Pervasive transcription constitutes a new level of eukaryotic genome regulation

dsRNA formation leads to preferential nuclear export and gene expression

When mRNAs have been transcribed and processed in the nucleus, they are exported to the cytoplasm for translation. This export is mediated by the export receptor heterodimer Mex67-Mtr2 in the yeast Saccharomyces cerevisiae (TAP-p15 in humans)1,2. Interestingly, many long non-coding RNAs (lncRNAs) also leave the nucleus but it is currently unclear why they move to the cytoplasm3. Here we show that antisense RNAs (asRNAs) accelerate mRNA export by annealing with their sense counterparts through the helicase Dbp2. These double-stranded RNAs (dsRNAs) dominate export compared with single-stranded RNAs (ssRNAs) because they have a higher capacity and affinity for the export receptor Mex67. In this way, asRNAs boost gene expression, which is beneficial for cells. This is particularly important when the expression program changes. Consequently, the degradation of dsRNA, or the prevention of its formation, is toxic for cells. This mechanism illuminates the general cellular occurrence of asRNAs and explains their nuclear export.

Global control of RNA polymerase II

RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.

Integrated analysis of long non-coding RNAs and mRNAs associated with condyloma acuminatum

Condyloma acuminatum (CA) is a prevalent sexually transmitted disease caused by low-risk human papillomavirus infection, characterized by high transmission and recurrence rates. Long non-coding RNAs (lncRNAs) play a crucial role in regulating gene transcription and are involved in various biological processes. Although recent studies have demonstrated the involvement of lncRNAs in cervical cancer, their expression profile and function in CA remain poorly understood. In this study, we aimed to identify messenger RNA (mRNA) and lncRNA expression patterns in CA using high-throughput lncRNA sequencing. We found that 3033 differentially expressed genes (DEGs) and 1090 differentially expressed lncRNAs (DELs) were significantly altered in CA compared to healthy controls. The results from quantitative reverse transcription polymerase chain reaction and immunohistochemical staining are in accordance with the observed trends in the sequencing data. Functional enrichment analysis revealed that upregulated DEGs in CA were involved in biological processes such as virus response, immune response, cell cycle regulation, the tumor necrosis factor signaling pathway, and the P53 signaling pathway. Co-expression network analysis identified potential target genes of DELs, with enrichment in biological processes such as cell differentiation, the intrinsic apoptotic signaling pathway, and pathways such as virus infection, pathways in cancer, T helper 17 cell differentiation, the mitogen-activated protein kinase signaling pathway, and the Wnt signaling pathway. Collectively, our findings indicate significant changes in the transcriptome profile, including mRNAs and lncRNAs, in CA compared to healthy controls. Our study provides new insights into the potential functions of lncRNAs in the pathogenesis of CA and identifies potential therapeutic targets for this disease.

Genome-Wide Identification and Characterization of Long Non-Coding RNAs Associated with Floral Scent Formation in Jasmine (Jasminum sambac)

Long non-coding RNAs (lncRNAs) have emerged as curial regulators of diverse biological processes in plants. Jasmine (Jasminum sambac) is a world-renowned ornamental plant for its attractive and exceptional flower fragrance. However, to date, no systematic screening of lncRNAs and their regulatory roles in the production of the floral fragrance of jasmine flowers has been reported. In this study, we identified a total of 31,079 novel lncRNAs based on an analysis of strand-specific RNA-Seq data from J. sambac flowers at different stages. The lncRNAs identified in jasmine flowers exhibited distinct characteristics compared with protein-coding genes (PCGs), including lower expression levels, shorter transcript lengths, and fewer exons. Certain jasmine lncRNAs possess detectable sequence conservation with other species. Expression analysis identified 2752 differentially expressed lncRNAs (DE_lncRNAs) and 8002 DE_PCGs in flowers at the full-blooming stage. DE_lncRNAs could potentially cis- and trans-regulate PCGs, among which DE_lincRNAs and their targets showed significant opposite expression patterns. The flowers at the full-blooming stage are specifically enriched with abundant phenylpropanoids and terpenoids potentially contributed by DE_lncRNA cis-regulated PCGs. Notably, we found that many cis-regulated DE_lncRNAs may be involved in terpenoid and phenylpropanoid/benzenoid biosynthesis pathways, which potentially contribute to the production of jasmine floral scents. Our study reports numerous jasmine lncRNAs and identifies floral-scent-biosynthesis-related lncRNAs, which highlights their potential functions in regulating the floral scent formation of jasmine and lays the foundations for future molecular breeding.

Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders

The haemostatic system is pivotal to maintaining vascular integrity. Multiple components involved in blood coagulation have central functions in inflammation and immunity. A derailed haemostasis is common in prevalent pathologies such as sepsis, cardiovascular disorders, and lately, COVID-19. Physiological mechanisms limit the deleterious consequences of a hyperactivated haemostatic system through adaptive changes in gene expression. While this is mainly regulated at the level of transcription, co- and posttranscriptional mechanisms are increasingly perceived as central hubs governing multiple facets of the haemostatic system. This layer of regulation modulates the biogenesis of haemostatic components, for example in situations of increased turnover and demand. However, they can also be 'hijacked' in disease processes, thereby perpetuating and even causally entertaining associated pathologies. This review summarizes examples and emerging concepts that illustrate the importance of posttranscriptional mechanisms in haemostatic control and crosstalk with the immune system. It also discusses how such regulatory principles can be used to usher in new therapeutic concepts to combat global medical threats such as sepsis or cardiovascular disorders.

Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer's disease

Modulation of brain olfactory (OR) and taste receptor (TASR) expression was recently reported in neurological diseases. However, there is still limited evidence of these genes' expression in the human brain and the transcriptional regulation mechanisms involved remain elusive. We explored the possible expression and regulation of selected OR and TASR in the human orbitofrontal cortex (OFC) of sporadic Alzheimer's disease (AD) and non-demented control specimens using quantitative real-time RT-PCR and ELISA. Global H3K9me3 amounts were measured on OFC total histone extracts, and H3K9me3 binding at each chemoreceptor locus was examined through native chromatin immunoprecipitation. To investigate the potential interactome of the repressive histone mark H3K9me3 in OFC specimens, native nuclear complex co-immunoprecipitation (Co-IP) was combined with reverse phase-liquid chromatography coupled to mass spectrometry analysis. Interaction between H3K9me3 and MeCP2 was validated by reciprocal Co-IP, and global MeCP2 levels were quantitated. We found that OR and TAS2R genes are expressed and markedly downregulated in OFC at early stages of sporadic AD, preceding the progressive reduction in their protein levels and the appearance of AD-associated neuropathology. The expression pattern did not follow disease progression suggesting transcriptional regulation through epigenetic mechanisms. We discovered an increase of OFC global H3K9me3 levels and a substantial enrichment of this repressive signature at ORs and TAS2Rs proximal promoter at early stages of AD, ultimately lost at advanced stages. We revealed the interaction between H3K9me3 and MeCP2 at early stages and found that MeCP2 protein is increased in sporadic AD. Findings suggest MeCP2 might be implicated in OR and TAS2R transcriptional regulation through interaction with H3K9me3, and as an early event, it may uncover a novel etiopathogenetic mechanism of sporadic AD.

Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs

Although long noncoding RNAs (lncRNAs) experience weaker evolutionary constraints and exhibit lower sequence conservation than coding genes, they can still conserve their features in various aspects. Here, we used multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1,731 conserved lncRNAs with 427 high-confidence ones meeting multiple criteria. Conserved lncRNAs, compared with non-conserved ones, generally have longer gene bodies, more exons and transcripts, stronger connections with human diseases, and are more abundant and widespread across different tissues. Transcription factor (TF) profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger regulation on conserved than non-conserved lncRNAs. Our study has reconciled some discrepant interpretations of lncRNA conservation and revealed a new set of transcriptional factors ruling the expression of conserved lncRNAs.

Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions

It is debated whether the pervasive intergenic transcription from eukaryotic genomes has functional significance or simply reflects the promiscuity of RNA polymerases. We approach this question by comparing chance promoter activities with the expression levels of intergenic regions in the model eukaryote Saccharomyces cerevisiae. We build a library of over 105 strains, each carrying a 120-nucleotide, chromosomally integrated, completely random sequence driving the potential transcription of a barcode. Quantifying the RNA concentration of each barcode in two environments reveals that 41-63% of random sequences have significant, albeit usually low, promoter activities. Therefore, even in eukaryotes, where the presence of chromatin is thought to repress transcription, chance transcription is prevalent. We find that only 1-5% of yeast intergenic transcriptions are unattributable to chance promoter activities or neighboring gene expressions, and these transcriptions exhibit higher-than-expected environment-specificity. These findings suggest that only a minute fraction of intergenic transcription is functional in yeast.

The noncoding RNA HIDDEN TREASURE 1 promotes phytochrome B-dependent seed germination by repressing abscisic acid biosynthesis

Light is a major environmental factor for seed germination. Red light-activated phytochrome B (phyB) promotes seed germination by modulating the dynamic balance of two phytohormones, gibberellic acid (GA) and abscisic acid (ABA). How phyB modulates ABA biosynthesis after perceiving a light signal is not yet well understood. Here, we identified the noncoding RNA HIDDEN TREASURE 1 (HID1) as a repressor of ABA biosynthesis acting downstream of phyB during Arabidopsis thaliana seed germination. Loss of HID1 function led to delayed phyB-dependent seed germination. Photoactivated phyB promoted the accumulation of HID1 in the radicle within 48 h of imbibition. Our transcriptomics analysis showed that HID1 and phyB co-regulate the transcription of a common set of genes involved in ABA and GA metabolism. Through a forward genetic screen, we identified three ABA biosynthesis genes, ABA DEFICIENT 1 (ABA1), ABA2, and ABA3, as suppressors of HID1. We further demonstrated that HID1 directly inhibits the transcription of 9-CIS-EPOXYCAROTENOID DIOXYGENASE (NCED9), a gene encoding a key rate-limiting enzyme of ABA biosynthesis. HID1 interacts with ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), an H3K4me3 methyltransferase, inhibiting its occupancy and H3K4me3 modification at the NCED9 locus. Our study reveals a nuclear mechanism of phyB signaling transmitted through HID1 to control the internal homeostasis of ABA and GA, which gradually optimizes the transcriptional network during seed germination.

Temporal regulation of head-on transcription at replication initiation sites

Head-on (HO) collisions between the DNA replication machinery and RNA polymerase over R-loop forming sequences (RLFS) are genotoxic, leading to replication fork blockage and DNA breaks. Current models suggest that HO collisions are avoided through replication initiation site (RIS) positioning upstream of active genes, ensuring co-orientation of replication fork movement and genic transcription. However, this model does not account for pervasive transcription, or intragenic RIS. Moreover, pervasive transcription initiation and CG-rich DNA is a feature of RIS, suggesting that HO transcription units (HO TUs) capable of forming R-loops might occur. Through mining phased GRO-seq data, and developing an informatics strategy to stringently identify RIS, we demonstrate that HO TUs containing RLFS occur at RIS in MCF-7 cells, and are downregulated at the G1/S phase boundary. Our analysis reveals a novel spatiotemporal relationship between transcription and replication, and supports the idea that HO collisions are avoided through transcriptional regulatory mechanisms.

Bacterial Transcription Factors Bind to Coding Regions and Regulate Internal Cryptic Promoters

Transcription factors (TFs) regulate transcription by binding to the specific sequences at the promoter region. However, the mechanisms and functions of TFs binding within the coding sequences (CDS) remain largely elusive in prokaryotes. To this end, we collected 409 data sets for bacterial TFs, including 104 chromatin immunoprecipitation sequencing (ChIP-seq) assays and 305 data sets from the systematic evolution of ligands by exponential enrichment (SELEX) in seven model bacteria. Interestingly, these TFs displayed the same binding capabilities for both coding and intergenic regions. Subsequent biochemical and genetic experiments demonstrated that several TFs bound to the coding regions and regulated the transcription of the binding or adjacent genes. Strand-specific RNA sequencing revealed that these CDS-binding TFs regulated the activity of the cryptic promoters, resulting in the altered transcription of the corresponding antisense RNA. TF RhpR hindered the transcriptional elongation of a subgenic transcript within a CDS. A ChIP-seq and Ribo-seq coanalysis revealed that RhpR influenced the translational efficiency of binding genes. Taken together, the present study reveals three regulatory mechanisms of CDS-bound TFs within individual genes, operons, and antisense RNAs, which demonstrate the variability of the regulatory mechanisms of TFs and expand upon the complexity of bacterial transcriptomes.

LncRNAs in Osteoarthritis

Osteoarthritis (OA) is a progressive joint disease that affects millions of older adults around the world. With increasing rates of incidence and prevalence worldwide, OA has become an enormous global socioeconomic burden on healthcare systems. Long non-coding ribonucleic acids (lncRNAs), essential functional molecules in many biological processes, are a group of non-coding RNAs that are greater than approximately 200 nucleotides in length. Fast-growing and recent developments in lncRNA research are captivating and represent a novel and promising field in understanding the complexity of OA pathogenesis. The involvement of lncRNAs in OA's pathological processes and their altered expressions in joint tissues, blood and synovial fluid make them attractive candidates for the diagnosis and treatment of OA. We focus on the recent advances in major regulator mechanisms of lncRNAs in the pathophysiology of OA and discuss potential diagnostic and therapeutic uses of lncRNAs for OA. We investigate how upregulation or downregulation of lncRNAs influences the pathogenesis of OA and how we can use lncRNAs to elucidate the molecular mechanism of OA. Furthermore, we evaluate how we can use lncRNAs as a diagnostic marker or therapeutic target for OA. Our study not only provides a comprehensive review of lncRNAs regarding OA's pathogenesis but also contributes to the elucidation of its molecular mechanisms and to the development of diagnostic and therapeutic approaches for OA.

