"Models of successive levels of resolution during individual gene transcription".

John H. Frenster ¹, and Jeannette A. Hovsepian ²,

Divisions of  ¹ Medical Oncology, and of  ² Diagnostic Imaging,
Stanford University School of Medicine, Stanford, California 94305, USA
Phone: 650/367-6483, e-mail:  frensterjh@aol.com ,  hovsepianj@aol.com , http://www.euchromatin.net/

Supported in part by a USPHS Research Career Development Award (CA-17857) from the National Cancer Institute.

Network simulation studies require integration of gene activity at several levels. Recent and on-going studies have revealed three levels of resolution showing pervasive interleaved transcription (Gingeras TR, "Mapping the strand-specific transcriptome of fission yeast", Nature Genetics 40: 935 (August, 2008). These studies have included the levels of multiple gene clusters, of overlapping primary transcripts, and of individual gene loci (ibid.). Newer studies have suggested a deeper level of resolution distinguishing transcription on one DNA strand from that on the opposing DNA strand within a single gene locus (Dutrow N, et al., "Dynamic transcriptome of S. pombe shown by RNA-DNA hybrid mapping", Nature Genetics 40: 977 (August, 2008). The products of such transcription include both coding and non-coding RNAs, sense and antisense orientations, and single and paired duplexes. Among the latter, the increasing importance of RNA-DNA and RNA-RNA duplexes during regulation of gene transcription is being recognized as crucial to gene selectivity and gene specificity. The recent studies of RNA-RNA  interactions within promoter sites and enhancer sites of the same gene product exemplifies such research (Schwartz JC, et al., "Antisense transcripts are targets for activating small RNAs", Nature Structural & Molecular Biology, 15: 842 (August, 2008), as does the study of individual genes on one chromosome and throughout the euchromatin of one cell (Mikkelsen TJ, et al., "Dissecting direct reprogramming through integrative genomic analysis", Nature 454: 49 (July 3. 2008). A preliminary network simulation of these data for several linked genes reveals driving forces from initiation levels which determine kinetics thoughout the particular gene network. These diverse data  re-assert the need and importance of high-resolution isolation techniques and comprehensive composite structures in analyzing network interactions within intact living cells.

References for Levels:

1a. Frenster JH, and Hovsepian JA,
"DNase-I Ultrastructural Probe Sites and Kissing Chromosomes".

1b. Tkacik G, Callan, CGJr , and Bialek W,
"Information flow and optimization in transcriptional regulation".

1c. Frenster JH, and Hovsepian JA, "Kissing Chromosomes and Paired Sense-Antisense RNA Synthesis".

2. Lanctôt C, Cheutin T, Cremer M, Cavalli G, and Cremer T, "Dynamic genome architecture in the nuclear space:  regulation of gene expression in three dimensions".

3. Frenster JH, and Hovsepian JA, "Ultrastructure  of Closed Loops within Euchromatin of Isolated Lymphocyte Nuclei".

4a. Hovsepian JA, and Frenster JH,
"Chromosome-Chromosome Contact Points and Paired Sense-Antisense RNA Synthesis".

4b. Frenster JH, and Hovsepian JA, "Ultrastructure of Euchromatin Contact Points between the Closed Loops of Adjacent Interphase Chromosomes".

5. Frenster JH, and Hovsepian JA,
"DNA-DNA Tetraplex Model of Paired Sense-Antisense RNA Synthesis".

6a. Place RF, Li L-C, Pookot D, Noonan EJ, and Dahiya R, "MicroRNA-373 induces expression of genes with complementary promoter sequences".

6b. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, and Rubin EM, "In vivo enhancer analysis of human conserved non-coding sequences".

7. Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T,  and  Ohta K,
"Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs".

8. Schwartz JC, Younger ST, Nguyen N-B, Hardy DB, Monia BP, Corey DR, and Janowski BA,
"Antisense transcripts are targets for activating small RNAs".

9. Durniak KJ, Bailey S, and Steitz TA,
"The Structure of a Transcribing T7 RNA Polymerase in Transition from Initiation to Elongation".

10a. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, and  Tyagi S,
"Imaging individual mRNA molecules using multiple singly labeled probes".

10b. Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, and Cairns BR,
"Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping".

