International Journal of Molecular Sciences

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15 pages, 4377 KiB

Open AccessArticle

Strong Activation of ID1, ID2, and ID3 Genes Is Coupled with the Formation of Vasculogenic Mimicry Phenotype in Melanoma Cells

by Nickolai A. Tchurikov, Amalia A. Vartanian, Elena S. Klushevskaya, Ildar R. Alembekov, Antonina N. Kretova, Viktoriya N. Lukicheva, Vladimir R. Chechetkin, Galina I. Kravatskaya, Vyacheslav S. Kosorukov and Yuri V. Kravatsky

Int. J. Mol. Sci. 2024, 25(17), 9291; https://doi.org/10.3390/ijms25179291 - 27 Aug 2024

Viewed by 988

Abstract

Gene expression patterns are very sensitive to external influences and are reflected in phenotypic changes. It was previously described that transferring melanoma cells from a plastic surface to Matrigel led to formation of de novo vascular networks—vasculogenic mimicry—that are characteristic to a stemness [...] Read more.

Gene expression patterns are very sensitive to external influences and are reflected in phenotypic changes. It was previously described that transferring melanoma cells from a plastic surface to Matrigel led to formation of de novo vascular networks—vasculogenic mimicry—that are characteristic to a stemness phenotype in aggressive tumors. Up to now there was no detailed data about the gene signature accompanying this process. Here, we show that this transfer shortly led to extremely strong epigenetic changes in gene expression in the melanoma cells. We observed that on Matrigel numerous genes controlling ribosome biogenesis were upregulated. However, most of the activated genes were inhibitors of the differentiation genes (ID1, ID2, and ID3). At the same time, the genes that control differentiation were downregulated. Both the upregulated and the downregulated genes are simultaneously targeted by different transcription factors shaping sets of co-expressed genes. The specific group of downregulated genes shaping contacts with rDNA genes are also associated with the H3K27me3 mark and with numerous lincRNAs and miRNAs. We conclude that the stemness phenotype of melanoma cells is due to the downregulation of developmental genes and formation of dedifferentiated cells. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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17 pages, 5456 KiB

Open AccessArticle

Melatonin Inhibits Testosterone Synthesis in Rooster Leydig Cells by Targeting CXCL14 through miR-7481-3p

by Haoran Xu, Jingxin Pu, Yunkun Teng, Qingyu Zhu, Lewei Guo, Jing Zhao, He Ding, Yi Fang, Xin Ma, Hongyu Liu, Jing Guo, Wenfa Lu and Jun Wang

Int. J. Mol. Sci. 2023, 24(23), 16552; https://doi.org/10.3390/ijms242316552 - 21 Nov 2023

Cited by 1 | Viewed by 1414

Abstract

Melatonin has been proved to be involved in testosterone synthesis, but whether melatonin participates in testosterone synthesis by regulating miRNA in Leydig cells is still unclear. The purpose of this study is to clarify the mechanism of melatonin on Leydig cells testosterone synthesis [...] Read more.

Melatonin has been proved to be involved in testosterone synthesis, but whether melatonin participates in testosterone synthesis by regulating miRNA in Leydig cells is still unclear. The purpose of this study is to clarify the mechanism of melatonin on Leydig cells testosterone synthesis from the perspective of miRNA. Our results showed that melatonin could significantly inhibit testosterone synthesis in rooster Leydig cells. miR-7481-3p and CXCL14 were selected as the target of melatonin based on RNA-seq and miRNA sequencing. The results of dual-luciferase reporter assays showed that miR-7481-3p targeted the 3′-UTR of CXCL14. The overexpression of miR-7481-3p significantly inhibited the expression of CXCL14 and restored the inhibitory role of melatonin testosterone synthesis and the expression of StAR, CYP11A1, and 3β-HSD in rooster Leydig cells. Similarly, interference with CXCL14 could reverse the inhibitory effect of melatonin on the level of testosterone synthesis and the expression of StAR, CYP11A1, and 3β-HSD in rooster Leydig cells. The RNA-seq results showed that melatonin could activate the PI3K/AKT signal pathway. Interference with CXCL14 significantly inhibited the phosphorylation level of PI3K and AKT, and the inhibited PI3K/AKT signal pathway could reverse the inhibitory effect of CXCL14 on testosterone synthesis and the expression of StAR, CYP11A1 and 3β-HSD in rooster Leydig cells. Our results indicated that melatonin inhibits testosterone synthesis by targeting miR-7481-3p/CXCL14 and inhibiting the PI3K/AKT pathway. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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13 pages, 2193 KiB

Open AccessArticle

The Evaluation of SHAPE-MaP RNA Structure Probing Protocols Reveals a Novel Role of Mn²⁺ in the Detection of 2′-OH Adducts

by Kamilla Grzywacz, Agnieszka Chełkowska-Pauszek, Marianna Plucinska-Jankowska and Marek Żywicki

Int. J. Mol. Sci. 2023, 24(9), 7890; https://doi.org/10.3390/ijms24097890 - 26 Apr 2023

Cited by 1 | Viewed by 3202

Abstract

Chemical probing, for decades, has been one of the most popular tools for studying the secondary structure of RNA molecules. Recently, protocols for simultaneous analysis of multiple RNAs have been developed, enabling in vivo transcriptome-wide interrogation of the RNA structure dynamics. One of [...] Read more.

Chemical probing, for decades, has been one of the most popular tools for studying the secondary structure of RNA molecules. Recently, protocols for simultaneous analysis of multiple RNAs have been developed, enabling in vivo transcriptome-wide interrogation of the RNA structure dynamics. One of the most popular methods is the selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP). In this study, we describe the evaluation of this protocol by addressing the influence of the reverse transcription enzymes, buffer conditions, and chemical probes on the properties of the cDNA library and the quality of mutational profiling-derived structural signals. Our results reveal a SuperScript IV (SSIV) reverse transcriptase as a more efficient enzyme for mutational profiling of SHAPE adducts and shed new light on the role of Mn²⁺ cations in the modulation of SSIV readthrough efficiency. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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18 pages, 12969 KiB

Open AccessArticle

Systematic Characterization and Regulatory Role of lncRNAs in Asian Honey Bees Responding to Microsporidian Infestation

by Zixin Wang, Siyi Wang, Xiaoxue Fan, Kaiyao Zhang, Jiaxin Zhang, Haodong Zhao, Xuze Gao, Yiqiong Zhang, Sijia Guo, Dingding Zhou, Qiming Li, Zhihao Na, Dafu Chen and Rui Guo

Int. J. Mol. Sci. 2023, 24(6), 5886; https://doi.org/10.3390/ijms24065886 - 20 Mar 2023

Cited by 2 | Viewed by 1935

Abstract

Long noncoding RNAs (lncRNAs) are pivotal regulators in gene expression and diverse biological processes, such as immune defense and host–pathogen interactions. However, little is known about the roles of lncRNAs in the response of the Asian honey bee (Apis cerana) to [...] Read more.

