Function Of Long Non-coding RNAs Research Articles

Long non-coding NEAT1 weakens the protective role of sevoflurane on myocardial ischemia/reperfusion injury by mediating the microRNA-140/RhoA axis.

The function of long non-coding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1) has been revealed in injury caused by myocardial ischemia/reperfusion (I/R), however, its association with Sevoflurane (Sev), an anesthetic effective for regulating inflammation and oxidative stress, is not yet clear in I/R injury. The aim of this study was to functionally validate and elucidate the mechanism-of-action for Sev-mediated NEAT1 in myocardial I/R injury. Firstly, reduced NEAT1 was revealed in myocardial I/R injured mice treated with Sev. Moreover, restoration of NEAT1 could repress the alleviating role of Sev in cardiac function, infarct size and myocardial apoptosis in mice, while miR-140 was remarkably enhanced in myocardial tissues from mice treated with Sev. Furthermore, miR-140 was suggested and authenticated as a downstream biomolecule of NEAT1 with the help of a bioinformatics tool. Interestingly, miR-140 inhibitor played the same role as NEAT1 overexpression on the cardiac function, infarct size and apoptosis of mice. Finally, it was manifested that RhoA was a putative target of miR-140, which functioned importantly in the Sev/miR-140-mediated myocardial I/R injury. All in all, NEAT1 knockdown contributed to Sev-mediated myocardial I/R injury alleviation via the miR-140/RhoA axis.

RETRACTED: LncRNA HOTAIR regulates the expression of E-cadherin to affect nasopharyngeal carcinoma progression by recruiting histone methylase EZH2 to mediate H3K27 trimethylation

Background/AimThere has been increasing evidence for the function of long non-coding RNA (lncRNA) in nasopharyngeal carcinoma (NPC). We aim to delve into the position of lncRNA HOX antisense intergenic RNA (HOTAIR), together with enhancer of zeste homolog 2 (EZH2), E-cadherin and trimethylation of lysine 27 on histone H3 (H3K27me3) in NPC. MethodsHOTAIR, EZH2, and E-cadherin expression in NPC tissues and cells were tested. NPC cell biological functions were examined through gain-of and loss-of function assays. The mechanism of lncRNA HOTAIR/E-cadherin/EZH2/H3K27 axis in NPC was decoded. ResultsLncRNA HOTAIR and EZH2 were highly expressed in NPC, and E-cadherin was lowly expressed. Down-regulation of HOTAIR or EZH2 inhibited NPC cell progression and tumor growth. HOTAIR recruited histone methylase EZH2 to mediate trimethylation of H3K27 and regulated E-cadherin expression. ConclusionHOTAIR inhibits E-cadherin by stimulating the trimethylation of H3K27 to promote NPC cell progression through recruiting histone methylase EZH2.

LncRNAs induce oxidative stress and spermatogenesis by regulating endoplasmic reticulum genes and pathways.

Oligozoospermia or low sperm count is a leading cause of male infertility worldwide. Despite decades of work on non-coding RNAs (ncRNAs) as regulators of spermatogenesis, fertilization, and male fertility, the literature on the function of long non-coding RNAs (lncRNAs) in human oligozoospermia is scarce. We integrated lncRNA and mRNA sequencing data from 12 human normozoospermic and oligozoospermic samples and comprehensively analyzed the function of differentially expressed lncRNAs (DE lncRNAs) and mRNAs (DE mRNAs) in male infertility. The target genes of DE lncRNAs were identified using a Gaussian graphical model. Gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were primarily enriched in protein transport and localization to the endoplasmic reticulum (ER). The lncRNA–mRNA co-expression network revealed cis- and trans-regulated target genes of lncRNAs. The transcriptome data implicated DE lncRNAs and DE mRNAs and their target genes in the accumulation of unfolded proteins in sperm ER, PERK-EIF2 pathway-induced ER stress, oxidative stress, and sperm cell apoptosis in individuals with oligozoospermia. These findings suggest that the identified lncRNAs and pathways could serve as effective therapeutic targets for male infertility.

