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Selected Papers from IEEE BIBM 2021 Workshop on Long Non-coding...
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Selected Papers from IEEE BIBM 2021 Workshop on Long Non-coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA)

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

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 9897

Special Issue Editors

Prof. Dr. Donald Adjeroh

E-Mail Website
Guest Editor
Lane Department of Computer Science & Electrical Engineering, West Virginia University (WVU), Morgantown, WV, USA
Interests: machine learning & computer vision; search algorithms & data structures; bioinformatics & computational biology; digital health
Prof. Dr. Xiaobo Zhou

E-Mail Website
Guest Editor
McGovern Medical School, and School of Biomedical Informatics, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA
Interests: bioinformatics; systems biology; imaging informatics; clinical informatics
Dr. Ivan Martinez

E-Mail Website
Guest Editor
Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV 26506, USA
Interests: miRNA biogenesis; lncRNA and cancer; human papillomavirus; coronaviruses; lung cancer; quiescence; senescence
Prof. Dr. Leonard Lipovich

E-Mail Website
Guest Editor
Department of Basic Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
Interests: lncRNA; long non-coding RNA; lincRNA; primate-specific genes; antisense; RNA therapeutics; precision medicine; GWAS; cancer; diabetes; transcriptome; proteogenomics
Dr. Tatiana Shkurat

E-Mail Website
Guest Editor
Academy of Biology and Biotechnologies, Southern Federal University, Rostov-on-Don, Russia
Interests: genetics; genomics; bioinformatics; biomedicine; synthetic biology; theoretical biology
Dr. Ekaterina Derevyanchuk

E-Mail Website
Guest Editor
Assoc. Prof. of the Genetics Department, Academy of Biology and Biotechnologies, Southern Federal University, Rostov-on-Don, Russia
Interests: molecular biology; human genetics; epigenetics; non-coding genome

Special Issue Information

Dear Colleagues,

This Special Issue comprises extended versions of selected papers and presentations from the IEEE BIBM 2021 Workshop on Long Non-Coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA), held on 9–12 December 2021, (https://community.wvu.edu/~daadjeroh/workshops/LNCRNA2021/). The LncRNA workshop was held in a mixed mode: both virtual/remote and face-to-face in Dubai, UAE.

Recent applications of high-throughput technologies in transcriptomics have changed our view of gene regulation and function. The discovery of the extensive transcription of large RNA transcripts, termed long noncoding RNAs (lncRNAs), has provided an important and novel perspective on the centrality of RNAs in gene regulation. LncRNAs are involved in various biological and cellular processes, such as genetic imprinting, chromatin remodeling, gene regulation and embryonic development. LncRNAs have been implicated in several chronic diseases, such as cancers, heart disease, etc. Given the abundance of lncRNAs, tens of thousands still need to be functionally characterized. Various types of genomic data on lncRNAs are currently available, including sequences, secondary/tertiary structures, transcriptome data, and their interactions with related proteins or genes. A key challenge is how to integrate data from a myriad of sources to determine the functions and regulatory mechanism of these ubiquitous lncRNAs. Computational studies of lncRNA secondary, tertiary structure, and lncRNA interactions with other molecules are in their infancy, and more work is still needed.

Authors of selected papers and invited presentations at the workshop were invited to submit extended versions of their work, including comprehensive review papers and research articles with unpublished, original research describing recent advances on topics related to this workshop, including, but not limited to:

  • lncRNA detection and biomarker discovery;
  • CLIP-Seq and RIP-Seq data analysis;
  • Prediction of physical binding between lncRNAs and DNAs and RNAs and protein;
  • Competition and interactions between lncRNA, miRNA, and mRNA;
  • Studying methylation regulating lncRNA functions;
  • Function prediction for lncRNAs;
  • Deep learning approaches to lncRNA/RNA binding protein prediction;
  • Computational approaches to analyzing lncRNAs;
  • lncRNA 3D secondary structures;
  • lncRNA–protein interactions;
  • lncRNA in epigenetic regulation;
  • lncRNA-associated disease network;
  • lncRNAs in plant genomics;
  • lncRNAs in phenotype–genotype problems;
  • lncRNAs and single-cell transcriptomics;
  • lncRNAs and spatial transcriptomics;
  • CRISPR/Cas9 and genome editing in lncRNAs.

Selected papers and presentations that have attracted the most interest on the web or that provide a particularly innovative contribution were gathered for publication. These papers were subjected to a peer review and have been published with the aim of attaining a rapid and wide dissemination of research results, developments, and applications. In addition, authors could submit their extended papers to this Special Issue after the workshop, so there was no need to wait for the submission deadline. All papers accepted for publication will be immediately published.

Prof. Dr. Donald Adjeroh
Prof. Dr. Xiaobo Zhou
Dr. Ivan Martinez
Prof. Dr. Leonard Lipovich
Dr. Tatiana Shkurat
Dr. Ekaterina Derevyanchuk
Guest Editors

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.

