Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain

Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons

Neurons are central to lifelong learning and memory, but ageing disrupts their morphology and function, leading to cognitive decline. Although epigenetic mechanisms are known to play crucial roles in learning and memory, neuron-specific genome-wide epigenetic maps into old age remain scarce, often being limited to whole-brain homogenates and confounded by glial cells. Here, we mapped H3K4me3, H3K27ac, and H3K27me3 in mouse neurons across their lifespan. This revealed stable H3K4me3 and global losses of H3K27ac and H3K27me3 into old age. We observed patterns of synaptic function gene deactivation, regulated through the loss of the active mark H3K27ac, but not H3K4me3. Alongside this, embryonic development loci lost repressive H3K27me3 in old age. This suggests a loss of a highly refined neuronal cellular identity linked to global chromatin reconfiguration. Collectively, these findings indicate a key role for epigenetic regulation in neurons that is inextricably linked with ageing.

Hidden regulators: the emerging roles of lncRNAs in brain development and disease

Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.

Neuronal dysfunction and gene modulation by non-coding RNA in Parkinson's disease and synucleinopathies

Over the last few decades, emerging evidence suggests that non-coding RNAs (ncRNAs) including long-non-coding RNA (lncRNA), microRNA (miRNA) and circular-RNA (circRNA) contribute to the molecular events underlying progressive neuronal degeneration, and a plethora of ncRNAs have been identified significantly misregulated in many neurodegenerative diseases, including Parkinson's disease and synucleinopathy. Although a direct link between neuropathology and causative candidates has not been clearly established in many cases, the contribution of ncRNAs to the molecular processes leading to cellular dysfunction observed in neurodegenerative diseases has been addressed, suggesting that they may play a role in the pathophysiology of these diseases. Aim of the present Review is to overview and discuss recent literature focused on the role of RNA-based mechanisms involved in different aspects of neuronal pathology in Parkinson's disease and synucleinopathy models.

A model for cis-regulation of transcriptional condensates and gene expression by proximal lncRNAs

Long noncoding RNAs (lncRNAs) perform several important functions in cells including cis-regulation of transcription. Barring a few specific cases, the mechanisms underlying transcriptional regulation by lncRNAs remain poorly understood. Transcriptional proteins can form condensates via phase separation at protein-binding loci (BL) on the genome (e.g., enhancers and promoters). lncRNA-coding genes are present at loci in close genomic proximity of these BL and these RNAs can interact with transcriptional proteins via attractive heterotypic interactions mediated by their net charge. Motivated by these observations, we propose that lncRNAs can dynamically regulate transcription in cis via charge-based heterotypic interactions with transcriptional proteins in condensates. To study the consequences of this mechanism, we developed and studied a dynamical phase-field model. We find that proximal lncRNAs can promote condensate formation at the BL. Vicinally localized lncRNA can migrate to the BL to attract more protein because of favorable interaction free energies. However, increasing the distance beyond a threshold leads to a sharp decrease in protein recruitment to the BL. This finding could potentially explain why genomic distances between lncRNA-coding genes and protein-coding genes are conserved across metazoans. Finally, our model predicts that lncRNA transcription can fine-tune transcription from neighboring condensate-controlled genes, repressing transcription from highly expressed genes and enhancing transcription of genes expressed at a low level. This nonequilibrium effect can reconcile conflicting reports that lncRNAs can enhance or repress transcription from proximal genes.

Roles of lncRNAs in brain development and pathogenesis: Emerging therapeutic opportunities

The human genome is pervasively transcribed, producing a majority of short and long noncoding RNAs (lncRNAs) that can influence cellular programs through a variety of transcriptional and post-transcriptional regulatory mechanisms. The brain houses the richest repertoire of long noncoding transcripts, which function at every stage during central nervous system development and homeostasis. An example of functionally relevant lncRNAs is species involved in spatiotemporal organization of gene expression in different brain regions, which play roles at the nuclear level and in transport, translation, and decay of other transcripts in specific neuronal sites. Research in the field has enabled identification of the contributions of specific lncRNAs to certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders, resulting in notions of potential therapeutic strategies that target these RNAs to recover the normal phenotype. Here, we summarize the latest mechanistic findings associated with lncRNAs in the brain, focusing on their dysregulation in neurodevelopmental or neurodegenerative disorders, their use as biomarkers for central nervous system (CNS) diseases in vitro and in vivo, and their potential utility for therapeutic strategies.

Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326-NKX3.2-Regulated Porcine Chondrocyte Differentiation

The porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In this study, RNA-seq analysis was used to profile the transcriptome (lncRNA, mRNA, and miRNA) of the thoracic intervertebral cartilage (TIC) at two time points (1 and 4 months) during vertebral column development in Yorkshire (Y) and Wuzhishan pigs (W). There were four groups: 1- (Y1) and 4-month-old (Y4) Yorkshire pigs and 1- (W1) and 4-month-old (W4) Wuzhishan pigs. In total, 161, 275, 86, and 126 differentially expressed (DE) lncRNAs, 1478, 2643, 404, and 750 DE genes (DEGs), and 74,51, 34, and 23 DE miRNAs (DE miRNAs) were identified in the Y4 vs. Y1, W4 vs. W1, Y4 vs. W4, and Y1 vs. W1 comparisons, respectively. Functional analysis of these DE transcripts (DETs) demonstrated that they had participated in various biological processes, such as cellular component organization or biogenesis, the developmental process, the metabolic process, bone development, and cartilage development. The crucial bone development-related candidate genes NK3 Homeobox 2 (NKX3.2), Wnt ligand secretion mediator (WLS), gremlin 1 (GREM1), fibroblast growth factor receptor 3 (FGFR3), hematopoietically expressed homeobox (HHEX), (collagen type XI alpha 1 chain (COL11A1), and Wnt Family Member 16 (WNT16)) were further identified by functional analysis. Moreover, lncRNA, miRNA, and gene interaction networks were constructed; a total of 55 lncRNAs, 6 miRNAs, and 7 genes formed lncRNA-gene, miRNA-gene, and lncRNA-miRNA-gene pairs, respectively. The aim was to demonstrate that coding and non-coding genes may co-regulate porcine spine development through interaction networks. NKX3.2 was identified as being specifically expressed in cartilage tissues, and it delayed chondrocyte differentiation. miRNA-326 regulated chondrocyte differentiation by targeting NKX3.2. The present study provides the first non-coding RNA and gene expression profiles in the porcine TIC, constructs the lncRNA-miRNA-gene interaction networks, and confirms the function of NKX3.2 in vertebral column development. These findings contribute to the understanding of the potential molecular mechanisms regulating pig vertebral column development. They expand our knowledge about the differences in body length between different pig species and provide a foundation for future studies.

Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

BACKGROUND

The growth and development of leaves and petioles have a significant effect on photosynthesis. Understanding the molecular mechanisms underlying leaf and petiole development is necessary for improving photosynthetic efficiency, cultivating varieties with high photosynthetic efficiency, and improving the yield of crops of which the leaves are foodstuffs. This study aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). The data were used to construct a competitive endogenous RNA (ceRNA) network to obtain insights into the mechanisms underlying leaf and petiole development.

RESULTS

The leaves and petioles of the 'PHL' inbred line of Chinese cabbage were used as research materials for whole transcriptome sequencing. A total of 10,646 differentially expressed (DE) mRNAs, 303 DElncRNAs, 7 DEcircRNAs, and 195 DEmiRNAs were identified between leaves and petioles. Transcription factors and proteins that play important roles in leaf and petiole development were identified, including xyloglucan endotransglucosylase/hydrolase, expansion proteins and their precursors, transcription factors TCP15 and bHLH, lateral organ boundary domain protein, cellulose synthase, MOR1-like protein, and proteins related to plant hormone biosynthesis. A ceRNA regulatory network related to leaf and petiole development was constructed, and 85 pairs of ceRNA relationships were identified, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA, and 2 DEmiRNA-DEcircRNA pairs. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaves and petioles were screened from transcriptome data, and their functions were explored through subcellular localization analysis and transgenic overexpression verification. BrLSH1, BrLSH2 and BrLSH3 were nuclear proteins, and BrLSH2 inhibited the growth and development of Arabidopsis thaliana.

CONCLUSIONS

This study identifies mRNAs and non-coding RNAs that may be involved in the development of leaves and petioles in Chinese cabbage, and establishes a ceRNA regulatory network related to development of the leaves and petioles, providing valuable genomic resources for further research on the molecular mechanisms underlying leaf and petiole development in this crop species.

Whole-transcriptome analyses of Sorghum leaves identify key mRNAs and ncRNAs associated with GA3-mediated alleviation of salt stress

Sorghum has recently attracted much attention for its tolerance in high salt environment. However, the effect and regulatory mechanism of the gibberellic acid (GA₃)-mediated alleviation of salt stress in sorghum remains unclear. Herein, we reported that a GA₃ concentration of 50 mg/L is optimal for sorghum ("Jitian 3") development under salt stress. We conducted a whole-transcriptome analysis between GA₃-treated and control sorghum leaves under salt stress, and we identified 1002 differentially expressed (DE)-messenger RNAs (mRNAs), 81 DE-long non-coding RNAs (lncRNAs), 7 DE-circular RNAs (circRNAs), and 26 DE-microRNA (miRNAs) in sorghum following GA₃ treatment. We also identified a majority of DE-mRNAs and non-coding RNAs (ncRNAs) targets that serve essential roles in phenylpropanoid biosynthesis and plant hormone networks. In addition, we generated a competitive endogenous RNA (ceRNA)-miRNA-target gene network, and 3 circRNAs (circRNA_2746, circRNA_6515, circRNA_5622), 4 lncRNAs (XR_002450182.1, XR_002452422.1, XR_002448510.1, XR_002448296.1) and 4 genes (LOC8056546, LOC8062245, LOC8061469, LOC8071960) probably act as valuable candidates for the regulation of the GA₃-mediated alleviation of salt stress in sorghum. Our findings uncovered potential mRNA and non-coding RNAs that contribute to GA₃ regulation, thus offering a basis for the future investigation of underlying mechanisms of salt stress in sorghum.

Identification of the Genes Encoding B3 Domain-Containing Proteins Related to Vernalization of Beta vulgaris

Vernalization is the process of exposure to low temperatures, which is crucial for the transition from vegetative to reproductive growth of plants. In this study, the global landscape vernalization-related mRNAs and long noncoding RNAs (lncRNAs) were identified in Beta vulgaris. A total of 22,159 differentially expressed mRNAs and 4418 differentially expressed lncRNAs were uncovered between the vernalized and nonvernalized samples. Various regulatory proteins, such as zinc finger CCCH domain-containing proteins, F-box proteins, flowering-time-related proteins FY and FPA, PHD finger protein EHD3 and B3 domain proteins were identified. Intriguingly, a novel vernalization-related lncRNA-mRNA target-gene co-expression regulatory network and the candidate vernalization genes, VRN1, VRN1-like, VAL1 and VAL2, encoding B3 domain-containing proteins were also unveiled. The results of this study pave the way for further illumination of the molecular mechanisms underlying the vernalization of B. vulgaris.

Transcriptome-Wide Study of mRNAs and lncRNAs Modified by m6A RNA Methylation in the Longissimus Dorsi Muscle Development of Cattle-Yak

Cattle-yak is a hybrid F₁ generation of cattle and yak, which has a history of more than 3000 years and has shown better production performance and higher economic benefits than those of yaks. However, up to now, there has been no study on the transcriptome-wide m⁶A methylation profile of bovine skeletal muscle and its potential biological function during muscle development. Here, we observed significant changes in the expression levels of muscle-related marker genes and methylation-related enzymes during the development of cattle-yak, and the overall m⁶A content in the Longissimus dorsi muscle of 18-month-old cattle-yak decreased significantly. A total of 36,602 peaks, 11,223 genes and 8388 lncRNAs were identified in the two groups, including 2989 differential peaks (427 up-regulated peaks and 2562 down-regulated peaks), 1457 differentially expressed genes (833 up-regulated genes and 624 down-regulated genes) and 857 differentially expressed lncRNAs (293 up-regulated lncRNAs and 564 down-regulated lncRNAs). GO and KEGG analysis revealed that they were significantly enriched in some muscle-related pathways (Wnt signaling pathway and MAPK signaling pathway) and high-altitude adaptation-related pathway (HIF-1 signaling pathway). Moreover, m⁶A abundance was positively correlated with gene expression levels, while it was negatively correlated with lncRNA expression levels. This indicates that m⁶A modification played an important role in the Longissimus dorsi muscle development of cattle-yak; however, the regulation mechanism of m⁶A-modified mRNA and lncRNA may be different. This study was the first report of transcriptome-wide m⁶A-modified mRNAs and lncRNAs atlas in the Longissimus dorsi muscle development of cattle-yak, one which will provide new perspectives for genetic improvement in bovines.

LncRNA RUS shapes the gene expression program towards neurogenesis

The chromatin-associated lncRNA RUS binds in the vicinity to neural differentiation-associated genes and regulates them in a context-dependent manner to enable proper neuron development.

The evolution of brain complexity correlates with an increased expression of long, noncoding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for “RNA upstream of Slitrk3.” The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.