Long intergenic non-coding RNA 00473 promotes proliferation and migration of gastric cancer via the miR-16-5p/CCND2 axis and by regulating AQP3

Gastric cancer (GC) is one of the most common malignancies worldwide, but its molecular mechanisms remain unclear. Increasing evidence indicates that long non-coding RNAs (LncRNAs) play a pivotal role in various cancers recently. Our present study focused on exploring the function of long intergenic non-coding RNA 00473 (LINC00473) in GC. In this study, we found that LINC00473 expression was aberrantly increased in tumor tissues compared with the paired para-cancerous tissues. The expression of high LINC00473 in GC was notably correlated with a higher risk of lymphatic metastasis, a higher incidence of vascular cancer embolus, and advanced TNM stage. Further experiments showed that the overexpression of LINC00473 could promote the proliferation and metastasis of GC cells both in vitro and in vivo. The apoptosis of GC cells increased significantly by the decrease of LINC00473. Mechanistically, LINC00473 could sponge miR-16-5p in the cytoplasm and relieve its suppression of CCND2. Moreover, AQP3 was found to be a significant downstream target gene for LINC00473 through RNA transcriptome sequencing, as demonstrated by qRT-PCR and western blot. Overexpression of LINC00473 can partially reverse the effects of AQP3 decrease on GC proliferation and metastasis. LINC00473 regulated AQP3 expression through CREB was confirmed by western blot. Our research indicates that LINC00473/miR-16-5p/CCND2 axis plays a role in the proliferation of GC and modulates AQP3 to influence GC cell metastasis, making it a potential therapeutic target for GC.

LncRNA SNHG14 promotes osteogenic differentiation of human bone marrow-derived mesenchymal stem cells via regulating miR-185-5p/WISP2 axis.

Osteogenic differentiation of human bone marrow-derived mesenchymal stem cells (hBMSCs) is vital for bone formation, and its dysfunction is linked to osteoporosis (OP). In this work, we explored the function of long non-coding RNA (lncRNA) small nucleolar RNA host gene 14 (SNHG14) in regulating osteogenic differentiation of hBMSCs. In the present study, the expression of SNHG14 in hBMSCs obtained from OP patients was measured by quantitative real-time polymerase chain reaction (qRT-PCR). SNHG14 was over-expressed or knocked down in hBMSCs, and the expression levels of OP-related genes (ALP, OCN, and OPN) in hBMSCs were detected by qRT-PCR and Western blot. StarBase database and miRanda database were used to predict the binding sites between SNHG14 and miR-185-5p, and between miR-185-5p and 3'UTR of WNT1 inducible signaling pathway protein 2 (WISP2), respectively. Luciferase reporter gene assay was used to validate the binding relationship between SNHG14 and miR-185-5p, and miR-185-5p and 3'UTR of WISP2, respectively. Here, we report that SNHG14 was significantly down-regulated in hBMSCs obtained from patients with OP. Overexpression of SNHG14 promoted osteogenic differentiation, while knockdown of SNHG14 worked oppositely. Mechanistically, miR-185-5p was demonstrated to be a target of SNHG14, and could reverse the function of SNHG14. Additionally, WISP2 was identified as a target gene of miR-185-5p in hBMSCs and could be indirectly regulated by SNHG14. Taken together, down-regulation of SNHG14 in hBMSCs accelerated the progression of OP via regulating miR-185-5p/WISP2 axis.

Expression profiles and potential functions of long noncoding RNAs and mRNAs in autoimmune pulmonary alveolar proteinosis patients.

Autoimmune pulmonary alveolar proteinosis (APAP) is a rare lung disease that may be associated with surfactant overaccumulation. To assess the function of long noncoding RNAs (lncRNAs) in APAP, we performed microarray analyses to identify differentially expressed (DE) lncRNAs and mRNAs between peripheral blood samples from five APAP patients and five healthy volunteers. In total, 12459 DE lncRNAs and 9331 DE mRNAs were identified in APAP patient samples. A qRT-PCR validation of 20 DE lncRNAs and 20 mRNAs indicated that 12 DE lncRNAs may be involved in the pathogenesis of APAP. Coding and noncoding co-expression (CNC) and competing endogenous RNA (ceRNA) regulatory networks were constructed with these 12 DE lncRNAs. Gene Ontology analysis of the downregulated mRNAs and the CNC network revealed that “ubiquitin-like protein transferase activity” was suppressed in APAP patient samples. Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that the “MAPK signaling pathway” was enriched in the ceRNA network. Gene Ontology analysis also indicated that mRNAs involved in many transmembrane ion transport processes were upregulated in APAP patients. The DE lncRNAs and mRNAs discovered in this study have elucidated the pathogenesis of APAP, and the CNC and ceRNA networks have provided novel insights for future functional research.

Breast Cancer and the Other Non-Coding RNAs.