Long noncoding RNAs (lncRNAs) are pivotal regulators in gene expression and diverse biological processes, such as immune defense and host–pathogen interactions. However, little is known about the roles of lncRNAs in the response of the Asian honey bee (Apis cerana) to microsporidian infestation. Based on our previously obtained high-quality transcriptome datasets from the midgut tissues of Apis cerana cerana workers at 7 days post inoculation (dpi) and 10 dpi with Nosema ceranae (AcT7 and AcT10 groups) and the corresponding un-inoculated midgut tissues (AcCK7 and AcCK10 groups), the transcriptome-wide identification and structural characterization of lncRNAs were conducted, and the differential expression pattern of lncRNAs was then analyzed, followed by investigation of the regulatory roles of differentially expressed lncRNAs (DElncRNAs) in host response. Here, 2365, 2322, 2487, and 1986 lncRNAs were, respectively, identified in the AcCK7, AcT7, AcCK7, and AcT10 groups. After removing redundant ones, a total of 3496 A. c. cerana lncRNAs were identified, which shared similar structural characteristics with those discovered in other animals and plants, such as shorter exons and introns than mRNAs. Additionally, 79 and 73 DElncRNAs were screened from the workers’ midguts at 7 dpi and 10 dpi, respectively, indicating the alteration of the overall expression pattern of lncRNAs in host midguts after N. ceranae infestation. These DElncRNAs could, respectively, regulate 87 and 73 upstream and downstream genes, involving a suite of functional terms and pathways, such as metabolic process and Hippo signaling pathway. Additionally, 235 and 209 genes co-expressed with DElncRNAs were found to enrich in 29 and 27 terms, as well as 112 and 123 pathways, such as ABC transporters and the cAMP signaling pathway. Further, it was detected that 79 (73) DElncRNAs in the host midguts at 7 (10) dpi could target 321 (313) DEmiRNAs and further target 3631 (3130) DEmRNAs. TCONS_00024312 and XR_001765805.1 were potential precursors for ame-miR-315 and ame-miR-927, while TCONS_00006120 was the putative precursor for both ame-miR-87-1 and ame-miR-87-2. These results together suggested that DElncRNAs are likely to play regulatory roles in the host response to N. ceranae infestation through the regulation of neighboring genes via a cis-acting effect, modulation of co-expressed mRNAs via trans-acting effect, and control of downstream target genes’ expression via competing endogenous RNA networks. Our findings provide a basis for disclosing the mechanism underlying DElncRNA-mediated host N. ceranae response and a new perspective into the interaction between A. c. cerana and N. ceranae. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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18 pages, 2805 KiB

Open AccessArticle

DNA Nanomachine (DNM) Biplex Assay for Differentiating Bacillus cereus Species

by Muhannad Ateiah, Erik R. Gandalipov, Aleksandr A. Rubel, Maria S. Rubel and Dmitry M. Kolpashchikov

Int. J. Mol. Sci. 2023, 24(5), 4473; https://doi.org/10.3390/ijms24054473 - 24 Feb 2023

Cited by 5 | Viewed by 2850

Abstract

Conventional methods for the detection and differentiation of Bacillus cereus group species have drawbacks mostly due to the complexity of genetic discrimination between the Bacillus cereus species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA [...] Read more.

Conventional methods for the detection and differentiation of Bacillus cereus group species have drawbacks mostly due to the complexity of genetic discrimination between the Bacillus cereus species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA by DNA nanomachine (DNM). The assay uses a universal fluorescent reporter and four all-DNA binding fragments, three of which are responsible for “opening up” the folded rRNA while the fourth stand is responsible for detecting single nucleotide variation (SNV) with high selectivity. Binding of the DNM to 16S rRNA results in the formation of the 10–23 deoxyribozyme catalytic core that cleaves the fluorescent reporter and produces a signal, which is amplified over time due to catalytic turnover. This developed biplex assay enables the detection of B. thuringiensis 16S rRNA at fluorescein and B. mycoides at Cy5 channels with a limit of detection of 30 × 10³ and 35 × 10³ CFU/mL, respectively, after 1.5 h with a hands-on time of ~10 min. The new assay may simplify the analysis of biological RNA samples and might be useful for environmental monitoring as a simple and inexpensive alternative to amplification-based nucleic acid analysis. The DNM proposed here may become an advantageous tool for detecting SNV in clinically significant DNA or RNA samples and can easily differentiate SNV under broadly variable experimental conditions and without prior amplification. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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17 pages, 6713 KiB

Open AccessArticle

Integrating Analysis to Identify Differential circRNAs Involved in Goat Endometrial Receptivity

by Wenjing Wang, Xupeng Zang, Yaokun Li, Dewu Liu, Linjun Hong and Guangbin Liu

Int. J. Mol. Sci. 2023, 24(2), 1531; https://doi.org/10.3390/ijms24021531 - 12 Jan 2023

Cited by 2 | Viewed by 2015

Abstract

Endometrial receptivity is one of the main factors underlying a successful pregnancy, with reports substantiating the fact that suboptimal endometrial receptivity accounts for two-thirds of early implantation event failures. The association between circRNAs and endometrial receptivity in the goat remains unclear. This study [...] Read more.

Endometrial receptivity is one of the main factors underlying a successful pregnancy, with reports substantiating the fact that suboptimal endometrial receptivity accounts for two-thirds of early implantation event failures. The association between circRNAs and endometrial receptivity in the goat remains unclear. This study aims to identify potential circRNAs and regulatory mechanisms related to goat endometrial receptivity. Therefore, the endometrial samples on day 16 of pregnancy and day 16 of the estrous cycle were analyzed using high-throughput RNA-seq and bioinformatics. The results show that 4666 circRNAs were identified, including 7 downregulated and 11 upregulated differentially expressed circRNAs (DE-circRNAs). Back-splicing and RNase R resistance verified the identified circRNAs. We predicted the competing endogenous RNA (ceRNA) regulatory mechanism and potential target genes of DE-circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these predicted target genes suggest that DE-circRNAs were significantly involved in establishing endometrial receptivity. Furthermore, Sanger sequencing, qPCR, correlation analysis and Fluorescence in Situ Hybridization (FISH) show that circ_MYRF derived from the host gene myelin regulatory factor (MYRF) might regulate the expression of interferon stimulating gene 15 (ISG15), thereby promoting the formation of endometrial receptivity. These novel findings may contribute to a better understanding of the molecular mechanisms regulating endometrial receptivity and promoting the maternal recognition of pregnancy (MRP). Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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15 pages, 2835 KiB

Open AccessArticle

Discovery and Functional Analysis of Secondary Hair Follicle miRNAs during Annual Cashmere Growth

by Minglin Wang, Han Dai, Shengda Sheng, Yanlei Liu, Shuyi Zhang, Wenlin Bai and Huiling Xue

Int. J. Mol. Sci. 2023, 24(2), 1063; https://doi.org/10.3390/ijms24021063 - 5 Jan 2023

Cited by 6 | Viewed by 1796

Abstract

Secondary hair follicles (SHFs) produce the thermoregulatory cashmere of goats. MicroRNAs (miRNAs) play indispensable roles in hair follicle formation and growth. However, most studies examining miRNAs related to cashmere have been performed on goat skin. It remains unclear which miRNAs are highly expressed [...] Read more.