High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes

The advent of massively parallel sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long noncoding RNAs (lncRNAs). Selected functional examples raised the possibility that lncRNAs, as a class, may maintain broad regulatory roles. Expression of lncRNAs is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory functions. A more detailed understanding of these regulatory roles may be obtained through careful examination of the precise timing of lncRNA expression relative to adjacent protein-coding genes. Despite the diversity of reported lncRNA regulatory mechanisms, where causal cis-regulatory relationships exist, lncRNA transcription is expected to precede changes in target gene expression. Using a high temporal resolution RNA-seq time course, we profiled the expression dynamics of several thousand lncRNAs and protein-coding genes in synchronized, transitioning human cells. Our findings reveal that lncRNAs are expressed synchronously with adjacent protein-coding genes. Analysis of lipopolysaccharide-activated mouse dendritic cells revealed the same temporal relationship observed in transitioning human cells. Our findings suggest broad-scale cis-regulatory roles for lncRNAs are not common. The strong association between lncRNAs and adjacent genes may instead indicate an origin as transcriptional by-products from active protein-coding gene promoters and enhancers.

Discovering functional motifs in long noncoding RNAs

Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

The Long Non-Coding RNA GOMAFU in Schizophrenia: Function, Disease Risk, and Beyond

Neuropsychiatric diseases are among the most common brain developmental disorders, represented by schizophrenia (SZ). The complex multifactorial etiology of SZ remains poorly understood, which reflects genetic vulnerabilities and environmental risks that affect numerous genes and biological pathways. Besides the dysregulation of protein-coding genes, recent discoveries demonstrate that abnormalities associated with non-coding RNAs, including microRNAs and long non-coding RNAs (lncRNAs), also contribute to the pathogenesis of SZ. lncRNAs are an actively evolving family of non-coding RNAs that harbor greater than 200 nucleotides but do not encode for proteins. In general, lncRNA genes are poorly conserved. The large number of lncRNAs specifically expressed in the human brain, together with the genetic alterations and dysregulation of lncRNA genes in the SZ brain, suggests a critical role in normal cognitive function and the pathogenesis of neuropsychiatric diseases. A particular lncRNA of interest is GOMAFU, also known as MIAT and RNCR2. Growing evidence suggests the function of GOMAFU in governing neuronal development and its potential roles as a risk factor and biomarker for SZ, which will be reviewed in this article. Moreover, we discuss the potential mechanisms through which GOMAFU regulates molecular pathways, including its subcellular localization and interaction with RNA-binding proteins, and how interruption to GOMAFU pathways may contribute to the pathogenesis of SZ.

Integrated lncRNA function upon genomic and epigenomic regulation

Although some long noncoding (lnc)RNAs are known since the 1950s, the past 25 years have uncovered myriad lncRNAs with diverse sequences, structures, and functions. The advent of high-throughput and sensitive technologies has further uncovered the vast heterogeneity of lncRNA-interacting molecules and patterns of expressed lncRNAs. We propose a unifying functional theme for the expansive family of lncRNAs. At an elementary level, the genomic program of gene expression is elicited via canonical transcription and post-transcriptional mRNA assembly, turnover, and translation. Building upon this regulation, an epigenomic program refines the basic genomic control by modifying chromatin architecture as well as DNA and RNA chemistry. Superimposed over the genomic and epigenomic programs, lncRNAs create an additional regulatory dimension: by interacting with the proteins and nucleic acids that regulate gene expression in the nucleus and cytoplasm, lncRNAs help establish robust, nimble, and specific transcriptional and post-transcriptional control. We describe our present understanding of lncRNA-coordinated control of protein programs and cell fate and discuss challenges and opportunities as we embark on the next 25 years of lncRNA discovery.

Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells

Central nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expressed in the nervous system and are predicted to act together to regulate neuronal development and function. Although some of these lncRNAs also bind and modulate the activity of the encoded transcription factors, the regulatory mechanisms controlling co-expression of neighbouring lncRNA-protein coding genes remain unclear. Here, we used high resolution NG Capture-C to map the cis-regulatory interaction landscape of the key neuro-developmental Paupar-Pax6 lncRNA-mRNA locus. The results define chromatin architecture changes associated with high Paupar-Pax6 expression in neurons and identify both promoter selective as well as shared cis-regulatory-promoter interactions involved in regulating Paupar-Pax6 co-expression. We discovered that the TCF7L2 transcription factor, a regulator of chromatin architecture and major effector of the Wnt signalling pathway, binds to a subset of these candidate cis-regulatory elements to coordinate Paupar and Pax6 co-expression. We describe distinct roles for Paupar in Pax6 expression control and show that the Paupar DNA locus contains a TCF7L2 bound transcriptional silencer whilst the Paupar transcript can act as an activator of Pax6. Our work provides important insights into the chromatin interactions, signalling pathways and transcription factors controlling co-expression of adjacent lncRNAs and protein coding genes in the brain.

Long noncoding RNAs as regulators of pediatric acute myeloid leukemia

Long noncoding RNAs (lncRNAs) are increasingly emerging as regulators across human development and disease, and many have been described in the context of hematopoiesis and leukemogenesis. These studies have yielded new molecular insights into the contribution of lncRNAs to AML development and revealed connections between lncRNA expression and clinical parameters in AML patients. In this mini review, we illustrate the versatile functions of lncRNAs in AML, with a focus on pediatric AML, and present examples that may serve as future therapeutic targets or predictive factors.

LncRNAs and Cardiovascular Disease

A novel class of RNA molecule emerged from human transcriptome sequencing studies termed long non-coding RNAs. These RNA molecules differ from other classes of non-coding RNAs such as microRNAs in their sizes, sequence motifs and structures. Studies have demonstrated that long non-coding RNAs play a prominent role in the development and progression of cardiovascular disease. They provide the cell with tiered levels of gene regulation interacting with DNA, other RNA molecules or proteins acting in various capacities to control a variety of cellular mechanisms. Cell specificity is a hallmark of lncRNA studies and they have been identified in macrophages, smooth muscle cells, endothelial cells and hepatocytes. Recent lncRNA studies have uncovered functional micropeptides encoded within lncRNA genes that can have a different function to the lncRNA. Disease associated mutations in the genome tend to occur in non-coding regions signifying the importance of non-coding genes in disease associations. There is a great deal of work to be done in the non-coding RNA field and tremendous therapeutic potential due to their cell type specificity. A better understanding of the functions and interactions of lncRNAs will inevitably have clinical implications.

Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

Anther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestris L. ssp. pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers of Arabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.

Current and Future Perspectives of Noncoding RNAs in Brain Function and Neuropsychiatric Disease

Noncoding RNAs (ncRNAs) represent the majority of the transcriptome and play important roles in regulating neuronal functions. ncRNAs are exceptionally diverse in both structure and function and include enhancer RNAs, long ncRNAs, and microRNAs, all of which demonstrate specific temporal and regional expression in the brain. Here, we review recent studies demonstrating that ncRNAs modulate chromatin structure, act as chaperone molecules, and contribute to synaptic remodeling and behavior. In addition, we discuss ncRNA function within the context of neuropsychiatric diseases, particularly focusing on addiction and schizophrenia, and the recent methodological developments that allow for better understanding of ncRNA function in the brain. Overall, ncRNAs represent an underrecognized molecular contributor to complex neuronal processes underlying neuropsychiatric disorders.