Breast cancer is very heterogenous and the most common gynaecological cancer, with various factors affecting its development. While its impact on human lives and national health budgets is still rising in almost all global areas, many molecular mechanisms affecting its onset and development remain unclear. Conventional treatments still prove inadequate in some aspects, and appropriate molecular therapeutic targets are required for improved outcomes. Recent scientific interest has therefore focused on the non-coding RNAs roles in tumour development and their potential as therapeutic targets. These RNAs comprise the majority of the human transcript and their broad action mechanisms range from gene silencing to chromatin remodelling. Many non-coding RNAs also have altered expression in breast cancer cell lines and tissues, and this is often connected with increased proliferation, a degraded extracellular environment, and higher endothelial to mesenchymal transition. Herein, we summarise the known abnormalities in the function and expression of long non-coding RNAs, Piwi interacting RNAs, small nucleolar RNAs and small nuclear RNAs in breast cancer, and how these abnormalities affect the development of this deadly disease. Finally, the use of RNA interference to suppress breast cancer growth is summarised.

Dysregulation of lncRNAs in Rheumatoid Arthritis: Biomarkers, Pathogenesis and Potential Therapeutic Targets.

Rheumatoid arthritis (RA) is a chronic autoimmune disease of unknown etiology, mainly manifested by persistent abnormal proliferation of fibroblast-like synoviocytes (FLSs), inflammation, synovial hyperplasia and cartilage erosion, accompanied by joint swelling and joint destruction. Abnormal expression or function of long noncoding RNAs (lncRNAs) are closely related to human diseases, including cancers, mental diseases, autoimmune diseases and others. The abnormal sequence and spatial structure of lncRNAs, the disorder expression and the abnormal interaction with the binding protein will lead to the change of gene expression in the way of epigenetic modification. Increasing evidence demonstrated that lncRNAs were involved in the activation of FLSs, which played a key role in the pathogenesis of RA. In this review, the research progress of lncRNAs in the pathogenesis of RA was systematically summarized, including the role of lncRNAs in the diagnosis of RA, the regulatory mechanism of lncRNAs in the pathogenesis of RA, and the intervention role of lncRNAs in the treatment of RA. Furthermore, the activated signal pathways, the role of DNA methylation and other mechanism have also been overview in this review.

Systematic and computational identification of Androctonus crassicauda long non-coding RNAs

The potential function of long non-coding RNAs in regulating neighbor protein-coding genes has attracted scientists’ attention. Despite the important role of lncRNAs in biological processes, a limited number of studies focus on non-model animal lncRNAs. In this study, we used a stringent step-by-step filtering pipeline and machine learning-based tools to identify the specific Androctonus crassicauda lncRNAs and analyze the features of predicted scorpion lncRNAs. 13,401 lncRNAs were detected using pipeline in A. crassicauda transcriptome. The blast results indicated that the majority of these lncRNAs sequences (12,642) have no identifiable orthologs even in closely related species and those considered as novel lncRNAs. Compared to lncRNA prediction tools indicated that our pipeline is a helpful approach to distinguish protein-coding and non-coding transcripts from RNA sequencing data of species without reference genomes. Moreover, analyzing lncRNA characteristics in A. crassicauda uncovered that lower protein-coding potential, lower GC content, shorter transcript length, and less number of isoform per gene are outstanding features of A. crassicauda lncRNAs transcripts.

Expression profiling and bioinformatics analysis of exosomal long noncoding RNAs in patients with myasthenia gravis by RNA sequencing.

BackgroundMyasthenia gravis (MG) is an autoimmune disease mediated by acetylcholine receptor antibodies. Exosomes were shown to be involved in the immune modulation and autoimmune diseases. However, the expression and function of exosomal long noncoding RNAs (lncRNAs) in MG are still unclear.MethodsWe conducted high‐throughput sequencing to detect the lncRNA profiles of serum exosomes in 6 MG patients (2 grade I, 2 grade IIa, and 2 grade IIb) and 6 healthy controls (HC). Then, differentially expressed (DE) lncRNAs with the greatest difference between the MG and HC groups were selected for further quantitative real‐time polymerase chain reaction (qRT‐PCR) validation in additional 30 MG patients and 10 HC. The DE lncRNAs were used to construct the coding/noncoding network and perform enrichment analysis.ResultsWe identified 378 significantly upregulated and 348 significantly downregulated lncRNAs in MG patients compared with HC. The top 5 lncRNAs (NR_104677.1, ENST00000583253.1, NR_046098.1, NR_022008.1, and ENST00000581362.1) were validated and shown to be significantly increased in the serum exosome of MG, and the expression level of NR_046098.1 significantly increased with the MG grading. Enrichment analysis showed that DE genes mainly participated in the basic biological regulation of MG and immune‐related pathways, such as autoimmune thyroid disease pathway and T‐cell receptor signaling pathway. A specific lncRNA‐miRNA‐mRNA regulatory network associated with the 5 lncRNAs, 14 MG‐related miRNAs and 30 mRNAs was constructed.ConclusionsWe conducted a comprehensive analysis of exosomal lncRNAs to reveal potential biomarkers for the MG diagnosis and severity assessment.