Secondary hair follicles (SHFs) produce the thermoregulatory cashmere of goats. MicroRNAs (miRNAs) play indispensable roles in hair follicle formation and growth. However, most studies examining miRNAs related to cashmere have been performed on goat skin. It remains unclear which miRNAs are highly expressed in SHFs or how miRNAs affect cashmere growth. In the present study, we isolated the SHFs under a dissecting microscope and analyzed the miRNA signatures during annual cashmere growth. Small-RNA sequencing followed by genome-wide expression analysis revealed that early anagen is a crucial phase for miRNA regulation of the cashmere growth, as revealed by two predominant groups of miRNAs. Although they exhibited opposite expression patterns, both groups demonstrated sharp changes of expression when in transit from early anagen to mid-anagen. In addition, we identified 96 miRNA signatures that were differentially expressed between different phases among 376 miRNAs. Functional analysis of the predicted target genes of highly expressed or differentially expressed miRNAs indicated that these miRNAs were involved in signal pathways associated with SHF development, regeneration, and regression. Furthermore, miR-143-3p was preferentially expressed in SHFs and Itga6 was identified as one of targets. The dual-luciferase and in situ hybridization assay demonstrated that miR-143-3p directly repressed the expression of Itga6, suggesting a possible novel role for miR-143-3p in cashmere growth. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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18 pages, 1825 KiB

Open AccessArticle

Sperm DNA Fragmentation and Sperm-Borne miRNAs: Molecular Biomarkers of Embryo Development?

by Anna Chiara Conflitti, Gaia Cicolani, Alessandra Buonacquisto, Francesco Pallotti, Fabiana Faja, Serena Bianchini, Giovanna Blaconà, Sabina Maria Bruno, Antonella Linari, Marco Lucarelli, Diletta Montanino, Ludovico Muzii, Andrea Lenzi, Francesco Lombardo and Donatella Paoli

Int. J. Mol. Sci. 2023, 24(2), 1007; https://doi.org/10.3390/ijms24021007 - 5 Jan 2023

Cited by 16 | Viewed by 2450

Abstract

The evaluation of morpho-functional sperm characteristics alone is not enough to explain infertility or to predict the outcome of Assisted Reproductive Technologies (ART): more sensitive diagnostic tools are needed in clinical practice. The aim of the present study was to analyze Sperm DNA [...] Read more.

The evaluation of morpho-functional sperm characteristics alone is not enough to explain infertility or to predict the outcome of Assisted Reproductive Technologies (ART): more sensitive diagnostic tools are needed in clinical practice. The aim of the present study was to analyze Sperm DNA Fragmentation (SDF) and sperm-borne miR-34c-5p and miR-449b-5p levels in men of couples undergoing ART, in order to investigate any correlations with fertilization rate, embryo quality and development. Male partners (n = 106) were recruited. Semen analysis, SDF evaluation and molecular profiling analysis of miR-34c-5p and miR-449b-5p (in 38 subjects) were performed. Sperm DNA Fragmentation evaluation- a positive correlation between SDF post sperm selection and the percentage of low-quality embryos and a negative correlation with viable embryo were found. SDF > 2.9% increased the risk of obtaining a non-viable embryo by almost 4-fold. Sperm miRNAs profile—we found an association with both miRNAs and sperm concentration, while miR-449b-5p is positively associated with SDF. Moreover, the two miRNAs are positively correlated. Higher levels of miR-34c-5p compared to miR-449b-5p increases by 14-fold the probability of obtaining viable embryos. This study shows that SDF, sperm miR-34c-5p, and miR-449b-5p have a promising role as biomarkers of semen quality and ART outcome. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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17 pages, 20401 KiB

Open AccessArticle

Unveiling the circRNA-Mediated Immune Responses of Western Honey Bee Larvae to Ascosphaera apis Invasion

by Yaping Ye, Xiaoxue Fan, Zongbing Cai, Ying Wu, Wende Zhang, Haodong Zhao, Sijia Guo, Peilin Feng, Qiming Li, Peiyuan Zou, Mengjun Chen, Nian Fan, Dafu Chen and Rui Guo

Int. J. Mol. Sci. 2023, 24(1), 613; https://doi.org/10.3390/ijms24010613 - 29 Dec 2022

Cited by 6 | Viewed by 4199

Abstract

Western honey bee (Apis mellifera), a eusocial insect with a superior economic and ecological value, is widely used in the beekeeping industry throughout the world. As a new class of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) participate in the modulation of [...] Read more.

Western honey bee (Apis mellifera), a eusocial insect with a superior economic and ecological value, is widely used in the beekeeping industry throughout the world. As a new class of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) participate in the modulation of considerable biological processes, such as the immune response via diverse manners. Here, the identification, characteristic investigation, and molecular verification of circRNAs in the Apis mellifera ligustica larval guts were conducted, and the expression pattern of larval circRNAs during the Ascosphaera apis infection was analyzed, followed by the exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 2083 circRNAs in the larval guts of A. m. ligustcia were identified, with a length distribution ranging from 106 nt to 92,798 nt. Among these, exonic circRNAs were the most abundant type and LG1 was the most distributed chromosome. Additionally, 25, 14, and 30 up-regulated circRNAs as well as 26, 25, and 62 down-regulated ones were identified in the A. apis-inoculated 4-, 5-, and 6-day-old larval guts in comparison with the corresponding un-inoculated larval guts. These DEcircRNAs were predicted to target 35, 70, and 129 source genes, which were relative to 12, 23, and 20 GO terms as well as 11, 10, and 27 KEGG pathways, including 5 cellular and humoral immune pathways containing apoptosis, autophagy, endocytosis, MAPK, Toll, and Imd signaling pathways. Furthermore, complex competing endogenous RNA (ceRNA) regulatory networks were detected to be formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The Target DEmRNAs were engaged in 24, 20, and 25 functional terms as well as 62, 80, and 159 pathways, including several vital immune defense-associated pathways, namely the lysosome, endocytosis, phagosome, autophagy, apoptosis, MAPK, Jak-STAT, Toll, and Imd signaling pathways. Finally, back-splicing sites within 15 circRNAs and the difference in the 9 DEcircRNAs’ expression between un-inoculated and A. apis-inoculated larval guts were confirmed utilizing molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions, but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. m. ligustica larvae against A. apis invasion. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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15 pages, 5203 KiB

Open AccessArticle

Cognate RNA-Binding Modes by the Alternative-Splicing Regulator MBNL1 Inferred from Molecular Dynamics

by Àlex L. González, Daniel Fernández-Remacha, José Ignacio Borrell, Jordi Teixidó and Roger Estrada-Tejedor

Int. J. Mol. Sci. 2022, 23(24), 16147; https://doi.org/10.3390/ijms232416147 - 18 Dec 2022

Cited by 1 | Viewed by 1787

Abstract

The muscleblind-like protein family (MBNL) plays a prominent role in the regulation of alternative splicing. Consequently, the loss of MBNL function resulting from sequestration by RNA hairpins triggers the development of a neuromuscular disease called myotonic dystrophy (DM). Despite the sequence and structural [...] Read more.