Long Non-Coding RNA Lacuna Regulates Neuronal Differentiation of Neural Stem Cells During Brain Development

Although long non-coding RNAs (lncRNAs) is one of the most abundant classes of RNAs encoded within the mammalian genome and are highly expressed in the adult brain, they remain poorly characterized and their roles in the brain development are not well understood. Here we identify the lncRNA Lacuna (also catalogued as NONMMUT071331.2 in NONCODE database) as a negative regulator of neuronal differentiation in the neural stem/progenitor cells (NSCs) during mouse brain development. In particular, we show that Lacuna is transcribed from a genomic locus near to the Tbr2/Eomes gene, a key player in the transition of intermediate progenitor cells towards the induction of neuronal differentiation. Lacuna RNA expression peaks at the developmental time window between E14.5 and E16.5, consistent with a role in neural differentiation. Overexpression experiments in ex vivo cultured NSCs from murine cortex suggest that Lacuna is sufficient to inhibit neuronal differentiation, induce the number of Nestin+ and Olig2+ cells, without affecting proliferation or apoptosis of NSCs. CRISPR/dCas9-KRAB mediated knockdown of Lacuna gene expression leads to the opposite phenotype by inducing neuronal differentiation and suppressing Nestin+ and Olig2+ cells, again without any effect on proliferation or apoptosis of NSCs. Interestingly, despite the negative action of Lacuna on neurogenesis, its knockdown inhibits Eomes transcription, implying a simultaneous, but opposite, role in facilitating the Eomes gene expression. Collectively, our observations indicate a critical function of Lacuna in the gene regulation networks that fine tune the neuronal differentiation in the mammalian NSCs.

Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis)

BACKGROUND

The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenous RNA (ceRNA) network that provides valuable information to better understand the vernalization response.

RESULTS

In this study, seeds sampled from the Chinese cabbage doubled haploid (DH) line 'FT' with or without vernalization treatment were used for whole-transcriptome sequencing. A total of 2702 differentially expressed (DE) mRNAs, 151 DE lncRNAs, 16 DE circRNAs, and 233 DE miRNAs were identified in the vernalization-treated seeds. Various transcription factors, such as WRKY, MYB, NAC, bHLH, MADS-box, zinc finger protein CONSTANS-like gene, and B3 domain protein, and regulatory proteins that play important roles in the vernalization pathway were identified. Additionally, we constructed a vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA‒DEmRNA, 67 DEmiRNA‒DElncRNA, and 12 DEmiRNA‒DEcircRNA interactions, in Chinese cabbage. Furthermore, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs, which are involved in the regulation of flowering time, floral organ formation, bolting, and flowering, were identified.

CONCLUSIONS

Our results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernalization in Chinese cabbage.

Characterization of Long Non-coding RNAs Modified by m6A RNA Methylation in Skeletal Myogenesis

Proper development of mammalian skeletal muscle relies on precise gene expression regulation. Our previous studies revealed that muscle development is regulated by both mRNA and long non-coding RNAs (lncRNAs). Accumulating evidence has demonstrated that N⁶-methyladenosine (m⁶A) plays important roles in various biological processes, making it essential to profile m⁶A modification on a transcriptome-wide scale in developing muscle. Patterns of m⁶A methylation in lncRNAs in developing muscle have not been uncovered. Here, we reveal differentially expressed lncRNAs and report temporal m⁶A methylation patterns in lncRNAs expressed in mouse myoblasts and myotubes by RNA-seq and methylated RNA immunoprecipitation (MeRIP) sequencing. Many lncRNAs exhibit temporal differential expression, and m⁶A-lncRNAs harbor the consensus m⁶A motif “DRACH” along lncRNA transcripts. Interestingly, we found that m⁶A methylation levels of lncRNAs are positively correlated with the transcript abundance of lncRNAs. Overexpression or knockdown of m⁶A methyltransferase METTL3 alters the expression levels of these lncRNAs. Furthermore, we highlight that the function of m⁶A genic lncRNAs might correlate to their nearby mRNAs. Our work reveals a fundamental expression reference of m⁶A-mediated epitranscriptomic modifications in lncRNAs that are temporally expressed in developing muscle.

Chart Mining: A Survey of Methods for Automated Chart Analysis

Charts are useful communication tools for the presentation of data in a visually appealing format that facilitates comprehension. There have been many studies dedicated to chart mining, which refers to the process of automatic detection, extraction and analysis of charts to reproduce the tabular data that was originally used to create them. By allowing access to data which might not be available in other formats, chart mining facilitates the creation of many downstream applications. This paper presents a comprehensive survey of approaches across all components of the automated chart mining pipeline, such as (i) automated extraction of charts from documents; (ii) processing of multi-panel charts; (iii) automatic image classifiers to collect chart images at scale; (iv) automated extraction of data from each chart image, for popular chart types as well as selected specialized classes; (v) applications of chart mining; and (vi) datasets for training and evaluation, and the methods that were used to build them. Finally, we summarize the main trends found in the literature and provide pointers to areas for further research in chart mining.

RNA Deregulation in Amyotrophic Lateral Sclerosis: The Noncoding Perspective

RNA metabolism is central to cellular physiopathology. Almost all the molecular pathways underpinning biological processes are affected by the events governing the RNA life cycle, ranging from transcription to degradation. The deregulation of these processes contributes to the onset and progression of human diseases. In recent decades, considerable efforts have been devoted to the characterization of noncoding RNAs (ncRNAs) and to the study of their role in the homeostasis of the nervous system (NS), where they are highly enriched. Acting as major regulators of gene expression, ncRNAs orchestrate all the steps of the differentiation programs, participate in the mechanisms underlying neural functions, and are crucially implicated in the development of neuronal pathologies, among which are neurodegenerative diseases. This review aims to explore the link between ncRNA dysregulation and amyotrophic lateral sclerosis (ALS), the most frequent motoneuron (MN) disorder in adults. Notably, defective RNA metabolism is known to be largely associated with this pathology, which is often regarded as an RNA disease. We also discuss the potential role that these transcripts may play as diagnostic biomarkers and therapeutic targets.

Long Non-coding RNAs in Pathogenesis of Neurodegenerative Diseases

Emerging evidence addresses the link between the aberrant epigenetic regulation of gene expression and numerous diseases including neurological disorders, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and Huntington’s disease (HD). LncRNAs, a class of ncRNAs, have length of 200 nt or more, some of which crucially regulate a variety of biological processes such as epigenetic-mediated chromatin remodeling, mRNA stability, X-chromosome inactivation and imprinting. Aberrant regulation of the lncRNAs contributes to pathogenesis of many diseases, such as the neurological disorders at the transcriptional and post-transcriptional levels. In this review, we highlight the latest research progress on the contributions of some lncRNAs to the pathogenesis of neurodegenerative diseases via varied mechanisms, such as autophagy regulation, Aβ deposition, neuroinflammation, Tau phosphorylation and α-synuclein aggregation. Meanwhile, we also address the potential challenges on the lncRNAs-mediated epigenetic study to further understand the molecular mechanism of the neurodegenerative diseases.

