exRNAdisease: An extracellular RNA transcriptome atlas in human diseases.

Extracellular RNAs (exRNAs) are types of RNAs that present outside of the cells with highly stable features. exRNAs have been shown to play important roles in aiding intercellular communication and regulating cellular processes. In clinical settings, exRNAs have the potential to serve as biomarkers indicating the presence of a disease.Recently, the high-throughput technologies such as RNA sequencing (RNAseq) and microarray have generated abundant exRNA expression data about various diseases. Thus, it is highly desirable to have a comprehensive database for disease-related exRNA transcriptome data detected in diverse body fluids. Here, a total of 88 previously published exRNA transcriptome datasets were collected. We developed a web-accessible database, exRNADisease, which is designed as a central repository for exRNAs from body fluids in human diseases and healthy controls. In the current version, a total of 18,265 samples were collected, which includes 10 body fluids and 78 human disease types. Six different types of RNAs were included (messenger RNAs, circular RNAs, long noncoding RNAs, microRNAs, transfer RNA fragments and PIWI-interacting RNA). Literature is also included to provide the robust evidence about the relationship between exRNAs and diseases. A user-friendly interface was constructed to conveniently search and browse disease-related exRNAs. exRNADisease will become a useful platform to provide genome-wide view of exRNA deregulation in human diseases and help to identify novel biomarkers. Availability and implementation: exRNAdisease can be freely accessible at http://www.origin-gene.cn/database/exRNAdisease/.

Mitochondrion-encoded circular RNAs are widespread and translatable in plants.

Nucleus-encoded circular RNAs (ncircRNAs) have been widely detected in eukaryotes, and most circRNA identification algorithms are designed to identify them. However, using these algorithms, few mitochondrion-encoded circRNAs (mcircRNAs) have been identified in plants, and the role of plant mcircRNAs has not yet been addressed. Here, we developed a circRNA identification algorithm, mitochondrion-encoded circRNA identifier, based on common features of plant mitochondrial genomes. We identified 7,524, 9,819, 1,699, 1,821, 1,809, and 5,133 mcircRNAs in maize (Zea mays), Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), tomato (Solanum lycopersicum), cucumber (Cucumis sativus), and grape (Vitis vinifera), respectively. These mcircRNAs were experimentally validated. Plant mcircRNAs had distinct characteristics from ncircRNAs, and they were more likely to be derived from RNA degradation but not intron backsplicing. Alternative circularization was prevalent in plant mitochondria, and most parental genomic regions hosted multiple mcircRNA isoforms, which have homogenous 5' termini but heterogeneous 3' ends. By analysis of mitopolysome and mitoribosome profiling data, 1,463 mcircRNAs bound to ribosomes were detected in maize and Arabidopsis. Further analysis of mass spectrometry-based proteomics data identified 358 mcircRNA-derived polypeptides. Overall, we developed a computational pipeline that efficiently identifies plant mcircRNAs, and we demonstrated mcircRNAs are widespread and translated in plants.

Unexpected expression of heat-activated transient receptor potential (TRP) channels in winter torpid bats and cold-activated TRP channels in summer active bats.

The ability to sense temperature changes is crucial for mammalian survival. Mammalian thermal sensing is primarily carried out by thermosensitive transient receptor potential channels (Thermo-TRPs). Some mammals hibernate to survive cold winter conditions, during which time their body temperature fluctuates dramatically. However, the underlying mechanisms by which these mammals regulate thermal responses remain unclear. Using quantitative real-time polymerase chain reaction (qRT-PCR) and the Western blotting, we found that Myotis ricketti bats had high levels of heat-activated TRPs (e.g., TRPV1 and TRPV4) during torpor in winter and cold-activated TRPs (e.g., TRPM8 and TRPC5) during active states in summer. We also found that laboratory mice had high mRNA levels of cold-activated TRPs (e.g., Trpm8 and Trpc5) under relatively hot conditions (i.e., 40 °C). These data suggest that small mammals up-regulate the expression of cold-activated TRPs even under warm or hot conditions. Binding site analysis showed that some homeobox (HOX) transcription factors (TFs) regulate the expression of hot- and cold-activated TRP genes and that some TFs of the Pit-Oct-Unc (POU) family regulate warm-sensitive and cold-activated TRP genes. The dual-luciferase reporter assay results demonstrated that TFs HOXA9, POU3F1, and POU5F1 regulate TRPC5 expression, suggesting that Thermo-TRP genes are regulated by multiple TFs of the HOX and POU families at different levels. This study provides insights into the adaptive mechanisms underlying thermal sensing used by bats to survive hibernation.

Two new triterpenoids from the leaves of Cyclocarya paliurus (Batalin) Iljinskaja.

