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Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs

MicroRNAs (miRNAs) are short non-coding RNAs that function in post-transcriptional gene silencing and mRNA regulation. Although the number of nucleotides of miRNAs ranges from 17 to 27, they are mostly made up of 22 nucleotides. The expression of miRNAs changes significantly in cancer, causing prote...

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Detalles Bibliográficos
Autores principales: Dogan, Senol, Spahiu, Emrulla, Cilic, Anis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9316571/
https://www.ncbi.nlm.nih.gov/pubmed/35885935
http://dx.doi.org/10.3390/genes13071152
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author Dogan, Senol
Spahiu, Emrulla
Cilic, Anis
author_facet Dogan, Senol
Spahiu, Emrulla
Cilic, Anis
author_sort Dogan, Senol
collection PubMed
description MicroRNAs (miRNAs) are short non-coding RNAs that function in post-transcriptional gene silencing and mRNA regulation. Although the number of nucleotides of miRNAs ranges from 17 to 27, they are mostly made up of 22 nucleotides. The expression of miRNAs changes significantly in cancer, causing protein alterations in cancer cells by preventing some genes from being translated into proteins. In this research, a structural analysis of 587 miRNAs that are differentially expressed in myeloid cancer was carried out. Length distribution studies revealed a mean and median of 22 nucleotides, with an average of 21.69 and a variance of 1.65. We performed nucleotide analysis for each position where Uracil was the most observed nucleotide and Adenine the least observed one with 27.8% and 22.6%, respectively. There was a higher frequency of Adenine at the beginning of the sequences when compared to Uracil, which was more frequent at the end of miRNA sequences. The purine content of each implicated miRNA was also assessed. A novel motif analysis script was written to detect the most frequent 3–7 nucleotide (3–7n) long motifs in the miRNA dataset. We detected CUG (42%) as the most frequent 3n motif, CUGC (15%) as a 4n motif, AGUGC (6%) as a 5n motif, AAGUGC (4%) as a 6n motif, and UUUAGAG (4%) as a 7n motif. Thus, in the second part of our study, we further characterized the motifs by analyzing whether these motifs align at certain consensus sequences in our miRNA dataset, whether certain motifs target the same genes, and whether these motifs are conserved within other species. This thorough structural study of miRNA sequences provides a novel strategy to study the implications of miRNAs in health and disease. A better understanding of miRNA structure is crucial to developing therapeutic settings.
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spelling pubmed-93165712022-07-27 Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs Dogan, Senol Spahiu, Emrulla Cilic, Anis Genes (Basel) Article MicroRNAs (miRNAs) are short non-coding RNAs that function in post-transcriptional gene silencing and mRNA regulation. Although the number of nucleotides of miRNAs ranges from 17 to 27, they are mostly made up of 22 nucleotides. The expression of miRNAs changes significantly in cancer, causing protein alterations in cancer cells by preventing some genes from being translated into proteins. In this research, a structural analysis of 587 miRNAs that are differentially expressed in myeloid cancer was carried out. Length distribution studies revealed a mean and median of 22 nucleotides, with an average of 21.69 and a variance of 1.65. We performed nucleotide analysis for each position where Uracil was the most observed nucleotide and Adenine the least observed one with 27.8% and 22.6%, respectively. There was a higher frequency of Adenine at the beginning of the sequences when compared to Uracil, which was more frequent at the end of miRNA sequences. The purine content of each implicated miRNA was also assessed. A novel motif analysis script was written to detect the most frequent 3–7 nucleotide (3–7n) long motifs in the miRNA dataset. We detected CUG (42%) as the most frequent 3n motif, CUGC (15%) as a 4n motif, AGUGC (6%) as a 5n motif, AAGUGC (4%) as a 6n motif, and UUUAGAG (4%) as a 7n motif. Thus, in the second part of our study, we further characterized the motifs by analyzing whether these motifs align at certain consensus sequences in our miRNA dataset, whether certain motifs target the same genes, and whether these motifs are conserved within other species. This thorough structural study of miRNA sequences provides a novel strategy to study the implications of miRNAs in health and disease. A better understanding of miRNA structure is crucial to developing therapeutic settings. MDPI 2022-06-26 /pmc/articles/PMC9316571/ /pubmed/35885935 http://dx.doi.org/10.3390/genes13071152 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
Dogan, Senol
Spahiu, Emrulla
Cilic, Anis
Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs
title Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs
title_full Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs
title_fullStr Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs
title_full_unstemmed Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs
title_short Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs
title_sort structural analysis of micrornas in myeloid cancer reveals consensus motifs
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9316571/
https://www.ncbi.nlm.nih.gov/pubmed/35885935
http://dx.doi.org/10.3390/genes13071152
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