LncRNA-CRNDE regulates BMSC chondrogenic differentiation and promotes cartilage repair in osteoarthritis through SIRT1/SOX9.

Osteoarthritis (OA) is the most common chronic and degenerative joint disease. Although traditional OA medications can partially relieve pain, these medications cannot completely cure OA. Therefore, it is particularly important to find an effective treatment for OA. This study explored the function of long non-coding RNA (lncRNA)-colorectal neoplasia differentially expressed gene (CRNDE) in the chondrogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) and the underlying molecular mechanism, aiming to develop a new treatment method for osteoarthritis. BMSCs were isolated from rat bone marrow using the gradient centrifugation method. And BMSC chondrogenic differentiation was induced with chondrogenic medium. The expression of lncRNA-CRNDE was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Silent information regulator factor 2-related enzyme 1(SIRT1) and cartilage marker genes Aggrecan and collagen 2 (α1) protein expression were researched using western blot. Alcian blue staining was employed to examine the content of cartilage matrix proteoglycan glycosaminoglycan (GAG). The interaction between lncRNA-CRNDE and SIRT1 was detected by RNA pull-down and RNA immunoprecipitation (RIP) assay. Ubiquitination experiments were performed to measure the ubiquitination level of SIRT1. The combination between SMAD ubiquitination regulatory factor 2 (SMURF2) and SIRT1, as well as SRY-related high-mobility-group box 9 (SOX9) and collagen 2 (α1) promoter, was detected by Co-immunoprecipitation or ChIP. With the prolongation of induction time, the expression of lncRNA-CRNDE, SIRT1, cartilage marker genes Aggrecan and collagen 2 (α1) in BMSC osteogenic differentiation was gradually increased. Also, the content of cartilage matrix proteoglycan GAG was gradually elevated with the extension of the induction time. Further increase in the expression of SIRT1, cartilage marker genes Aggrecan and collagen 2 (α1) by overexpression of lncRNA-CRNDE also indicated elevated GAG content. RNA pull-down and RIP assay confirmed the binding between lncRNA-CRNDE and SIRT1. qRT-PCR and western blot showed that interference with lncRNA-CRNDE significantly inhibited the protein expression of SIRT1. BMSCs transfected with si-CRNDE increased ubiquitination levels of SIRT1 mediated by the E3 ligase SMURF2, leading to the reduced protein stability of SIRT1. However, overexpression of lncRNA-CRNDE increased the binding ability of SOX9 and collagen 2 (α1) promoter, which was reversed by the simultaneous transfection ofCRNDE overexpression (pcDNA-CRNDE) and SIRT1small interferingRNA (si-SIRT1). lncRNA-CRNDE regulates BMSC chondrogenic differentiation to promote cartilage repair in osteoarthritis through SIRT1/SOX9.

CRISPR-Cas13-Mediated Knockdown of lncRNA-GACAT3 Inhibited Cell Proliferation and Motility, and Induced Apoptosis by Increasing p21, Bax, and E-Cadherin Expression in Bladder Cancer.

The current study is to investigate the expression pattern and biological function of long non-coding RNA Focally gastric cancer-associated transcript3 (GACAT3) in bladder cancer. Real-time quantitative qPCR was used to detect the expression level of GACAT-3 in tumor tissues and paired normal tissues. Human bladder cancer T24 and 5637 cell lines were transiently transfected with specific CRISPR-Cas13 or negative control CRISPR-Cas13. Cell migration, proliferation, and apoptosis were measured by using wound healing assay CCK-8 assay and Caspase-3 ELISA assay, respectively. The expression changes of p21, Bax, and E-cadherin after knockdown of GACAT3 were detected by using Western blot. The results demonstrated that GACAT3 was up-regulated in bladder cancer tissues than that in the paired normal tissues. Inhibition of cell proliferation, increased apoptosis, and decreased motility were observed in T24 and 5637 cell lines transfected by CRISPR-Cas13 targeting GACAT3. Downregulation of GACAT3 increased p21, Bax, and E-cadherin expression and silencing these genes could eliminate the phenotypic changes induced by knockdown of GACAT3. A ceRNA mechanism for GACAT3 was also revealed. By using CRISPR-Cas13 biotechnology, we suggested that GACAT3 may be a novel target for diagnosis and treatment of bladder cancer.