Two previously undescribed triterpenoids (1-2), along with thirteen known compounds (3-15) were isolated from a CHCl3-soluble extract of the leaves of Cyclocarya paliurus. Their structures were established on the basis of chemical and spectroscopic approaches. These compounds were assessed for their therapeutic effects on diabetic nephropathy (DN)-evoked fibrosis through High-Glucose and transforming growth factor-ß1 (TGF-ß1) challenged HK-2 cells. Among them, compounds 3, 5 and 8 could remarkedly decrease the level of fibronectin to relieve DN with 27.66 ± 2.77%, 6.09 ± 0.57% and 17.74 ± 5.83% inhibition rate at 10 µM, 10 µM and 1 µM, respectively.

Four new dammarane triterpenoid glycosides from the leaves of Cyclocarya paliurus and their SIRT1 activation activities.

Four new C-11 monosaccharide attached dammarane triterpenoid glycosides cypaliurusides SV (1-4), along with nine known dammarane triterpenoid glycosides (5-13) were isolated from a CHCl3-soluble extract of the leaves of Cyclocarya paliurus. All characterized compounds were assayed for their cytotoxicities against HepG2 cells and 10 compounds were evaluated for the agonistic effects on sirtuin1 (SIRT1). The results showed that compounds 1, 5 and 6 were strongly cytotoxic in HepG2 cell line. Two dammarane triterpenoid glycosides 3 and 10 exhibited agonistic activities on SIRT1 with IC50 of 10 µM and 20 µM, respectively.

Translation and functional roles of circular RNAs in human cancer.

Circular RNAs (circRNAs) are a new class of non-coding RNAs formed by covalently closed loops through backsplicing. Recent methodologies have enabled in-depth characterization of circRNAs for identification and potential functions. CircRNAs play important roles in various biological functions as microRNA sponges, transcriptional regulators and combining with RNA binding proteins. Recent studies indicated that some cytoplasmic circRNAs can be effectively translated into detectable peptides, which enlightened us on the importance of circRNAs in cellular physiology function. Internal Ribosome Entry site (IRES)- and N6-methyladenosines (m6A)-mediated cap-independent translation initiation have been suggested to be potential mechanism for circRNA translation. To date, several translated circRNAs have been uncovered to play pivotal roles in human cancers. In this review, we introduced the properties and functions of circRNAs, and characterized the possible mechanism of translation initiation and complexity of the translation ability of circRNAs. We summarized the emerging functions of circRNA-encoded proteins in human cancer. The works on circRNA translation will open a hidden human proteome, and enhance us to understand the importance of circRNAs in human cancer, which has been poorly explored so far.

Adaptation of the FK506 binding protein 1B to hibernation in bats.

Hibernation is an adaptive strategy used by some animals to cope with cold and food shortage. The heart rate, overall energy need, body temperature, and many other physiological functions are greatly reduced during torpor but promptly return to normal levels upon arousal. The heartbeat of torpid bats can be hundreds fold lower than that of active bats, indicating that hibernating bats have a remarkable ability to control excitation-contraction coupling in cardiac muscle. FKBP1B (calstabin 2), a peptidyl-prolyl cis-trans isomerase, is critical for the regulation of excitation-contraction coupling. Whether FKBP1B is adapted to hibernation in bats is not known. Evolutionary analyses showed that the ω values of the Fkbp1b genes of 25 mammalian species are all less than 1, and amino acid sequence alignments revealed that FKBP1B proteins are highly conserved in mammals. The expression of the Fkbp1b gene was found to be elevated at both mRNA and protein levels in two distantly related bats (Rhinolophus ferrumequinum in Yinpterochiroptera and Myotis ricketti in Yangochiroptera) during torpor. Transcription factors such as YY1 and SPs were bioinformatically determined to have a higher binding affinity to the potential regulatory regions of Fkbp1b genes in hibernating than in non-hibernating mammals. This study provides new insights into the molecular evolution of Fkbp1b in adaptation to bat hibernation.

HCMDB: the human cancer metastasis database.

Metastasis is the main event leading to death in cancer patients. Over the past decade, high-throughput technologies have provided genome-wide view of transcriptomic changes associated with cancer metastases. Many microarray and RNA sequencing studies have addressed metastases-related expression patterns in various types of cancer, and the number of relevant works continues to increase rapidly. These works have characterized genes that orchestrate the metastatic phenotype of cancer cells. However, these expression data have been deposited in various repositories, and efficiently analyzing these data is still difficult because of the lack of an integrated data mining platform. To facilitate the in-depth analyses of transcriptome data on metastasis, it is quite important to make a comprehensive integration of these metastases-related expression data. Here, we presented a database, HCMDB (the human cancer metastasis database, http://hcmdb.i-sanger.com/index), which is freely accessible to the research community query cross-platform transcriptome data on metastases. HCMDB is developed and maintained as a useful resource for building the systems-biology understanding of metastasis.

The Genomes of Two Bat Species with Long Constant Frequency Echolocation Calls.

Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats-the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats. Pseudogenization of some vision-related genes in rhinolophoid bats was observed, suggesting that these genes have undergone relaxed natural selection. An extensive contraction of olfactory receptor gene repertoires was observed in the lineage leading to the common ancestor of bats. Further extensive gene contractions can be observed in the branch leading to the rhinolophoid bats. Such concordance suggested that molecular changes at one sensory gene might have direct consequences for genes controlling for other sensory modalities. To characterize the population genetic structure and patterns of evolution, we re-sequenced the genome of 20 great leaf-nosed bats from four different geographical locations of China. The result showed similar sequence diversity values and little differentiation among populations. Moreover, evidence of genetic adaptations to high altitudes in the great leaf-nosed bats was observed. Taken together, our work provided a useful resource for future research on the evolution of bats.

Understanding the combinatorial action of transcription factors and microRNA regulation from regions of open chromatin.

Transcriptional regulatory cascades are always triggered through the combinatorial interplay between transcription factors (TFs) and microRNAs (miRNAs) in eukaryotes. However, it is still a very substantial undertaking to dynamically profile their coordinated actions. In this work, we compared the differences in TFBS numbers between miRNA targets and non-targets, and found that miRNA targets tend to have more TFBS numbers. With the attempt to comprehensively understand the combinatorial action of TF and miRNA regulation from regions of open chromatin, we retrieved recently published DNase I hypersensitive sites (DHSs) across different human cell lines. The result showed that the differences are more statistically significant in DHS regions than non-DHS regions. Next, we trained classifiers for miRNA targets and non-targets. The result showed that TFBSs located in DHS regions achieved a competitive performance when discriminating miRNA targets and non-targets, whereas the performance of classifiers using TFBSs located in non-DHS regions is close to that of a random classifier. After the DHSs were divided into intergenic, transcription start sites (TSSs) and gene body DHS regions based on their genomic locations, only TFBSs located in TSS DHS regions provided a competitive performance. Our results provide us a clue that the coordinated activity of miRNAs and TFs describing the mechanism of gene expression control should be examined in a dynamic perspective.

Coordinated action of histone modification and microRNA regulations in human genome.

Both histone modifications and microRNAs (miRNAs) play pivotal role in gene expression regulation. Although numerous studies have been devoted to explore the gene regulation by miRNA and epigenetic regulations, their coordinated actions have not been comprehensively examined. In this work, we systematically investigated the combinatorial relationship between miRNA and epigenetic regulation by taking advantage of recently published whole genome-wide histone modification data and high quality miRNA targeting data. The results showed that miRNA targets have distinct histone modification patterns compared with non-targets in their promoter regions. Based on this finding, we proposed a machine learning approach to fit predictive models on the task to discern whether a gene is targeted by a specific miRNA. We found a considerable advantage in both sensitivity and specificity in diverse human cell lines. Finally, we found that our predicted miRNA targets are consistently annotated with Gene Ontology terms. Our work is the first genome-wide investigation of the coordinated action of miRNA and histone modification regulations, which provide a guide to deeply understand the complexity of transcriptional regulation.

Adaptation of peroxisome proliferator-activated receptor alpha to hibernation in bats.

BACKGROUND: Hibernation is a survival mechanism in the winter for some animals. Fat preserved instead of glucose produced is the primary fuel during winter hibernation of mammals. Many genes involved in lipid metabolism are regulated by the peroxisome proliferator-activated receptor alpha (PPARα). The role of PPARα in hibernation of mammals remains largely unknown. Using a multidisciplinary approach, we investigated whether PPARα is adapted to hibernation in bats. RESULTS: Evolutionary analyses revealed that the ω value of Pparα of the ancestral lineage of hibernating bats in both Yinpterochiroptera and Yangochiroptera was lower than that of non-hibernating bats in Yinpterochiroptera, suggesting that a higher selective pressure acts on Pparα in hibernating bats. PPARα expression was found to be increased at both mRNA and protein levels in distantly related bats (Rhinolophus ferrumequinum and Hipposideros armiger in Yinpterochiroptera and Myotis ricketti in Yangochiroptera) during their torpid episodes. Transcription factors such as FOXL1, NFYA, NFYB, SP1, TBP, and ERG were bioinformatically determined to have a higher binding affinity to the potential regulatory regions of Pparα in hibernating than in non-hibernating mammals. Genome-wide bioinformatic analyses of 64 mammalian species showed that PPARα has more potential target genes and higher binding affinity to these genes in hibernating than in non-hibernating mammals. CONCLUSIONS: We conclude that PPARα is adapted to hibernation in bats based on the observations that Pparα has a more stringent functional constraint in the ancestral lineage of hibernating bats and a higher level of expression in hibernating than in non-hibernating bats. We also conclude that PPARα plays a very important role in hibernation as hibernators have more PPARα target genes than non-hibernators, and PPARα in hibernators has a higher binding affinity for its target genes than in non-hibernators.