @}
Departments of  ¹Medicine and  ² Radiology,
Stanford University School of Medicine, Stanford, California 94305

^@ Present Address: Physicians’ Educational Series, Atherton, CA 94027-5446
Phone:  +1 650 367 6483;  Fax:  +1 650 364 1773;  E-mail:  frenster@euchromatin.net
* Supported in part by a USPHS Research Career Development Award (CA-17857) from the National Cancer Institute to JHF.

Queueing, renewal, and feedback have been quantitatively analyzed within enzyme, cellular and organ systems (http://www.euchromatin.org/systems1.htm), and can now be studied within gene systems. Recent data indicate that non-coding nuclear RNA species function as co-activators of eukaryotic gene transcription (Science 296:1260 (2002). Such RNA de-repressors are capable of forming RNA-RNA duplexes with the non-coding 5’ leaders of pre-mRNA that are liberated during splicing of pre-mRNA. As transcription and splicing proceed, increasing concentrations of gene-specific 5’ leader RNA accumulate within the cell nucleus, and compete with gene-specific promoter DNA for gene-specific de-repressor RNA. Because RNA-RNA duplexes are thermodynamically more stable than are DNA-RNA duplexes, rising concentrations of gene-specific 5’ leader RNA capture gene-specific de-repressor RNA from the DNA promoter site, forming RNA-RNA duplexes, and reducing DNA transcription initiation at the promoter site. Base-sequence pairing may be restricted to as little as 10 nucleotides in length of RNA or DNA, and may be shared among promoters at different gene sites, allowing for cross-activation of several promoters from the same population of de-repressor RNA. Such cross-activation of multiple genes, with feedback inhibition by RNA-RNA duplex formation after excessive transcription, is compatible with the original version (Science 165: 349 (1969) of multi-gene regulation theory.

Introduction:

Systems biology involves the application of computer, engineering and mathematical methods to the analysis of the complexity, throughput, robustness, modularity, feedback, and fragility of biological systems (Csete and Doyle, 2002). The focus of such studies can include the large number of interacting variables, the queueing and renewal of throughputs (Frenster, 1965a), the activity of superimposed feedback and feed-forward  control systems, and the high selectivity and specificity of multi-gene and metabolic systems (Ravasz et al, 2002). The techniques include large array synchronous sampling, modeling, and simulation of the observed biological behavior curves.

Selective gene transcription is a complex genetic molecular process, involving up to 100 distinct molecular species at each initiation site. It has been modeled for mammalian cells (Frenster, 1965b), and these data have been incorporated into a multi-gene regulation model (Britten and Davidson, 1969). The special features of feedback at single genes have been added (Frenster and Herstein, 1973), and the most recent results for gene transcription in bacteria have been modeled (Grundy, et al, 2002).
...
Conclusions:

A study of previous models of gene regulation in eukaryotes reveals increasing support for the role of RNA activators of transcription initiation, and for the functional significance of the DNA template strand 5’ to the transcription start locus, known as 5’-leader loci.

New studies in bacteria have revealed a 5’-leader RNA that plays the major role in feedback control of single-locus antitermination transcription (Grundy FJ, et al, 2002). “The transcripts of genes regulated by this mechanism contain a 200- to 300-nt untranslated leader that includes a factor-independent (intrinsic) transcription termination signal and a competing anti-terminator structure”. A single codon pairing between the two relevant 5’-leader RNA species may be sufficient for a full effect. This RNA-RNA feedback mechanism “provides a further example of the ability of RNA to carry out complex interactions in the absence of protein-cofactors”.

5’-leader DNA and the corresponding 5’-leader RNA  have been previously identified in eukaryote systems as operon sites and operon RNA involved in feedback control systems at specific gene loci (Herstein PR, and Frenster JH, 1972). Although gene clusters and perhaps functional operons have recently been identified in eukaryote systems (Blumenthal T, et al, 2002), most eukaryote promoter sites involve cis and/or trans  relationships to single gene loci (Britten RJ, and Davidson EH, 1969).

RNA feedback mechanisms operating at single gene loci exist in eukaryote and prokaryote gene systems, and may be further analyzed by biological feedback analysis methods (Csete ME, and Doyle JC, 2002).

00. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, and Barabasi A-L, “Hierarchical Organization of     Modularity in Metabolic Networks”, Science vol. 297, no. 5586, pp. 1551-1555 (August 30, 2002).

0. Csete ME, and Doyle JC, “Reverse Engineering of Biological Complexity”, Science vol. 295, no. 5560, pp. 1664-1669 (March 1, 2002).

1. Grundy FJ, Winkler WC, and Henkin TM, "tRNA-Mediated Transcription Antitermination in vitro: Codon-Anticodon Pairing Independent of the Ribosome", Proc. Natl. Acad. Sci. USA, vol. 99, no. 17, pp. 11121-11126 (August 20, 2002).

2. Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL,
Duke K, Kiraly M, and Kim SK, "A Global Analysis of Caenorhabditis elegans Operons".

3. Young BA, Gruber TM, and Gross CA, "Views of Transcription Initiation".

4. Jelinek W, and Leinwand L, "Low molecular weight RNAs hydrogen-bonded to nuclear and
     cytoplasmic poly(A)-terminated RNA from cultured Chinese hamster ovary cells", Cell 15, 205 (1978).

5. Frenster JH, "Nuclear Polyanions as De-repressors of Synthesis of Ribonucleic Acid".

6. Frenster JH, "A Model of Specific De-repression within Interphase Chromatin".

7. Britten RJ, and Davidson EH, "Gene Regulation for Higher Cells: A Theory".

8. Herstein PR, and Frenster JH, "Mated Models of Gene Regulation in Eukaryotes".

9. Frenster JH, and Herstein PR, "Gene De-Repression".

10. Frenster JH, “Analysis of Queueing and Renewal within Human Systems”.

11. Frenster JH, "Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".

12. Hovsepian JA, and Frenster JH, "RNA-Induced Melting of DNA during Selective Gene Transcription".