The muscleblind-like protein family (MBNL) plays a prominent role in the regulation of alternative splicing. Consequently, the loss of MBNL function resulting from sequestration by RNA hairpins triggers the development of a neuromuscular disease called myotonic dystrophy (DM). Despite the sequence and structural similarities between the four zinc-finger domains that form MBNL1, recent studies have revealed that the four binding domains have differentiated splicing activity. The dynamic behaviors of MBNL1 ZnFs were simulated using conventional molecular dynamics (cMD) and steered molecular dynamics (sMD) simulations of a structural model of MBNL1 protein to provide insights into the binding selectivity of the four zinc-finger (ZnF) domains toward the GpC steps in YGCY RNA sequence. In accordance with previous studies, our results suggest that both global and local residue fluctuations on each domain have great impacts on triggering alternative splicing, indicating that local motions in RNA-binding domains could modulate their affinity and specificity. In addition, all four ZnF domains provide a distinct RNA-binding environment in terms of structural sampling and mobility that may be involved in the differentiated MBNL1 splicing events reported in the literature. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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18 pages, 3681 KiB

Open AccessArticle

Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping

by Stefanie A. Köhler, Lisa Brandl, Pamela L. Strissel, Laura Gloßner, Arif B. Ekici, Miriam Angeloni, Fulvia Ferrazzi, Veronika Bahlinger, Arndt Hartmann, Matthias W. Beckmann, Markus Eckstein and Reiner Strick

Int. J. Mol. Sci. 2022, 23(18), 10267; https://doi.org/10.3390/ijms231810267 - 6 Sep 2022

Cited by 2 | Viewed by 2235

Abstract

Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known [...] Read more.

Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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17 pages, 13238 KiB

Open AccessArticle

Functional Characterization of Two RNA Methyltransferase Genes METTL3 and METTL14 Uncovers the Roles of m⁶A in Mediating Adaptation of Plutella xylostella to Host Plants

by Bei-Bei Wang, Ying-Fang Lai, Fei-Fei Li, Lu Jiao, Qing-Xuan Qiao, Shan-Yu Li, Xiu-Juan Xiang, Huang Liao, Min-Sheng You and Wei-Yi He

Int. J. Mol. Sci. 2022, 23(17), 10013; https://doi.org/10.3390/ijms231710013 - 2 Sep 2022

Cited by 4 | Viewed by 2055

Abstract

N⁶-methyladenosine (m⁶A) is one of the major epigenetic modifications in eukaryotes. Although increasing functions of m⁶A have been identified in insects, its role in Plutella xylostella L. for host plant adaptation remains unclear. In the current study, [...] Read more.

N⁶-methyladenosine (m⁶A) is one of the major epigenetic modifications in eukaryotes. Although increasing functions of m⁶A have been identified in insects, its role in Plutella xylostella L. for host plant adaptation remains unclear. In the current study, we show that the m⁶A content of P. xylostella was relatively low in different developmental stages and tissues, with no significant differences. Two RNA methyltransferase genes, PxMETTL3 (methyltransferase-like 3) and PxMETTL14 (methyltransferase-like 14), were identified and characterized. PxMETTL3 could be transcribed into two transcripts, and PxMETTL14 had only one transcript; both of these genes were highly expressed in egg and adult stages and reproductive tissues. The CRISPR/Cas9-mediated knockout of PxMETTL3 (ΔPxMETTL3-2) or PxMETTL14 (ΔPxMETTL14-14) confirmed their function in m⁶A installation into RNA. Furthermore, upon transfer from an artificial diet to the host plant, the mutant strains were affected in terms of larval and pupal weight or adult emergence rate, while the wildtype (WT) strain did not exhibit any difference. In addition, the fecundity and egg hatching rate of the WT strain decreased significantly, whereas only the ΔPxMETTL14-14 mutant strain displayed significantly decreased fecundity. There seemed to be a tradeoff between the stress adaptation and reproduction in P. xylostella mediated by m⁶A modification. During host transfer, the expression of PxMETTL14 was consistent with the change in m⁶A content, which implied that PxMETTL14 could respond to host plant defense effectively, and may regulate m⁶A content. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially expressed transcripts with changes in m⁶A levels revealed that the potential functions of m⁶A-related genes may be involved in steroid biosynthesis for larval performance and metabolic pathways for adult reproduction. Overall, our work reveals an epigenetic regulation mechanism for the rapid adaptation of P. xylostella to variations in the host environment. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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14 pages, 4132 KiB

Open AccessArticle

MicroRNA Let-7a, -7e and -133a Attenuate Hypoxia-Induced Atrial Fibrosis via Targeting Collagen Expression and the JNK Pathway in HL1 Cardiomyocytes

by Chien-Hsien Lo, Li-Ching Li, Shun-Fa Yang, Chin-Feng Tsai, Yao-Tsung Chuang, Hsiao-Ju Chu and Kwo-Chang Ueng

Int. J. Mol. Sci. 2022, 23(17), 9636; https://doi.org/10.3390/ijms23179636 - 25 Aug 2022

Cited by 11 | Viewed by 2402

Abstract

Fibrosis is a hallmark of atrial structural remodeling. The main aim of this study was to investigate the role of micro-ribonucleic acids (miRNAs) in the modulation of fibrotic molecular mechanisms in response to hypoxic conditions, which may mediate atrial fibrosis. Under a condition [...] Read more.