Phosphorylation-dependent association of human chromatin protein PC4 to linker histone H1 regulates genome organization and transcription

Human Positive Coactivator 4 (PC4) is a multifaceted chromatin protein involved in diverse cellular processes including genome organization, transcription regulation, replication, DNA repair and autophagy. PC4 exists as a phospho-protein in cells which impinges on its acetylation by p300 and thereby affects its transcriptional co-activator functions via double-stranded DNA binding. Despite the inhibitory effects, the abundance of phosphorylated PC4 in cells intrigued us to investigate its role in chromatin functions in a basal state of the cell. We found that casein kinase-II (CKII)-mediated phosphorylation of PC4 is critical for its interaction with linker histone H1. By employing analytical ultracentrifugation and electron microscopy imaging of in vitro reconstituted nucleosomal array, we observed that phospho-mimic (PM) PC4 displays a superior chromatin condensation potential in conjunction with linker histone H1. ATAC-sequencing further unveiled the role of PC4 phosphorylation to be critical in inducing chromatin compaction of a wide array of coding and non-coding genes in vivo. Concordantly, phospho-PC4 mediated changes in chromatin accessibility led to gene repression and affected global histone modifications. We propose that the abundance of PC4 in its phosphorylated state contributes to genome compaction contrary to its co-activator function in driving several cellular processes like gene transcription and autophagy.

The emerging roles of N6-methyladenosine (m6A)-modified long non-coding RNAs in human cancers

N⁶-methyladenosine (m⁶A) epitranscriptional modifications widely exist in RNA, which play critical roles in RNA metabolism and biogenesis processes. Long non-coding RNAs (lncRNAs) are class of non-coding RNAs longer than 200 nucleotides without protein-coding ability. LncRNAs participate in a large number of vital biological progressions. With the great improvement of molecular biology, m⁶A and lncRNAs are attracting more attention from researchers and scholars. In this review, we overview the current status of m⁶A and lncRNAs based on the latest research, and propose some viewpoints for future research perspectives.

Classification of Hepatocellular Carcinoma Based on N6-Methylandenosine–Related lncRNAs Profiling

HCC is one of the most common types of malignancies worldwide and the fourth-leading cause of cancer deaths. Thus, there is an urgent need to search for novel targeted therapies in HCC. 186 m6a-related lncRNAs were screened for subsequent analysis. Two distinct m6A modification clusters were identified to be associated with the overall prognosis in TCGA-LIHC based on the m6A-related lncRNAs profiling, followed by univariate Cox regression analysis. In addition, four m6A-related lncRNAs prognostic signatures were developed and validated that could predict the OS of HCC patients, followed by univariate Cox regression, LASSO regression, and multivariate Cox regression analysis. Moreover, four m6A-related lncRNAs were identified to be related to HCC prognosis. ESTIMATE was used to evaluate the stromal score, immune score, ESTIMATE score, and tumor purity of each HCC sample. ssGSEA was performed to identify the enrichment levels of 29 immune signatures in each sample. Finally, quantitative real-time polymerase chain reaction shown that KDM4A-AS1, BACE1-AS, and NRAV expressions were upregulated in HCC patients. We proved that our m6A-related lncRNAs signature had powerful and robust ability for predicting OS of different HCC subgroups.

Long RNA-Mediated Chromatin Regulation in Fission Yeast and Mammals

As part of a complex network of genome control, long regulatory RNAs exert significant influences on chromatin dynamics. Understanding how this occurs could illuminate new avenues for disease treatment and lead to new hypotheses that would advance gene regulatory research. Recent studies using the model fission yeast Schizosaccharomyces pombe (S. pombe) and powerful parallel sequencing technologies have provided many insights in this area. This review will give an overview of key findings in S. pombe that relate long RNAs to multiple levels of chromatin regulation: histone modifications, gene neighborhood regulation in cis and higher-order chromosomal ordering. Moreover, we discuss parallels recently found in mammals to help bridge the knowledge gap between the study systems.

In vivo discovery of RNA proximal proteins via proximity-dependent biotinylation

RNA molecules function as messenger RNAs (mRNAs) that encode proteins and noncoding transcripts that serve as adaptor molecules, structural components, and regulators of genome organization and gene expression. Their function and regulation are largely mediated by RNA binding proteins (RBPs). Here we present RNA proximity labelling (RPL), an RNA-centric method comprising the endonuclease-deficient Type VI CRISPR-Cas protein dCas13b fused to engineered ascorbate peroxidase APEX2. RPL discovers target RNA proximal proteins in vivo via proximity-based biotinylation. RPL applied to U1 identified proteins involved in both U1 canonical and noncanonical functions. Profiling of poly(A) tail proximal proteins uncovered expected categories of RBPs and provided additional evidence for 5'-3' proximity and unexplored subcellular localizations of poly(A)+ RNA. Our results suggest that RPL allows rapid identification of target RNA binding proteins in native cellular contexts, and is expected to pave the way for discovery of novel RNA-protein interactions important for health and disease.

Tissue-specific analysis of Coffea arabica L. transcriptome revealed potential regulatory roles of lncRNAs

Long non-coding RNAs (lncRNAs) play pivot roles in regulating mRNA expression in eukaryotic organisms without coding any proteins. In the current study, a comprehensive analysis of 260 published RNA-Seq datasets collected from different tissues (fruits, leaves, stems, and roots) of Coffea arabica L. was performed to discover potential lncRNAs. A total of 10,564 unique lncRNAs were identified. Our results showed that 77.14% of the lncRNAs were intergenic and 60.39% of them are located within 5 Kbp from the partner gene. In general, all the identified lncRNAs showed shorter lengths, fewer number of exons, and lower expression levels as compared to mRNAs in different studied tissues. Several lncRNAs were determined as differentially expressed (DE) in fruits as compared to leaves, stems, or roots. The functional characterization of the DE lncRNAs revealed their roles in regulating significant biological processes in different tissues of C. arabica. The current study provides a comprehensive analysis and dataset of lncRNAs in C. arabica that could be utilized in further studies concerning the roles of these molecules in plant cells.

