Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis

A method for evaluating of RNA's coding potential using the interaction effects of open reading frames and high-energy scalograms

The identification and function determination of long non-coding RNAs (lncRNAs) can help to better understand the transcriptional regulation in both normal development and disease pathology, thereby demanding methods to distinguish them from protein-coding (pcRNAs) after obtaining sequencing data. Many algorithms based on the statistical, structural, physical, and chemical properties of the sequences have been developed for evaluating the coding potential of RNA to distinguish them. In order to design common features that do not rely on hyperparameter tuning and optimization and are evaluated accurately, we designed a series of features from the effects of open reading frames (ORFs) on their mutual interactions and with the electrical intensity of sequence sites to further improve the screening accuracy. Finally, the single model constructed from our designed features meets the strong classifier criteria, where the accuracy is between 82% and 89%, and the prediction accuracy of the model constructed after combining the auxiliary features equal to or exceed some best classification tools. Moreover, our method does not require special hyper-parameter tuning operations and is species insensitive compared to other methods, which means this method can be easily applied to a wide range of species. Also, we find some correlations between the features, which provides some reference for follow-up studies.

GAS5 which is regulated by Lhx8 promotes the recovery of learning and memory in rats with cholinergic nerve injury

Damage to the cholinergic system in central nervous system injuries such as traumatic brain injury (TBI) and neurodegenerative diseases leads to impaired learning and cognition. Neural stem cells (NSCs) have self-renewal capacity and multi-directional differentiation potential and considered the best source of cells for cell replacement therapy. However, how to promote the differentiation of NSCs into neurons is a major challenge in current research. Lhx8 has a specific effect on the development of the cholinergic nervous system, but its exact function is unclear. In this study, we found that Lhx8 could regulate the expression of Growth arrest-specific (GAS)5 which has been implicated in cancer but was less studied in the nervous system. Additionally, results from PCR, fluorescence in situ hybridization, and immunocytochemical analyses showed that GAS5 is mainly expressed in the cytoplasm of hippocampal neural stems cells and promotes their differentiation into neurons; the Morris water maze test demonstrated that GAS5 overexpression restored learning and memory in rats with cholinergic injury. These findings indicate that GAS5, which is regulated by Lhx8, improve brain function following cholinergic nerve injury.

Long noncoding RNA mediates stroke-induced neurogenesis

Neurogenesis contributes to poststroke recovery. Long noncoding RNAs (lncRNAs) participate in the regulation of stem cell self-renewal and differentiation. However, the role of lncRNAs in stroke-induced neurogenesis remains unknown. In this study, we found that H19 was the most highly upregulated lncRNA in neural stem cells (NSCs) of the subventricular zone (SVZ) of rats subjected to focal cerebral ischemia. Deletion of H19 suppressed cell proliferation, promoted cell death, and blocked NSC differentiation. RNA sequencing analysis revealed that genes deregulated by H19 knockdown were those that are involved in transcription, apoptosis, proliferation, cell cycle, and response to hypoxia. H19 knockdown significantly increased the transcription of cell cycle-related genes including p27, whereas overexpression of H19 substantially reduced expression of these genes through the interaction with chromatin remodeling proteins EZH2 and SUZ12. Moreover, H19 regulated neurogenesis-related miRNAs. Inactivation of H19 in NSCs of ischemic rats attenuated spontaneous functional recovery after stroke. Collectively, our data provide novel insights into the epigenetic regulation of lncRNAs in stroke-induced neurogenesis.

The functions of long non-coding RNAs in neural stem cell proliferation and differentiation

The capacities for neural stem cells (NSCs) self-renewal with differentiation are need to be precisely regulated for ensuring brain development and homeostasis. Recently, increasing number of studies have highlighted that long non-coding RNAs (lncRNAs) are associated with NSC fate determination during brain development stages. LncRNAs are a class of non-coding RNAs more than 200 nucleotides without protein-coding potential and function as novel critical regulators in multiple biological processes. However, the correlation between lncRNAs and NSC fate decision still need to be explored in-depth. In this review, we will summarize the roles and molecular mechanisms of lncRNAs focusing on NSCs self-renewal, neurogenesis and gliogenesis over the course of neural development, still more, dysregulation of lncRNAs in all stage of neural development have closely relationship with development disorders or glioma. In brief, lncRNAs may be explored as effective modulators in NSCs related neural development and novel biomarkers for diagnosis and prognosis of neurological disorders in the future.