FAM207BP, a pseudogene-derived lncRNA, facilitates proliferation, migration and invasion of lung adenocarcinoma cells and acts as an immune-related prognostic factor

AimsThis study aimed to characterize the functions of pseudogene-derived long non-coding RNA (lncRNA) FAM207BP in lung adenocarcinoma (LUAD). Materials and methodsThrough the Cancer Genome Atlas (TCGA)-Genotype Tissue Expression (GTEx) database, FAM207BP expression was detected in LUAD and normal tissues. Overall survival (OS) and disease-free survival (DFS) analysis was presented using log-rank test or univariate Cox regression analysis. The relationships between FAM207BP expression and clinical features were analyzed. FAM207BP expression was validated in LUAD tissues and cells using RT-qPCR. Cell viability of LUAD cells was evaluated after silencing or overexpressing FAM207BP. Furthermore, migrated and invasive abilities were examined by Transwell and scratch assays. The correlation between FAM207BP expression and the immune infiltration levels was analyzed. Gene Set Enrichment Analysis (GSEA) was performed for high- and low-expression of FAM207BP using C2 collection in the Molecular Signatures Database (MSigDB) database. Key findingsFAM207BP expression was distinctly higher in LUAD than normal tissues. Patients with its high expression indicated worse OS and DFS time. FAM207BP expression was significantly related to gender. RT-qPCR results confirmed that FAM207BP was significantly highly expressed in LUAD tissues and cells. Knockdown of FAM207BP distinctly suppressed cellular viability, migration and invasion for LUAD cells. Also, its expression was negatively related to B cell infiltration levels. GSEA results indicated that high FAM207BP expression was involved in regulation of gene expression. Its low expression was related to immune response. SignificancePseudogene-derived lncRNA FAM207BP could induce proliferation and migration of LUAD cells, which could act as an immune-related prognostic factor.

LncRNA MYLK-AS1 acts as an oncogene by epigenetically silencing large tumor suppressor 2 (LATS2) in gastric cancer

ABSTRACT Extensive studies showed the vital function of long noncoding RNAs (lncRNAs) in the pathological and physiological progression of tumors. Previous evidence has indicated that lncRNA MYLK Antisense RNA 1 (MYLK-AS1) acts as an oncogene to facilitate the progression of several tumors. Nevertheless, little is known about its biological role in gastric cancer (GC). Our report intended to probe the underlying mechanism and function of MYLK-AS1 in GC. Results revealed that MYLK-AS1 showed an upregulated level in GC. It was worth mentioning that upregulated MYLK-AS1 caused the unfavorable clinical outcome in GC patients. Functional assays indicated that MYLK-AS1 silencing retarded the proliferation, cell cycle, migration, and invasion in GC. Besides, in vivo assay validated that MYLK-AS1 deficiency also restrained tumor growth. Through in-depth mechanism exploration, MYLK-AS1 was uncovered to bind with wnhancer of zeste homolog 2 (EZH2), an epigenetic inhibitor, to inhibit the level of Large Tumor Suppressor 2 (LATS2), thereby exerting carcinogenicity. Conclusively, our research highlighted the importance of MYLK-AS1 in GC, indicating that MYLK-AS1 might be an effective biomarker for GC.

Genome-Scale Perturbation of Long Noncoding RNA Expression Using CRISPR Interference.

CRISPR-mediated interference (CRISPRi), a robust and specific system for programmably repressing transcription, provides a versatile tool for systematically characterizing the function of long noncoding RNAs (lncRNAs). When used with highly parallel, lentiviral pooled screening approaches, CRISPRi enables the targeted knockdown of tens of thousands of lncRNA-expressing loci in a single screen. Here we describe the use of CRISPRi to target lncRNA loci in a pooled screen, using cell growth and proliferation as an example of a phenotypic readout. Considerations for custom lncRNA-targeting libraries, alternative phenotypic readouts, and orthogonal validation approaches are also discussed.

