MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome
Complete 3′UTRs unambiguously assigned to specific mRNA isoforms from the Atlantic salmon full-length (FL) transcriptome were collected into a 3′UTRome. miRNA response elements (MREs) and other cis-regulatory motifs were subsequently predicted and assigned to 3′UTRs of all FL-transcripts. The MicroS...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-09-01
|
| Series: | Non-Coding RNA |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2311-553X/7/4/61 |
| _version_ | 1827670627694149632 |
|---|---|
| author | Sigmund Ramberg Rune Andreassen |
| author_facet | Sigmund Ramberg Rune Andreassen |
| author_sort | Sigmund Ramberg |
| collection | DOAJ |
| description | Complete 3′UTRs unambiguously assigned to specific mRNA isoforms from the Atlantic salmon full-length (FL) transcriptome were collected into a 3′UTRome. miRNA response elements (MREs) and other cis-regulatory motifs were subsequently predicted and assigned to 3′UTRs of all FL-transcripts. The MicroSalmon GitHub repository provides all results. RNAHybrid and sRNAtoolbox tools predicted the MREs. UTRscan and the Teiresias algorithm predicted other 3′UTR cis-acting motifs, both known vertebrate motifs and putative novel motifs. MicroSalmon provides search programs to retrieve all FL-transcripts targeted by a miRNA (median number 1487), all miRNAs targeting an FL-transcript (median number 27), and other cis-acting motifs. As thousands of FL-transcripts may be targets of each miRNA, additional experimental strategies are necessary to reduce the likely true and relevant targets to a number that may be functionally validated. Low-complexity motifs known to affect mRNA decay in vertebrates were over-represented. Many of these were enriched in the terminal end, while purine- or pyrimidine-rich motifs with unknown functions were enriched immediately downstream of the stop codon. Furthermore, several novel complex motifs were over-represented, indicating conservation and putative function. In conclusion, MicroSalmon is an extensive and useful, searchable resource for study of Atlantic salmon transcript regulation by miRNAs and cis-acting 3′UTR motifs. |
| first_indexed | 2024-03-10T03:25:44Z |
| format | Article |
| id | doaj.art-c92c56d6f78846fca1ff84db7af6d03e |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-10T03:25:44Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-c92c56d6f78846fca1ff84db7af6d03e2023-11-23T09:52:58ZengMDPI AGNon-Coding RNA2311-553X2021-09-01746110.3390/ncrna7040061MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon TranscriptomeSigmund Ramberg0Rune Andreassen1Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, NorwayDepartment of Life Sciences and Health, Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, 0167 Oslo, NorwayComplete 3′UTRs unambiguously assigned to specific mRNA isoforms from the Atlantic salmon full-length (FL) transcriptome were collected into a 3′UTRome. miRNA response elements (MREs) and other cis-regulatory motifs were subsequently predicted and assigned to 3′UTRs of all FL-transcripts. The MicroSalmon GitHub repository provides all results. RNAHybrid and sRNAtoolbox tools predicted the MREs. UTRscan and the Teiresias algorithm predicted other 3′UTR cis-acting motifs, both known vertebrate motifs and putative novel motifs. MicroSalmon provides search programs to retrieve all FL-transcripts targeted by a miRNA (median number 1487), all miRNAs targeting an FL-transcript (median number 27), and other cis-acting motifs. As thousands of FL-transcripts may be targets of each miRNA, additional experimental strategies are necessary to reduce the likely true and relevant targets to a number that may be functionally validated. Low-complexity motifs known to affect mRNA decay in vertebrates were over-represented. Many of these were enriched in the terminal end, while purine- or pyrimidine-rich motifs with unknown functions were enriched immediately downstream of the stop codon. Furthermore, several novel complex motifs were over-represented, indicating conservation and putative function. In conclusion, MicroSalmon is an extensive and useful, searchable resource for study of Atlantic salmon transcript regulation by miRNAs and cis-acting 3′UTR motifs.https://www.mdpi.com/2311-553X/7/4/61Atlantic salmonmiRNAmicroRNAcis-regulatory elements3′UTR |
| spellingShingle | Sigmund Ramberg Rune Andreassen MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome Non-Coding RNA Atlantic salmon miRNA microRNA cis-regulatory elements 3′UTR |
| title | MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome |
| title_full | MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome |
| title_fullStr | MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome |
| title_full_unstemmed | MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome |
| title_short | MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome |
| title_sort | microsalmon a comprehensive searchable resource of predicted microrna targets and 3 utr cis regulatory elements in the full length sequenced atlantic salmon transcriptome |
| topic | Atlantic salmon miRNA microRNA cis-regulatory elements 3′UTR |
| url | https://www.mdpi.com/2311-553X/7/4/61 |
| work_keys_str_mv | AT sigmundramberg microsalmonacomprehensivesearchableresourceofpredictedmicrornatargetsand3utrcisregulatoryelementsinthefulllengthsequencedatlanticsalmontranscriptome AT runeandreassen microsalmonacomprehensivesearchableresourceofpredictedmicrornatargetsand3utrcisregulatoryelementsinthefulllengthsequencedatlanticsalmontranscriptome |