Fibrosis is a hallmark of atrial structural remodeling. The main aim of this study was to investigate the role of micro-ribonucleic acids (miRNAs) in the modulation of fibrotic molecular mechanisms in response to hypoxic conditions, which may mediate atrial fibrosis. Under a condition of hypoxia induced by a hypoxia chamber, miRNA arrays were used to identify the specific miRNAs associated with the modulation of fibrotic genes. Luciferase assay, real-time polymerase chain reaction, immunofluorescence and Western blotting were used to investigate the effects of miRNAs on the expressions of the fibrotic markers collagen I and III (COL1A, COL3A) and phosphorylation levels of the stress kinase c-Jun N-terminal kinase (JNK) pathway in a cultured HL-1 atrial cardiomyocytes cell line. COL1A and COL3A were found to be the direct regulatory targets of miR-let-7a, miR-let-7e and miR-133a in hypoxic atrial cardiac cells in vitro. The expressions of COL1A and COL3A were influenced by treatment with miRNA mimic and antagomir while hypoxia-induced collagen expression was inhibited by the delivery of miR-133a, miR-let-7a or miR-let-7e. The JNK pathway was critical in the pathogenesis of atrial fibrosis. The JNK inhibitor SP600125 increased miRNA expressions and repressed the fibrotic markers COL1A and COL3A. In conclusion, MiRNA let-7a, miR-let-7e and miR-133a play important roles in hypoxia-related atrial fibrosis by inhibiting collagen expression and post-transcriptional repression by the JNK pathway. These novel findings may lead to the development of new therapeutic strategies. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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13 pages, 2845 KiB

Open AccessArticle

DNA Methylation Mediates lncRNA2919 Regulation of Hair Follicle Regeneration

by Bohao Zhao, Jiali Li, Ming Liu, Naisu Yang, Zhiyuan Bao, Xiyu Zhang, Yingying Dai, Jiawei Cai, Yang Chen and Xinsheng Wu

Int. J. Mol. Sci. 2022, 23(16), 9481; https://doi.org/10.3390/ijms23169481 - 22 Aug 2022

Cited by 6 | Viewed by 2544

Abstract

Hair follicles (HFs) are organs that periodically regenerate during the growth and development of mammals. Long non-coding RNAs (lncRNAs) are non-coding RNAs with crucial roles in many biological processes. Our previous study identified that lncRNA2919 is highly expressed in catagen during the HF [...] Read more.

Hair follicles (HFs) are organs that periodically regenerate during the growth and development of mammals. Long non-coding RNAs (lncRNAs) are non-coding RNAs with crucial roles in many biological processes. Our previous study identified that lncRNA2919 is highly expressed in catagen during the HF cycle. In this study, the in vivo rabbit model was established using intradermal injection of adenovirus-mediated lncRNA2919. The results showed that lncRNA2919 decreased HF depth and density and contributed to HF regrowth, thereby indicating that lncRNA2919 plays a negative role in HF regeneration. Moreover, methylation levels of the lncRNA2919 promoter at different HF cycle stages were detected through bisulfite sequencing. The key CpG site that negatively correlates with lncRNA2919 expression during the HF cycle was identified. 5-Aza-dc-induced demethylation upregulated lncRNA2919 expression, and the core promoter region of lncRNA2919 was verified on the basis of luciferase activity. Furthermore, we found that DNA methylation could prevent the binding of EGR1 to the lncRNA2919 promoter region, thereby affecting the transcriptional expression of lncRNA2919. Collectively, DNA methylation inhibits the transcriptional expression of lncRNA2919, which plays a vital role in the HF cycle and HF regrowth. These findings contribute to the basic theory of epigenetics in HF biology and provide references for further research in HF disease treatment and animal wool production. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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20 pages, 5485 KiB

Open AccessArticle

GcvB Regulon Revealed by Transcriptomic and Proteomic Analysis in Vibrio alginolyticus

by Bing Liu, Jianxiang Fang, Huizhen Chen, Yuehong Sun, Shan Yang, Qian Gao, Ying Zhang and Chang Chen

Int. J. Mol. Sci. 2022, 23(16), 9399; https://doi.org/10.3390/ijms23169399 - 20 Aug 2022

Cited by 6 | Viewed by 2466

Abstract

Vibrio alginolyticus is a widely distributed marine bacterium that is a threat to the aquaculture industry as well as human health. Evidence has revealed critical roles for small RNAs (sRNAs) in bacterial physiology and cellular processes by modulating gene expression post-transcriptionally. GcvB is [...] Read more.

Vibrio alginolyticus is a widely distributed marine bacterium that is a threat to the aquaculture industry as well as human health. Evidence has revealed critical roles for small RNAs (sRNAs) in bacterial physiology and cellular processes by modulating gene expression post-transcriptionally. GcvB is one of the most conserved sRNAs that is regarded as the master regulator of amino acid uptake and metabolism in a wide range of Gram-negative bacteria. However, little information about GcvB-mediated regulation in V. alginolyticus is available. Here we first characterized GcvB in V. alginolyticus ZJ-T and determined its regulon by integrated transcriptome and quantitative proteome analysis. Transcriptome analysis revealed 40 genes differentially expressed (DEGs) between wild-type ZJ-T and gcvB mutant ZJ-T-ΔgcvB, while proteome analysis identified 50 differentially expressed proteins (DEPs) between them, but only 4 of them displayed transcriptional differences, indicating that most DEPs are the result of post-transcriptional regulation of gcvB. Among the differently expressed proteins, 21 are supposed to be involved in amino acid biosynthesis and transport, and 11 are associated with type three secretion system (T3SS), suggesting that GcvB may play a role in the virulence besides amino acid metabolism. RNA-EMSA showed that Hfq binds to GcvB, which promotes its stability. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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15 pages, 3487 KiB

Open AccessArticle

Microvesicles and Microvesicle-Associated microRNAs Reflect Glioblastoma Regression: Microvesicle-Associated miR-625-5p Has Biomarker Potential

by Natalia Simionescu, Miruna Nemecz, Anca-Roxana Petrovici, Ioan Sebastian Nechifor, Razvan-Cristian Buga, Marius Gabriel Dabija, Lucian Eva and Adriana Georgescu

Int. J. Mol. Sci. 2022, 23(15), 8398; https://doi.org/10.3390/ijms23158398 - 29 Jul 2022

Cited by 9 | Viewed by 2132

Abstract

Glioblastoma (GB) is the most aggressive and recurrent form of brain cancer in adults. We hypothesized that the identification of biomarkers such as certain microRNAs (miRNAs) and the circulating microvesicles (MVs) that transport them could be key to establishing GB progression, recurrence and [...] Read more.