The role of the multifaceted long non-coding RNAs: A nuclear-cytosolic interplay to regulate hyaluronan metabolism

In the extracellular matrix (ECM), the glycosaminoglycan (GAG) hyaluronan (HA) has different physiological roles favouring hydration, elasticity and cell survival. Three different isoforms of HA synthases (HAS1, 2, and 3) are responsible for the production of HA. In several pathologies the upregulation of HAS enzymes leads to an abnormal HA accumulation causing cell dedifferentiation, proliferation and migration thus favouring cancer progression, fibrosis and vascular wall thickening. An intriguing new player in HAS2 gene expression regulation and HA production is the long non-coding RNA (lncRNA) hyaluronan synthase 2 antisense 1 (HAS2-AS1). A significant part of mammalian genomes corresponds to genes that transcribe lncRNAs; they can regulate gene expression through several mechanisms, being involved not only in maintaining the normal homeostasis of cells and tissues, but also in the onset and progression of different diseases, as demonstrated by the increasing number of studies published through the last decades. HAS2-AS1 is no exception: it can be localized both in the nucleus and in the cytosol, regulating cancer cells as well as vascular smooth muscle cells behaviour.

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Hyaluronan is a component of the extracellular matrix and is synthetised by three isoenzymes named HAS1, 2, and 3.

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In several pathologies an upregulation of HAS2 leads to an abnormal accumulation of HA.

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The long non-coding RNA is a new specific epigenetic regulator of HAS2.

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In the nucleus HAS2-AS1 modulates chromatin structure around HAS2 promoter increasing transcription.

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In the cytosol, HAS2-AS1 can interact with several miRNAs altering the expression of several genes as well as can stabilise HAS2 mRNA forming RNA: RNA duplex.

The impact of non-coding RNAs on normal stem cells

Self-renewal and differentiation into diverse cells are two main characteristics of stem cells. These cells have important roles in development and homeostasis of different tissues and are supposed to facilitate tissue regeneration. Function of stem cells is regulated by dynamic interactions between external signaling, epigenetic factors, and molecules that regulate expression of genes. Among the highly appreciated regulators of function of stem cells are long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). Impact of miR-342-5p, miR-145, miR-1297, miR-204-5p, miR-132, miR-128-3p, hsa-miR-302, miR-26b-5p and miR-10a are among miRNAs that regulate function of stem cells. Among lncRNAs, AK141205, ANCR, MEG3, Pnky, H19, TINCR, HULC, EPB41L4A-AS1 and SNHG7 have important roles in the regulation of stem cells. In the current paper, we aimed at reviewing the importance of miRNAs and lncRNAs in differentiation of stem cells both in normal and diseased conditions. For this purpose, we searched PubMed/Medline and google scholar databases using "stem cell" AND "lncRNA", or "long non-coding RNA", or "microRNA" or "miRNA".

Non-Coding, RNAPII-Dependent Transcription at the Promoters of rRNA Genes Regulates Their Chromatin State in S. cerevisiae

Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.

Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum

Long non-coding RNAs (lncRNAs) are a type of non-coding transcripts having length of more than 200 nucleotides lacking protein-coding ability. In the present study, 12807 lncRNAs were identified in Capsicum annuum tissues exposed to abiotic stress conditions viz. heat, cold, osmotic and salinity stress. Expression analysis of lncRNAs in different treatment conditions demonstrates their stress-specific expression. Thirty lncRNAs were found to act as precursors for 10 microRNAs (miRNAs) of C. annuum. Additionally, a total of 1807 lncRNAs were found to interact with 194 miRNAs which targeted 621 mRNAs of C. annuum. Among these, 344 lncRNAs were found to act as target mimics for 621 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that out of those 621 gene sequences, 546 were tagged with GO terms, 105 Enzyme Code (EC) numbers were assigned to 246 genes and 223 genes are found to be involved in 63 biological pathways. In this report, we have highlighted the prospective role of lncRNAs in different abiotic stress conditions by interacting with miRNAs and regulating stress responsive transcription factors (TFs) such as DoF, WRKY, MYB, bZIP and ERF in C. annuum.

Role of long non-coding RNAs on the regulation of Nrf2 in chronic diseases

Studies have identified dysregulated long non-coding RNA (lncRNA) in several diseases at transcriptional, translational, and post-translational levels. Although our mechanistic knowledge on the regulation of lncRNAs is still limited, one of the mechanisms of action attributed is binding and regulating transcription factors, thus controlling gene expression and protein function. One such transcription factor is nuclear factor erythroid 2-related factor 2 (Nrf2), which plays a critical biological role in maintaining cellular homeostasis at multiple levels in physiological and pathophysiological conditions. The levels of Nrf2 were found to be down-regulated in many chronic diseases, signifying that Nrf2 can be a key therapeutic target. Few lncRNAs like lncRNA ROR, ENSMUST00000125413, lncRNA ODRUL, Nrf2-lncRNA have been associated with the Nrf2 signaling pathway in response to various stimuli, including stress. This review discusses the regulation of Nrf2 in different responses and the potential role of specific lncRNA in modulating its transcriptional activities. This review further helps to enhance our knowledge on the regulatory role of the critical antioxidant transcription factor, Nrf2.

Blood-based Biomarkers of Alzheimer's Disease: The Long and Winding Road

BACKGROUND

Blood-based biomarkers can be very useful in formulating new diagnostic and treatment proposals in the field of dementia, especially in Alzheimer's disease (AD). However, due to the influence of several factors on the reproducibility and reliability of these markers, their clinical use is still very uncertain. Thus, up-to-date knowledge about the main blood biomarkers that are currently being studied is extremely important in order to discover clinically useful and applicable tools, which could also be used as novel pharmacological strategies for the AD treatment.

METHODS

A narrative review was performed based on the current candidates of blood-based biomarkers for AD to show the main results from different studies, focusing on their clinical applicability and association with AD pathogenesis.

OBJECTIVE

The aim of this paper was to carry out a literature review on the major blood-based biomarkers for AD, connecting them with the pathophysiology of the disease.

RESULTS

Recent advances in the search of blood-based AD biomarkers were summarized in this review. The biomarkers were classified according to the topics related to the main hallmarks of the disease such as inflammation, amyloid, and tau deposition, synaptic degeneration and oxidative stress. Moreover, molecules involved in the regulation of proteins related to these hallmarks were described, such as non-coding RNAs, neurotrophins, growth factors and metabolites. Cells or cellular components with the potential to be considered as blood-based AD biomarkers were described in a separate topic.

CONCLUSION

A series of limitations undermine new discoveries on blood-based AD biomarkers. The lack of reproducibility of findings due to the small size and heterogeneity of the study population, different analytical methods and other assay conditions make longitudinal studies necessary in this field to validate these structures, especially when considering a clinical evaluation that includes a broad panel of these potential and promising blood-based biomarkers.

Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice

BACKGROUND

Long non-coding RNAs (LncRNAs) have emerged as important regulators in many physiological processes in plant. By high-throughput RNA-sequencing, many pathogen-associated LncRNAs were mapped in various plants, and some of them were proved to be involved in plant defense responses. The rice blast disease caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases in rice. However, M. oryzae-induced LncRNAs in rice is yet to be studied.

FINDINGS

We investigated rice LncRNAs that were associated with the rice blast fungus. Totally 83 LncRNAs were up-regulated after blast fungus infection and 78 were down-regulated. Of them, the natural antisense transcripts (NATs) were the most abundant. The expression of some LncRNAs has similar pattern with their host genes or neighboring genes, suggesting a cis function of them in regulating gene transcription level. The deferentially expressed (DE) LncRNAs and genes co-expression analysis revealed some LncRNAs were associated with genes known to be involved in pathogen resistance, and these genes were enriched in terpenoid biosynthesis and defense response by Gene Ontology (GO) enrichment analysis. Interestingly, one of up-regulated DE-intronic RNA was derived from a jasmonate (JA) biosynthetic gene, lipoxygenase RLL (LOX-RLL). Levels of JAs were significantly increased after blast fungus infection. Given that JA is known to regulate blast resistance in rice, we suggested that LncRNA may be involved in JA-mediated rice resistance to blast fungus.

CONCLUSIONS

This study identified blast fungus-responsive LncRNAs in rice, which provides another layer of candidates that regulate rice and blast fungus interactions.

A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer

Although enhancers play critical roles in cancer, quantifying enhancer activities in clinical samples remains challenging, especially for super-enhancers. Enhancer activities can be inferred from enhancer RNA (eRNA) signals, which requires enhancer transcription loci definition. Only a small proportion of human eRNA loci has been precisely identified, limiting investigations of enhancer-mediated oncogenic mechanisms. Here, we characterize super-enhancer regions using aggregated RNA sequencing (RNA-seq) data from large cohorts. Super-enhancers usually contain discrete loci featuring sharp eRNA expression peaks. We identify >300,000 eRNA loci in ∼377 Mb super-enhancer regions that are regulated by evolutionarily conserved, well-positioned nucleosomes and are frequently dysregulated in cancer. The eRNAs provide explanatory power for cancer phenotypes beyond that provided by mRNA expression through resolving intratumoral heterogeneity with enhancer cell-type specificity. Our study provides a high-resolution map of eRNA loci through which super-enhancer activities can be quantified by RNA-seq and a user-friendly data portal, enabling a broad range of biomedical investigations.

The Role of Small Noncoding RNA in DNA Double-Strand Break Repair

DNA damage is a common phenomenon promoted through a variety of exogenous and endogenous factors. The DNA damage response (DDR) pathway involves a wide range of proteins, and as was indicated, small noncoding RNAs (sncRNAs). These are double-strand break-induced RNAs (diRNAs) and DNA damage response small RNA (DDRNA). Moreover, RNA binding proteins (RBPs) and RNA modifications have also been identified to modulate diRNA and DDRNA function in the DDR process. Several theories have been formulated regarding the synthesis and function of these sncRNAs during DNA repair; nevertheless, these pathways’ molecular details remain unclear. Here, we review the current knowledge regarding the mechanisms of diRNA and DDRNA biosynthesis and discuss the role of sncRNAs in maintaining genome stability.

Functional impacts of non-coding RNA processing on enhancer activity and target gene expression

Tight regulation of gene expression is orchestrated by enhancers. Through recent research advancements, it is becoming clear that enhancers are not solely distal regulatory elements harboring transcription factor binding sites and decorated with specific histone marks, but they rather display signatures of active transcription, showing distinct degrees of transcription unit organization. Thereby, a substantial fraction of enhancers give rise to different species of non-coding RNA transcripts with an unprecedented range of potential functions. In this review, we bring together data from recent studies indicating that non-coding RNA transcription from active enhancers, as well as enhancer-produced long non-coding RNA transcripts, may modulate or define the functional regulatory potential of the cognate enhancer. In addition, we summarize supporting evidence that RNA processing of the enhancer-associated long non-coding RNA transcripts may constitute an additional layer of regulation of enhancer activity, which contributes to the control and final outcome of enhancer-targeted gene expression.

Long noncoding RNAs shape transcription in plants

The advent of novel high-throughput sequencing techniques has revealed that eukaryotic genomes are massively transcribed although only a small fraction of RNAs exhibits protein-coding capacity. In the last years, long noncoding RNAs (lncRNAs) have emerged as regulators of eukaryotic gene expression in a wide range of molecular mechanisms. Plant lncRNAs can be transcribed by alternative RNA polymerases, acting directly as long transcripts or can be processed into active small RNAs. Several lncRNAs have been recently shown to interact with chromatin, DNA or nuclear proteins to condition the epigenetic environment of target genes or modulate the activity of transcriptional complexes. In this review, we will summarize the recent discoveries about the actions of plant lncRNAs in the regulation of gene expression at the transcriptional level.

Histone deacetylases 1 and 2 silence cryptic transcription to promote mitochondrial function during cardiogenesis

Cryptic transcription occurs widely across the eukaryotic genome; however, its regulation during vertebrate development is not understood. Here, we show that two class I histone deacetylases, Hdac1 and Hdac2, silence cryptic transcription to promote mitochondrial function in developing murine hearts. Mice lacking Hdac1 and Hdac2 in heart exhibit defective developmental switch from anaerobic to mitochondrial oxidative phosphorylation (OXPHOS), severe defects in mitochondrial mass, mitochondrial function, and complete embryonic lethality. Hdac1/Hdac2 promotes the transition to OXPHOS by enforcing transcriptional fidelity of metabolic gene programs. Mechanistically, Hdac1/Hdac2 deacetylates histone residues including H3K23, H3K14, and H4K16 to suppress cryptic transcriptional initiation within the coding regions of actively transcribed metabolic genes. Thus, Hdac1/2-mediated epigenetic silencing of cryptic transcription is essential for mitochondrial function during early vertebrate development.

