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...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-03-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/6/3014 |
| _version_ | 1797471011648569344 |
|---|---|
| author | Nickolai A. Tchurikov Elena S. Klushevskaya Ildar R. Alembekov Anastasiia S. Bukreeva Antonina N. Kretova Vladimir R. Chechetkin Galina I. Kravatskaya Yuri V. Kravatsky |
| author_facet | Nickolai A. Tchurikov Elena S. Klushevskaya Ildar R. Alembekov Anastasiia S. Bukreeva Antonina N. Kretova Vladimir R. Chechetkin Galina I. Kravatskaya Yuri V. Kravatsky |
| author_sort | Nickolai A. Tchurikov |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T19:43:31Z |
| format | Article |
| id | doaj.art-92946db2facd4fda99d180b95d64cc75 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T19:43:31Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-92946db2facd4fda99d180b95d64cc752023-11-24T01:30:37ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01236301410.3390/ijms23063014Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAsNickolai A. Tchurikov0Elena S. Klushevskaya1Ildar R. Alembekov2Anastasiia S. Bukreeva3Antonina N. Kretova4Vladimir R. Chechetkin5Galina I. Kravatskaya6Yuri V. Kravatsky7Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaSmall 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.https://www.mdpi.com/1422-0067/23/6/3014small ribosomal RNAs (srRNAs)rDNA fragmentsHEK293Tepigeneticstranscriptional silencingtranscriptional activation |
| spellingShingle | Nickolai A. Tchurikov Elena S. Klushevskaya Ildar R. Alembekov Anastasiia S. Bukreeva Antonina N. Kretova Vladimir R. Chechetkin Galina I. Kravatskaya Yuri V. Kravatsky Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs International Journal of Molecular Sciences small ribosomal RNAs (srRNAs) rDNA fragments HEK293T epigenetics transcriptional silencing transcriptional activation |
| 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 | small ribosomal RNAs (srRNAs) rDNA fragments HEK293T epigenetics transcriptional silencing transcriptional activation |
| url | https://www.mdpi.com/1422-0067/23/6/3014 |
| work_keys_str_mv | AT nickolaiatchurikov fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas AT elenasklushevskaya fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas AT ildarralembekov fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas AT anastasiiasbukreeva fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas AT antoninankretova fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas AT vladimirrchechetkin fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas AT galinaikravatskaya fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas AT yurivkravatsky fragmentsofrdnagenesscatteredoverthehumangenomearetargetsofsmallrnas |