Published Papers (5 papers)

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Research

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15 pages, 22736 KiB  
Article
LncRNA PNKY Is Upregulated in Breast Cancer and Promotes Cell Proliferation and EMT in Breast Cancer Cells
by Forough Hakiminia, Firooz Jannat Alipoor, Mostafa Keshavarz and Malek Hossein Asadi
Non-Coding RNA 2023, 9(2), 25; https://doi.org/10.3390/ncrna9020025 - 06 Apr 2023
Cited by 1 | Viewed by 2003
Abstract
Long non-coding RNAs (lncRNAs) are known to be important regulators in different cellular processes and are implicated in various human diseases. Recently, lncRNA PNKY has been found to be involved in pluripotency and differentiation of embryonic and postnatal neural stem cells (NSCs); however, [...] Read more.
Long non-coding RNAs (lncRNAs) are known to be important regulators in different cellular processes and are implicated in various human diseases. Recently, lncRNA PNKY has been found to be involved in pluripotency and differentiation of embryonic and postnatal neural stem cells (NSCs); however, its expression and function in cancer cells is still unclear. In the present study, we observed the expression of PNKY in various cancer tissues, including brain, breast, colorectal, and prostate cancers. In particular, we demonstrated that lncRNA PNKY was significantly upregulated in breast tumors, especially high-grade tumors. Knock down experiments indicated that the suppression of PNKY in breast cancer cells could restrict their proliferation by promoting apoptosis, senescence, and cell cycle disruption. Moreover, the results demonstrated that PNKY may play a crucial role in the cell migration of breast cancer cells. We further found that PNKY may trigger EMT in breast cancer cells by upregulating miR-150 and restricting the expression of Zeb1 and Snail. This study is the first to provide new evidence on the expression and biological function of PNKY in cancer cells and its potential contribution to tumor growth and metastasis. Full article
(This article belongs to the Special Issue Selected Papers from IEEE BIBM 2021 Workshop on Long Non-coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA))
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11 pages, 280 KiB  
Article
The Role of Genetic Variants in the Long Non-Coding RNA Genes MALAT1 and H19 in the Pathogenesis of Childhood Obesity
by Tatiana Pavlovna Shkurat, Manar Ammar, Olga Bocharova, Elena Teplyakova, Anzhela Aleksandrova, Ruba Ali and Leonard Lipovich
Non-Coding RNA 2023, 9(2), 22; https://doi.org/10.3390/ncrna9020022 - 30 Mar 2023
Cited by 1 | Viewed by 1806
Abstract
Long non-coding RNAs (lncRNAs) play important roles in the maintenance of metabolic homeostasis. Recently, many studies have suggested that lncRNAs, such as Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and Imprinted Maternally Expressed Transcript (H19), might participate in the pathogenesis of metabolic disorders [...] Read more.
Long non-coding RNAs (lncRNAs) play important roles in the maintenance of metabolic homeostasis. Recently, many studies have suggested that lncRNAs, such as Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and Imprinted Maternally Expressed Transcript (H19), might participate in the pathogenesis of metabolic disorders such as obesity. We conducted a case-control study with 150 Russian children and adolescents aged between 5 and 17 years old in order to assess the statistical association between the single nucleotide polymorphisms (SNPs) rs3200401 in MALAT1 and rs217727 in H19, and the risk of developing obesity in this population. We further explored the possible association of rs3200401 and rs217727 with BMI Z-score and insulin resistance. The MALAT1 rs3200401 and H19 rs217727 SNPs were genotyped using Taqman SNP genotyping assay. The MALAT1 rs3200401 SNP was identified as a risk factor for childhood obesity (p < 0.05) under the dominant and allelic models, and the CT heterozygous genotype was associated with the risk of increased BMI and with insulin resistance. The H19 rs217727 SNP had no significant association with obesity risk (all p > 0.05). Our findings thus suggest that MALAT1 SNP rs3200401 is a potential indicator of obesity susceptibility and pathogenesis in children and adolescents. Full article
(This article belongs to the Special Issue Selected Papers from IEEE BIBM 2021 Workshop on Long Non-coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA))
14 pages, 2492 KiB  
Article
Activity-Dependent Non-Coding RNA MAPK Interactome of the Human Epileptic Brain
by Allison Kirchner, Fabien Dachet, Leonard Lipovich and Jeffrey A. Loeb
Non-Coding RNA 2023, 9(1), 3; https://doi.org/10.3390/ncrna9010003 - 04 Jan 2023
Cited by 1 | Viewed by 2118
Abstract
The human brain has evolved to have extraordinary capabilities, enabling complex behaviors. The uniqueness of the human brain is increasingly posited to be due in part to the functions of primate-specific, including human-specific, long non-coding RNA (lncRNA) genes, systemically less conserved than protein-coding [...] Read more.
The human brain has evolved to have extraordinary capabilities, enabling complex behaviors. The uniqueness of the human brain is increasingly posited to be due in part to the functions of primate-specific, including human-specific, long non-coding RNA (lncRNA) genes, systemically less conserved than protein-coding genes in evolution. Patients who have surgery for drug-resistant epilepsy are subjected to extensive electrical recordings of the brain tissue that is subsequently removed in order to treat their epilepsy. Precise localization of brain tissues with distinct electrical properties offers a rare opportunity to explore the effects of brain activity on gene expression. Here, we identified 231 co-regulated, activity-dependent lncRNAs within the human MAPK signaling cascade. Six lncRNAs, four of which were antisense to known protein-coding genes, were further examined because of their high expression and potential impact on the disease phenotype. Using a model of repeated depolarizations in human neuronal-like cells (Sh-SY5Y), we show that five out of six lncRNAs were electrical activity-dependent, with three of four antisense lncRNAs having reciprocal expression patterns relative to their protein-coding gene partners. Some were directly regulated by MAPK signaling, while others effectively downregulated the expression of the protein-coding genes encoded on the opposite strands of their genomic loci. These lncRNAs, therefore, likely contribute to highly evolved and primate-specific human brain regulatory functions that could be therapeutically modulated to treat epilepsy. Full article
(This article belongs to the Special Issue Selected Papers from IEEE BIBM 2021 Workshop on Long Non-coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA))
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Review