RNA at DNA Double-Strand Breaks: The Challenge of Dealing with DNA:RNA Hybrids

RNA polymerase II is recruited to DNA double-strand breaks (DSBs), transcribes the sequences that flank the break and produces a novel RNA type that has been termed damage-induced long non-coding RNA (dilncRNA). DilncRNAs can be processed into short, miRNA-like molecules or degraded by different ribonucleases. They can also form double-stranded RNAs or DNA:RNA hybrids. The DNA:RNA hybrids formed at DSBs contribute to the recruitment of repair factors during the early steps of homologous recombination (HR) and, in this way, contribute to the accuracy of the DNA repair. However, if not resolved, the DNA:RNA hybrids are highly mutagenic and prevent the recruitment of later HR factors. Here recent discoveries about the synthesis, processing, and degradation of dilncRNAs are revised. The focus is on RNA clearance, a necessary step for the successful repair of DSBs and the aim is to reconcile contradictory findings on the effects of dilncRNAs and DNA:RNA hybrids in HR.

A human somatic cell culture system for modelling gene silencing by transcriptional interference

Transcriptional interference and transcription through regulatory elements (transcriptional read-through) are implicated in gene silencing and the establishment of DNA methylation. Transcriptional read-through is needed to seed DNA methylation at imprinted genes in the germ line and can lead to aberrant gene silencing by DNA methylation in human disease. To enable the study of parameters and factors influencing transcriptional interference and transcriptional read-through at human promoters, we established a somatic cell culture system. At two promoters of imprinted genes (UBE3A and SNRPN) and two promoters shown to be silenced by aberrant transcriptional read-through in human disease (MSH2 and HBA2) we tested, if transcriptional read-through is sufficient for gene repression and the acquisition of DNA methylation. Induction of transcriptional read-through from the doxycycline-inducible CMV promoter resulted in consistent repression of all downstream promoters, independent of promoter type and orientation. Repression was dependent on ongoing transcription, since withdrawal of induction resulted in reactivation. DNA methylation was not acquired at any of the promoters. Overexpression of DNMT3A and DNMT3L, factors needed for DNA methylation establishment in oocytes, was still not sufficient for the induction of DNA methylation. This indicates that induction of DNA methylation has more complex requirements than transcriptional read-through and the presence of de novo DNA methyltransferases.

MIR221HG Is a Novel Long Noncoding RNA that Inhibits Bovine Adipocyte Differentiation

Adipogenesis is a complicated but precisely orchestrated process mediated by a series of transcription factors. Our previous study has identified a novel long noncoding RNA (lncRNA) that was differentially expressed during bovine adipocyte differentiation. Because this lncRNA overlaps with miR-221 in the genome, it was named miR-221 host gene (MIR221HG). The purpose of this study was to clone the full length of MIR221HG, detect its subcellular localization, and determine the effects of MIR221HG on bovine adipocyte differentiation. The 5′ rapid amplification of cDNA ends (RACE) and 3′ RACE analyses demonstrated that MIR221HG is a transcript of 1064 nucleotides, is located on the bovine X chromosome, and contains a single exon. Bioinformatics analyses suggested that MIR221HG is an lncRNA and the promoter of MIR221HG includes the binding consensus sequences of the forkhead box C1 (FOXC1) and krüppel-like factor5 (KLF5). The semi-quantitative PCR and quantitative real-time PCR (qRT-PCR) of nuclear and cytoplasmic fractions revealed that MIR221HG mainly resides in the nucleus. Inhibition of MIR221HG significantly increased adipocyte differentiation, as indicated by a dramatic increment in the number of mature adipocytes and in the expression of the respective adipogenic markers, peroxisome proliferator-activated receptor γ (PPARγ), CCAAT/enhancer-binding protein α (C/EBPα), and fatty acid binding protein 4 (FABP4). Our results provide a basis for elucidating the mechanism by which MIR221HG regulates adipocyte differentiation.

lncRNA Rmst acts as an important mediator of BMP9-induced osteogenic differentiation of mesenchymal stem cells (MSCs) by antagonizing Notch-targeting microRNAs

Understanding the bone and musculoskeletal system is essential to maintain the health and quality of life of our aging society. Mesenchymal stem cells (MSCs) can undergo self-renewal and differentiate into multiple tissue types including bone. We demonstrated that BMP9 is the most potent osteogenic factors although molecular mechanism underlying BMP9 action is not fully understood. Long noncoding RNAs (lncRNAs) play important regulatory roles in many physiological and/or pathologic processes. Here, we investigated the role of lncRNA Rmst in BMP9-induced osteogenic differentiation of MSCs. We found that Rmst was induced by BMP9 through Smad signaling in MSCs. Rmst knockdown diminished BMP9-induced osteogenic, chondrogenic and adipogenic differentiation in vitro, and attenuated BMP9-induced ectopic bone formation. Silencing Rmst decreased the expression of Notch receptors and ligands. Bioinformatic analysis predicted Rmst could directly bind to eight Notch-targeting miRNAs, six of which were downregulated by BMP9. Silencing Rmst restored the expression of four microRNAs (miRNAs). Furthermore, an activating Notch mutant NICD1 effectively rescued the decreased ALP activity caused by Rmst silencing. Collectively, our results strongly suggest that the Rmst-miRNA-Notch regulatory axis may play an important role in mediating BMP9-induced osteogenic differentiation of MSCs.

Si vis pacem para bellum: A prospective in silico analysis of miRNA-based plant defenses against fungal infections

Fungal pathogens are an important threat for plant crops, being responsible for important reductions of production yields and a consequent economic impact. Among the molecular mediators of fungal infections of plant crops, non-coding RNAs (ncRNAs) have been described as relevant players either in the plant immune responses and mechanism of defense or in the colonization of plant tissues by fungi. Acting as a mechanism of defense, some plant small ncRNAs such as miRNAs and tasiRNAs can be secreted by cells and directed to target the transcriptome of pathogenic fungi, triggering an RNAi-like interference mechanism able to silence the expression of specific fungal genes. The detailed knowledge of this mechanism of defense against fungal pathogens could open new possibilities for the protection of human important crops. To infer putative functional relationships mediated by ncRNA communication, we performed a prospective analysis to determine potential plant miRNAs able to target the genome of fungal pathogens, which resulted in the description of enriched specific plant miRNA families and their putative fungal targets that could be further studied in the context of plant-fungi interactions. The expression profile of specific members of the enriched miRNAs families showed an infection-dependent behavior in laboratory models of infection. Plant miRNAs showed sequence complementarity with coding genes of their cognate fungal pathogens. Plant miRNAs could potentially target fungal genes belonging to functional families related to stress response, membrane architecture, vacuolar transport, membrane traffic, and anabolic processes. Families of specific infection-responsive miRNAs are included in the putative plant defense mechanism.

Identification and dynamic quantification of regulatory elements using total RNA

The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 billion years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.

LINC00565 promotes proliferation and inhibits apoptosis of gastric cancer by targeting miR-665/AKT3 axis

Background

Numerous studies have shown that long noncoding RNA (lncRNA) is involved in gastric cancer (GC). A relevant microarray containing gastric cancer-related lncRNAs was downloaded from The Cancer Genome Atlas database.