11. Ebisuya M, Yamamoto T, Nakajima M,  and  Nishida E,
"Ripples from neighbouring transcription".

12. Singh J, Saxena A, Christodoulou J, and Ravine D,
"MECP2 genomic structure and function: insights from ENCODE".

13. Veyrieras J-B, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, and Pritchard JK,
"High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation".

14a. Lin S-L, Chang DC, Chang-Lin S, Lin C-H, Wu DTS, Chen DT, and Ying S-Y,
"Mir-302 reprograms human skin cancer cells into a pluripotent ES-cell-like state".

14b. Kumar MS, Erkeland SJ, Pester RE, Chen CY, Ebert MS, Sharp PA, and  Jacks T.,
"Suppression of non-small cell lung tumor development by the let-7 microRNA family".

14c. DeCarvalho S, "Effect of RNA from Normal Human Marrow on Leukaemic Marrow In-Vivo".

15a. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu A-L, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, and  Humphries RK,
"In-depth characterization of the microRNA transcriptome in a leukemia progression model".

15b. Frenster JH, and Hovsepian JA, "Models of  Embryonic RNA Initiating and Reverting Adult Neoplasms".

16. Sarrió D, Rodriguez-Pinilla SM, Hardisson D, Cano A, Moreno-Bueno G, and Palacios J,
"Epithelial-Mesenchymal Transition in Breast Cancer Relates to the Basal-like Phenotype",
Cancer Research 68, 989-997, February 15, 2008.

17a. Prabhakar S, Visel A,  Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, FitzPatrick DR, Afzal V, Pennacchio LA, Rubin EM, and Noonan JP,
"Human-Specific Gain of Function in a Developmental Enhancer".

17b. Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, and Haussler D,
"An RNA gene expressed during cortical development evolved rapidly in humans".

18a.Tay Y, Zhang J, Thomson AM, Lim B,  and  Rigoutso  I,
"MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation".

18b. Ma J, Ratan A, Raney BJ, Suh BB, Miller W, and Haussler D,
"The infinite sites model of genome evolution".

19. Frenster JH, "Selective control of DNA helix openings during gene regulation".

20a. Frenster JH, "Single-Cell Analysis of DNase I-Sensitive Sites during Neoplastic and Normal Cell Differentiation within Human Bone Marrow."

20b. Frenster JH, Allfrey VG, and Mirsky AE, "Repressed and Active Chromatin Isolated from Interphase Lymphocytes".

21. Chen B, Dodge ME, Tang W, Lu J, Ma Z, Fan C-W, Wei S, Hao W, Kilgore J, Williams NS, Roth MG, Amatruda JF, Chen C, and  Lum L, "Small molecule–mediated disruption of Wnt-dependent signaling in tissue regeneration and cancer".

22a.  Hebert C, Norris K, Scheper MA, Nikitakis N, and Sauk JJ, "High mobility group A2 is a target for miRNA-98 in head and neck squamous cell carcinoma",

22b. Frenster JH, "Nuclear polyanions as de-repressors of synthesis of ribonucleic acid".

23. Frenster JH, "Nuclear polyanions as de-repressors of synthesis of ribonucleic acid".

24.  Frenster JH, "Ultrastructure and function of  heterochromatin and euchromatin".

25a. Frenster JH, "Selective gene de-repression by de-repressor RNA".

25b. Storz G, "An expanding universe of non-coding RNAs".

Reference:

Frenster JH, "Single-Cell Analysis of DNase I-Sensitive Sites during Neoplastic and Normal Cell Differentiation within Human Bone Marrow."

The interior of the DNA double helix is hydrophobic, and this force is altered in that portion of the DNA molecule which opens to form the transcription bubble:

1. Herskovits TT, Singer SJ, and Guiduschek EP, Arch. Biochem. Biophys. 94: 99 (1961);
2. Sinanoglu O, and Abdulnur S, Fed. Proc. 24: Suppl. 15, S 12 (1965).

Those interior portions of RNA molecules which form double helices are similarly hydrophobic, and this force is also altered when the RNA molecule opens.