Glioblastoma (GB) is the most aggressive and recurrent form of brain cancer in adults. We hypothesized that the identification of biomarkers such as certain microRNAs (miRNAs) and the circulating microvesicles (MVs) that transport them could be key to establishing GB progression, recurrence and therapeutic response. For this purpose, circulating MVs were isolated from the plasma of GB patients (before and after surgery) and of healthy subjects and characterized by flow cytometry. OpenArray profiling and the individual quantification of selected miRNAs in plasma and MVs was performed, followed by target genes’ prediction and in silico survival analysis. It was found that MVs’ parameters (number, EGFRvIII and EpCAM) decreased after the surgical resection of GB tumors, but the inter-patient variability was high. The expression of miR-106b-5p, miR-486-3p, miR-766-3p and miR-30d-5p in GB patients’ MVs was restored to control-like levels after surgery: miR-106b-5p, miR-486-3p and miR-766-3p were upregulated, while miR-30d-5p levels were downregulated after surgical resection. MiR-625-5p was only identified in MVs isolated from GB patients before surgery and was not detected in plasma. Target prediction and pathway analysis showed that the selected miRNAs regulate genes involved in cancer pathways, including glioma. In conclusion, miR-625-5p shows potential as a biomarker for GB regression or recurrence, but further in-depth studies are needed. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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24 pages, 3610 KiB

Open AccessArticle

Circ-LocNet: A Computational Framework for Circular RNA Sub-Cellular Localization Prediction

by Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Muhammad Imran Malik, Andreas Dengel and Sheraz Ahmed

Int. J. Mol. Sci. 2022, 23(15), 8221; https://doi.org/10.3390/ijms23158221 - 26 Jul 2022

Cited by 4 | Viewed by 2895

Abstract

Circular ribonucleic acids (circRNAs) are novel non-coding RNAs that emanate from alternative splicing of precursor mRNA in reversed order across exons. Despite the abundant presence of circRNAs in human genes and their involvement in diverse physiological processes, the functionality of most circRNAs remains [...] Read more.

Circular ribonucleic acids (circRNAs) are novel non-coding RNAs that emanate from alternative splicing of precursor mRNA in reversed order across exons. Despite the abundant presence of circRNAs in human genes and their involvement in diverse physiological processes, the functionality of most circRNAs remains a mystery. Like other non-coding RNAs, sub-cellular localization knowledge of circRNAs has the aptitude to demystify the influence of circRNAs on protein synthesis, degradation, destination, their association with different diseases, and potential for drug development. To date, wet experimental approaches are being used to detect sub-cellular locations of circular RNAs. These approaches help to elucidate the role of circRNAs as protein scaffolds, RNA-binding protein (RBP) sponges, micro-RNA (miRNA) sponges, parental gene expression modifiers, alternative splicing regulators, and transcription regulators. To complement wet-lab experiments, considering the progress made by machine learning approaches for the determination of sub-cellular localization of other non-coding RNAs, the paper in hand develops a computational framework, Circ-LocNet, to precisely detect circRNA sub-cellular localization. Circ-LocNet performs comprehensive extrinsic evaluation of 7 residue frequency-based, residue order and frequency-based, and physio-chemical property-based sequence descriptors using the five most widely used machine learning classifiers. Further, it explores the performance impact of K-order sequence descriptor fusion where it ensembles similar as well dissimilar genres of statistical representation learning approaches to reap the combined benefits. Considering the diversity of statistical representation learning schemes, it assesses the performance of second-order, third-order, and going all the way up to seventh-order sequence descriptor fusion. A comprehensive empirical evaluation of Circ-LocNet over a newly developed benchmark dataset using different settings reveals that standalone residue frequency-based sequence descriptors and tree-based classifiers are more suitable to predict sub-cellular localization of circular RNAs. Further, K-order heterogeneous sequence descriptors fusion in combination with tree-based classifiers most accurately predict sub-cellular localization of circular RNAs. We anticipate this study will act as a rich baseline and push the development of robust computational methodologies for the accurate sub-cellular localization determination of novel circRNAs. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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19 pages, 3894 KiB

Open AccessArticle

Differential MicroRNA Expression in Porcine Endometrium Related to Spontaneous Embryo Loss during Early Pregnancy

by Shengchen Gu, Xupeng Zang, Lei Jiang, Ting Gu, Fanming Meng, Sixiu Huang, Gengyuan Cai, Zicong Li, Zhenfang Wu and Linjun Hong

Int. J. Mol. Sci. 2022, 23(15), 8157; https://doi.org/10.3390/ijms23158157 - 24 Jul 2022

Cited by 5 | Viewed by 2421

Abstract

Litter size is an important indicator to measure the production capacity of commercial pigs. Spontaneous embryo loss is an essential factor in determining sow litter size. In early pregnancy, spontaneous embryo loss in porcine is as high as 20–30% during embryo implantation. However, [...] Read more.

Litter size is an important indicator to measure the production capacity of commercial pigs. Spontaneous embryo loss is an essential factor in determining sow litter size. In early pregnancy, spontaneous embryo loss in porcine is as high as 20–30% during embryo implantation. However, the specific molecular mechanism underlying spontaneous embryo loss at the end of embryo implantation remains unknown. Therefore, we comprehensively used small RNA sequencing technology, bioinformatics analysis, and molecular experiments to determine the microRNA (miRNA) expression profile in the healthy and arresting embryo implantation site of porcine endometrium on day of gestation (DG) 28. A total of 464 miRNAs were identified in arresting endometrium (AE) and healthy endometrium (HE), and 139 differentially expressed miRNAs (DEMs) were screened. We combined the mRNA sequencing dataset from the SRA database to predict the target genes of these miRNAs. A quantitative real-time PCR assay identified the expression levels of miRNAs and mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed target genes of DEMs, mainly enriched in epithelial development and amino acids metabolism-related pathways. We performed fluorescence in situ hybridization (FISH) and the dual-luciferase report gene assay to confirm miRNA and predicted target gene binding. miR-205 may inhibit its expression by combining 3′-untranslated regions (3′ UTR) of tubulointerstitial nephritis antigen-like 1 (TINAGL1). The resulting inhibition of angiogenesis in the maternal endometrium ultimately leads to the formation of arresting embryos during the implantation period. This study provides a reference for the effect of miRNA on the successful implantation of pig embryos in early gestation. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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Review

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13 pages, 923 KiB

Open AccessReview

Potential Roles of m6A and FTO in Synaptic Connectivity and Major Depressive Disorder

by Haruka Mitsuhashi and Corina Nagy

Int. J. Mol. Sci. 2023, 24(7), 6220; https://doi.org/10.3390/ijms24076220 - 25 Mar 2023

Cited by 11 | Viewed by 2949

Abstract

RNA modifications known as epitranscriptomics have emerged as a novel layer of transcriptomic regulation. Like the well-studied epigenetic modifications characterized in DNA and on histone-tails, they have been shown to regulate activity-dependent gene expression and play a vital role in shaping synaptic connections [...] Read more.