Methods

qRT-PCR was used to analyze LINC00565 and AKT3 expression in tumor tissues and cell lines. Proliferative, colony formation and apoptotic abilities of GC cells after transfection of sh-LINC00565 were determined by CCK-8, colony formation assay and flow cytometry, respectively. RIP was enrolled to detect the interaction between LINC00565, AKT3 and miR-665. Dual luciferase assay was used to confirm the relation between miR-665 and LINC00565 and AKT3.

Results

Expression level of LINC00565 in GC tissue was highly expressed in GC, which was negatively correlated to prognosis of GC patients. The results showed that knockdown of LINC00565 decreased proliferative and colony formation abilities, and induced apoptosis of GC cells. Pearson analysis showed that LINC00565 was positively correlated with AKT3. Besides, AKT3 was significantly up-regulated in GC. In addition, knockdown of LINC00565 down-regulated AKT3. In order to explore the mechanism, we found that miR-665 could bind to LINC00565 by bioinformatics. Dual-luciferase reporter gene assay and RIP assay both verified the binding relationship between miR-665 and AKT3. Finally, rescue experiments were carried out to explore whether AKT3 could reverse the anti-cancer effect of low-level LINC00565 on GC development.

Conclusion

In summary, the expression of LINC00565 is upregulated in GC. LINC00565 can be used as the sponge of miR-665 to up-regulate the expression of AKT3, thus promoting the progression of GC.

SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers

Super-enhancers (SEs) are enriched with a cluster of mediator binding sites, which are major contributors to cell-type-specific gene expression. Currently, a large quantity of long non-coding RNAs has been found to be transcribed from or to interact with SEs, which constitute super-enhancer associated long non-coding RNAs (SE-lncRNAs). These SE-lncRNAs play essential roles in transcriptional regulation through controlling SEs activity to regulate a broad range of physiological and pathological processes, especially tumorigenesis. However, the pathological functions of SE-lncRNAs in tumorigenesis are still obscure. In this paper, we characterized 5056 SE-lncRNAs and their associated genes by analysing 102 SE data sets. Then, we analysed their expression profiles and prognostic information derived from 19 cancer types to identify cancer-related SE-lncRNAs and to explore their potential functions. In total, 436 significantly differentially expressed SE-lncRNAs and 2035 SE-lncRNAs with high prognostic values were identified. Additionally, 3935 significant correlations between SE-lncRNAs and their regulatory genes were further validated by calculating their correlation coefficients in each cancer type. Finally, the SELER database incorporating the aforementioned data was provided for users to explore their physiological and pathological functions to comprehensively understand the blocks of living systems.

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.

A Potential Role for the Noncoding Transcriptome in Psychiatric Disorders

Understanding the complexity and regular function of the human brain is an unresolved challenge that hampers the identification of disease-contributing components and mechanisms of psychiatric disorders. It is accepted that the majority of psychiatric disorders result from a complex interaction of environmental and heritable factors, and efforts to determine, for example, genetic variants contributing to the pathophysiology of these diseases are becoming increasingly successful. We also continue to discover new molecules with unknown functions that might play a role in brain physiology. One such class of polymeric molecules is noncoding RNAs; though discovered years ago, they have only recently started to receive careful attention. Furthermore, recent technological advances in the field of molecular genetics and high-throughput sequencing have facilitated the discovery of a broad spectrum of RNAs that show no obvious coding potential but may provide additional layers of complexity and regulation to the molecular mechanisms underlying psychiatric disorders. Their exquisite enrichment and expression profiles in the brain may point to important functions of these RNAs in health and disease. This review will therefore aim to provide insight into the expression of noncoding RNAs in the brain, their function, and potential role in psychiatric disorders.

New lncRNA annotation reveals extensive functional divergence of the transcriptome in maize

Long non-coding RNAs (lncRNAs), whose sequences are approximately 200 bp or longer and unlikely to encode proteins, may play an important role in eukaryotic gene regulation. Although the latest maize (Zea mays L.) reference genome provides an essential genomic resource, genome-wide annotations of maize lncRNAs have not been updated. Here, we report on a large transcriptomic dataset collected from 749 RNA sequencing experiments across different tissues and stages of the maize reference inbred B73 line and 60 from its wild relative teosinte. We identified 18,165 high-confidence lncRNAs in maize, of which 6,873 are conserved between maize and teosinte. We uncovered distinct genomic characteristics of conserved lncRNAs, non-conserved lncRNAs, and protein-coding transcripts. Intriguingly, Shannon entropy analysis showed that conserved lncRNAs are likely to be expressed similarly to protein-coding transcripts. Co-expression network analysis revealed significant variation in the degree of co-expression. Furthermore, selection analysis indicated that conserved lncRNAs are more likely than non-conserved lncRNAs to be located in regions subject to recent selection, indicating evolutionary differentiation. Our results provide the latest genome-wide annotation and analysis of maize lncRNAs and uncover potential functional divergence between protein-coding, conserved lncRNA, and non-conserved lncRNA genes, demonstrating the high complexity of the maize transcriptome.

Rapid evolution of protein diversity by de novo origination in Oryza

New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation. Using pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments, we detected at least 175 de novo open reading frames in the focal species O. sativa subspecies japonica, which were all detected in RNA sequencing-based transcriptomes. Mass spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo genes. In recent divergence of Oryza, an average of 51.5 de novo genes per million years were generated and retained. We observed evolutionary patterns in which excess indels and early transcription were favoured in origination with a stepwise formation of gene structure. These data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection.

Contribution of spurious transcription to intellectual disability disorders

During the development of multicellular organisms, chromatin-modifying enzymes orchestrate the establishment of gene expression programmes that characterise each differentiated cell type. These enzymes also contribute to the maintenance of cell type-specific transcription profiles throughout life. But what happens when epigenomic regulation goes awry? Genomic screens in experimental models of intellectual disability disorders (IDDs) caused by mutations in epigenetic machinery-encoding genes have shown that transcriptional dysregulation constitutes a hallmark of these conditions. Here, we underscore the connections between a subset of chromatin-linked IDDs and spurious transcription in brain cells. We also propose that aberrant gene expression in neurons, including both the ectopic transcription of non-neuronal genes and the activation of cryptic promoters, may importantly contribute to the pathoaetiology of these disorders.