Long Noncoding RNAs and Human Liver Disease

Long noncoding RNAs (lncRNAs) are pervasively transcribed in the genome, exhibit a diverse range of biological functions, and exert effects through a variety of mechanisms. The sheer number of lncRNAs in the human genome has raised important questions about their potential biological significance and roles in human health and disease. Technological and computational advances have enabled functional annotation of a large number of lncRNAs. Though the number of publications related to lncRNAs has escalated in recent years, relatively few have focused on those involved in hepatic physiology and pathology. We provide an overview of evolving lncRNA classification systems and characteristics and highlight important advances in our understanding of the contribution of lncRNAs to liver disease, with a focus on nonalcoholic steatohepatitis, hepatocellular carcinoma, and cholestatic liver disease. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Involvement of non-coding RNAs during infection of rice by Acidovorax oryzae

The expression of non-coding RNAs (ncRNAs) has been observed in a variety of bacteria. However, the function of ncRNAs and their regulatory targets are largely unknown, and few ncRNAs are found to be associated with bacterial virulence. The bacterial brown stripe pathogen Acidovorax oryzae (Ao) RS-1 shows a high level of condition-dependent differential expression of ncRNA, which we identified in a genome wide screen. We experimentally validated 66 differentially expressed ncRNAs using an integrative analysis of conservative genome sequences and transcriptomic data during in vivo interaction of the bacterial pathogen with the rice plant. To test the relevance of the differentially expressed ncRNAs, we chose four with different positions within the genome, and with different secondary structures and promoter activities. The results show that the overexpression of the four ncRNAs caused a significant change in virulence-related phenotypes, resistance to various environmental stresses, expression of secretion systems and effector proteins, while changing the expression of ncRNA putative target genes. We conclude that these ncRNAs are examples for the inherent regulatory roles for many of the observed ncRNAs in response to changing conditions such as host interaction or environmental adaption.

The Emerging Role of Long Non-Coding RNAs and MicroRNAs in Neurodegenerative Diseases: A Perspective of Machine Learning

Neurodegenerative diseases (NDs) are characterized by progressive neuronal dysfunction and death of brain cells population. As the early manifestations of NDs are similar, their symptoms are difficult to distinguish, making the timely detection and discrimination of each neurodegenerative disorder a priority. Several investigations have revealed the importance of microRNAs and long non-coding RNAs in neurodevelopment, brain function, maturation, and neuronal activity, as well as its dysregulation involved in many types of neurological diseases. Therefore, the expression pattern of these molecules in the different NDs have gained significant attention to improve the diagnostic and treatment at earlier stages. In this sense, we gather the different microRNAs and long non-coding RNAs that have been reported as dysregulated in each disorder. Since there are a vast number of non-coding RNAs altered in NDs, some sort of synthesis, filtering and organization method should be applied to extract the most relevant information. Hence, machine learning is considered as an important tool for this purpose since it can classify expression profiles of non-coding RNAs between healthy and sick people. Therefore, we deepen in this branch of computer science, its different methods, and its meaningful application in the diagnosis of NDs from the dysregulated non-coding RNAs. In addition, we demonstrate the relevance of machine learning in NDs from the description of different investigations that showed an accuracy between 85% to 95% in the detection of the disease with this tool. All of these denote that artificial intelligence could be an excellent alternative to help the clinical diagnosis and facilitate the identification diseases in early stages based on non-coding RNAs.

Emerging Role of Long Noncoding RNAs in Perioperative Neurocognitive Disorders and Anesthetic-Induced Developmental Neurotoxicity

Preclinical investigations in animal models have consistently demonstrated neurobiological changes and life-long cognitive deficits following exposure to widely used anesthetics early in life. However, the mechanisms by which these exposures affect brain function remain poorly understood, therefore, limiting the efficacy of current diagnostic and therapeutic options in human studies. The human brain exhibits an abundant expression of long noncoding RNAs (lncRNAs). These biologically active transcripts play critical roles in a diverse array of functions, including epigenetic regulation. Changes in lncRNA expression have been linked with brain development, normal CNS processes, brain injuries, and the development of neurodegenerative diseases, and many lncRNAs are known to have brain-specific expression. Aberrant lncRNA expression has also been implicated in areas of growing importance in anesthesia-related research, including anesthetic-induced developmental neurotoxicity (AIDN), a condition defined by neurological changes occurring in patients repeatedly exposed to anesthesia, and the related condition of perioperative neurocognitive disorder (PND). In this review, we detail recent advances in PND and AIDN research and summarize the evidence supporting roles for lncRNAs in the brain under both normal and pathologic conditions. We also discuss lncRNAs that have been linked with PND and AIDN, and conclude with a discussion of the clinical potential for lncRNAs to serve as diagnostic and therapeutic targets for the prevention of these neurocognitive disorders and the challenges facing the identification and characterization of associated lncRNAs.

From Junk to Function: LncRNAs in CNS Health and Disease

Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.

LncRNAs as putative biomarkers and therapeutic targets for Parkinson's disease

Parkinson's disease (PD) is known as one of the most common degenerative disorders related to the damage of the central nervous system (CNS). This brain disorder is also characterized by the formation of Lewy bodies in the cytoplasm of the dopaminergic neurons in the substantia nigra pars compacta (SNc), which consequently leads to motor and non-motor symptoms. With regard to the growing trend in the number of cases with PD and its effects on individuals, families, and communities, immediate treatments together with diagnostic methods are required. In this respect, long non-coding ribonucleic acids (lncRNAs) represent a large class of ncRNAs with more than 200 nucleotides in length, playing key roles in some important processes including gene expression, cell differentiation, genomic imprinting, apoptosis, and cell cycle. They are highly expressed in the CNS and previous studies have further reported that the expression profile of lncRNAs is disrupted in human diseases such as neurodegenerative disorders. Since the levels of some lncRNAs change over time in the brains of patients with PD, a number of previous studies have examined their potentials as biomarkers for this brain disorder. Therefore, the main purpose of this study was to review the advances in the related literature on lncRNAs as diagnostic, therapeutic, and prognostic biomarkers for PD.

Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function

The extraordinary cellular diversity and the complex connections established within different cells types render the nervous system of vertebrates one of the most sophisticated tissues found in living organisms. Such complexity is ensured by numerous regulatory mechanisms that provide tight spatiotemporal control, robustness and reliability. While the unusual abundance of long noncoding RNAs (lncRNAs) in nervous tissues was traditionally puzzling, it is becoming clear that these molecules have genuine regulatory functions in the brain and they are essential for neuronal physiology. The canonical view of RNA as predominantly a 'coding molecule' has been largely surpassed, together with the conception that lncRNAs only represent 'waste material' produced by cells as a side effect of pervasive transcription. Here we review a growing body of evidence showing that lncRNAs play key roles in several regulatory mechanisms of neurons and other brain cells. In particular, neuronal lncRNAs are crucial for orchestrating neurogenesis, for tuning neuronal differentiation and for the exact calibration of neuronal excitability. Moreover, their diversity and the association to neurodegenerative diseases render them particularly interesting as putative biomarkers for brain disease. Overall, we foresee that in the future a more systematic scrutiny of lncRNA functions will be instrumental for an exhaustive understanding of neuronal pathophysiology.

Long Noncoding RNA Expression Profiles of Rat Extrasynaptic and Synaptic Neurons Expressing the N-methyl-D-Aspartate Receptor Revealed by Microarray Analysis

PURPOSE

To study the 24-hour expression of long noncoding RNAs (lncRNAs) in synaptic and extrasynaptic neurons expressing N-methyl-D-aspartate receptor (NMDAR), and normal neuronal cultures, via microarray analysis.

MATERIALS AND METHODS

Cortical neurons from embryonic (day E18) Sprague-Dawley rats were used for primary neuronal culture. NMDAR activation was blocked and the cells were then incubated for 6 hours. Total RNA was extracted, quantified, and analyzed for purity and integrity. Double-stranded cDNA was synthesized, followed by quantile normalization, quantitative polymerase chain reaction validation, and data analysis. The interactions between transcription factors and lncRNAs were analyzed by Pearson correlation.

RESULTS

The lncRNA profiles were obtained after synaptic and extrasynaptic NMDAR activation of rat cortical neuron cultures for 24 hours. In total, 251 lncRNAs were consistently upregulated, and 335 were downregulated, after extrasynaptic NMDAR activation compared with normal neurons. After synaptic NMDAR activation, only 9 lncRNAs were upregulated and 2 were downregulated.

CONCLUSIONS

Differential expression of lncRNAs after synaptic and extrasynaptic NMDAR activation suggests that lncRNAs may be responsible for extrasynaptic NMDAR-induced neurodegeneration.

Long Noncoding RNA Fos Downstream Transcript Is Developmentally Dispensable but Vital for Shaping the Poststroke Functional Outcome

[Figure: see text].

Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression

Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-coding RNA (lncRNA) in bovine tissues, and a previous study characterizes (lncRNA) in macrophages infected with MAP in vitro. In this study, we aim to characterize the lncRNA in macrophages from cows naturally infected with MAP. From 15 herds, feces and blood samples were collected for each cow older than 24 months, twice yearly over 3–5 years. Paired samples were analyzed by fecal PCR and blood ELISA. We used RNA-seq data to study lncRNA in macrophages from 33 JD(+) and 33 JD(–) dairy cows. We performed RNA-seq analysis using the “new Tuxedo” suite. We characterized lncRNA using logistic regression and multilayered neural networks and used DESeq2 for differential expression analysis and Panther and Reactome classification systems for gene ontology (GO) analysis. The study identified 13,301 lncRNA, 605 of which were novel lncRNA. We found seven genes close to differentially expressed lncRNA, including CCDC174, ERI1, FZD1, TWSG1, ZBTB38, ZNF814, and ZSCAN4. None of the genes associated with susceptibility to JD have been cited in the literature. LncRNA target genes were significantly enriched for biological process GO terms involved in immunity and nucleic acid regulation. These include the MyD88 pathway (TLR5), GO:0043312 (neutrophil degranulation), GO:0002446 (neutrophil-mediated immunity), and GO:0042119 (neutrophil activation). These results identified lncRNA with potential roles in host immunity and potential candidate genes and pathways through which lncRNA might function in response to MAP infection.

Comparative genomics in the search for conserved long noncoding RNAs

Long noncoding RNAs (lncRNAs) have emerged as prominent regulators of gene expression in eukaryotes. The identification of lncRNA orthologs is essential in efforts to decipher their roles across model organisms, as homologous genes tend to have similar molecular and biological functions. The relatively high sequence plasticity of lncRNA genes compared with protein-coding genes, makes the identification of their orthologs a challenging task. This is why comparative genomics of lncRNAs requires the development of specific and, sometimes, complex approaches. Here, we briefly review current advancements and challenges associated with four levels of lncRNA conservation: genomic sequences, splicing signals, secondary structures and syntenic transcription.

Long non-coding RNAs in motor neuron development and disease

Long non-coding RNAs (lncRNAs) are RNAs that exceed 200 nucleotides in length and that are not translated into proteins. Thousands of lncRNAs have been identified with functions in processes such as transcription and translation regulation, RNA processing, and RNA and protein sponging. LncRNAs show prominent expression in the nervous system and have been implicated in neural development, function and disease. Recent work has begun to report on the expression and roles of lncRNAs in motor neurons (MNs). The cell bodies of MNs are located in cortex, brainstem or spinal cord and their axons project into the brainstem, spinal cord or towards peripheral muscles, thereby controlling important functions such as movement, breathing and swallowing. Degeneration of MNs is a pathological hallmark of diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. LncRNAs influence several aspects of MN development and disruptions in these lncRNA-mediated effects are proposed to contribute to the pathogenic mechanisms underlying MN diseases (MNDs). Accumulating evidence suggests that lncRNAs may comprise valuable therapeutic targets for different MNDs. In this review, we discuss the role of lncRNAs (including circular RNAs [circRNAs]) in the development of MNs, discuss how lncRNAs may contribute to MNDs and provide directions for future research.

Associating divergent lncRNAs with target genes by integrating genome sequence, gene expression and chromatin accessibility data

Recent RNA knockdown experiments revealed that a dozen divergent long noncoding RNAs (lncRNAs) positively regulate the transcription of genes in cis. Here, to understand the regulatory mechanism of divergent lncRNAs, we proposed a computational model IRDL (Identify the Regulatory Divergent LncRNAs) to associate divergent lncRNAs with target genes. IRDL took advantage of the cross-tissue paired expression and chromatin accessibility data in ENCODE and a dozen experimentally validated divergent lncRNA target genes. IRDL integrated sequence similarity, co-expression and co-accessibility features, battled the scarcity of gold standard datasets with an increasingly learning framework and identified 446 and 977 divergent lncRNA-gene regulatory associations for mouse and human, respectively. We found that the identified divergent lncRNAs and target genes correlated well in expression and chromatin accessibility. The functional and pathway enrichment analysis suggests that divergent lncRNAs are strongly associated with developmental regulatory transcription factors. The predicted loop structure validation and canonical database search indicate a scaffold regulatory model for divergent lncRNAs. Furthermore, we computationally revealed the tissue/cell-specific regulatory associations considering the specificity of lncRNA. In conclusion, IRDL provides a way to understand the regulatory mechanism of divergent lncRNAs and hints at hundreds of tissue/cell-specific regulatory associations worthy for further biological validation.