Intracellular foci of hydrophobic forces are currently under intense investigation:

1. Nicolas Giovambattista, Carlos F. Lopez, Peter J. Rossky, and Pablo G. Debenedetti,
"Hydrophobicity of protein surfaces: Separating geometry from chemistry",
 PNAS  February 19, 2008   vol. 105  no. 7  2274-2279

2. Jeetain Mittal and Gerhard Hummer,
"Static and dynamic correlations in water at hydrophobic interfaces",
    Published online before print December 11, 2008, doi: 10.1073/pnas.0809029105
http://www.pnas.org/content/early/2008/12/11/0809029105.abstract?etoc

A variety of physical forces bind primary ligands to DNA or to other transcription factor ligands. The hydrophobic forces include the hydrophobic solute-solvent interactions between DNA and water (19), and  the stacking (van der Waal's) interactions between the successive bases of the same or opposing DNA strand (22).

The hydrophilic forces include the hydrogen bond interactions between the complementary bases of the opposing DNA strands (20), and the electrostatic charge interactions between the phosphate groups of the same or opposing DNA strands (21).

"Recent investigations have revealed that template DNA is found natively in the form of single-stranded loops during the active transcription of selected portions of the genome in higher organisms (1, 2). Conversely, during repression of such transcription the DNA is found natively in the form of double-stranded helices (1, 2). A variety of organic molecules which function in vivo as inhibitors or stimulators of RNA synthesis within pre-selected portions of the genome (2) have been shown to be capable of a reversible physical binding to DNA in vivo or in vitro. Each of these inhibitors or stimulators binds preferentially to either single-stranded or to double-stranded DNA. In every case for which adequate data are available (Table 2), a strong correlation exists between the form of DNA preferred for binding and the effect of the ligand on RNA synthesis within pre-selected portions of the genome.

Table 2. Correlation of the Preferred Form of DNA for Binding with the Effect on RNASynthesis.

Primary DNA Ligand	Preferred Form of DNA for Binding	Effect of Ligand on RNA Synthesis
.	.	.
Histones	Double-Stranded (ref. 3)	Inhibition (refs. 4, 5)
Polylysine	Double-Stranded (ref. 3)	Inhibition (ref. 5)
Actinomycin D	Double-Stranded (ref. 6)	Inhibition (ref. 7)
Acridine Orange	Double-Stranded (ref. 8)	Inhibition (ref. 8)
Chloroquine	Double-Stranded (ref. 9)	Inhibition (ref. 9)
Testosterone	Single-Stranded (ref. 10)	Stimulation (ref. 11)
Estradiol	Single-Stranded (ref. 10)	Stimulation (ref. 12)
Methylcholanthrene	Single-Stranded (ref. 13)	Stimulation (ref. 14)
RNA Polymerase II	Single-Stranded (ref. 15)	Stimulation (ref. 16)
Antisense RNA	Single-Stranded (ref. 17)	Stimulation (ref. 18)

These strong correlations suggest that such primary ligands may exert their characteristic effects on RNA synthesis by preferentially stabilizing either the inactive helical form or the active loop form of DNA (2, 10) in the equilibrium:

Secondary ligands do not bind DNA directly, but bind primary ligands in a ligand-counter ligand complex.

Ligand References:

The mechanisms of such preferential binding to either double-stranded helical DNA or to single-stranded loop DNA are little understood. Preliminary thermodynamic analyses have revealed that the equilibrium between the helical and the loop forms of DNA can be shifted during binding by an effect of the ligand on one or more of the physical forces existing within the DNA-solvent system. These forces include:

(a). The hydrophobic solute-solvent interactions between DNA and water (19);

(b). The hydrogen bond interactions between the complementary bases of the opposing DNA strands (20);

(c). The electrostatic charge interactions between the phosphate groups of the same or opposing DNA strands (21);

(d). The stacking (van der Waal's) interactions between the successive bases of the same or opposing DNA strand (22).

In addition, the ability of particular ligands to:

(e). Cross-link opposing DNA strands (23), or to:

(f). Fit sterically into certain regions of the DNA molecule (23)

is of importance in the inhibition or stimulation of RNA synthesis. Thus, both histone-type inhibitors and actinomycins bind preferentially to double-stranded helical DNA by utilizing properties (e) and (f) (23). In addition, histones alter physical force (c) (3), while actinomycins may alter forces (a), (c) and (d) (6). By contrast, both testosterone-type stimulators and oestradiol-type stimulators bind preferentially to single-stranded loop DNA by utilizing property (f) (24), and by altering physical forces (a) and (d) (24). Before such inhibitors or stimulators can bind to DNA and alter the rates of RNA synthesis they must often be first concentrated within the particular sensitive tissue by specific, non-DNA binding agents (12, 25).