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17 pages, 1115 KiB  
Review
More than the SRY: The Non-Coding Landscape of the Y Chromosome and Its Importance in Human Disease
by Emily S. Westemeier-Rice, Michael T. Winters, Travis W. Rawson and Ivan Martinez
Non-Coding RNA 2024, 10(2), 21; https://doi.org/10.3390/ncrna10020021 - 10 Apr 2024
Viewed by 825
Abstract
Historically, the Y chromosome has presented challenges to classical methodology and philosophy of understanding the differences between males and females. A genetic unsolved puzzle, the Y chromosome was the last chromosome to be fully sequenced. With the advent of the Human Genome Project [...] Read more.
Historically, the Y chromosome has presented challenges to classical methodology and philosophy of understanding the differences between males and females. A genetic unsolved puzzle, the Y chromosome was the last chromosome to be fully sequenced. With the advent of the Human Genome Project came a realization that the human genome is more than just genes encoding proteins, and an entire universe of RNA was discovered. This dark matter of biology and the black box surrounding the Y chromosome have collided over the last few years, as increasing numbers of non-coding RNAs have been identified across the length of the Y chromosome, many of which have played significant roles in disease. In this review, we will uncover what is known about the connections between the Y chromosome and the non-coding RNA universe that originates from it, particularly as it relates to long non-coding RNAs, microRNAs and circular RNAs. Full article
(This article belongs to the Special Issue Selected Papers from IEEE BIBM 2021 Workshop on Long Non-coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA))
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Other

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6 pages, 423 KiB  
Systematic Review
Polymorphism rs2383207 of CDKN2B-AS and Susceptibility to Atherosclerosis: A Mini Review
by Sofia Vladimorovna Timofeeva, Tatiana Alexandrovna Sherchkova and Tatiana Pavlovna Shkurat
Non-Coding RNA 2022, 8(6), 78; https://doi.org/10.3390/ncrna8060078 - 18 Nov 2022
Cited by 1 | Viewed by 1581
Abstract
We conducted this meta-analysis to estimate associations between CDKN2B antisense (CDKN2B-AS) rs2383207 polymorphism and susceptibility to atherosclerosis. A systematic literature research of Google Scholar and PubMed was performed to identify eligible studies. Overall, eight studies were included for meta-analyses. The association was assessed [...] Read more.
We conducted this meta-analysis to estimate associations between CDKN2B antisense (CDKN2B-AS) rs2383207 polymorphism and susceptibility to atherosclerosis. A systematic literature research of Google Scholar and PubMed was performed to identify eligible studies. Overall, eight studies were included for meta-analyses. The association was assessed by statistical odds’ ratio (OR) with 95% confidence interval (CI). RevMan software (Cochrane Collaboration, 5.3. Copenhagen) was used for the meta-analysis. Pooled overall analyses showed that rs2383207 polymorphism was associated with the risk of atherosclerosis in the whole population. Additional analyses by ethnicity revealed that rs2383207 polymorphism was associated with susceptibility to atherosclerosis in Asians and Caucasians. Our results suggest that rs2383207, might serve as genetic biomarkers of atherosclerosis. Further, studies will be required to confirm the observed association. Full article
(This article belongs to the Special Issue Selected Papers from IEEE BIBM 2021 Workshop on Long Non-coding RNAs: Mechanism, Function, and Computational Analysis (BIBM-LncRNA))
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