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MirtronStructDB: A Comprehensive Database of Mirtrons with Predicted Secondary Structures

[version 1; peer review: 2 approved with reservations]
PUBLISHED 06 Aug 2024
Author details Author details
OPEN PEER REVIEW
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Abstract

Motivation

Mirtrons, a vital category of non-canonical microRNAs (miRNAs) originating from exon-intron boundaries through splicing mechanisms, play crucial roles in cellular processes. However, existing databases lack the latest data and structural information, hindering understandings of mirtron formation and functions.

Results

We introduce MirtronStructDB, an online database addressing these gaps by incorporating over 350 novel mirtrons. Significantly, it provides corresponding predicted RNA secondary structures, offering a deeper understanding of the functional roles and mechanisms of all mirtrons. This enhances previous repositories, offering a total of 4,209 mirtron records spanning 25 species from 46 publications. Our database contributes for unraveling patterns and functions in mirtrons across species and diverse structural features. MirtronStructDB allows users to freely browse, search, visualize, and download data via a user-friendly interface.

Availability

MirtronStructDB is accessible at: http://www.bio8.cs.hku.hk/msdb/.

Contact

lishumin@connect.hku.hk, rbluo@cs.hku.hk

Keywords

Mirtron, Secondary Structure

Introduction

Mirtrons are a vital category of non-canonical microRNAs (miRNAs). MicroRNAs represent a crucial class of small RNAs that play significant roles in various post-transcriptional cellular processes.1 Conventionally, miRNAs are processed from longer primary transcripts, known as pri-miRNAs, via sequential enzymatic cleavage steps involving the Drosha or Dicer proteins. However, a distinct class of miRNAs, termed mirtrons, have been identified that they follow an alternative processing pathway. Mirtrons originate from exon-intron boundaries through splicing and are independent of Drosha or Dicer cleavage. The initial detection of mirtrons occurred in D. melanogaster and C. elegans2 and subsequent studies confirmed their presence in mammals,3 plants,4 and viruses.5 Notably, mirtrons have demonstrated involvement in diverse biological processes, including cell development and cancer.6 To facilitate the exploration of mirtrons, an organized database, MirtronDB, was launched in 2019, collecting 3,833 precursors or mature mirtrons across 18 species.7 However, MirtronDB is limited by the absence of the latest data and, more significantly, structural information—a critical factor in miRNA maturation and distinguishing canonical and non-canonical miRNAs.8

To address these limitations, we present MirtronStructDB, an updated database that offers corresponding secondary structures of all mirtrons, along with an addition of over 350 novel mirtrons that are currently unavailable in existing databases. Furthermore, our user-friendly web interface provides browsing, searching, visualization, and downloading of all stored data. Through timely updates and comprehensive structural information, MirtronStructDB aims to contribute to the advancement of mirtron research and facilitate investigations into their functional roles and mechanisms. MirtronStructDB is publicly accessible at: http://www.bio8.cs.hku.hk/msdb/.

Methods

Implementation

Data collection and processing

MirtronStructDB was constructed through a two-fold data collection strategy (Figure 1A). Initially, we obtained the data from mirtronDB7 by downloading their available information as a primary source. Subsequently, we conducted a comprehensive literature search using the term ‘mirtron OR mirtrons’ from PubMed to collect additional publications related to mirtron discoveries. All the collected data underwent a standardization process and was integrated into MirtronStructDB. In cases where certain fields were missing from the original papers, temporarily placeholders (‘tbu’ indicating ‘to be updated’) were employed. To augment the database and investigate the functions and mechanisms of diverse mirtrons, we predicted the RNA secondary structures for all the collected data with sequence information. This prediction was performed through the RNAstructure Web Server with default parameters.9

ecce27f2-7da3-451f-b162-5db880d5a07b_figure1.gif

Figure 1. Data collection and web interface of MirtronStructDB.

A) Workflow of data collection and preprocessing. B) Main modules of MirtronStructDB: search and filter, browse by species, demonstration and download.

In summary, MirtronStructDB offers a comprehensive dataset comprising 1,569 precursors and 2,640 mature mirtrons spanning 25 species, sourced from 46 publications. Of these, 163 precursors and 223 mature mirtrons were first documented in a dedicated mirtron database. And 9 species were first collected and reported in MirtronStructDB. In addition, a total of 12,555 RNA secondary structures were predicted for better understandings of the functional roles and mechanisms of mirtrons. Detailed information was provided in Data availability statement.

Web application implementation

The online web server was developed with the Flask web framework (v1.1.4) (https://github.com/pallets/flask) as the backend. It is deployed on an Ubuntu Linux server equipped with 48 Intel Xeon CPUs and 189GB of memory. All data is stored in a SQLite database, managed by the SQLAlchemy toolkit (v2.5.1) (https://www.sqlalchemy.org/).