Epigenetic mechanisms of neurodegenerative diseases and acute brain injury

Epigenetic modifications are emerging as major players in the pathogenesis of neurodegenerative disorders and susceptibility to acute brain injury. DNA and histone modifications act together with non-coding RNAs to form a complex gene expression machinery that adapts the brain to environmental stressors and injury response. These modifications influence cell-level operations like neurogenesis and DNA repair to large, intricate processes such as brain patterning, memory formation, motor function and cognition. Thus, epigenetic imbalance has been shown to influence the progression of many neurological disorders independent of aberrations in the genetic code. This review aims to highlight ways in which epigenetics applies to several commonly researched neurodegenerative diseases and forms of acute brain injury as well as shed light on the benefits of epigenetics-based treatments.

Long non-coding RNA profiling in LPS-induced intestinal inflammation model: New insight into pathogenesis

LPS can induce an inflammatory immune response in the intestine, and long non-coding RNA (lncRNA) is involved in the process of inflammatory disease. However, the biological role of lncRNA in the intestinal inflammation of piglets remains unclear. In this study, the lncRNA expression profile of the ileal mucosa of piglets challenged by LPS was analysed using lncRNA sequencing. In total, 112 novel lncRNAs were predicted, of which 58 were up-regulated and 54 down-regulated following LPS challenge. Expression of 15 selected lncRNAs was validated by quantitative PCR. We further investigated the target genes of lncRNA that were enriched in the signalling pathways involved in the inflammatory immune response by utilising Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes analysis, with cell adhesion molecules and mTOR signalling pathway identified. In addition, the co-expression networks between the differentially expressed lncRNAs and the target mRNAs were constructed, with seven core lncRNAs identified, which also demonstrated that the relationship between lncRNAs and the target genes was highly correlated. Our study offers important information about the lncRNAs of the mucosal immune system in piglets and provides new insights into the inflammatory mechanism of LPS challenge, which might serve as a novel target to control intestinal inflammation.

Long non-coding RNAs in nucleus pulposus cell function and intervertebral disc degeneration

Intervertebral disc degeneration (IDD) is the major cause of low back pain which incurs a significant public-health and economic burden. The aetiology of IDD is complex, with developmental, genetic, biomechanical and biochemical factors contributing to the disease development. Deregulated phenotypes of nucleus pulposus cells, including aberrant differentiation, apoptosis, proliferation and extracellular matrix deposition, are involved in the initiation and progression of IDD. Non-coding RNAs, including long non-coding RNAs (lncRNAs), have recently been identified as important regulators of gene expression. Research into their roles in IDD has been very active over the past 5 years. Our review summarizes current research regarding the roles of deregulated lncRNAs (eg, RP11-296A18.3, TUG1, HCG18) in modulating nucleus pulposus cell functions in IDD. These exciting findings suggest that specific modulation of lncRNAs or their downstream signalling pathways might be an attractive approach for developing novel therapeutics for IDD.

