Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs.

Nickolai A Tchurikov,Antonina N Kretova,Anastasiia S Bukreeva,Elena S Klushevskaya,Vladimir R Chechetkin,Yuri V Kravatsky,Ildar R Alembekov,Galina I Kravatskaya

doi:10.3390/ijms23063014

Nickolai A Tchurikov, Antonina N Kretova + Show 6 more

Open Access

https://doi.org/10.3390/ijms23063014

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Abstract

Small noncoding RNAs of different origins and classes play several roles in the regulation of gene expression. Here, we show that diverged and rearranged fragments of rDNA units are scattered throughout the human genome and that endogenous small noncoding RNAs are processed by the Microprocessor complex from specific regions of ribosomal RNAs shaping hairpins. These small RNAs correspond to particular sites inside the fragments of rDNA that mostly reside in intergenic regions or the introns of about 1500 genes. The targets of these small ribosomal RNAs (srRNAs) are characterized by a set of epigenetic marks, binding sites of Pol II, RAD21, CBP, and P300, DNase I hypersensitive sites, and by enrichment or depletion of active histone marks. In HEK293T cells, genes that are targeted by srRNAs (srRNA target genes) are involved in differentiation and development. srRNA target genes are enriched with more actively transcribed genes. Our data suggest that remnants of rDNA sequences and srRNAs may be involved in the upregulation or downregulation of a specific set of genes in human cells. These results have implications for diverse fields, including epigenetics and gene therapy.

Highlights

RNA molecules are capable of recognizing complementary genomic regions [1]
DGCR8 directly recognizes the RNA substrates and is involved in the initial step of miRNA biogenesis and in the fate of different classes of RNAs, including ribosomal RNAs and several hundred mRNAs, as well as snoRNAs and long noncoding RNAs (lncRNAs) [12]. Small rDNA-derived RNAs (srRNAs) mostly correspond to the 28S gene [6] and are not random products formed during rRNA degradation, but correspond to a new class of small RNAs that deserves further investigation [13]
There Are Thousands of Unique srRNAs srRNAs were selected from the sequenced library of RNAs that were isolated by crosslinking immunoprecipitation using antibodies to DGCR8 [12]

Summary

Introduction

RNA molecules are capable of recognizing complementary genomic regions [1]. The pervasive transcription of RNA likely gives rise to RNA copies of the entire genome [2]. It was shown that rDNA clusters shape interchromosomal contacts within different genomic regions in HEK293T cells and that the contact sites are enriched with small noncoding RNAs, suggesting the RNA-mediated nature of the contacts [10,11]. These data prompted us to study whether srRNAs are involved in these contacts, and we investigated the origin and the target sites of srRNAs. For this study, we used the 20–50-nt long RNAs associated with DGCR8—a Microprocessorcomplex subunit—that was isolated by crosslinking immunoprecipitation in HEK293T cells [12]. DGCR8 ( known as Pasha) directly recognizes the RNA substrates and is involved in the initial step of miRNA biogenesis and in the fate of different classes of RNAs, including ribosomal RNAs and several hundred mRNAs, as well as snoRNAs and lncRNAs [12]. srRNAs mostly correspond to the 28S gene [6] and are not random products formed during rRNA degradation, but correspond to a new class of small RNAs that deserves further investigation [13]

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