"Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells".

Jiang Han*, Daniel Kim ¹, and Kevin V. Morris*^{, @},

*Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037;
¹ Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010

^@ To whom correspondence should be addressed. E-mail:  kmorris@scripps.edu

siRNAs targeted to gene promoters can direct epigenetic modifications that result in transcriptional gene silencing in human cells. It is not clear whether the antisense strand of the siRNAs bind directly to DNA or to a sense-stranded RNA transcript corresponding to the known promoter region. We present evidence that an RNA polymerase II expressed mRNA containing an extended 5' untranslated region that overlaps the gene promoter is required for RNA-directed epigenetic modifications and transcriptional silencing of the RNA-targeted promoter. These promoter-associated RNAs were detected by their hybridization to the antisense strand of the complementary promoter-directed siRNA. Antisense phosphorothioate oligodeoxynucleotides were used to degrade the promoter-associated RNA transcripts, the loss of which abrogated the effect of siRNA-mediated transcriptional gene silencing, as well as the complexing of the siRNA with the silent state histone methyl mark and the promoter-associated RNA. These data demonstrate that low-copy promoter-associated RNAstranscribed through RNAPII promoters are recognized by the antisense strand of the siRNA and function as a recognition motif to direct epigenetic silencing complexes to the corresponding targeted promoters to mediate transcriptional silencing in human cells.

Model for RNA-directed TGS in human cells.

(A) The promoter-associated RNA model of RNA-mediated TGS proposes that a variant species of mRNA, a promoter-associated mRNA, essentially containing an extended 5' UTR, is recognized by the antisense strand of siRNAs or possibly endogenous antisense RNAs during RNAPII-mediated transcription of the RNA-targeted promoter.

(B) The antisense strand of the siRNA might then guide a putative transcriptional silencing complex (possibly composed of DNMT3A, Ago-1, HDAC-1, and/or EZH2) to the targeted promoter where histone modifications result and the initial gene-silencing event.

(C) The initial silencing event or prolonged suppression of the siRNA-targeted promoter may result in heterchromatization of the local siRNA-targeted genomic region and is not, based on these data, thought to be the result of slicing of the low-copy promoter-associated RNA but rather due to a recruitment of chromatin remodeling factors or complexes to the targeted promoter that result in the gene silencing event.

In this complex study by Jiang Han, Daniel Kim , and Kevin Morris, it is shown that new RNA transcripts target downstream promoters, and play a complicated role in epigenetic controls of gene transcription.

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A Brief History of Activator RNA:

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).