RNA modifications known as epitranscriptomics have emerged as a novel layer of transcriptomic regulation. Like the well-studied epigenetic modifications characterized in DNA and on histone-tails, they have been shown to regulate activity-dependent gene expression and play a vital role in shaping synaptic connections in response to external stimuli. Among the hundreds of known RNA modifications, N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes. Through recognition of its binding proteins, m6A can regulate various aspects of mRNA metabolism and is essential for maintaining higher brain functions. Indeed, m6A is highly enriched in synapses and is involved in neuronal plasticity, learning and memory, and adult neurogenesis. m6A can also respond to environmental stimuli, suggesting an important role in linking molecular and behavioral stress. This review summarizes key findings from fields related to major depressive disorder (MDD) including stress and learning and memory, which suggest that activity-dependent m6A changes may, directly and indirectly, contribute to synaptic connectivity changes underlying MDD. Furthermore, we will highlight the roles of m6A and FTO, a m6A eraser, in the context of depressive-like behaviors. Although we have only begun to explore m6A in the context of MDD and psychiatry, elucidating a link between m6A and MDD presents a novel molecular mechanism underlying MDD pathogenesis. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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27 pages, 1581 KiB

Open AccessReview

Modulation of AKT Pathway-Targeting miRNAs for Cancer Cell Treatment with Natural Products

by Jun-Ping Shiau, Ya-Ting Chuang, Ching-Yu Yen, Fang-Rong Chang, Kun-Han Yang, Ming-Feng Hou, Jen-Yang Tang and Hsueh-Wei Chang

Int. J. Mol. Sci. 2023, 24(4), 3688; https://doi.org/10.3390/ijms24043688 - 12 Feb 2023

Cited by 9 | Viewed by 2804

Abstract

Many miRNAs are known to target the AKT serine-threonine kinase (AKT) pathway, which is critical for the regulation of several cell functions in cancer cell development. Many natural products exhibiting anticancer effects have been reported, but their connections to the AKT pathway (AKT [...] Read more.

Many miRNAs are known to target the AKT serine-threonine kinase (AKT) pathway, which is critical for the regulation of several cell functions in cancer cell development. Many natural products exhibiting anticancer effects have been reported, but their connections to the AKT pathway (AKT and its effectors) and miRNAs have rarely been investigated. This review aimed to demarcate the relationship between miRNAs and the AKT pathway during the regulation of cancer cell functions by natural products. Identifying the connections between miRNAs and the AKT pathway and between miRNAs and natural products made it possible to establish an miRNA/AKT/natural product axis to facilitate a better understanding of their anticancer mechanisms. Moreover, the miRNA database (miRDB) was used to retrieve more AKT pathway-related target candidates for miRNAs. By evaluating the reported facts, the cell functions of these database-generated candidates were connected to natural products. Therefore, this review provides a comprehensive overview of the natural product/miRNA/AKT pathway in the modulation of cancer cell development. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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16 pages, 2957 KiB

Open AccessReview

The Origin of Translation: Bridging the Nucleotides and Peptides

by Xuyuan Guo and Meng Su

Int. J. Mol. Sci. 2023, 24(1), 197; https://doi.org/10.3390/ijms24010197 - 22 Dec 2022

Cited by 3 | Viewed by 3108

Abstract

Extant biology uses RNA to record genetic information and proteins to execute biochemical functions. Nucleotides are translated into amino acids via transfer RNA in the central dogma. tRNA is essential in translation as it connects the codon and the cognate amino acid. To [...] Read more.

Extant biology uses RNA to record genetic information and proteins to execute biochemical functions. Nucleotides are translated into amino acids via transfer RNA in the central dogma. tRNA is essential in translation as it connects the codon and the cognate amino acid. To reveal how the translation emerged in the prebiotic context, we start with the structure and dissection of tRNA, followed by the theory and hypothesis of tRNA and amino acid recognition. Last, we review how amino acids assemble on the tRNA and further form peptides. Understanding the origin of life will also promote our knowledge of artificial living systems. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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12 pages, 807 KiB

Open AccessReview

The Polyvalent Role of NF90 in RNA Biology

by Giuseppa Grasso and Rosemary Kiernan

Int. J. Mol. Sci. 2022, 23(21), 13584; https://doi.org/10.3390/ijms232113584 - 5 Nov 2022

Viewed by 2389

Abstract

Double-stranded RNA-binding proteins (dsRBPs) are major players in the regulation of gene expression patterns. Among them, Nuclear Factor 90 (NF90) has a plethora of well-known functions in viral infection, transcription, and translation as well as RNA stability and degradation. In addition, NF90 has [...] Read more.

Double-stranded RNA-binding proteins (dsRBPs) are major players in the regulation of gene expression patterns. Among them, Nuclear Factor 90 (NF90) has a plethora of well-known functions in viral infection, transcription, and translation as well as RNA stability and degradation. In addition, NF90 has been identified as a regulator of microRNA (miRNA) maturation by competing with Microprocessor for the binding of pri-miRNAs in the nucleus. NF90 was recently shown to control the biogenesis of a subset of human miRNAs, which ultimately influences, not only the abundance, but also the expression of the host gene and the fate of the mRNA target repertoire. Moreover, recent evidence suggests that NF90 is also involved in RNA-Induced Silencing Complex (RISC)-mediated silencing by binding to target mRNAs and controlling their translation and degradation. Here, we review the many, and growing, functions of NF90 in RNA biology, with a focus on the miRNA pathway and RISC-mediated gene silencing. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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21 pages, 2256 KiB

Open AccessReview

Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane

by Luciane Santini, Leonardo Yoshida, Kaique Dias de Oliveira, Carolina Gimiliani Lembke, Augusto Lima Diniz, Geraldo Cesar Cantelli, Milton Yutaka Nishiyama-Junior and Glaucia Mendes Souza

Int. J. Mol. Sci. 2022, 23(19), 11603; https://doi.org/10.3390/ijms231911603 - 1 Oct 2022

Cited by 4 | Viewed by 2205

Abstract

Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there [...] Read more.

Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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22 pages, 1797 KiB

Open AccessReview

Insights Gained from RNA Editing Targeted by the CRISPR-Cas13 Family

by Li Liu and De-Sheng Pei

Int. J. Mol. Sci. 2022, 23(19), 11400; https://doi.org/10.3390/ijms231911400 - 27 Sep 2022

Cited by 13 | Viewed by 6090

Abstract

Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely developed for DNA targeting and formed a set of mature precision gene-editing systems. However, the basic research and application of the CRISPR-Cas system in RNA [...] Read more.

Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely developed for DNA targeting and formed a set of mature precision gene-editing systems. However, the basic research and application of the CRISPR-Cas system in RNA is still in its early stages. Recently, the discovery of the CRISPR-Cas13 type VI system has provided the possibility for the expansion of RNA targeting technology, which has broad application prospects. Most type VI Cas13 effectors have dinuclease activity that catalyzes pre-crRNA into mature crRNA and produces strong RNA cleavage activity. Cas13 can specifically recognize targeted RNA fragments to activate the Cas13/crRNA complex for collateral cleavage activity. To date, the Cas13X protein is the smallest effector of the Cas13 family, with 775 amino acids, which is a promising platform for RNA targeting due to its lack of protospacer flanking sequence (PFS) restrictions, ease of packaging, and absence of permanent damage. This study highlighted the latest progress in RNA editing targeted by the CRISPR-Cas13 family, and discussed the application of Cas13 in basic research, nucleic acid diagnosis, nucleic acid tracking, and genetic disease treatment. Furthermore, we clarified the structure of the Cas13 protein family and their molecular mechanism, and proposed a future vision of RNA editing targeted by the CRISPR-Cas13 family. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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20 pages, 1649 KiB

Open AccessReview

Circular RNAs Involved in the Regulation of the Age-Related Pathways

by Siqi Wang, Feng Xiao, Jiamei Li, Xiaolan Fan, Zhi He, Taiming Yan, Mingyao Yang and Deying Yang

Int. J. Mol. Sci. 2022, 23(18), 10443; https://doi.org/10.3390/ijms231810443 - 9 Sep 2022

Cited by 8 | Viewed by 2867

Abstract

Circular RNAs (circRNAs) are a class of covalently circular noncoding RNAs that have been extensively studied in recent years. Aging is a process related to functional decline that is regulated by signal transduction. An increasing number of studies suggest that circRNAs can regulate [...] Read more.

