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ncRNA
Special Issues
Systematic Analysis of lncRNA Structures and Functions
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Systematic Analysis of lncRNA Structures and Functions

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: closed (20 April 2022) | Viewed by 12461

Special Issue Editor

Prof. Dr. Shizuka Uchida

E-Mail Website
Guest Editor
Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark
Interests: bioinformatics; cardiovascular system; circRNA; database; epitranscriptomics; lncRNA; miRNA; non-coding RNA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advances in next-generation sequencing, particularly RNA sequencing (RNA-seq), have led to the discovery of long non-coding RNAs (lncRNAs), whose number surpasses that of protein-coding genes. With the rise of single-cell RNA-seq (scRNA-seq), many cell-type-specific lncRNAs have been identified, yet the functions of lncRNAs remain largely unknown. As proteins have numerous functions, it is natural to assume that a myriad of functions for lncRNAs are waiting to be uncovered. By definition, lncRNAs are non-protein-coding transcripts. Thus, it is essential to examine the sequence structures of lncRNAs to determine the functions of lncRNAs. Currently, there are over 170 known RNA modifications (e.g., A-to-I RNA editing, m6A methylation, and pseudouridylation) that can affect the structures and functions of RNAs, including lncRNAs. This Special Issue on the Systematic Analysis of lncRNA Structures and Functions aims to unravel the diverse functional roles of lncRNAs by focusing on systematic approaches using bioinformatics, computational biology, and/or systems biology approaches coupled with experimental validation.

Dr. Shizuka Uchida
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Non-Coding RNA is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Bioinformatics
  • computational biology
  • epitranscriptomics
  • lncRNAs
  • systems biology

Published Papers (3 papers)

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Research

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7 pages, 373 KiB  
Article
HiMoRNA: A Comprehensive Database of Human lncRNAs Involved in Genome-Wide Epigenetic Regulation
by Evgeny Mazurov, Alexey Sizykh and Yulia A. Medvedeva
Non-Coding RNA 2022, 8(1), 18; https://doi.org/10.3390/ncrna8010018 - 08 Feb 2022
Cited by 3 | Viewed by 2731
Abstract
Long non-coding RNAs (lncRNAs) play an important role in genome regulation. Specifically, many lncRNAs interact with chromatin, recruit epigenetic complexes and in this way affect large-scale gene expression programs. However, the experimental data about lncRNA-chromatin interactions is still limited. The majority of experimental [...] Read more.
Long non-coding RNAs (lncRNAs) play an important role in genome regulation. Specifically, many lncRNAs interact with chromatin, recruit epigenetic complexes and in this way affect large-scale gene expression programs. However, the experimental data about lncRNA-chromatin interactions is still limited. The majority of experimental protocols do not provide any insight into the mechanics of lncRNA-based genome-wide epigenetic regulation. Here we present the HiMoRNA (Histone-Modifying RNA) database, a resource containing correlated lncRNA–epigenetic changes in specific genomic locations genome-wide. HiMoRNA integrates a large amount of multi-omics data to characterize the effects of lncRNA on epigenetic modifications and gene expression. The current release of HiMoRNA includes more than five million associations in humans for ten histone modifications in multiple genomic loci and 4145 lncRNAs. HiMoRNA provides a user-friendly interface to facilitate browsing, searching and retrieving of lncRNAs associated with epigenetic profiles of various chromatin loci. Analysis of the HiMoRNA data suggests that several lncRNA including JPX might be involved not only in regulation of XIST locus but also in direct establishment or maintenance of X-chromosome inactivation. We believe that HiMoRNA is a convenient and valuable resource that can provide valuable biological insights and greatly facilitate functional annotation of lncRNAs. Full article
(This article belongs to the Special Issue Systematic Analysis of lncRNA Structures and Functions)
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Review

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14 pages, 1946 KiB  
Review
Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions
by Henry E. Miller, Mirolyuba Ilieva, Alexander J. R. Bishop and Shizuka Uchida
Non-Coding RNA 2022, 8(2), 23; https://doi.org/10.3390/ncrna8020023 - 28 Mar 2022
Cited by 9 | Viewed by 3754
Abstract
Long non-coding RNAs (lncRNAs) belong to a class of non-protein-coding RNAs with their lengths longer than 200 nucleotides. Most of the mammalian genome is transcribed as RNA, yet only a small percent of the transcribed RNA corresponds to exons of protein-coding genes. Thus, [...] Read more.
Long non-coding RNAs (lncRNAs) belong to a class of non-protein-coding RNAs with their lengths longer than 200 nucleotides. Most of the mammalian genome is transcribed as RNA, yet only a small percent of the transcribed RNA corresponds to exons of protein-coding genes. Thus, the number of lncRNAs is predicted to be several times higher than that of protein-coding genes. Because of sheer number of lncRNAs, it is often difficult to elucidate the functions of all lncRNAs, especially those arising from their relationship to their binding partners, such as DNA, RNA, and proteins. Due to their binding to other macromolecules, it has become evident that the structures of lncRNAs influence their functions. In this regard, the recent development of epitranscriptomics (the field of study to investigate RNA modifications) has become important to further elucidate the structures and functions of lncRNAs. In this review, the current status of lncRNA structures and functions influenced by epitranscriptomic marks is discussed. Full article
(This article belongs to the Special Issue Systematic Analysis of lncRNA Structures and Functions)
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Other

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18 pages, 3020 KiB  
Hypothesis
Secondary Structural Model of MALAT1 Becomes Unstructured in Chronic Myeloid Leukemia and Undergoes Structural Rearrangement in Cervical Cancer
by Matthew C. Wang, Phillip J. McCown, Grace E. Schiefelbein and Jessica A. Brown
Non-Coding RNA 2021, 7(1), 6; https://doi.org/10.3390/ncrna7010006 - 13 Jan 2021
Cited by 6 | Viewed by 4669
Abstract
Long noncoding RNAs (lncRNAs) influence cellular function through binding events that often depend on the lncRNA secondary structure. One such lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), is upregulated in many cancer types and has a myriad of protein- and miRNA-binding sites. Recently, [...] Read more.
Long noncoding RNAs (lncRNAs) influence cellular function through binding events that often depend on the lncRNA secondary structure. One such lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), is upregulated in many cancer types and has a myriad of protein- and miRNA-binding sites. Recently, a secondary structural model of MALAT1 in noncancerous cells was proposed to form 194 hairpins and 13 pseudoknots. That study postulated that, in cancer cells, the MALAT1 structure likely varies, thereby influencing cancer progression. This work analyzes how that structural model is expected to change in K562 cells, which originated from a patient with chronic myeloid leukemia (CML), and in HeLa cells, which originated from a patient with cervical cancer. Dimethyl sulfate-sequencing (DMS-Seq) data from K562 cells and psoralen analysis of RNA interactions and structure (PARIS) data from HeLa cells were compared to the working structural model of MALAT1 in noncancerous cells to identify sites that likely undergo structural alterations. MALAT1 in K562 cells is predicted to become more unstructured, with almost 60% of examined hairpins in noncancerous cells losing at least half of their base pairings. Conversely, MALAT1 in HeLa cells is predicted to largely maintain its structure, undergoing 18 novel structural rearrangements. Moreover, 50 validated miRNA-binding sites are affected by putative secondary structural changes in both cancer types, such as miR-217 in K562 cells and miR-20a in HeLa cells. Structural changes unique to K562 cells and HeLa cells provide new mechanistic leads into how the structure of MALAT1 may mediate cancer in a cell-type specific manner. Full article
(This article belongs to the Special Issue Systematic Analysis of lncRNA Structures and Functions)
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