All the foregoing inhibitory or stimulatory ligands (Table 2) except antisense RNA are molecules which are capable of reacting with all portions of the DNA genome non-selectively. RNA by contrast is capable of a selective interaction with specific portions of the DNA genome (17). It is this selective ability which appears to be the basis for its role as the agent of specific de-repression of RNA synthesis during selective transcription of the genome (1, 2, 18). In a similar fashion, polyoma viral DNA binds preferentially to single-stranded host DNA (26). The result of such oncogenic viral DNA interaction with the host DNA genome is a de-repression of host DNA synthesis and of host enzyme synthesis (27, 28). A concurrent selective de-repression of host RNA synthesis is also likely (27).

Ligand References:

1. Frenster JH, Nature 206: 1269 (1965).

2. Frenster JH, Nature 208: 894 (1965);
Frenster JH, in "The Chromosomes: Structural and Functional Aspects", edit. by Dawe CJ, and Yerganian G, (Williams and Wilkins, Inc., Baltimore, 1965).

3. Akinrimisi EO, Bonner J, and Ts'o POP, J. Mol. Biol. 11: 128 (1965).

4. Huang RC, and Bonner J, Proc. U.S. Nat. Acad. Sci. 48: 1216 (1962);
Allfrey VG, and Mirsky AE, Proc. U.S. Nat. Acad. Sci. 48: 1590 (1962).

5. Allfrey VG, Littau VC, and Mirsky AE, Proc. U.S. Nat. Acad. Sci. 49: 414 (1963).

6. Haselkorn R, Science 143: 682 (1964);
Reich E, Science 143: 684 (1964);
Gellert M, Smith CE, Neville D, and Felsenfeld G, J. Mol. Biol. 11: 445 (1965).

7. Reich E, Franklin RM, Shatkin AJ, and Tatum EL, Proc. U.S. Nat. Acad. Sci. 48: 1238 (1962).

8. Lerman LS, J. Cell. Comp. Physiol., Suppl. 1, 1(1964).

9. Cohen SN, and Yielding LK, J. Biol. Chem. 240: 3123 (1965);
Cohen SN, and Yielding LK, Proc. U.S. Nat. Acad. Sci. 54: 521 (1965).

10. Ts'o POP, and Lu P, Proc. U.S. Nat. Acad. Sci. 51: 17 (1964).

11. Kochakian CD, Hill J, and Harrison DG, Endocrinology 74: 635 (1964);
Loeb PM, and Wilson JD, Clin. Res. 13: 45 (1965).

12. Talwar GP, Segal SJ, Evans A, and Davidson OW, Proc. U.S. Nat. Acad. Sci. 52: 1059 (1964).

13. Robert F, J. Chim. Phys. 60: 684 (1963).

14. Loeb LA, and Gelboin HV, Proc. U.S. Nat. Acad. Sci. 52: 1219 (1964).

15. Berg P, Kornberg RD, Fancher H, and Dieckmann M, Biochem. Biophys. Res. Comm. 18: 932 (1965).

16. Chamberlin M, and Berg P, Proc. U.S. Nat. Acad. Sci. 48: 81 (1962);
Chamberlin M, and Berg P, J. Mol. Biol. 8: 297 (1964).

17. Schildkraut CL, Marmur J, Fresco JR, and Doty P, J. Biol. Chem. 236: PC 2 (1961);
McCarthy BJ, and Hoyer BH, Proc. U.S. Nat. Acad. Sci. 52: 915 (1964).

18. Frenster JH, Nature 206: 680 (1965).

19. Herskovits TT, Singer SJ, and Guiduschek EP, Arch. Biochem. Biophys. 94: 99 (1961);
Sinanoglu O, and Abdulnur S, Fed. Proc. 24: Suppl. 15, S 12 (1965).

20.Watson JD, and Crick FHC, Nature 171: 737, 964 (1953).