Detection and Characterization of Ribosome-Associated Long Noncoding RNAs.

Ribosome profiling shows potential for studying the function of long noncoding RNAs (lncRNAs). We introduce a bioinformatics pipeline for detecting ribosome-associated lncRNAs (ribo-lncRNAs) from ribosome profiling data. Further, we describe a machine-learning approach for the characterization of ribo-lncRNAs based on their sequence features. Scripts for ribo-lncRNA analysis can be accessed at ( https://ribolnc.hamadalab.com/ ).

Long non-coding RNA PWRN2 regulates cytotoxicity in an in vitro model of age-related macular degeneration

BackgroundAge-related macular degeneration (AMD) may lead to irreversibly vision loss among aging populations. In this work, in an in vitro AMD cell model, we examined the expression and function of long non-coding RNA, Prader-Willi Region Non-Protein Coding RNA 2 (PWRN2) in injured human retinal pigment epithelial cells. MethodARPE-19 cell line was maintained in vitro and treated with multi-module stressful conditions, including hydrogen peroxide (H2O2) tert-butylhydroperoxide (t-BuOOH) and ultraviolet B (UVB). Multi-module-stressor-induced cell death was monitored by a viability assay, and PWRN2 expression by qRT-PCR. PWRN2 was either downregulated or upregulated in ARPE-19 cells. The effects of PWRN2 downregulation or upregulation on t-BuOOH-induced cell death, cellular apoptosis and mitochondrial injuries were then quantitatively evaluated. ResultsMulti-module stressful conditions induced cell death and PWRN2 upregulation in ARPE-19 cells in vitro. We created ARPE-19 subpopulations with either downregulated or upregulated PWRN2 expressions. Quantitative assays demonstrated that, PWRN2 downregulation effectively alleviated t-BuOOH-induced cell death, apoptosis and various-type of mitochondrial injuries. On the other hand, PWRN2 upregulation worsened t-BuOOH-induced cellular damages in ARPE-19 cells. ConclusionWe demonstrated that downregulating PWRN2 protected multi-module-stressor-induced cell death, apoptosis and mitochondrial injuries in human retinal pigment epithelial cells, suggesting PWRN2 may be an active factor in human AMD.

Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle

Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs (lincRNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi muscle (LDM) during embryonic development. We identified a total of 739 lincRNA transcripts, which were distributed on all chromosomes except the chromosome Y, and analyzed their molecular characteristics. Compared to protein-coding genes, lincRNAs showed shorter transcripts, longer exons, fewer exons and higher tissue specificity. In addition, the abundance of lincRNAs in five embryonic development stages were analyzed and 45 differentially expressed lincRNAs were screened, three of which were highly expressed in LDM during porcine embryonic development. Finally, we predicted the potential target genes and functions of the lincRNAs, and identified 1 537 cis-target genes and 8 571 trans-target genes. Furthermore, we identified two key candidate lincRNAs involved in muscle development, XLOC_024652 and XLOC_001832, for post-trial validation. Our results provide a genome-wide resource of lincRNAs which are potentially involved in porcine embryonic skeletal muscle development and lay a foundation for the further study of their functions.

NF-\u03baB-mediated lncRNA AC007271.3 promotes carcinogenesis of oral squamous cell carcinoma by regulating miR-125b-2-3p/Slug

Oral squamous cell carcinoma (OSCC) is the most common oral cancer. The molecular mechanisms of this disease are not fully understood. Our previous studies confirmed that dysregulated function of long non-coding RNA (lncRNA) AC007271.3 was associated with a poor prognosis and overexpression of AC007271.3 promoted cell proliferation, migration, invasion, and inhibited cell apoptosis in vitro, and promoted tumor growth in vivo. However, the underlying mechanisms of AC007271.3 dysregulation remained obscure. In this study, our investigation showed that AC007271.3 functioned as competing endogenous RNA by binding to miR-125b-2-3p and by destabilizing primary miR-125b-2, resulted in the upregulating expression of Slug, which is a direct target of miR-125b-2-3p. Slug also inhibited the expression of E-cadherin but N-cadherin, vimentin, and β-catenin had no obvious change. The expression of AC007271.3 was promoted by the canonical nuclear factor-κB (NF-κB) pathway. Taken together, these results suggested that the classical NF-κB pathway-activated AC007271.3 regulates EMT by miR-125b-2-3p/Slug/E-cadherin axis to promote the development of OSCC, implicating it as a novel potential target for therapeutic intervention in this disease.

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.