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

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 com...

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Autores principales: Tchurikov, Nickolai A., Klushevskaya, Elena S., Alembekov, Ildar R., Bukreeva, Anastasiia S., Kretova, Antonina N., Chechetkin, Vladimir R., Kravatskaya, Galina I., Kravatsky, Yuri V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954558/
https://www.ncbi.nlm.nih.gov/pubmed/35328433
http://dx.doi.org/10.3390/ijms23063014
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author Tchurikov, Nickolai A.
Klushevskaya, Elena S.
Alembekov, Ildar R.
Bukreeva, Anastasiia S.
Kretova, Antonina N.
Chechetkin, Vladimir R.
Kravatskaya, Galina I.
Kravatsky, Yuri V.
author_facet Tchurikov, Nickolai A.
Klushevskaya, Elena S.
Alembekov, Ildar R.
Bukreeva, Anastasiia S.
Kretova, Antonina N.
Chechetkin, Vladimir R.
Kravatskaya, Galina I.
Kravatsky, Yuri V.
author_sort Tchurikov, Nickolai A.
collection PubMed
description 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.
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spelling pubmed-89545582022-03-26 Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs Tchurikov, Nickolai A. Klushevskaya, Elena S. Alembekov, Ildar R. Bukreeva, Anastasiia S. Kretova, Antonina N. Chechetkin, Vladimir R. Kravatskaya, Galina I. Kravatsky, Yuri V. Int J Mol Sci Article 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. MDPI 2022-03-10 /pmc/articles/PMC8954558/ /pubmed/35328433 http://dx.doi.org/10.3390/ijms23063014 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tchurikov, Nickolai A.
Klushevskaya, Elena S.
Alembekov, Ildar R.
Bukreeva, Anastasiia S.
Kretova, Antonina N.
Chechetkin, Vladimir R.
Kravatskaya, Galina I.
Kravatsky, Yuri V.
Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs
title Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs
title_full Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs
title_fullStr Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs
title_full_unstemmed Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs
title_short Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs
title_sort fragments of rdna genes scattered over the human genome are targets of small rnas
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954558/
https://www.ncbi.nlm.nih.gov/pubmed/35328433
http://dx.doi.org/10.3390/ijms23063014
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