21. Kotin L, J. Mol. Biol. 7: 309 (1963);
Schildkraut CL, and Lifson S, Biopolymers 3: 195 (1965).

22. Luzzati V, Mathis A, Masson F, and Witz J, J. Mol. Biol. 10: 28 (1964);
Holcombe DN, and Tinoco jun. I, Biopolymers 3: 121 (1965).

23. Wilkens MHF, Zubay G, and Wilson HR, J. Mol. Biol. 1: 179 (1959);
Luzzati V, and Nicolaieff A, J. Mol. Biol. 7: 142 (1963);
Hamilton LD, Fuller W, and Reich E, Nature 198: 538 (1963);
Lloyd PH, and Peacocke AR, Biochim. Biophys. Acta 95: 522 (1964).

24. Minck A, Scott JF, and Engel LL, Biochim. Biophys. Acta 26: 397 (1957).

25. Noteboom WD, and Gorski J, Arch. Biochem. Biophys. 111: 559 (1965).

26. Axelrod D, Habel K, and Bolton ET, Science 146: 1466 (1964).

27. Dulbecco R, Hartwell LH, and Vogt M, Proc. U.S. Nat. Acad. Sci. 53: 403 (1965).

28. Kit S, Dubbs DR, Anken M, and Melnick JL, J. Cell Biol. 27: 52A (1965)."

3D Mapping of Competing Ligand Factors during Single Gene Transcription.

Several layers of transcription factors are present during the selection and initiation phases of individual gene transcription. The DNA coding sequence within open-looped and/or paired euchromatin 10 nm microfibrils is exposed to a growing cluster of primary ligands to DNA . Primary ligands may encounter counter-ligands in their immediate vicinity, thus forming ligand-counter ligand complexes.

Hydrophobic ligands are bound preferably to single-stranded portions of DNA and/or RNA.

1. The first ligand layer consists of small RNA molecules, synthesized in  upstream or downstream cis- or trans- enhancer loci. Such enhancer RNAs find their preferred binding sites in complementary RNA molecules within the promoter regions of the selected gene.

2. The second layer finds the sense-DNA template already covered by the first layer of ligands. This second layer is also antagonized by intruding antisense-DNA kiss sequences on the same or other chromosomes within the cell. As a consequence, second layer ligands, whether they are  histones, RNAs, proteins, lipids, hormones, or drug molecules, may not gain or retain direct contact with the sense-DNA template during active gene transcription.

RNA Polymerase II and other necessary enzymes are recruited between the layers into the growing transcription clusters early in the initiation stage.

3, 4, and 5. The third, fourth and fifth layers include sequences for binding to other euchromatin, heterochromatin, and nuclear membrane sites, respectively.

1. Several layers of transcription factors are present during the selection and initiation phases of individual gene transcription. The DNA coding sequence within open-looped and/or paired euchromatin 10 nm microfibrils is exposed to a growing cluster of ligands to DNA. Primary ligands may encounter counter-ligands in their immediate vicinity, thus forming ligand-counter ligand complexes. Hydrophobic ligands are bound preferably to single-stranded portions of DNA and/or RNA.

2. The first ligand layer consists of small RNA molecules, synthesized in  upstream or downstream cis- or trans- enhancer loci. Such enhancer RNAs find their preferred binding sites in complementary RNA molecules within the promoter regions of the selected gene.

3. The second layer finds the sense-DNA template already covered by the first layer of ligands. This second layer is also antagonized by intruding antisense-DNA kiss sequences from the same or other chromosomes within the cell. As a consequence, second layer ligands, whether they are  histones, RNAs, proteins, lipids, hormones, or drug molecules, may not gain or retain direct contact with the sense-DNA template during active gene transcription.

4. RNA Polymerase II and other necessary enzymes are recruited between the layers into the growing transcription clusters  early in the initiation stage.

5. The third, fourth and fifth layers include sequences for binding to other euchromatin, heterochromatin, and nuclear membrane sites, respectively

In this new study of Transcription Clusters of ligands to DNA, it is demonstrated that the DNA transcription bubble is the scene for both hydrophobic and hydrophilic forces, engaged in intimate competition for binding sites on the DNA template during the selection and initiation phases of gene transcription.

1. Frenster JH, and Hovsepian JA, "Models of  Embryonic RNA Initiating and Reverting Adult Neoplasms". Section 6 (Cancer Genetics) of the XX International Congress of Genetics, "Understanding Living Systems", Berlin, Germany, July 12-17, 2008.

