Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA
Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we devel...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-09-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/22/18/9757 |
| _version_ | 1797518970212843520 |
|---|---|
| author | Marine Lambert Abderrahim Benmoussa Idrissa Diallo Katheryn Ouellet-Boutin Véronique Dorval Nathalie Majeau Charles Joly-Beauparlant Arnaud Droit Alain Bergeron Bernard Têtu Yves Fradet Frédéric Pouliot Patrick Provost |
| author_facet | Marine Lambert Abderrahim Benmoussa Idrissa Diallo Katheryn Ouellet-Boutin Véronique Dorval Nathalie Majeau Charles Joly-Beauparlant Arnaud Droit Alain Bergeron Bernard Têtu Yves Fradet Frédéric Pouliot Patrick Provost |
| author_sort | Marine Lambert |
| collection | DOAJ |
| description | Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5′ Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought. |
| first_indexed | 2024-03-10T07:35:48Z |
| format | Article |
| id | doaj.art-778f942ddc6a4232b45aa9de2ba5ab73 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T07:35:48Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-778f942ddc6a4232b45aa9de2ba5ab732023-11-22T13:27:04ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-09-012218975710.3390/ijms22189757Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNAMarine Lambert0Abderrahim Benmoussa1Idrissa Diallo2Katheryn Ouellet-Boutin3Véronique Dorval4Nathalie Majeau5Charles Joly-Beauparlant6Arnaud Droit7Alain Bergeron8Bernard Têtu9Yves Fradet10Frédéric Pouliot11Patrick Provost12CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaCHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, CanadaUsing a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5′ Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.https://www.mdpi.com/1422-0067/22/18/9757RNA sequencingsmall RNAnon-coding RNART-qPCR5.8S rRNA |
| spellingShingle | Marine Lambert Abderrahim Benmoussa Idrissa Diallo Katheryn Ouellet-Boutin Véronique Dorval Nathalie Majeau Charles Joly-Beauparlant Arnaud Droit Alain Bergeron Bernard Têtu Yves Fradet Frédéric Pouliot Patrick Provost Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA International Journal of Molecular Sciences RNA sequencing small RNA non-coding RNA RT-qPCR 5.8S rRNA |
| title | Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA |
| title_full | Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA |
| title_fullStr | Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA |
| title_full_unstemmed | Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA |
| title_short | Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA |
| title_sort | identification of abundant and functional dodecarnas dornas derived from ribosomal rna |
| topic | RNA sequencing small RNA non-coding RNA RT-qPCR 5.8S rRNA |
| url | https://www.mdpi.com/1422-0067/22/18/9757 |
| work_keys_str_mv | AT marinelambert identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT abderrahimbenmoussa identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT idrissadiallo identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT katherynouelletboutin identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT veroniquedorval identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT nathaliemajeau identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT charlesjolybeauparlant identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT arnauddroit identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT alainbergeron identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT bernardtetu identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT yvesfradet identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT fredericpouliot identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna AT patrickprovost identificationofabundantandfunctionaldodecarnasdornasderivedfromribosomalrna |