Impaired expression of the COSMOC/MOCOS gene unit in ASD patient stem cells

Autism spectrum disorders (ASD) are complex neurodevelopmental disorders with a very large number of risk loci detected in the genome. However, at best, each of them explains rare cases, the majority being idiopathic. Genomic data on ASD derive mostly from post-mortem brain analyses or cell lines derived from blood or patient-specific induced pluripotent stem cells (iPSCS). Therefore, the transcriptional and regulatory architecture of the nervous system, particularly during early developmental periods, remains highly incomplete. To access the critical disturbances that may have occurred during pregnancy or early childhood, we recently isolated stem cells from the nasal cavity of anesthetized patients diagnosed for ASD and compared them to stem cells from gender-matched control individuals without neuropsychiatric disorders. This allowed us to discover MOCOS, a non-mutated molybdenum cofactor sulfurase-coding gene that was under-expressed in the stem cells of most ASD patients of our cohort, disturbing redox homeostasis and synaptogenesis. We now report that a divergent transcription upstream of MOCOS generates an antisense long noncoding RNA, to which we coined the name COSMOC. Surprisingly, COSMOC is strongly under-expressed in all ASD patients of our cohort with the exception of a patient affected by Asperger syndrome. Knockdown studies indicate that loss of COSMOC reduces MOCOS expression, destabilizes lipid and energy metabolisms of stem cells, but also affects neuronal maturation and splicing of synaptic genes. Impaired expression of the COSMOC/MOCOS bidirectional unit might shed new lights on the origins of ASD that could be of importance for future translational studies.

Long Non-coding RNA Expression Profiling Identifies a Four-Long Non-coding RNA Prognostic Signature for Isocitrate Dehydrogenase Mutant Glioma

Background: Isocitrate dehydrogenase (IDH) mutant is one of the most robust and important genetic aberrations in glioma. However, the underlying regulation mechanism of long non-coding RNA (lncRNA) in IDH mutant glioma has not been systematically portrayed.

Methods:In this work, 775 IDH mutant glioma samples with transcriptome data, including 167 samples from the Chinese Glioma Genome Atlas (CGGA) RNAseq dataset, 390 samples from The Cancer Genome Atlas (TCGA) dataset, 79 samples from GSE16011 dataset, and 139 samples from CGGA microarray dataset, were enrolled. R language and GraphPad Prism software were applied for the statistical analysis and graphical work.

Results: By comparing the differentially lncRNA genes between IDH mutant and IDH wild-type glioma samples, a four-lncRNA (JAG1, PVT1, H19, and HAR1A) signature was identified in IDH mutant glioma patients. The signature model was established based on the expression level and the regression coefficient of the four lncRNA genes. IDH mutant glioma samples could be successfully stratified into low-risk and high-risk groups in CGGA RNAseq, TCGA, GSE16011, and CGGA microarray databases. Meanwhile, multivariate Cox analysis showed that the four-lncRNA signature was an independent prognostic biomarker after adjusting for other clinicopathologic factors. Moreover, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the immune response and cellular metabolism were significantly associated with the four-lncRNA risk signature.

Conclusion: Taken together, the four-lncRNA risk signature was identified as a novel prognostic marker for IDH mutant glioma patients and may potentially lead to improvements in the lives of glioma patients.

RNA, Genome Output and Input

RNA, the transcriptional output of genomes, not only templates protein synthesis or directly engages in catalytic functions, but can feed back to the genome and serve as regulatory input for gene expression. Transcripts affecting the RNA abundance of other genes act by mechanisms similar to and in concert with protein factors that control transcription. Through recruitment or blocking of activating and silencing complexes to specific genomic loci, RNA and protein factors can favor transcription or lower the local gene expression potential. Most regulatory proteins enter nuclei from all directions to start the search for increased affinity to specific DNA sequences or to other proteins nearby genuine gene targets. In contrast, RNAs emerge from spatial point sources within nuclei, their encoding genes. A transcriptional burst can result in the local appearance of multiple nascent RNA copies at once, in turn increasing local nucleic acid density and RNA motif abundance before diffusion into the nuclear neighborhood. The confined initial localization of regulatory RNAs causing accumulation of protein co-factors raises the intriguing possibility that target specificity of non-coding, and probably coding, RNAs is achieved through gene/RNA positioning and spatial proximity to regulated genomic regions. Here we review examples of positional cis conservation of regulatory RNAs with respect to target genes, spatial proximity of enhancer RNAs to promoters through DNA looping and RNA-mediated formation of membrane-less structures to control chromatin structure and expression. We speculate that linear and spatial proximity between regulatory RNA-encoding genes and gene targets could possibly ease the evolutionary pressure on maintaining regulatory RNA sequence conservation.

LncRNA-MAP3K4 regulates vascular inflammation through the p38 MAPK signaling pathway and cis-modulation of MAP3K4

Chronic vascular inflammation plays a key role in the pathogenesis of atherosclerosis. Long non-coding RNAs (lncRNAs) have emerged as essential inflammation regulators. We identify a novel lncRNA termed lncRNA-MAP3K4 that is enriched in the vessel wall and regulates vascular inflammation. In the aortic intima, lncRNA-MAP3K4 expression was reduced by 50% during the progression of atherosclerosis (chronic inflammation) and 70% during endotoxemia (acute inflammation). lncRNA-MAP3K4 knockdown reduced the expression of key inflammatory factors (eg, ICAM-1, E-selectin, MCP-1) in endothelial cells or vascular smooth muscle cells and decreased monocytes adhesion to endothelium, as well as reducing TNF-α, IL-1β, COX2 expression in macrophages. Mechanistically, lncRNA-MAP3K4 regulates inflammation through the p38 MAPK signaling pathway. lncRNA-MAP3K4 shares a bidirectional promoter with MAP3K4, an upstream regulator of the MAPK signaling pathway, and regulates its transcription in cis. lncRNA-MAP3K4 and MAP3K4 show coordinated expression in response to inflammation in vivo and in vitro. Similar to lncRNA-MAP3K4, MAP3K4 knockdown reduced the expression of inflammatory factors in several different vascular cells. Furthermore, lncRNA-MAP3K4 and MAP3K4 knockdown showed cooperativity in reducing inflammation in endothelial cells. Collectively, these findings unveil the role of a novel lncRNA in vascular inflammation by cis-regulating MAP3K4 via a p38 MAPK pathway.

Genome-wide analysis of long non-coding RNA expression profile in lung adenocarcinoma compared to spinal metastasis

Background

Long non-coding RNAs (lncRNAs) play important roles in tumor metastasis. The aim of the present study was to investigate their expression profile and potential functions in spinal metastasis (SM) of lung adenocarcinoma.

Methods

We conducted lncRNA and mRNA expression in lung adenocarcinoma and its SM tissue using microarray analysis. Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) revealed 10 differentially expressed lncRNAs. Gene ontology and pathway analysis were performed to test the gene effect. Possible target genes of lncRNAs were predicted based on precise algorithms.

