John H. Frenster ^{1, @} and Jeannette A. Hovsepian ^{2, @}

Departments of ¹ Medicine and of ² Radiology, Stanford University School of Medicine, Stanford, California  94305, USA,

^@ Present Addresses: RNA Research, Physicians’ Educational Series, Atherton, CA  94027-5446 USA.
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 J.H.F.

Although mammalian chromatin is normally reprogrammed during late telophase after each cell division (1, 2), it is also possible to reprogram chromatin during the longer cycle phases of interphase (3). Calf thymus interphase lymphocytes were used as a source both of isolated active euchromatin 10 nm microfibrils and of isolated repressed masses of heterochromatin (4). Isolated active euchromatin contained a 5-fold excess of constituent RNA compared to isolated repressed heterochromatin. When isolated total nuclear RNA of calf thymus lymphocytes was added to incubations of isolated repressed heterochromatin, a marked activation of DNA transcription within heterochromatin was observed. This new activity within isolated heterochromatin was almost equal to the basal transcription activity found within isolated euchromatin. When isolated total nuclear RNA of calf thymus lymphocytes was added to parallel incubations of isolated active euchromatin, no further increase of DNA transcription was observed over that seen within basal euchromatin incubations, while addition of yeast total RNA was actually inhibitory at lower concentrations, regaining basal levels only at higher concentrations of added yeast RNA. These data suggest a displacement of endogenous thymus activator RNA (5) by exogenous yeast activator RNA, resulting in a decrease in thymus euchromatin DNA transcription, with a rise in euchromatin DNA transcription to basal states only at higher replacement doses of yeast activator RNA. A simple model of thymus activator RNA displacement and yeast activator RNA replacement during chromatin reprogramming accounts for the observed phenomena.

Glossary for:  "Subjects of Study in Cell and Chromatin Reprogramming":

Summary of:  "Activator RNA Exchange during Interphase Chromatin Reprogramming".

Model for:  "RNA-Induced Chromatin Remodeling and DNA Melting during Selective Gene Transcription".

1. Prasanth KV, Sacco-Bubulya PA, Prasanth SG, and Spector DL, "Sequential Entry of Components of Gene Expression Machinery into Daughter Nuclei",   Mol. Biol. Cell, 14: 1043 (2003).

2. Frenster JH, and Hovsepian JA,  "Overshoot in Late Telophase for RNA Re-Programming of Mitotic Chromatin",  RNA 2003, 211 (2003).

3. Frenster JH, "Yeast  RNA  Re-Programming  of  Already-Active  Mammalian Chromatin".  RNA 2002, 592 (2002).

4. Frenster JH, "Activation of DNA Transcription within Repressed Chromatin by Nuclear RNA Species",    RNA 2001, 237 (2001).

5. Hovsepian JA, and Frenster JH, "RNA-Induced Melting of DNA during Selective Gene Transcription",
Molec. Biol. Cell, vol. 13, supp. p. 239a (November, 2002).

6. Kuwabara T, Hsieh J, Nakashima K, Taira K, and Gage FH, "A Small Modulatory dsRNA Specifies the Fate of Adult Neural Stem Cells". Cell,  vol. 116, no. 6, pp.779-793  (19 March 2004).

1. Byrne JA, Simonsson S, Western PS, and Gurdon JB, "Nuclei of Adult Mammalian Somatic Cells are Directly Reprogrammed to oct-4 Stem Cell Gene Expression by Amphibian Oocytes", Current Biology, vol 13, no. 14, pp. 1206-1213 (July 15, 2003).

2. Li L, Connelly MC, Wetmore C, Curran T, and Morgan JI, "Mouse Embryos Cloned from Brain Tumors", Cancer Research vol. 63, no. 11, pp. 2733-2736 (June 1, 2003).

3. Goldstein L, “Stable Nuclear RNA Returns to Post-Division Nuclei Following Release to Cytoplasm during Mitosis”, Exp. Cell Res. vol. 89,  no. 2, pp. 421-425 (December, 1974).

4. Geiss G, Jin G, Guo J, Bumgarner R, Katze MG, and Sen GC, "A Comprehensive View of Regulation of Gene Expression by Double-Stranded RNA-Mediated Cell Signaling", J. Biol. Chem. vol. 276, pp. 30178-30182 (2001).

5. Persengiev SP, Zhu X and Green MR, "Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs)",  RNA, vol. 10, no. 1, pp. 12-18 (January, 2004).

6. Gottesfeld JM,  and Barbas III CF, "RNA as a Transcriptional Activator", Chemistry and Biology, vol 10, no.7, pp. 584-585 (July, 2003).

7. Xie H , Ye M , Feng R , and Graf T, "Stepwise Reprogramming of B Cells into Macrophages", Cell, vol 117, no. 5, pp. 663-676 (May 28, 2004).

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 Presentatuion).

For Further Information and Feedback:
E-mail: frenster@euchromatin.net