Mechanistic principles of chromatin remodeling guided by siRNAs and miRNAs

Abstract

Small RNAs can guide chromatin remodeling in mammalian cells, but the mechanisms involved are poorly understood. Previous reports have shown a requirement for overlapping transcription and the involvement of Argonaute (Ago) proteins. Here, we use the Regulatory Domain (RD) of the INK4/ARF locus as an experimental platform susceptible to siRNA-guided chromatin remodeling to interrogate about the mechanisms involved. We show that siRNA-guided chromatin remodeling of RD requires overlapping transcription, and targets the transcribed strand, but not the template strand, supporting an RNA:RNA recognition mechanism between the small RNA and the nascent RNA transcript. We found that heterochromatin formation can be triggered both by perfectly-matched double-stranded RNA precursors, as well as, by imperfectly-matched double-stranded RNA precursors. These observations, together with the fact that promoters are often subjected to overlapping transcription, open the possibility that miRNAs could also be able to guide heterochromatin formation at promoters. We demonstrate this possibility showing that miRNAs miR17-5p and miR20a from the oncomiR cluster miR-17-92 can induce heterochromatic features in promoters that undergo overlapping transcription and possess sequence complementarity to the miRNA seed region. These results unveil a new level of gene regulation by miRNAs.

Ectopic expression of the histone methyltransferase Ezh2 in haematopoietic stem cells causes myeloproliferative disease

“…Total RNA was isolated from PB, BM, spleen and other tissues with the Trizol reagent (Invitrogen), and treated essentially as described 48 , using the primers listed in Supplementary Table S2. Gene expression analysis is described in Supplementary Information.…”

“…ChIP was performed essentially as described 48 . Antibodies for immunoprecipitation were rabbit polyclonals to H3K27me3, H3K9me3, H2Aub1, IgM, Ezh2 and H3K4me3 (all from Upstate; 1:2,500).…”

microRNA: New Players in Metastatic Process

“…To complicate the already intricate scenario, it has been recently reported that miRNAs can bind to ribonucleoproteins in a seed sequence and a RISC-independent manner and then interfere with their RNA binding functions (decoy activity) [15] . Three studies have reported that miRNAs can also regulate gene expression at the transcriptional level by direct binding to the DNA [16][17][18].…”

Phospho-ΔNp63α/microRNA network modulates epigenetic regulatory enzymes in squamous cell carcinomas

“…8,[12][13][14][15][16][17] Certain microRNAs were shown to mediate epigenetic regulation of gene transcription and cell metabolism, the induction of cell death, cell cycle arrest, autophagy, and senescence. 8,[18][19][20][21][22] On one hand, microRNAs were shown to directly bind the gene promoter and gene terminus sequences, thereby modulating specific gene expression at the transcription level. [23][24][25][26] On the other hand, transcriptional deregulation in cancer cells may lead to altered transcription of specific microRNA genes.…”