The frontend of MirtronStructDB with a user-friendly design, crafted using Bootstrap (v3) (https://getbootstrap.com/) and adminLTE (v2.4.18) (https://github.com/ColorlibHQ/AdminLTE), and dynamically generated through the JINJA2 templating engine (v2.11.3) (https://jinja.palletsprojects.com/en/3.1.x/templates/). The web service is hosted by Apache2 and Gunicore modules, guaranteeing high performance and stability.

Operation

MirtronStructDB is available to the community through its web-based interface and is freely available. It can also be run locally with a typically 2GB RAM and a dual-core CPU. It is compatible with popular web browsers, including Microsoft Edge, Google Chrome, Firefox and Safari.

The web portal has three primary modules: search and filter, browse by species, and demonstration and download. The overview is shown in Figure 1B. Users can either start with search and filter or browse by species to get the mirtron list and then select individual mirtrons to view their details. Usages listed below:

Search and filter: To facilitate the use of MirtronStructDB, a search and filter can be performed through clicking the ‘Search’ button from the top navigation bar. Users can type the IDs of mirBase, host gene symbols, DOIs or keywords of papers in the search box to retrieve all relevant mirtrons. Additionally, users can apply filters based on preferred species and sources to customize their search results.

Browse by species: We also provide a gallery page which categorizing mirtrons by species. Users can access it through clicking ‘Browse’ button of the navigation bar. Mirtron summaries for each species are presented, and users can explore detailed information by clicking on individual species.

Demonstration and download: Individual mirtrons can be accessed through the mirtron detail page. Two sections were shown: The first section includes basic information including the species, corresponding precursors or mature mirtrons, sequences, strand, chromosome position, source papers, etc. The second section displays predicted secondary structures. Users are flexible to explore and download data based on their own needs.

Discussion

MirtronStructDB is a comprehensive database with an extensive collection of over 350 novel mirtrons accompanied by their predicted secondary structures. This database not only presents an updated catalog of mirtrons across diverse species but also provide structural insights into the entire spectrum of mirtrons. MirtronStructDB make it feasible for experimental biologists seeking identification of relevant mirtrons for distinct species, sources, or specific research requirements. Furthermore, MirtronStructDB offers computational biologists an opportunity to delve into its rich information, particularly the sequence contexts and structural features it provides. With the accumulated data of mirtronStructDB, we anticipate the emergence of novel computational methods to expedite the prediction and identification of mirtrons across a broader spectrum of species. This advancement is expected to deepen our understanding of the unique formation mechanisms and functions of mirtrons.

Ethics and consent

Ethical approval and consent were not required.

Author contributions

R. L. And S. L. conceived the study. S. L. designed the web interface and the analyses. F. W. C., L. C., J. S., and S. S. A. evaluated the analysis results. All authored drafted and approved the manuscript.

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how to cite this article
Li S, Chow FWN, Chen L et al. MirtronStructDB: A Comprehensive Database of Mirtrons with Predicted Secondary Structures [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:899 (https://doi.org/10.12688/f1000research.153905.1)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Open Peer Review

Current Reviewer Status: ?
Key to Reviewer Statuses VIEW
ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 1
VERSION 1
PUBLISHED 06 Aug 2024
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Reviewer Report 19 Sep 2024
Lachlan Coin, The University of Melbourne, Melbourne, Victoria, Australia 
Approved with Reservations
VIEWS 7
Shunmin Li and co-authors have developed a database for Mirton structures, which looks like a useful resource for the community. Mirtons are an important subclass of micro-RNA and new resources for exploring their role in biology and medicine are valuable.
... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Coin L. Reviewer Report For: MirtronStructDB: A Comprehensive Database of Mirtrons with Predicted Secondary Structures [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:899 (https://doi.org/10.5256/f1000research.168861.r312746)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Views
19
Cite
Reviewer Report 21 Aug 2024
Panos Kakoulidis, National and Kapodistrian University of Athens, Athens, Greece 
Approved with Reservations
VIEWS 19
The authors have created an up-to-date online database that hosts data about mirtrons. The dataset of the database is an extension of a previously published database. The user can browse the data by species. Alternatively, the user can search for ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Kakoulidis P. Reviewer Report For: MirtronStructDB: A Comprehensive Database of Mirtrons with Predicted Secondary Structures [version 1; peer review: 2 approved with reservations]. F1000Research 2024, 13:899 (https://doi.org/10.5256/f1000research.168861.r312748)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.

Comments on this article Comments (0)

Version 1
VERSION 1 PUBLISHED 06 Aug 2024
Comment
Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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