2. Schwartz JC, Younger ST, Nguyen N-B, Hardy DB, Monia BP, Corey DR, and Janowski BA,
"Antisense transcripts are targets for activating small RNAs".

3. Frenster JH, and Hovsepian JA,  “Models of Embryonic Gene-Induced Initiation and Reversion of Adult Neoplasms”.

4. Ogawa Y, Sun BK, and Lee JT,
"Intersection of the RNA Interference and X-Inactivation Pathways".

5. Place RF, Li L-C, Pookot D, Noonan EJ, and Dahiya R, "MicroRNA-373 induces expression of genes with complementary promoter sequences".

6. Borel C, Gagnebin M, Gehrig C, Kriventseva EV, Zdobnov EM, and Antonarakis SE,
"Mapping of Small RNAs in the Human ENCODE Regions".

7. Zhu X, Ling J, Zhang L, Pi W, Wu M, and Tuan D, "A facilitated tracking and transcription mechanism of long-range enhancer function".

8. Frenster JH, and Hovsepian JA, "DNase-I Ultrastructural Probe Sites and Kissing Chromosomes".

9. Han J, Kim D, and Morris KV, "Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells".

10. Murray JI, Bao Z, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, and Waterston RH,
"Automated analysis of embryonic gene expression with cellular resolution in C. elegans",
Nature Methods - vol. 5; no. 8, pp. 703 - 709 (August, 2008)
http://www.nature.com/nmeth/journal/v5/n8/abs/nmeth.1228.html.

11. Meisner LF,  and Frenster JH,
"In Vivo Evolution within Radiation-Induced Clones of Human Lymphocytes".

12. Prabhakar S, Visel A,  Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, FitzPatrick DR, Afzal V, Pennacchio LA, Rubin EM, and Noonan JP,
"Human-Specific Gain of Function in a Developmental Enhancer".

13. Ozsolak F, Poling LL, Wang Z, Liu H, X. Liu XS, Roeder RG, Zhang X, Song JS, and Fisher DE,
"Chromatin structure analyses identify miRNA promoters."

1. Stephen Buratowski. "Gene Expression--Where to Start?"

2. Leighton J. Core, Joshua J. Waterfall, and John T. Lis,
"Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters".

3. Amy C. Seila, J. Mauro Calabrese, Stuart S. Levine, Gene W. Yeo, Peter B. Rahl, Ryan A. Flynn, Richard A. Young, and Phillip A. Sharp, "Divergent Transcription from Active Promoters".

4. Yiping He, Bert Vogelstein, Victor E. Velculescu, Nickolas Papadopoulos, and Kenneth W. Kinzler,
"The Antisense Transcriptomes of Human Cells".

5. Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen, Marianne S. Christensen, Christophe K. Mapendano, Mikkel H. Schierup, and Torben Heick Jensen,
"RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters".

6. Raphaël Riclet, Mariam Chendeb, Jean-Luc Vonesch, Dirk Koczan, Hans-Juergen Thiesen, Régine Losson, and Florence Cammas,
"Disruption of the Interaction between Transcriptional Intermediary Factor 1b and Heterochromatin Protein 1 Leads to a Switch from DNA Hyper- to Hypomethylation and H3K9 to H3K27 Trimethylation on the MEST Promoter Correlating with Gene Reactivation".

7. Zhong Wang, Mark Gerstein, and Michael Snyder,
"RNA-Seq: a revolutionary tool for transcriptomics".

8. Anna Saramäki, Sarah Diermeier, Ruth Kellner, Heidi Laitinen, Sami Väisänen,  and Carsten Carlberg,
"Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1a,25-dihydroxyvitamin D3".

9. Yasuhiro Tomaru, Misato Nakanishi, Hisashi Miura, Yasumasa Kimura, Hiroki Ohkawa, Yusuke Ohta, Yoshihide Hayashizaki, and Masanori Suzuki,
"Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi".

Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:
Links to Selective Gene Transcription:
Links to RNA-Induced Epigenetics:
Links to RNA-Induced Embryogenesis:
Links to RNA and Biological Causality:
Links to Reprogramming and Neoplasia:

A Brief History of Activator RNA:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA". (PowerPoint Presentation).