INTERRELATION OF PRIONS WITH NON-CODING RNAS

Prions are alternative infectious conformations for some cellular proteins. For the protein PrPC(PrP – prion protein, С – common), a prion conformation, called PrPSc(S – scrapie), is pathological. For example, in mammals the PrPScprion causes transmissible spongiform encephalopathies accumulating in the brain tissues of PrPScaggregates that have amyloid properties. MicroRNAs and long non-coding RNAs can be translated into functional peptides. These peptides can have a regulatory effect on genes from which their non-coding RNAs are transcribed. It has been assumed that prions, like peptides, due to the presence of specific domains, can also activate certain non-coding RNAs. Some of the activated non-coding RNAs can catalyze the formation of new prions from normal protein, playing their role in the pathogenesis of prion diseases. Confirmation of this assumption is the presence of the association of alleles of microRNA with the development of the disease, which indicates the role of the specific sequences of noncoding RNAs in the catalysis of prion formation. In the brain tissues of patients with prion diseases, as well as in exosomes containing an abnormal PrPScisoform, changes in the levels of microRNA have been observed. A possible cause is the interaction of the spatial domains of PrPScwith the sequences of the non-coding RNA genes, which causes a change in their expression. MicroRNAs, in turn, affect the synthesis of long non-coding RNAs. We hypothesize that long noncoding RNAs and possibly microRNAs can interact with PrPCcatalyzing its transformation into PrPSc. As a result, the number of PrPScincreases exponentially. In the brain of animals and humans, transposon activity has been observed, which has a regulatory effect on the differentiation of neuronal stem cells. Transposons form the basis of domain structures of long non-coding RNAs. In addition, they are important sources of microRNA. Since prion diseases can arise as sporadic and hereditary cases, and hereditary predisposition is important for the development of pathology, we hypothesize the role of individual features of activation of transposons in the pathogenesis of prion diseases. The activation of transposons in the brain at certain stages of development, as well as under the influence of stress, is reflected in the peculiarities of expression of specific non-coding RNAs that are capable of catalyzing the transition of the PrPCprotein to PrPSc. Research in this direction can be the basis for targeted anti-microRNA therapy of prion diseases.

Long non-coding RNA DANCR promotes cell proliferation, migration, invasion and resistance to apoptosis in esophageal cancer

BACKGROUND

Long non-coding RNAs (lncRNAs) have important effects on the development and progression of multiple carcinomas. Our studies aimed to investigate the expression of lncRNA DANCR in esophageal squamous cell carcinoma (ESCC) tissues and paracancerous tissues, and to explore its effect on the cell biological characteristics of ESCC ECA109 cells.

METHODS

The expression of DANCR was detected by qRT-PCR in human ESCC tissues and paracancerous normal tissues in ESCC patients. Small interfering RNA (siRNA) was transfected to knock down the expression of DANCR and interference efficiency was analyzed by qRT-PCR in ECA109 cells. MTT, wound healing, Transwell, TUNEL and flow cytometry (FCM) assay was used to measure the influence of DANCR on proliferation, invasion, migration and apoptosis in ECA109 cells, respectively.

RESULTS

The expression of DANCR in ESCC tissues and ESCC cells was significantly higher compared with that in the adjacent normal tissues (P<0.05). Furthermore, cell proliferation, migration and invasion were significantly suppressed by knock-down mediated down-regulation of DANCR expression. On the contrary, cell apoptosis was promoted by silencing of DANCR.

CONCLUSIONS

According to our research, the expression of DANCR was up-regulated in human ESCC tissues, and the important role that DANCR played in ESCC cells was similar to an oncogene. Therefore, silencing of lncRNA DANCR could have potentially beneficial effects on the prognostic and therapy for ESCC in the future.

The Role of Transposable Elements in Emergence of Metazoa

Systems initially emerged for protecting genomes against insertions of transposable elements and represented by mechanisms of splicing regulation, RNA-interference, and epigenetic factors have played a key role in the evolution of animals. Many studies have shown inherited transpositions of mobile elements in embryogenesis and preservation of their activities in certain tissues of adult organisms. It was supposed that on the emergence of Metazoa the self-regulation mechanisms of transposons related with the gene networks controlling their activity could be involved in intercellular cell coordination in the cascade of successive divisions with differentiated gene expression for generation of tissues and organs. It was supposed that during evolution species-specific features of transposons in the genomes of eukaryotes could form the basis for creation of dynamically related complexes of systems for epigenetic regulation of gene expression. These complexes could be produced due to the influence of noncoding transposon-derived RNAs on DNA methylation, histone modifications, and processing of alternative splicing variants, whereas the mobile elements themselves could be directly involved in the regulation of gene expression in cis and in trans. Transposons are widely distributed in the genomes of eukaryotes; therefore, their activation can change the expression of specific genes. In turn, this can play an important role in cell differentiation during ontogenesis. It is supposed that transposons can form a species-specific pattern for control of gene expression, and that some variants of this pattern can be favorable for adaptation. The presented data indicate the possible influence of transposons in karyotype formation. It is supposed that transposon localization relative to one another and to protein-coding genes can influence the species-specific epigenetic regulation of ontogenesis.