Results

Microarray analysis found many significantly differentially expressed lncRNAs and mRNAs in lung adenocarcinoma compared with SM. qRT-PCR results aligned with those of the microarray analysis. The expression level of 10 lncRNAs showed the same trend (P<0.05). Biologic pathways known to be involved in cancer were identified among the differentially expressed mRNAs; these include cell adhesion molecules (related to 42 genes), focal adhesion (related to 31 genes), cytokine-cytokine receptor interaction (related to 48 genes), and extracellular matrix-receptor interaction (related to 23 genes). About 9,458 lncRNAs were found to have cis- or trans-genes. A total of 2,317 cis target genes were discovered to be abnormally expressed and could be regulated by lncRNAs in SM of lung adenocarcinoma.

Conclusions

Our results offer a genome-wide differential expression of lncRNA in lung adenocarcinoma and SM, as well as laying the foundation for further investigations of lncRNAs correlated with lung adenocarcinoma metastasis.

Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus

Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs), yet the biological functions of most of them remain unknown. A particularly rich repertoire of lncRNAs found in mammalian brain and in the early embryo. We used RNA-seq and computational analysis to prioritize lncRNAs that may regulate commitment of pluripotent cells to a neuronal fate and perturbed their expression prior to neuronal differentiation. Knockdown by RNAi of two highly conserved and well-expressed lncRNAs, Reno1 (2810410L24Rik) and lnc-Nr2f1, decreased the expression of neuronal markers and led to massive changes in gene expression in the differentiated cells. We further show that the Reno1 locus forms increasing spatial contacts during neurogenesis with its adjacent protein-coding gene Bahcc1. Loss of either Reno1 or Bahcc1 leads to an early arrest in neuronal commitment, failure to induce a neuronal gene expression program, and to global reduction in chromatin accessibility at regions that are marked by the H3K4me3 chromatin mark at the onset of differentiation. Reno1 and Bahcc1 thus form a previously uncharacterized circuit required for the early steps of neuronal commitment.

Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

Background

Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics.

Results

In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log₂ (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.

Conclusions

These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

Long non coding RNAs involved in MAPK pathway mechanism mediates diabetic neuropathic pain

Diabetes is the largest global epidemic of the 21st century, and the cost of diabetes and its complications comprise about 12% of global health expenditure. Diabetic neuropathy is the most common complication of diabetes, affecting up to 50% of patients over the course of their disease. Among them, 30%-50% develop neuropathic pain, which has typical symptoms that originate from the toes and progress to foot ulcers and seriously influence quality of life. The pathogenesis of diabetic neuropathic pain (DNP) is complicated and incompletely understood and there is no effective treatment except supportive treatment. Long noncoding RNAs (lncRNAs), a class of noncoding RNAs exceeding 200 nucleotides in length, have been shown to play key roles in fundamental cellular processes, and are considered to be potential targets for treatment. Recent research indicates that lncRNA is involved in the pathogenesis of DNP. Certain overexpressed lncRNAs can enhance the purinergic receptor-mediated neuropathic pain in peripheral ganglia and inflammatory cytokines are released due to receptors activated by adenosine triphosphate. In recent years, our laboratory also has been exploring the relationship and pathogenesis between lncRNAs and DNP. In this review, we focus on the recent progress in functional lncRNAs associated with DNP and investigate their roles related to respective receptors.

Identification of antisense lncRNAs targeting GSK3β as a regulator in major depressive disorder

Aim: To identify lncRNAs targeting GSK3β in MDD. Materials & methods: The levels of GSK3β and its three targeting lncRNAs (gsk3β antisense AS1, AS2 and AS3) were detected in 52 patients with major depressive disorder (MDD) before and after 8 weeks of escitalopram treatment. The functional study was evaluated using the silence of lncR-gsk3βAS2/3. The correlation between lncRNA-gsk3β and 89 MDD patients was analyzed. Human neuron progenitor cells were used to investigate the functional role of lncRNA-gsk3β in MDD. Results: All three lncRNAs were downregulated in MDD patients but upregulated after treatment. Inhibition of gsk3βAS2/3 reduced GSK3β expression and its phosphorylation levels in the neuron progenitor cells. Conclusion: Our findings suggest that lncRNA-gsk3βAS3 regulates GSK3β activity in MDD and has potential as a novel therapeutic target.

A long non-coding RNA GATA6-AS1 adjacent to GATA6 is required for cardiomyocyte differentiation from human pluripotent stem cells

Long noncoding RNAs (lncRNAs) are crucial in many cellular processes, yet relatively few have been shown to regulate human cardiomyocyte differentiation. Here, we demonstrate an essential role of GATA6 antisense RNA 1 (GATA6-AS1) in cardiomyocyte differentiation from human pluripotent stem cells (hPSCs). GATA6-AS1 is adjacent to cardiac transcription factor GATA6. We found that GATA6-AS1 was nuclear-localized and transiently upregulated along with GATA6 during the early stage of cardiomyocyte differentiation. The knockdown of GATA6-AS1 did not affect undifferentiated cell pluripotency but inhibited cardiomyocyte differentiation, as indicated by no or few beating cardiomyocytes and reduced expression of cardiomyocyte-specific proteins. Upon cardiac induction, the knockdown of GATA6-AS1 decreased GATA6 expression, altered Wnt-signaling gene expression, and reduced mesoderm development. Further characterization of the intergenic region between genomic regions of GATA6-AS1 and GATA6 indicated that the expression of GATA6-AS1 and GATA6 were regulated by a bidirectional promoter within the intergenic region. Consistently, GATA6-AS1 and GATA6 were co-expressed in several human tissues including the heart, similar to the mirror expression pattern of GATA6-AS1 and GATA6 during cardiomyocyte differentiation. Overall, these findings reveal a previously unrecognized and functional role of lncRNA GATA6-AS1 in controlling human cardiomyocyte differentiation.

Noncoding RNAs and Midbrain DA Neurons: Novel Molecular Mechanisms and Therapeutic Targets in Health and Disease

Midbrain dopamine neurons have crucial functions in motor and emotional control and their degeneration leads to several neurological dysfunctions such as Parkinson's disease, addiction, depression, schizophrenia, and others. Despite advances in the understanding of specific altered proteins and coding genes, little is known about cumulative changes in the transcriptional landscape of noncoding genes in midbrain dopamine neurons. Noncoding RNAs-specifically microRNAs and long noncoding RNAs-are emerging as crucial post-transcriptional regulators of gene expression in the brain. The identification of noncoding RNA networks underlying all stages of dopamine neuron development and plasticity is an essential step to deeply understand their physiological role and also their involvement in the etiology of dopaminergic diseases. Here, we provide an update about noncoding RNAs involved in dopaminergic development and metabolism, and the related evidence of these biomolecules for applications in potential treatments for dopaminergic neurodegeneration.