Avian Intestinal Mucus Modulates Campylobacter jejuni Gene Expression in a Host-Specific Manner

Campylobacter jejuni is a leading cause of bacterial foodborne illness in humans worldwide. However, C. jejuni naturally colonizes poultry without causing pathology where it resides deep within mucus of the cecal crypts. Mucus may modulate the pathogenicity of C. jejuni in a species-specific manner, where it is pathogenic in humans and asymptomatic in poultry. Little is known about how intestinal mucus from different host species affects C. jejuni gene expression. In this study we characterized the growth and transcriptome of C. jejuni NCTC11168 cultured in defined media supplemented with or without mucus isolated from avian (chicken or turkey) or mammalian (cow, pig, or sheep) sources. C. jejuni showed substantially improved growth over defined media, with mucus from all species, showing that intestinal mucus was an energy source for C. jejuni. Seventy-three genes were differentially expressed when C. jejuni was cultured in avian vs. mammalian mucus. Genes associated with iron acquisition and resistance to oxidative stress were significantly increased in avian mucus. Many of the differentially expressed genes were flanked by differentially expressed antisense RNA asRNA, suggesting a role in gene regulation. This study highlights the interactions between C. jejuni and host mucus and the impact on gene expression, growth and invasion of host cells, suggesting important responses to environmental cues that facilitate intestinal colonization. IMPORTANCE  Campylobacter jejuni infection of humans is an important health problem world-wide and is the leading bacterial cause of foodborne illnesses in U.S. The main route for exposure for humans is consumption of poultry meat contaminated during processing. C. jejuni is frequently found in poultry, residing within the mucus of the intestinal tract without causing disease. It is not clear why C. jejuni causes disease in some animals and humans, while leaving birds without symptoms. To understand its activity in birds, we characterized C. jejuni responses to poultry mucus to identify genes turned on in the intestinal tract of birds. We identified genes important for colonization and persistence within the poultry gut, turned on when C. jejuni was exposed to poultry mucus. Our findings are an important step in understanding how C. jejuni responds and interacts in the poultry gut, and may identify ways to reduce C. jejuni in birds.

The Involvement of Long Noncoding RNAs in Response to Plant Stress

Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved mechanisms which allow them to adapt to abiotic stresses through alterations in gene expression and metabolism. In recent years, studies have investigated the role of long noncoding RNA (lncRNA) in regulating gene expression in plants and characterized their involvement in various biological functions through their regulation of DNA methylation, DNA structural modifications, histone modifications, and RNA-RNA interactions. Genome-wide transcriptome analyses have identified various types of noncoding RNAs (ncRNAs) that respond to abiotic stress. These ncRNAs are in addition to the well-known housekeeping ncRNAs, such as rRNAs, tRNAs, snoRNAs, and snRNAs. In this review, recent research pertaining to the role of lncRNAs in the response of plants to abiotic stress is summarized and discussed.

Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling

DNA double-strand breaks (DSBs) jeopardize genome integrity and can-when repaired unfaithfully-give rise to structural rearrangements associated with cancer. Exogenous agents such as ionizing radiation or chemotherapy can invoke DSBs, but a vast amount of breakage arises during vital endogenous DNA transactions, such as replication and transcription. Additionally, chromatin looping involved in 3D genome organization and gene regulation is increasingly recognized as a possible contributor to DSB events. In this review, we first discuss insights into the mechanisms of endogenous DSB formation, showcasing the trade-off between essential DNA transactions and the intrinsic challenges that these processes impose on genomic integrity. In the second part, we highlight emerging methods for genome-wide profiling of DSBs, and discuss future directions of research that will help advance our understanding of genome-wide DSB formation and repair.

lncRNA involvement in hepatocellular carcinoma metastasis and prognosis

Eukaryotic lncRNAs are RNA molecules defined to be greater than 200 bp in length that are not translated to a protein and operate through several mechanisms, including participating in chromatin remodeling and methylation, influencing the integrity and stability of proteins and complexes, or acting as a sponge for miRNA inhibition. A number of recent studies have concentrated on the relationship between long non-coding RNAs (lncRNAs) and cancer. Hepatocellular carcinoma (HCC) is the most prevalent histological type of liver tumors, accounting for about 80 % of the cases worldwide. Lack of proper molecular markers for diagnosis of HCC and treatment evaluation is a significant problem. Dysregulated expression of HCC-related lncRNAs such as MEG-3, MALAT1, HULC, HOTAIR, and H19 have been identified and closely related with tumorigenesis, metastasis, prognosis and diagnosis. In this review, we summarized recent highlighted functions and molecular mechanisms of the most extensively studied lncRNAs in the pathophysiology of hepatocellular carcinoma and their potential for serving as probable therapeutic targets.

Long noncoding RNAs involve in resistance to Verticillium dahliae, a fungal disease in cotton

Long noncoding RNAs (lncRNAs) have several known functions in plant development, but their possible roles in responding to plant disease remain largely unresolved. In this study, we described a comprehensive disease-responding lncRNA profiles in defence against a cotton fungal disease Verticillium dahliae. We further revealed the conserved and specific characters of disease-responding process between two cotton species. Conservatively for two cotton species, we found the expression dominance of induced lncRNAs in the Dt subgenome, indicating a biased induction pattern in the co-existing subgenomes of allotetraploid cotton. Comparative analysis of lncRNA expression and their proposed functions in resistant Gossypium barbadense cv. '7124' versus susceptible Gossypium hirsutum cv. 'YZ1' revealed their distinct disease response mechanisms. Species-specific (LS) lncRNAs containing more SNPs displayed a fiercer inducing level postinfection than the species-conserved (core) lncRNAs. Gene Ontology enrichment of LS lncRNAs and core lncRNAs indicates distinct roles in the process of biotic stimulus. Further functional analysis showed that two core lncRNAs, GhlncNAT-ANX2- and GhlncNAT-RLP7-silenced seedlings, displayed an enhanced resistance towards V. dahliae and Botrytis cinerea, possibly associated with the increased expression of LOX1 and LOX2. This study represents the first characterization of lncRNAs involved in resistance to fungal disease and provides new clues to elucidate cotton disease response mechanism.

Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species

Organelle genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both organelle- and nuclear-encoded machinery. Next generation sequencing (NGS) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate organelle genome transcription. However, most of the available eukaryotic RNA-sequencing (RNA-seq) data are used to study nuclear transcription only, even though large numbers of organelle-derived reads can typically be mined from these experiments. Here, we use publicly available RNA-seq data to assess organelle genome transcription in 59 diverse plastid-bearing species. Our RNA mapping analyses unraveled pervasive (full or near-full) transcription of mitochondrial, plastid, and nucleomorph genomes. In all cases, 85% or more of the organelle genome was recovered from the RNA data, including noncoding (intergenic and intronic) regions. These results reinforce the idea that organelles transcribe all or nearly all of their genomic material and are dependent on post-transcriptional processing of polycistronic transcripts. We explore the possibility that transcribed intergenic regions are producing functional noncoding RNAs, and that organelle genome noncoding content might provide raw material for generating regulatory RNAs.