Circular RNAs (circRNAs) are a class of covalently circular noncoding RNAs that have been extensively studied in recent years. Aging is a process related to functional decline that is regulated by signal transduction. An increasing number of studies suggest that circRNAs can regulate aging and multiple age-related diseases through their involvement in age-related signaling pathways. CircRNAs perform several biological functions, such as acting as miRNA sponges, directly interacting with proteins, and regulating transcription and translation to proteins or peptides. Herein, we summarize research progress on the biological functions of circRNAs in seven main age-related signaling pathways, namely, the insulin-insulin-like, PI3K-AKT, mTOR, AMPK, FOXO, p53, and NF-κB signaling pathways. In these pathways, circRNAs mainly function as miRNA sponges. In this review, we suggest that circRNAs are widely involved in the regulation of the main age-related pathways and are potential biomarkers for aging and age-related diseases. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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19 pages, 1460 KiB

Open AccessReview

Host mRNA Analysis of Periodontal Disease Patients Positive for Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans and Tannerella forsythia

by Ramona Gabriela Ursu, Luminita Smaranda Iancu, Elena Porumb-Andrese, Costin Damian, Roxana Gabriela Cobzaru, Giorgio Nichitean, Carmen Ripa, Darius Sandu and Ionut Luchian

Int. J. Mol. Sci. 2022, 23(17), 9915; https://doi.org/10.3390/ijms23179915 - 31 Aug 2022

Cited by 5 | Viewed by 3139

Abstract

Periodontal disease is a frequent pathology worldwide, with a constantly increasing prevalence. For the optimal management of periodontal disease, there is a need to take advantage of actual technology to understand the bacterial etiology correlated with the pathogenic mechanisms, risk factors and treatment [...] Read more.

Periodontal disease is a frequent pathology worldwide, with a constantly increasing prevalence. For the optimal management of periodontal disease, there is a need to take advantage of actual technology to understand the bacterial etiology correlated with the pathogenic mechanisms, risk factors and treatment protocols. We analyzed the scientific literature published in the last 5 years regarding the recent applications of mRNA analysis in periodontal disease for the main known bacterial species considered to be the etiological agents: Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans and Tannerella forsythia. We identified new pathogenic mechanisms, therapeutic target genes and possible pathways to prevent periodontal disease. The mRNA analysis, as well as the important technological progress in recent years, supports its implementation in the routine management of periodontal disease patients. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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55 pages, 945 KiB

Open AccessReview

Expression of MicroRNAs in Sepsis-Related Organ Dysfunction: A Systematic Review

by Aniello Maiese, Andrea Scatena, Andrea Costantino, Enrica Chiti, Carla Occhipinti, Raffaele La Russa, Marco Di Paolo, Emanuela Turillazzi, Paola Frati and Vittorio Fineschi

Int. J. Mol. Sci. 2022, 23(16), 9354; https://doi.org/10.3390/ijms23169354 - 19 Aug 2022

Cited by 16 | Viewed by 3624

Abstract

Sepsis is a critical condition characterized by increased levels of pro-inflammatory cytokines and proliferating cells such as neutrophils and macrophages in response to microbial pathogens. Such processes lead to an abnormal inflammatory response and multi-organ failure. MicroRNAs (miRNA) are single-stranded non-coding RNAs with [...] Read more.

Sepsis is a critical condition characterized by increased levels of pro-inflammatory cytokines and proliferating cells such as neutrophils and macrophages in response to microbial pathogens. Such processes lead to an abnormal inflammatory response and multi-organ failure. MicroRNAs (miRNA) are single-stranded non-coding RNAs with the function of gene regulation. This means that miRNAs are involved in multiple intracellular pathways and thus contribute to or inhibit inflammation. As a result, their variable expression in different tissues and organs may play a key role in regulating the pathophysiological events of sepsis. Thanks to this property, miRNAs may serve as potential diagnostic and prognostic biomarkers in such life-threatening events. In this narrative review, we collect the results of recent studies on the expression of miRNAs in heart, blood, lung, liver, brain, and kidney during sepsis and the molecular processes in which they are involved. In reviewing the literature, we find at least 122 miRNAs and signaling pathways involved in sepsis-related organ dysfunction. This may help clinicians to detect, prevent, and treat sepsis-related organ failures early, although further studies are needed to deepen the knowledge of their potential contribution. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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14 pages, 1278 KiB

Open AccessBrief Report

Preinitiation Complex Loading onto mRNAs with Long versus Short 5′ TLs

by Benjamin Weiss, Pascale Jaquier-Gubler and Joseph Alphonsus Curran

Int. J. Mol. Sci. 2022, 23(21), 13369; https://doi.org/10.3390/ijms232113369 - 2 Nov 2022

Viewed by 1665

Abstract

The first step in translation initiation consists in the recruitment of the small ribosome onto the mRNA. This preinitiation complex (PIC) loads via interactions with eIF4F that has assembled on the 5′ cap. It then scans the 5′ TL (transcript leader) to locate [...] Read more.

The first step in translation initiation consists in the recruitment of the small ribosome onto the mRNA. This preinitiation complex (PIC) loads via interactions with eIF4F that has assembled on the 5′ cap. It then scans the 5′ TL (transcript leader) to locate a start site. The molecular architecture of the PIC-mRNA complex over the cap is beginning to be resolved. As part of this, we have been examining the role of the 5′ TL length. We observed in vivo initiation events on AUG codons positioned within 3 nts of the 5′ cap and robust initiation in vitro at start sites immediately downstream of the 5′ end. Ribosomal toe-printing confirmed the positioning of these codons within the P site, indicating that the ribosome reads from the +1 position. To explore differences in the eIF4E-5′ cap interaction in the context of long versus short TL, we followed the fate of the eIF4E-cap interaction using a novel solid phase in vitro expression assay. We observed that ribosome recruitment onto a short TL disrupts the eIF4E-cap contact releasing all the mRNA from the solid phase, whereas with a long the mRNA distributes between both phases. These results are discussed in the context of current recruitment models. Full article

(This article belongs to the Special Issue Molecular Biology of RNA: Recent Progress)

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